RetrogeneDB ID: retro_pabe_2463

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:117204575..117206437(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TOX4
• Ensembl ID: ENSPPYG00000005598
• Aliases: None
• Description: TOX high mobility group box family member 4 [Source:RefSeq peptide;Acc:NP_001126876]

Sequence

>retro_pabe_2463
ATGGAGTTTCCTGGAGGAAATGACAATTACCTGACGATCACAGGGCCTTCACACTCCTTCCTGTCAGGGGCTGAGACATT
CCATACACCAAGCCTGGGTGACGAGGAATTTGAAATCCCACCTATCTCTTTGGATTCTGATCCCTCATTGGCTGTCTCAG
ATGTGGTTGACCCTTTGATAACCTGGCAGACCCTTCCTCTTCACAAGATGGCAGTGCTTCAGCCCAGTATGGGGTCCAGA
CATTGGACATGCTCTGTAGGTATGACCCATGGCTTGATGGAGCAAGGCAGGGGCTCCTCAGTGGAGACTTGATCATGGAC
TTGAACCACTCTATAGGAACCCAATATAGTGCCAACCCACCTGTTACAATTGATGTACTAATGATAGCCATGACATCTGA
CTTGATGGGGCATAGCCAGTTGACCACCATTGATCAGTCAGAACTGAGTTTCCAACTGGGTTTGAGCTTAGGGGGTGGCA
CCATCCTGCCACCTGCCCAGTCACCTGAAGATCATCTTTCAACCACCCCTTCACCTACTAGTTCACTTCACGAGGTTGGT
ACTGAGGATTTCCGGAGGCAAATTTCCAGCCAGAAGACAGTGGTGGTGGAAGCAGGGAAAAAGCAGAAGGTCCCAAAGAA
GAGAAAAAAGAAAGATCCTAATGAACCTCAGAAACCAGTTTCAGCATATGCTTTATTCTTTCATGATACACAGGCTGCCA
TCAAGGGACAGAATCCTATTGCCACTTTTGGTGAGGTTTCAAAAATTGTGGCCTCCATGTGGGATAGTCTTGGAGAGGAG
CAAAAACAGATATATAAGAGGAAAACTGAGGCTGCCAAGAAAGAGTATCTGAAGGCACTGGCTGCTTACAAAGACAACCA
GGAGTGTCAGGCCACTGTGAAAACAGCAGAATTGGATCCAGCACCACCATCACAAACTCCTTCTCCAACTCCTATGGCTA
CTGTTGACCCAGCATCTCCAGCACCAGCTTCAACAGAGCCCCCTGCCCTGTCCCCATCCATTGTTGTTAACTCCACCCTT
TCACCCTATTTGGCAAACCAGGCATCTTCAGGAGCTGGGGGTCAGCCCAATATCACCAAGTTGATTATTACCAAACAAAC
GTTGCCCTCTTCCATTACTATGTCTCAAGGAGGGATGGTTACTGCTATCCCAGCCACAGTAGTGACCTCCTGGGGGCTCC
AACTAGGCCAAACCAGTACAGCTACTATCCAGCCCAGTCAACAAGCCCAGATTGTCACTCGGTCAGTGTTGCAGGCAGCA
GCAGCAGCTGCTGCTGTTGCTTCTATGCAACTGCCTCCACCCCGACTACAGCCTCCTCCAGTATAACAGATGCCACGCCC
CCGACTCAGCAGCAAGTTACCATTCTGCAGCAGCCTCCTCCACTCCAGGCCATGAAACAGCCTCCACCTCAGAAAGTTCG
AATCAATTTACGGCAACAGCTACCTCCTCTGCAGATCAAGAGTGTGCCTCCACTCACTTTGAAAATGCAGACTACCTTAG
TCCCACCAACTGTGGAAAGTAGTCCTGAGCAGCCTATGAGCAATAGCCCTGAGGCCCATACAGTGGAGGCAACTTCTCCT
GAGACTATCTGTGAGATGATCACAGATGTAGTTCCTGAGGTTGAGTCTTCTTCTCAGATGGATGTTGAATTGGTGAGTGG
GTCTCCTGTGGCACTGTCACCCCAGCCTCGATGTGTGATTGTCTGGTTGTGAGAATCCTCCCATTGTGAGTAAGGACTGG
GACAATGAATGCTGCAGCAATGAGTGTGTGGTGAAGCACTGCAGGGATGTATTCTTGGCCTGGGTAGCCTCTAGAAATTC
AAACACAGTGGTGTTTGTGAAA

Alignment

ORF - retro_pabe_2463 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.96 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MEFPGGNDNYLTITGPSHPFLSGAETFHTPSLGDEEFEIPPISLDSDPSLAVSDVVGH-FDDLADPSSSQ
          MEFPGGNDNYLTITGPSH.FLSGAETFHTPSLGDEEFEIPPISLDSDPSLAVSDVV...FD.LADPSSSQ
Retrocopy MEFPGGNDNYLTITGPSHSFLSGAETFHTPSLGDEEFEIPPISLDSDPSLAVSDVVDP<FDNLADPSSSQ

Parental  DGSFSAQYGVQTLDM-PVGMTHGLMEQGGG-LLSGGLTMDLDHSIGTQYSANPPVTIDVPMTDMTSGLMG
          DGS.SAQYGVQTLDM..VGMTHGLMEQG.G.LLSG.L.MDL.HSIGTQYSANPPVTIDV.M..MTS.LMG
Retrocopy DGSASAQYGVQTLDM>SVGMTHGLMEQGRG<LLSGDLIMDLNHSIGTQYSANPPVTIDVLMIAMTSDLMG

Parental  HSQLTTIDQSELSSQLGLSLGGGTILPPAQSPEDRLSTTPSPTSSLHEDGVEDFRRQLPSQKTVVVEAGK
          HSQLTTIDQSELS.QLGLSLGGGTILPPAQSPED.LSTTPSPTSSLHE.G.EDFRRQ..SQKTVVVEAGK
Retrocopy HSQLTTIDQSELSFQLGLSLGGGTILPPAQSPEDHLSTTPSPTSSLHEVGTEDFRRQISSQKTVVVEAGK

Parental  KQKAPKKRKKKDPNEPQKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDSLGEEQKQVYKRKTE
          KQK.PKKRKKKDPNEPQKPVSAYALFF.DTQAAIKGQNP.ATFGEVSKIVASMWDSLGEEQKQ.YKRKTE
Retrocopy KQKVPKKRKKKDPNEPQKPVSAYALFFHDTQAAIKGQNPIATFGEVSKIVASMWDSLGEEQKQIYKRKTE

Parental  AAKKEYLKALAAYKDNQECQATVETVELDPAPPSQTPSPPPMATVDPGIQPASIVATPALSPSIVVNSTL
          AAKKEYLKALAAYKDNQECQATV.T.ELDPAPPSQTPSP.PMATVDP..........PALSPSIVVNSTL
Retrocopy AAKKEYLKALAAYKDNQECQATVKTAELDPAPPSQTPSPTPMATVDPASPAPASTEPPALSPSIVVNSTL

Parental  SPSYVNQASSGAGGRAQYS-LIITKQMLPSSITMSQ-GWVTVIPATVVTSRG-QLGQTSTATIQPSQQAQ
          SP...NQASSGAGG......LIITKQ.LPSSITMSQ.G.VT.IPATVVTS.G.QLGQTSTATIQPSQQAQ
Retrocopy SPYLANQASSGAGGQPNITKLIITKQTLPSSITMSQGGMVTAIPATVVTSWGLQLGQTSTATIQPSQQAQ

Parental  IVTRSVLQAAAAAAAAASMQLPPPRLQPPPLQQMPQ-PPTQQQVTIL-SPPPLQAMQQPRTSEKFESNLQ
          IVTRSVLQAAAAAAA.ASMQLPPPRLQPPP..QMP..PPTQQQVTIL..PPPLQAM.QP....K...NL.
Retrocopy IVTRSVLQAAAAAAAVASMQLPPPRLQPPPV*QMPR<PPTQQQVTILQQPPPLQAMKQP-PPQKVRINLR

Parental  QQPPPLQIKSV-PTTLKIAELPLPPTVESSPERPMNNSP-AHTVEATS-ETICEMITDVVPEVESPSQMD
          QQ.PPLQIKSV.P.TLK......PPTVESSPE.PM.NSP.AHTVEATS.ETICEMITDVVPEVES.SQMD
Retrocopy QQLPPLQIKSVPPLTLKMQTTLVPPTVESSPEQPMSNSPEAHTVEATSPETICEMITDVVPEVESSSQMD

Parental  VELVSGSPVALSPQPRCV-RSGCENPPIVSKDWDNEYCSNECVVKHCRDVFLAWVASRNSNTVVFVK
          VELVSGSPVALSPQPRCV..SGCENPPIVSKDWDNE.CSNECVVKHCRDVFLAWVASRNSNTVVFVK
Retrocopy VELVSGSPVALSPQPRCV>LSGCENPPIVSKDWDNECCSNECVVKHCRDVFLAWVASRNSNTVVFVK

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	14.93 RPM	40.31 RPM
SRP007412_cerebellum	6.44 RPM	21.16 RPM
SRP007412_heart	4.03 RPM	15.56 RPM
SRP007412_kidney	6.13 RPM	19.72 RPM
SRP007412_liver	2.88 RPM	10.28 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2463 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2463 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2463 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2970
Pan troglodytes	retro_ptro_2008

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006261	1 retrocopy	retro_amel_858,
Canis familiaris	ENSCAFG00000005647	2 retrocopies	retro_cfam_1625, retro_cfam_1698,
Choloepus hoffmanni	ENSCHOG00000000714	2 retrocopies	retro_chof_2239, retro_chof_631,
Homo sapiens	ENSG00000092203	1 retrocopy	retro_hsap_2970,
Macropus eugenii	ENSMEUG00000010501	1 retrocopy	retro_meug_1384,
Mustela putorius furo	ENSMPUG00000000181	1 retrocopy	retro_mputfur_718,
Mus musculus	ENSMUSG00000016831	1 retrocopy	retro_mmus_11,
Nomascus leucogenys	ENSNLEG00000014556	1 retrocopy	retro_nleu_2027,
Pongo abelii	ENSPPYG00000005598	1 retrocopy	retro_pabe_2463 ,
Pan troglodytes	ENSPTRG00000006126	1 retrocopy	retro_ptro_2008,
Sus scrofa	ENSSSCG00000029203	1 retrocopy	retro_sscr_361,