RetrogeneDB ID: retro_hsap_2523

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 21:32434046..32435487(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000228941
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: UBE3A
• Ensembl ID: ENSG00000114062
• Aliases: UBE3A, ANCR, AS, E6-AP, EPVE6AP, HPVE6A
• Description: ubiquitin protein ligase E3A [Source:HGNC Symbol;Acc:12496]

Sequence

>retro_hsap_2523
GATTTTAAAGATGTGACTTACTTAACAGAAGAGAAGGTATATGAAATTACTGAATTATGTAGAGAAAGAGAGGATTATTC
CCCCTTAACTGTGTTATTGGAAGAGTTTTTTCTAGTGCTGAGGCATTGGTAGAGAGCTTCTGGAAAGCTAAACAACACAC
CAAGGAAGAACTGAAGTCTCTTCAAGCAAAGGATGAAGAGAAGAATGAAAATGAAAAGGCAAAAGCTGCATGTTCTGCTG
CTGCTATGGAAGAAGACTCAGAAGCATCTTCCTCAAGCACAGGTGATAGCTCACAGGGAGACAACAATTTGCAAAAATTA
GGCCCTGATGATGTGTCTGTGGATACTGATTCCATTAGAAGGGTCTACACCAGATTGCTCTCTAATGAAAAAATTGAAAT
TGCCTTTCTCAATGCACTTGTATATTTGTCACCTAACGTGGAATGTGACTTGATGTATCACAAGGTATACTCTCAAGATC
CTAATTATCTGAATTTGTTCATTATAGTAATGGAGAACAGAAATCTCCACAGTCCTGAATATCTGGAAATGGCTTTGCCA
TTATTTTGCAAAGCAATGAGCAAGCTACCCCTTGCAGCCCAAGGAAAGCTGATCAGACTGTGGTCTAAATACAATGCAGA
CCAGATTCGGAGAATGATGGAGACAGTTCAGCAACTTATTACTTACAAAGTCATAAGCAACGAATTTAACAGTCAAAATC
TGGTGAATGATGATGATGCCATTGTTGCTGCTTCGAAGTGCTTGAAAATGATTTACTATGCAAATGGTAGTGGGAGGGGA
AGTGGACACAAATCACAGTGAGGAAGATGATGAAGAGCCCATCCCTGAGTCCAGTGAGCTGACACTTCAGGAGCTTTTGG
AAGAAGAGAGAAGAAACAAGAAAGGTCCTTGAGTGGACCCCCTGGAAAATGAACTTGGTGTTAAAACCCTGGATTGTCAA
AAATCCCTTATCCCTTTTGAAGAGTTTATTAATGAACCACTGAAGGAGGTTCTAGAAATGCATAAAGATTATACTGTTTT
CAAAGTAGAAACAGAACAAATTCTCTTTTATGACATACCCCTTTTTAGCGTATGCTGTCACAAAGAATTTGGGATTATAT
TATGACAATAGAATTCGCATGTACAGTGAACGAAGAATCACTGTTCTCTACAGCTTAGTTCAAGGACAGCAGTTGAATCC
ATATTTGAGACTCATTGTTAGATGTGACCATATCATAGATGATGCACTTGTCCGGCTAGAGATGATCACTATGGAAAATC
CTGCAGACTTGAAGCAGTTCTATGTGGAATTTGAAGGAGAACAAGGTGAGGGAGGTGTTTCCAAATAATTTTTTCAGCTG
GTCGTGGAGGAAATCTTCAATCCAGATATTGGTATGTTCACGTACGATGAACTTACAAAATTGTTTTGGTTTAATCCATC
T

Alignment

ORF - retro_hsap_2523 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.32 %
• Parental protein coverage: 56.81 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DFKDVTYLTEEKVYEILELCREREDYSPLIR-VIGRVFSSAEALVQSFRKVKQHTKEELKSLQAKDEDKD
          DFKDVTYLTEEKVYEI.ELCREREDYSPL...VIGRVFSSAEALV.SF.K.KQHTKEELKSLQAKDE.K.
Retrocopy DFKDVTYLTEEKVYEITELCREREDYSPLTV<VIGRVFSSAEALVESFWKAKQHTKEELKSLQAKDEEKN

Parental  EDEKEKAACSAAAMEEDSEASSSRIGDSSQGDNNLQKLGPDDVSVDIDAIRRVYTRLLSNEKIETAFLNA
          E.EK.KAACSAAAMEEDSEASSS..GDSSQGDNNLQKLGPDDVSVD.D.IRRVYTRLLSNEKIE.AFLNA
Retrocopy ENEKAKAACSAAAMEEDSEASSSSTGDSSQGDNNLQKLGPDDVSVDTDSIRRVYTRLLSNEKIEIAFLNA

Parental  LVYLSPNVECDLTYHNVYSRDPNYLNLFIIVMENRNLHSPEYLEMALPLFCKAMSKLPLAAQGKLIRLWS
          LVYLSPNVECDL.YH.VYS.DPNYLNLFIIVMENRNLHSPEYLEMALPLFCKAMSKLPLAAQGKLIRLWS
Retrocopy LVYLSPNVECDLMYHKVYSQDPNYLNLFIIVMENRNLHSPEYLEMALPLFCKAMSKLPLAAQGKLIRLWS

Parental  KYNADQIRRMMETFQQLITYKVISNEFNSRNLVNDDDAIVAASKCLKMVYYAN-VVGGEVDTNHNEEDDE
          KYNADQIRRMMET.QQLITYKVISNEFNS.NLVNDDDAIVAASKCLKM.YYAN.VVGGEVDTNH.EEDDE
Retrocopy KYNADQIRRMMETVQQLITYKVISNEFNSQNLVNDDDAIVAASKCLKMIYYAN>VVGGEVDTNHSEEDDE

Parental  EPIPESSELTLQELLGEERRNKKGPRVDPLETELGVKTLDCRKPLIPFEEFINEPLNEVLEMDKDYTFFK
          EPIPESSELTLQELL.EERRNKKGP.VDPLE.ELGVKTLDC.K.LIPFEEFINEPL.EVLEM.KDYT.FK
Retrocopy EPIPESSELTLQELLEEERRNKKGP*VDPLENELGVKTLDCQKSLIPFEEFINEPLKEVLEMHKDYTVFK

Parental  VETENKFSFMTCP-FILNAVTKNLGLYYDNRIRMYSERRITVLYSLVQGQQLNPYLRLKVRRDHIIDDAL
          VETE....F...P.F...AVTKNLGLYYDNRIRMYSERRITVLYSLVQGQQLNPYLRL.VR.DHIIDDAL
Retrocopy VETE-QILFYDIP>FLAYAVTKNLGLYYDNRIRMYSERRITVLYSLVQGQQLNPYLRLIVRCDHIIDDAL

Parental  VRLEMIAMENPADLKKQLYVEFEGEQGVDEGGVSKEFFQLVVEEIFNPDIGMFTYDESTKLFWFNPS
          VRLEMI.MENPADL.KQ.YVEFEGEQG..EGGVSK.FFQLVVEEIFNPDIGMFTYDE.TKLFWFNPS
Retrocopy VRLEMITMENPADL-KQFYVEFEGEQG--EGGVSK*FFQLVVEEIFNPDIGMFTYDELTKLFWFNPS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
bodymap2_adipose	0.00 RPM	75.18 RPM
bodymap2_adrenal	0.00 RPM	84.15 RPM
bodymap2_brain	0.00 RPM	133.77 RPM
bodymap2_breast	0.00 RPM	78.68 RPM
bodymap2_colon	0.00 RPM	116.63 RPM
bodymap2_heart	0.00 RPM	122.69 RPM
bodymap2_kidney	0.00 RPM	106.71 RPM
bodymap2_liver	0.00 RPM	48.69 RPM
bodymap2_lung	0.00 RPM	72.82 RPM
bodymap2_lymph_node	0.00 RPM	76.99 RPM
bodymap2_ovary	0.00 RPM	125.38 RPM
bodymap2_prostate	0.00 RPM	108.01 RPM
bodymap2_skeletal_muscle	0.02 RPM	145.30 RPM
bodymap2_testis	0.06 RPM	137.70 RPM
bodymap2_thyroid	0.00 RPM	166.64 RPM
bodymap2_white_blood_cells	0.00 RPM	110.51 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_2523 was not detected

EST

No EST(s) were mapped for retro_hsap_2523 retrocopy.

TSS

No TSS is located nearby retro_hsap_2523 retrocopy 5' end.

Lab

retro_hsap_2523 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2523 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1468
Gorilla gorilla	retro_ggor_1575
Pongo abelii	retro_pabe_1855

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003764	1 retrocopy	retro_cjac_2048,
Homo sapiens	ENSG00000114062	1 retrocopy	retro_hsap_2523 ,
Gorilla gorilla	ENSGGOG00000003955	1 retrocopy	retro_ggor_1575,
Pongo abelii	ENSPPYG00000006272	1 retrocopy	retro_pabe_1855,
Pan troglodytes	ENSPTRG00000006829	1 retrocopy	retro_ptro_1468,