Gene: HLA-A (ENSG00000206503) - Structural variants - Homo_sapiens

Transcript ID	Name	bp	Protein	Biotype	CCDS	UniProt Match	RefSeq	Flags
ENST00000396634.1	HLA-A-001	1868	365aa	Gene/transcipt that contains an open reading frame (ORF).Protein coding	CCDS34373	A0ZXY8 A5PHP7 A7MAP4 B1PKY1 B4DVC4 B6ECH2 B6VA02 B8XRE8 B8YCR7 C4PFZ1 C5IZQ3 C5IZR4 C5J027 C5J029 C6K4E3 C6K4G0 C6K4H0 C6K4H3 C6K4H8 C6K4I1 C6K4I6 C6K4J6 C8CH66 C8XTN7 C8XTN9 C8XTP7 C8XTP8 C9E1E7 C9E1E8 C9WEL1 C9WEL2 C9WEL3 D0AB29 D0EZJ9 D0EZK0 D0RAY3 D1MYY8 D3U442 D3U454 D3U484 D5FHG0 D5FHK5 D5FHM1 D5FHM3 D5FHM5 D5FHN7 D5FHQ9 D5FIG9 D5G2J2 D5M8E4 D5M8G1 D5M8G4 D6MJF7 D6MKY9 D6ML01 D6ML06 D6ML09 D6ML10 D6ML16 D6ML18 D6ML33 D6ML35 D6ML40 D6ML42 D6ML44 D6ML54 D6ML55 D6ML56 D6MLJ1 D6MLJ4 D6MLK2 D6MLL1 D6MLM4 D6MLN3 D6MLN9 D7NNM6 D7NNR5 D7NNS2 D7NNT3 D7NNT6 D7NNT9 D7NNU1 D7NP92 D7NP98 D7NPA3 D7NSP0 E0WBX1 E0WBX4 E0X9K2 E0YTI1 E0YTI8 E2D5K9 E2D5L9 E2D5M3 E2DH82 E3SG86 E5DCM0 E5DCM2 E5DCM4 E7BBA1 E7BY85 E7BY93 E8ZF52 E9LY00 E9LY02 E9LY14 F2VNC4 F2VND0 F2VNE0 F2VNF2 F2VNF7 F2VNG0 F2VNH0 F2VNH3 F2X5X9 F2X5Y0 F2X604 F4YU20 F4YU26 F6IQV7 F6KRM4 F6KRP1 F8R110 F8R119 F8R8I1 F8RHB9 F8RHC2 F8RHD1 G0WVA0 G0WVA6 G0ZDS9 G0ZMF4 G0ZMG3 G0ZMG4 G0ZMG9 G1DUW4 G1ENY5 G1EP05 G1EP18 G1EP19 G1EP50 G1EP55 G1EP71 G1EP78 G1EP88 G1EP95 G1EP96 G1EP98 G1EPB1 G3DR81 G9HW24 G9I2J6 H2BDP5 H2BE80 H6UV68 H6UV69 H6UV72 H9BQ78 I1W1L8 I2B2Z9 I3QHQ4 I3UI47 I3UI58 I6NS19 I6NS25 I6QU16 I6SJ64 J7F8L2 J7FNZ2 J7GM07 J9PWL3 J9PWV5 J9TNR8 J9UP83 K7P558 K7P562 K7P5B6 K7P5E0 K7P5U2 K7P5W6 K7P600 K7WPD7 K9L7Y8 K9LCM8 K9LDJ0 L0BVP5 L7PH13 L7PHU7 L7PHV2 M1F5P2 M1FWW6 M1FYE3 M1FYE6 M1KE04 M1SQT4 M4N6L9 M9P8Z4 M9PAA4 M9PAA7 M9PNR0 O19689 O78081 O78085 O78086 P04439 P13746 P16188 Q0MSI1 Q1M2R8 Q29840 Q2L4E7 Q5XLD1 Q861Q7 Q8HWS5 Q9MYA8 Q9TQ84 Q9UEX6 R4I3H2 R4I501 R9WYX8 S4TZE1 S4TZI2 S5CRT1	-	A single transcript chosen for a gene which is the most conserved, most highly expressed, has the longest coding sequence and is represented in other key resources, such as NCBI and UniProt. This is defined in detail on http://www.ensembl.org/info/genome/genebuild/canonical.htmlEnsembl Canonical, A subset of the GENCODE transcript set, containing only 5' and 3' complete transcripts at protein-coding genes.GENCODE Basic,
ENST00000376806.5	HLA-A-002	1854	371aa	Gene/transcipt that contains an open reading frame (ORF).Protein coding		A0ZXY8 A5PHP7 B6ECH2 B6VA02 B8XRE8 B8YCR7 C4PFZ1 C5IZQ3 C5IZR4 C5J027 C5J029 C6K4E3 C6K4G0 C6K4H0 C6K4H3 C6K4H8 C6K4I1 C6K4I6 C6K4J6 C8CH66 C8XTN7 C8XTN9 C8XTP7 C8XTP8 C9E1E7 C9E1E8 C9WEL1 C9WEL2 C9WEL3 D0AB29 D0EZJ9 D0EZK0 D0RAY3 D1MYY8 D3U442 D3U454 D3U484 D5FHG0 D5FHK5 D5FHM1 D5FHM3 D5FHM5 D5FHN7 D5FHQ9 D5FIG9 D5G2J2 D5M8E4 D5M8G1 D5M8G4 D6MJF7 D6MKY9 D6ML01 D6ML06 D6ML09 D6ML10 D6ML16 D6ML18 D6ML33 D6ML35 D6ML40 D6ML42 D6ML44 D6ML54 D6ML55 D6ML56 D6MLJ1 D6MLJ4 D6MLK2 D6MLL1 D6MLM4 D6MLN3 D6MLN9 D7NNM6 D7NNR5 D7NNS2 D7NNT3 D7NNT6 D7NNT9 D7NNU1 D7NP92 D7NP98 D7NPA3 D7NSP0 E0WBX1 E0WBX4 E0X9K2 E0YTI1 E0YTI8 E2D5K9 E2D5L9 E2D5M3 E2DH82 E3SG86 E5DCM0 E5DCM2 E5DCM4 E7BBA1 E7BY85 E7BY93 E8ZF52 E9LY00 E9LY02 E9LY14 F2VNC4 F2VND0 F2VNE0 F2VNF2 F2VNF7 F2VNG0 F2VNH0 F2VNH3 F2X5X9 F2X5Y0 F2X604 F4YU20 F4YU26 F6IQV7 F6KRM4 F6KRP1 F8R110 F8R119 F8R8I1 F8RHB9 F8RHC2 F8RHD1 G0WVA0 G0WVA6 G0ZDS9 G0ZMF4 G0ZMG3 G0ZMG4 G0ZMG9 G1DUW4 G1ENY5 G1EP05 G1EP18 G1EP19 G1EP50 G1EP55 G1EP71 G1EP78 G1EP88 G1EP95 G1EP96 G1EP98 G1EPB1 G3DR81 G9HW24 G9I2J6 H2BDP5 H2BE80 H6UV68 H6UV69 H6UV72 H9BQ78 I1W1L8 I2B2Z9 I3QHQ4 I3UI47 I3UI58 I6NS19 I6NS25 I6QU16 I6SJ64 J7F8L2 J7FNZ2 J7GM07 J9PWL3 J9PWV5 J9TNR8 J9UP83 K7P558 K7P562 K7P5B6 K7P5E0 K7P5U2 K7P5W6 K7P600 K7WPD7 K9L7Y8 K9LCM8 K9LDJ0 L0BVP5 L7PH13 L7PHU7 L7PHV2 M1F5P2 M1FWW6 M1FYE3 M1FYE6 M1KE04 M1SQT4 M4N6L9 M9P8Z4 M9PAA4 M9PAA7 M9PNR0 O78081 O78085 O78086 Q0MSI1 Q1M2R8 Q2L4E7 Q5SRN5 Q5XLD1 Q861Q7 Q8HWS5 Q9MYA8 Q9TQ84 Q9UEX6 R4I3H2 R4I501 R9WYX8 S4TZE1 S4TZI2 S5CRT1	-	A subset of the GENCODE transcript set, containing only 5' and 3' complete transcripts at protein-coding genes.GENCODE Basic,
ENST00000376809.5	HLA-A-201	1548	365aa	Gene/transcipt that contains an open reading frame (ORF).Protein coding	CCDS34373	A0ZXY8 A5PHP7 A7MAP4 B1PKY1 B4DVC4 B6ECH2 B6VA02 B8XRE8 B8YCR7 C4PFZ1 C5IZQ3 C5IZR4 C5J027 C5J029 C6K4E3 C6K4G0 C6K4H0 C6K4H3 C6K4H8 C6K4I1 C6K4I6 C6K4J6 C8CH66 C8XTN7 C8XTN9 C8XTP7 C8XTP8 C9E1E7 C9E1E8 C9WEL1 C9WEL2 C9WEL3 D0AB29 D0EZJ9 D0EZK0 D0RAY3 D1MYY8 D3U442 D3U454 D3U484 D5FHG0 D5FHK5 D5FHM1 D5FHM3 D5FHM5 D5FHN7 D5FHQ9 D5FIG9 D5G2J2 D5M8E4 D5M8G1 D5M8G4 D6MJF7 D6MKY9 D6ML01 D6ML06 D6ML09 D6ML10 D6ML16 D6ML18 D6ML33 D6ML35 D6ML40 D6ML42 D6ML44 D6ML54 D6ML55 D6ML56 D6MLJ1 D6MLJ4 D6MLK2 D6MLL1 D6MLM4 D6MLN3 D6MLN9 D7NNM6 D7NNR5 D7NNS2 D7NNT3 D7NNT6 D7NNT9 D7NNU1 D7NP92 D7NP98 D7NPA3 D7NSP0 E0WBX1 E0WBX4 E0X9K2 E0YTI1 E0YTI8 E2D5K9 E2D5L9 E2D5M3 E2DH82 E3SG86 E5DCM0 E5DCM2 E5DCM4 E7BBA1 E7BY85 E7BY93 E8ZF52 E9LY00 E9LY02 E9LY14 F2VNC4 F2VND0 F2VNE0 F2VNF2 F2VNF7 F2VNG0 F2VNH0 F2VNH3 F2X5X9 F2X5Y0 F2X604 F4YU20 F4YU26 F6IQV7 F6KRM4 F6KRP1 F8R110 F8R119 F8R8I1 F8RHB9 F8RHC2 F8RHD1 G0WVA0 G0WVA6 G0ZDS9 G0ZMF4 G0ZMG3 G0ZMG4 G0ZMG9 G1DUW4 G1ENY5 G1EP05 G1EP18 G1EP19 G1EP50 G1EP55 G1EP71 G1EP78 G1EP88 G1EP95 G1EP96 G1EP98 G1EPB1 G3DR81 G9HW24 G9I2J6 H2BDP5 H2BE80 H6UV68 H6UV69 H6UV72 H9BQ78 I1W1L8 I2B2Z9 I3QHQ4 I3UI47 I3UI58 I6NS19 I6NS25 I6QU16 I6SJ64 J7F8L2 J7FNZ2 J7GM07 J9PWL3 J9PWV5 J9TNR8 J9UP83 K7P558 K7P562 K7P5B6 K7P5E0 K7P5U2 K7P5W6 K7P600 K7WPD7 K9L7Y8 K9LCM8 K9LDJ0 L0BVP5 L7PH13 L7PHU7 L7PHV2 M1F5P2 M1FWW6 M1FYE3 M1FYE6 M1KE04 M1SQT4 M4N6L9 M9P8Z4 M9PAA4 M9PAA7 M9PNR0 O19689 O78081 O78085 O78086 P04439 P13746 P16188 Q0MSI1 Q1M2R8 Q29840 Q2L4E7 Q5XLD1 Q861Q7 Q8HWS5 Q9MYA8 Q9TQ84 Q9UEX6 R4I3H2 R4I501 R9WYX8 S4TZE1 S4TZI2 S5CRT1	NM_002116.7	A subset of the GENCODE transcript set, containing only 5' and 3' complete transcripts at protein-coding genes.GENCODE Basic,
ENST00000376802.2	HLA-A-003	1334	299aa	Gene/transcipt that contains an open reading frame (ORF).Protein coding		A0ZXY8 A5PHP7 B6ECH2 B6VA02 B8XRE8 B8YCR7 C4PFZ1 C5IZQ3 C5IZR4 C5J027 C5J029 C6K4E3 C6K4G0 C6K4H0 C6K4H3 C6K4H8 C6K4I1 C6K4I6 C6K4J6 C8CH66 C8XTN7 C8XTN9 C8XTP7 C8XTP8 C9E1E7 C9E1E8 C9WEL1 C9WEL2 C9WEL3 D0AB29 D0EZJ9 D0EZK0 D0RAY3 D1MYY8 D3U442 D3U454 D3U484 D5FHG0 D5FHK5 D5FHM1 D5FHM3 D5FHM5 D5FHN7 D5FHQ9 D5FIG9 D5G2J2 D5M8E4 D5M8G1 D5M8G4 D6MJF7 D6MKY9 D6ML01 D6ML06 D6ML09 D6ML10 D6ML16 D6ML18 D6ML33 D6ML35 D6ML40 D6ML42 D6ML44 D6ML54 D6ML55 D6ML56 D6MLJ1 D6MLJ4 D6MLK2 D6MLL1 D6MLM4 D6MLN3 D6MLN9 D7NNM6 D7NNR5 D7NNS2 D7NNT3 D7NNT6 D7NNT9 D7NNU1 D7NP92 D7NP98 D7NPA3 D7NSP0 E0WBX1 E0WBX4 E0X9K2 E0YTI1 E0YTI8 E2D5K9 E2D5L9 E2D5M3 E2DH82 E3SG86 E5DCM0 E5DCM2 E5DCM4 E7BBA1 E7BY85 E7BY93 E8ZF52 E9LY00 E9LY02 E9LY14 F2VNC4 F2VND0 F2VNE0 F2VNF2 F2VNF7 F2VNG0 F2VNH0 F2VNH3 F2X5X9 F2X5Y0 F2X604 F4YU20 F4YU26 F6KRM4 F6KRP1 F8R110 F8R119 F8R8I1 F8RHB9 F8RHC2 F8RHD1 G0WVA0 G0WVA6 G0ZDS9 G0ZMF4 G0ZMG3 G0ZMG4 G0ZMG9 G1DUW4 G1ENY5 G1EP05 G1EP18 G1EP19 G1EP50 G1EP55 G1EP71 G1EP78 G1EP88 G1EP95 G1EP96 G1EP98 G1EPB1 G3DR81 G9HW24 G9I2J6 H2BDP5 H2BE80 H6UV68 H6UV69 H6UV72 H9BQ78 I1W1L8 I2B2Z9 I3QHQ4 I3UI47 I3UI58 I6NS19 I6NS25 I6QU16 I6SJ64 J7F8L2 J7FNZ2 J7GM07 J9PWL3 J9PWV5 J9TNR8 J9UP83 K7P558 K7P562 K7P5B6 K7P5E0 K7P5U2 K7P5W6 K7P600 K7WPD7 K9L7Y8 K9LCM8 K9LDJ0 L0BVP5 L7PH13 L7PHU7 L7PHV2 M1F5P2 M1FWW6 M1FYE3 M1FYE6 M1KE04 M1SQT4 M4N6L9 M9P8Z4 M9PAA4 M9PAA7 M9PNR0 O78081 O78085 O78086 Q0MSI1 Q1M2R8 Q2L4E7 Q5SRN7 Q5XLD1 Q861Q7 Q8HWS5 Q9MYA8 Q9TQ84 Q9UEX6 R4I3H2 R4I501 R9WYX8 S4TZE1 S4TZI2 S5CRT1	-	A subset of the GENCODE transcript set, containing only 5' and 3' complete transcripts at protein-coding genes.GENCODE Basic,
ENST00000496081.1	HLA-A-004	1786	No protein	An alternatively spliced transcript believed to contain intronic sequence relative to other, coding, transcripts of the same gene.Retained intron		-	-	-
ENST00000495183.1	HLA-A-005	1766	No protein	An alternatively spliced transcript believed to contain intronic sequence relative to other, coding, transcripts of the same gene.Retained intron		-	-	-
ENST00000461903.1	HLA-A-007	1352	No protein	An alternatively spliced transcript believed to contain intronic sequence relative to other, coding, transcripts of the same gene.Retained intron		-	-	-
ENST00000479320.1	HLA-A-006	1334	No protein	An alternatively spliced transcript believed to contain intronic sequence relative to other, coding, transcripts of the same gene.Retained intron		-	-	-

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Structural variants

Name	Chr:bp	Genomic size (bp)	Class	Source Study	Study description
nsv3877040	6:60107-171054786	170994680170,994,680	CNV	dbVar:nstd102	NCBI database of human genomic structural variation: Structural Variants with clinical assertions, submitted to ClinVar by external labs.
nsv3879811	6:108666-170980171	170871506170,871,506	CNV	dbVar:nstd102	NCBI database of human genomic structural variation: Structural Variants with clinical assertions, submitted to ClinVar by external labs.
nsv429572	6:149661-171051005	0-	CNV	DGVa:nstd11	Database of Genomic Variants Archive: Walter 2009 "Acquired copy number alterations in adult acute myeloid leukemia genomes." PMID:19651600
nsv995521	6:156974-46757028	4660005546,600,055	CNV	DGVa:nstd37	Database of Genomic Variants Archive: International Standards for Cytogenetic Array Consortium
nsv3913920	6:156974-46757028	4660005546,600,055	CNV	dbVar:nstd102	NCBI database of human genomic structural variation: Structural Variants with clinical assertions, submitted to ClinVar by external labs.
nsv2779086	6:156975-170919482	170762508170,762,508	CNV	DGVa:nstd37	Database of Genomic Variants Archive: International Standards for Cytogenetic Array Consortium
nsv3887898	6:156975-170919482	170762508170,762,508	CNV	dbVar:nstd102	NCBI database of human genomic structural variation: Structural Variants with clinical assertions, submitted to ClinVar by external labs.
nsv429610	6:165632-42731115	0-	CNV	DGVa:nstd11	Database of Genomic Variants Archive: Walter 2009 "Acquired copy number alterations in adult acute myeloid leukemia genomes." PMID:19651600
nsv3889814	6:165632-170919470	170753839170,753,839	CNV	dbVar:nstd102	NCBI database of human genomic structural variation: Structural Variants with clinical assertions, submitted to ClinVar by external labs.
nsv1034188	6:183203-32144931	3196172931,961,729	CNV	DGVa:nstd100	Database of Genomic Variants Archive: Coe 2014 "Refining analyses of copy number variation identifies specific genes associated with developmental delay." PMID:25217958
nsv538047	6:183203-32144931	3196172931,961,729	CNV	DGVa:nstd54	Database of Genomic Variants Archive: Cooper 2011 "A copy number variation morbidity map of developmental delay." PMID:21841781
esv3762841	6:301661-80232360	7993070079,930,700	CNV	DGVa:estd192	Database of Genomic Variants Archive: Catalogue of Somatic Mutations in Cancer (COSMIC) version 71
nsv1028942	6:389422-30956360	3056693930,566,939	CNV	DGVa:nstd100	Database of Genomic Variants Archive: Coe 2014 "Refining analyses of copy number variation identifies specific genes associated with developmental delay." PMID:25217958
nsv538068	6:389422-30956360	3056693930,566,939	CNV	DGVa:nstd54	Database of Genomic Variants Archive: Cooper 2011 "A copy number variation morbidity map of developmental delay." PMID:21841781
esv3765692	6:397378-38235171	3783779437,837,794	CNV	DGVa:estd192	Database of Genomic Variants Archive: Catalogue of Somatic Mutations in Cancer (COSMIC) version 71
esv3775941	6:1213284-53150633	5193735051,937,350	tandem duplication	DGVa:estd192	Database of Genomic Variants Archive: Catalogue of Somatic Mutations in Cancer (COSMIC) version 71
nsv916283	6:3224544-30624967	2740042427,400,424	CNV	DGVa:nstd37	Database of Genomic Variants Archive: International Standards for Cytogenetic Array Consortium
nsv3920564	6:3224544-30624967	2740042427,400,424	CNV	dbVar:nstd102	NCBI database of human genomic structural variation: Structural Variants with clinical assertions, submitted to ClinVar by external labs.
esv3762705	6:4887407-156625591	151738185151,738,185	CNV	DGVa:estd192	Database of Genomic Variants Archive: Catalogue of Somatic Mutations in Cancer (COSMIC) version 71
esv3768947	6:5064247-46965915	4190166941,901,669	tandem duplication	DGVa:estd192	Database of Genomic Variants Archive: Catalogue of Somatic Mutations in Cancer (COSMIC) version 71
esv3794867	6:5429377-37462708	3203333232,033,332	tandem duplication	DGVa:estd192	Database of Genomic Variants Archive: Catalogue of Somatic Mutations in Cancer (COSMIC) version 71
esv3808392	6:5750165-157209357	151459193151,459,193	tandem duplication	DGVa:estd192	Database of Genomic Variants Archive: Catalogue of Somatic Mutations in Cancer (COSMIC) version 71
esv3771386	6:6410741-66467500	6005676060,056,760	CNV	DGVa:estd192	Database of Genomic Variants Archive: Catalogue of Somatic Mutations in Cancer (COSMIC) version 71
nsv482953	6:7100001-30400000	2330000023,300,000	CNV	DGVa:nstd41	Database of Genomic Variants Archive: Iafrate 2004 "Detection of large-scale variation in the human genome." PMID:15286789
esv3802211	6:7109110-35043691	2793458227,934,582	tandem duplication	DGVa:estd192	Database of Genomic Variants Archive: Catalogue of Somatic Mutations in Cancer (COSMIC) version 71

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No copy number variant probes associated with this variant.

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Gene: HLA-A ENSG00000206503

Structural variants

Structural variants