RetrogeneDB ID: retro_ptro_2008

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:115084271..115086134(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TOX4
• Ensembl ID: ENSPTRG00000006126
• Aliases: TOX4, C14orf92
• Description: TOX high mobility group box family member 4 [Source:HGNC Symbol;Acc:20161]

Sequence

>retro_ptro_2008
ATGGAGTCTCCCGGAGGAAATGACAATTACCTGACGATCACAGGGCCTTTACACCTCTTCCTGTCAGGGGCCGAGACATT
CCATACACCAAGCTTAGGTGATGAAGAATTTGAAATCCCACCTATCTCTTTGGATTCTGATCCCTCATTGGCTGTCTCAG
ATGTGGTTGACCACTTTGATGACCTGGCAGACCCTTCCTCTTCACAGGATGGCAGTGCTTCAGCCCAGTATGGGGTCCAG
ACATTGGACATGCTGTGTGGGCATGACCCATGGCTTGATGGAGCAAGGTGGAGGCTCCTCAGTGGAGGCTTGATCATGGA
CTTAAACCACTCTATAGGAACTCAGTATAGTGCCAACTCACCTGTTACAATTGATGTACTAATGATAGACATGACATCTG
ACTTGATGGGGCATAGCCAGTTGACCACCATTGATCAGTCAGAACTGAGTTTCCAACTGGGTTTGAGCTTACGGGGTGGC
ACCATCCTGCCACCTGCCCAGTCACCTGAAGATCGTATTTCAACCACCCCTTCACCTACTAGTTCACTTCACGAGGTTGG
TGTTGAGGATTTCTGGAGGCAAATTTCCAGCCAGAAGACAGTGGTGGTGGAAGCAGGGAAAAAGCAGAAGGTCCCAAAGA
AGAGAAAAAAGAAAGATCCTAATGAACCTCAGAAACCAGTTTCAGCATATGCTTTATTCTTTCCTGATACACGGGCTGCC
ATCAAGGGACAGAATCCTAATGCCACTTTTGGTGAGGTTTCAAAAATTGTGGCCTCCATGTGGGATAGTCTTGGAGAGGA
GCAAAAACAGATATATAAGAGGAAAACTGAGGCTGCCAAGAAAGAGTATCTGAAGACACTGGCTGCTTACAAAGACAACC
AGGAGTGTCAGGCCACTGTGGAAACAGCGGAATTGGATCCAGCACCACCATCACAAACTCCTTCTCCACCTCCTATGGCT
ACTGTTGACCCAGCGTCTCCAGCACCAGCTTCAACAGAGCCCCCTGCCCTGTCCCCATCCATTGTTGTTAACTCCACCCT
TTCATCCTATGTGGCAAACCAGGCATCTTCAGGAGCTGGGGGTCAGCCCAATATCACCAAGTTGATTATTACCAAACAAA
CGTTGCCCTCTTCCATTACTATGTCTCAGGGAGGGATGGTTACTGCTATCCTAGCCACAGTGGTGACCTCCTGGGGGCTC
CAACTAGACCCAACCAGTACAGCCACTATCCAGCCCAGTCAACAAGCCCAGATTGTCACTCGGTCAGTGTTGCAGGCAGC
AGCAGCAGCTGCTACTGTTGCTTCTATGCGACTGCCTCCACCCCGACTACAGCCCCCTCCATTATAACAGATGCCACAGC
CCCTGACTCAGCAGCAAGTTACCATTCTGCAGCAGCCTCCTCCACTCCAGGCCATGCAACAGCCTCCACCTCAGAAAGTT
CAAATCAATTTACAGCAACAGCTACCTCCTCTGCAGATCAAGAGTGTGCCTCCACTCACTTTGAAAATGCAGACTACCTA
AGTCCCACCAACTGTGGAAAGTAGTCCTGAGCGGCCTATGAACAATAGTCCTGAGGCCCATACAGTGGAGGCAACTTCTC
CTGAGACCATCTGTGAGATGATCACAGATGTAGTTCCTGATGTTGAGTCTTCTTCTCAGATGGATGTTGAATTGGTGAGT
GGGTCTCCTGTGGCACTGTCACCCCAGCCTTGATGTGTGATGTCTGGTTGTGAGAATCCTCCCATTGTGAGTAAGGACTG
GGACAATGACTGCTGCAGCAATGAGTGTGTGGTGAAGCACTGCAGGGATGTATTCTTGGCCTGGGTAGCCTCTAGAAATT
CAAACACAGTGGTGTTTGTGAAG

Alignment

ORF - retro_ptro_2008 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.97 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MEFPGGNDNYLTITGPSHPFLSGAETFHTPSLGDEEFEIPPISLDSDPSLAVSDVVGHFDDLADPSSSQD
          ME.PGGNDNYLTITGP.H.FLSGAETFHTPSLGDEEFEIPPISLDSDPSLAVSDVV.HFDDLADPSSSQD
Retrocopy MESPGGNDNYLTITGPLHLFLSGAETFHTPSLGDEEFEIPPISLDSDPSLAVSDVVDHFDDLADPSSSQD

Parental  GSFSAQYGVQTLDMP-VGMTHGLMEQGGG-LLSGGLTMDLDHSIGTQYSANPPVTIDVPMTDMTSGLMGH
          GS.SAQYGVQTLDM..VGMTHGLMEQGGG.LLSGGL.MDL.HSIGTQYSAN.PVTIDV.M.DMTS.LMGH
Retrocopy GSASAQYGVQTLDML>VGMTHGLMEQGGG<LLSGGLIMDLNHSIGTQYSANSPVTIDVLMIDMTSDLMGH

Parental  SQLTTIDQSELSSQLGLSLGGGTILPPAQSPEDRLSTTPSPTSSLHEDGVEDFRRQLSSQKTVVVEAGKK
          SQLTTIDQSELS.QLGLSL.GGTILPPAQSPEDR.STTPSPTSSLHE.GVEDF.RQ.SSQKTVVVEAGKK
Retrocopy SQLTTIDQSELSFQLGLSLRGGTILPPAQSPEDRISTTPSPTSSLHEVGVEDFWRQISSQKTVVVEAGKK

Parental  QKAPKKRKKKDPNEPQKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDSLGEEQKQVYKRKTEA
          QK.PKKRKKKDPNEPQKPVSAYALFF.DT.AAIKGQNPNATFGEVSKIVASMWDSLGEEQKQ.YKRKTEA
Retrocopy QKVPKKRKKKDPNEPQKPVSAYALFFPDTRAAIKGQNPNATFGEVSKIVASMWDSLGEEQKQIYKRKTEA

Parental  AKKEYLKALAAYKDNQECQATVETVELDPAPSSQTPSPPPMATVDPASPAPASIEPPALSPSIVVNSTLS
          AKKEYLK.LAAYKDNQECQATVET.ELDPAP.SQTPSPPPMATVDPASPAPAS.EPPALSPSIVVNSTLS
Retrocopy AKKEYLKTLAAYKDNQECQATVETAELDPAPPSQTPSPPPMATVDPASPAPASTEPPALSPSIVVNSTLS

Parental  SYVANQASSGAGGQPNITKLIITKQMLPSSITMSQGGMVTVIPATVVTSRGLQLGQTSTATIQPSQQAQI
          SYVANQASSGAGGQPNITKLIITKQ.LPSSITMSQGGMVT.I.ATVVTS.GLQL..TSTATIQPSQQAQI
Retrocopy SYVANQASSGAGGQPNITKLIITKQTLPSSITMSQGGMVTAILATVVTSWGLQLDPTSTATIQPSQQAQI

Parental  VTRSVLQAAAAAAAAASMQLPPPRLQPPPLQQMPQPPTQQQVTILQQPPPLQAMQQPPPQKVRINLQQQP
          VTRSVLQAAAAAA..ASM.LPPPRLQPPPL.QMPQP.TQQQVTILQQPPPLQAMQQPPPQKV.INLQQQ.
Retrocopy VTRSVLQAAAAAATVASMRLPPPRLQPPPL*QMPQPLTQQQVTILQQPPPLQAMQQPPPQKVQINLQQQL

Parental  PPLQIKSVPLPTLKMQTTLVPPTVESSPERPMNNSPEAHTVEATSPETICEMITDVVPEVESPSQMDVEL
          PPLQIKSVP..TLKMQTT.VPPTVESSPERPMNNSPEAHTVEATSPETICEMITDVVP.VES.SQMDVEL
Retrocopy PPLQIKSVPPLTLKMQTT*VPPTVESSPERPMNNSPEAHTVEATSPETICEMITDVVPDVESSSQMDVEL

Parental  VSGSPVALSPQPRCVRSGCENPPIVSKDWDNEYCSNECVVKHCRDVFLAWVASRNSNTVVFVK
          VSGSPVALSPQP.CV.SGCENPPIVSKDWDN..CSNECVVKHCRDVFLAWVASRNSNTVVFVK
Retrocopy VSGSPVALSPQP*CVMSGCENPPIVSKDWDNDCCSNECVVKHCRDVFLAWVASRNSNTVVFVK

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	0.07 RPM	52.64 RPM
SRP007412_cerebellum	0.11 RPM	72.74 RPM
SRP007412_heart	0.03 RPM	51.24 RPM
SRP007412_kidney	0.03 RPM	49.71 RPM
SRP007412_liver	0.00 RPM	32.05 RPM
SRP007412_testis	0.11 RPM	94.84 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2008 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2008 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2008 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2970
Pongo abelii	retro_pabe_2463

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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,