RetrogeneDB ID: retro_pabe_1855

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 21:31904365..31905802(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: UBE3A
• Ensembl ID: ENSPPYG00000006272
• Aliases: None
• Description: ubiquitin-protein ligase E3A [Source:RefSeq peptide;Acc:NP_001126699]

Sequence

>retro_pabe_1855
GATTTTAAAGATGTGACTTACTTAACAGAAGAGAAGGTATATGAAATTACTGAATTATGTAGAGAAAGAGAGGATTATTC
CCCCTTAATTGTGTTATTGGAAGAGTTTTTTCTGGTGCTGAGGCATTGGTAGAGAGCTTCCGGAAAGCTAAACAACACAC
CAAGGAAGAACTGAAGTCTCCTCAAGCAAGGGATGAAGAGAAGGATGAAAATGAAAAGGAAAAAGCTGCATGTTCTGCTG
CTGCTATGGAAGAAGACTCAGAAGCATCTTCCTTAAGCACAGGTGATAGCTCACAGGGAGACAACAATTTGCAAAAATTA
GTCCCTGATGATGTGTCTGTGGATATTGATGCCATTAGAAGGGTCTACACCAGATTGCTCTCTAATGAAGAAATTGAAAC
TGCCTTTCTGAATGCACTTGTATGTTTGTCACCTAACATGGAATGTGACTTGATGTATCACAACGTGTACTCTCAAGATC
CTAATTATCTGAATTTGTTCATTATAGTAATGGAGAACAGAAATCTCCACAGTCCTGAATATCTGGAAATGGCTTTGCCA
TTATTTTGCAAAGCAATGAGCAAGCTACCCCTTGCAGCCCAAGGAAAACTGATCAGACTGTGGTCTAAATACAATGCAGA
CCAGATTCGGAGAACGATGGAGACATTTCAGCAACTTATTACTTACAAAGTCATAAGCAACGAATTTAACAGTCGAAATC
TAGTGAATGATGATGATGCCATTGTTGCTGCTTCGAAGTGCTTGAAAATGATTTACTATGCAAATGGTAGTGGGAGGGGA
AGTGGACACAAATCACAGTGAGGAAGATGATGAAGAGCCCATCCCTGAGTCCAGTGAGCTGACACTTCAGGAGCTTTTGG
AAGAAGAGAGAAGAAACAAGAAAGGTCCTTGAGTGGACCCCCTGGAAAATGAACTTGGTGTTAAAACCCTGGATTGTCGA
AAATCCCTTATCCCTTTTGAAGAGTTTATTAATGAACCACTGAAGGAGGTTCTAGAAATGCATAAAGATTATACTGTTTT
CAAAGTAGAAACAGAACAAATTCTCTTTTATGACATACCCCTTTTTAGTGTATGCTGTCACAAAGAATTTGGGATTATAT
TATGACTATAGAATTCGCATGTACAGTGAACGAAGAATCACTGTTCTCTACAGCTTAGTTCAAGGACAGCAGTTGAATCC
ATATTTGAGACTTATTGTTAGATGTGACCATATCATGATGATCCACTTGTCTGGCTAGAGATGATCACTATGGAAAATCC
TGCAGACTTGAAGCAGTTCTATGTGGAATTTGAAGGAGAACAAGGTGAGGGAGGTGTTTCCAAATAATTTTTTCAGCTGG
TTGTGGAGGAAATCTTCAATCCAGATATTGGTATGTTCACGTACAATGAACTTACAAAATTGTTTTGGTTTAATCCA

Alignment

ORF - retro_pabe_1855 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.89 %
• Parental protein coverage: 56.77 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  DFKDVTYLTEEKVYEILELRREREDYSPLIH-VIGGVFSSAEALVQSFRKVKQHTKEELKS-LAKDEDKD
          DFKDVTYLTEEKVYEI.EL.REREDYSPLI..VIG.VFS.AEALV.SFRK.KQHTKEELKS..A.DE.KD
Retrocopy DFKDVTYLTEEKVYEITELCREREDYSPLIV<VIGRVFSGAEALVESFRKAKQHTKEELKSPQARDEEKD

Parental  EDEKEKAACSAAAMEEDSEASSSRIGDSSQGDNNLQKLGPDDVSVDIDAIRRVYTRLLSNEKIETAFLNA
          E.EKEKAACSAAAMEEDSEASS...GDSSQGDNNLQKL.PDDVSVDIDAIRRVYTRLLSNE.IETAFLNA
Retrocopy ENEKEKAACSAAAMEEDSEASSLSTGDSSQGDNNLQKLVPDDVSVDIDAIRRVYTRLLSNEEIETAFLNA

Parental  LVYLSPNVECDLTYHNVYSRDPNYLNLFIIVMENRNLHSPEYLEMALPLFCKAMSKLPLAAQGKLIRLWS
          LV.LSPN.ECDL.YHNVYS.DPNYLNLFIIVMENRNLHSPEYLEMALPLFCKAMSKLPLAAQGKLIRLWS
Retrocopy LVCLSPNMECDLMYHNVYSQDPNYLNLFIIVMENRNLHSPEYLEMALPLFCKAMSKLPLAAQGKLIRLWS

Parental  KYNADQIRRMMETFQQLITYKVISNEFNSRNLVNDDDAIVAASKCLKMVYYAN-VVGGEVDTNHNEEDDE
          KYNADQIRR.METFQQLITYKVISNEFNSRNLVNDDDAIVAASKCLKM.YYAN.VVGGEVDTNH.EEDDE
Retrocopy KYNADQIRRTMETFQQLITYKVISNEFNSRNLVNDDDAIVAASKCLKMIYYAN>VVGGEVDTNHSEEDDE

Parental  EPIPESSELTLQELLGEERRNKKGPRVDPLETELGVKTLDCRKPLIPFEEFINEPLNEVLEMDKDYTFFK
          EPIPESSELTLQELL.EERRNKKGP.VDPLE.ELGVKTLDCRK.LIPFEEFINEPL.EVLEM.KDYT.FK
Retrocopy EPIPESSELTLQELLEEERRNKKGP*VDPLENELGVKTLDCRKSLIPFEEFINEPLKEVLEMHKDYTVFK

Parental  VETENKFSFMTCP-FILNAVTKNLGLYYDNRIRMYSERRITVLYSLVQGQQLNPYLRLKVRRDHII-DDA
          VETE....F...P.F...AVTKNLGLYYD.RIRMYSERRITVLYSLVQGQQLNPYLRL.VR.DHI..DD.
Retrocopy VETE-QILFYDIP>FLVYAVTKNLGLYYDYRIRMYSERRITVLYSLVQGQQLNPYLRLIVRCDHIM<DDP

Parental  LVRLEMIAMENPADLKKQLYVEFEGEQGVDEGGVSKEFFQLVVEEIFNPDIGMFTYDESTKLFWFNP
          LV.LEMI.MENPADL.KQ.YVEFEGEQG..EGGVSK.FFQLVVEEIFNPDIGMFTY.E.TKLFWFNP
Retrocopy LVWLEMITMENPADL-KQFYVEFEGEQG--EGGVSK*FFQLVVEEIFNPDIGMFTYNELTKLFWFNP

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
SRP007412_brain_prefrontal_cortex	0.22 RPM	34.83 RPM
SRP007412_cerebellum	0.73 RPM	43.65 RPM
SRP007412_heart	0.21 RPM	25.44 RPM
SRP007412_kidney	0.10 RPM	19.16 RPM
SRP007412_liver	0.09 RPM	14.54 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1855 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1855 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1855 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2523
Pan troglodytes	retro_ptro_1468
Gorilla gorilla	retro_ggor_1575

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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,