RetrogeneDB ID: retro_ptro_3136

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:80316582..80317832(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: WBP11
• Ensembl ID: ENSPTRG00000004724
• Aliases: None
• Description: None

Sequence

>retro_ptro_3136
AGATCTACATCATCCACCAAGAGTGGAAACTTTATGAAACCCATAGACCAAGCCCAAAAGGAAGCCCGGAAGAGAGAATT
GAAGAAGAGCAAAAAACAGCACATGATGGTTCCAGCTCCAGTTTTAAGGATGAAGGATCCCAAACAGATTATCTGAGACA
TGGAGAAATTGGATGAAATGGAGTTTAACCCAGTATAACAGCCACAACTAAATGAGAAAGTATTAAAAGACAAGCATAAA
AAGCTGCGTGAAACCTTTGGTATTCTACGACTCTATGAAAAAGAGAATCCAGATATTTACAAAGAACTGAGAAAGCTAGA
AGTAGAGTATAAACAGAAGAGGGCTCAACTTAGTCAATATTTTGATGCCGTCAAGAATGCTCTGCATGTGGAAATGGAGA
GTATTCCTTTGTGAGATATGCCACATATTCCTTCCAACATTTTGATCCAAGACATTCCACTTCCTGGTGCCCAGCCACCC
TCCATCCTTAAGAAAACCTCAGCCTATGGACGTCCAACTCGGGCAGTTTCTATCCTGGCTCTTCTTGGACATGGTGTTCC
ACGTTCGCCCCATGGCAGAAAACCTCTTTGCCCTCTCTCTGGCCCACCTCCTCCTCAAGTCGTGCAGATGTACGGCCGTA
AAGTGTGTTTCGCCCTAGATCTTCCCCCACGTAGGCGAGATGAAGACATATTTTATAGTCCTGCACTTGCCCAGAGAGGT
CATGATGATGATGTTTCTAGCACCAGTGAAGATGATGGCTATCCTGAGGACATGGATCAAGATAAGCATGATGAAAGTAC
TGATGACAGTGACACCAACGGATCAGATGGAGAAAGTGAGGAGGATGAATTTGTGCACCATGATGATGGTGAGAGAGACA
ACAATGAAGAAAAGAAGTCAGATCCTAGTGTACAGTTTGCAAATATGCCTGGAAAATCAAGGAAAAAAAGAAGAACATGA
AGGAACTAACTCCTCTTCAAGCTATGATGCTTCGTATGGCAGGTCAAGAAATCCCTGAGGAGTGATGGGCAGTAGAAGAA
TTTTCAGCGGACGGTGATGAAGATGATTCTGATGACTCTGAAGCAGAAAAGCAATCATAAAAACAGAATAAAGAAGAATC
TCATGCTGATGGCACATCCACTGCTTCTTCATAGCAGCAGGCTCCCCCGCGGTCTGCTCCTCCTTCTCAGATACAAGCAC
CTCCCATGCCAGGACCACCACCTCTTGGACCACCACCTGCTCTACCATTA

Alignment

ORF - retro_ptro_3136 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.11 %
• Parental protein coverage: 65.21 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RSTSSTKSGKFMNPTDQARKEARKRELKKNKKQRMMVRAAVLKMKDPKQIIRDMEKLDEMEFNPVQQPQL
          RSTSSTKSG.FM.P.DQA.KEARKRELKK.KKQ.MMV.A.VL.MKDPKQII.DMEKLDEMEFNPV.QPQL
Retrocopy RSTSSTKSGNFMKPIDQAQKEARKRELKKSKKQHMMVPAPVLRMKDPKQII*DMEKLDEMEFNPV*QPQL

Parental  NEKVLKDKRKKLRETFERILRLYEKENPDIYKELRKLEVEYEQKRAQLSQYFDAVKNAQHVEVESIPLPD
          NEKVLKDK.KKLRETF..ILRLYEKENPDIYKELRKLEVEY.QKRAQLSQYFDAVKNA.HVE.ESIPL.D
Retrocopy NEKVLKDKHKKLRETFG-ILRLYEKENPDIYKELRKLEVEYKQKRAQLSQYFDAVKNALHVEMESIPL*D

Parental  MPHAPSNILIQDIPLPGAQPPSILKKTSAYGPPTRAVSILPLLGHGVPRLPPGRKPPGPPPGPPPPQVVQ
          MPH.PSNILIQDIPLPGAQPPSILKKTSAYG.PTRAVSIL.LLGHGVPR.P.GRKP..P..GPPPPQVVQ
Retrocopy MPHIPSNILIQDIPLPGAQPPSILKKTSAYGRPTRAVSILALLGHGVPRSPHGRKPLCPLSGPPPPQVVQ

Parental  MYGRKVGFALDLPPRRRDEDMLYSPELAQRGHDDDVSSTSEDDGYPEDMDQDKHDDSTDDSDTDKSDGES
          MYGRKV.FALDLPPRRRDED..YSP.LAQRGHDDDVSSTSEDDGYPEDMDQDKHD.STDDSDT..SDGES
Retrocopy MYGRKVCFALDLPPRRRDEDIFYSPALAQRGHDDDVSSTSEDDGYPEDMDQDKHDESTDDSDTNGSDGES

Parental  DGDEFVHRDDGERDNNEEKKSGLSVRFADMPGKSRK-KKKNMKELTPLQAMMLRMAGQEIPEEGREVEEF
          ..DEFVH.DDGERDNNEEKKS..SV.FA.MPGKSRK.KKKNMKELTPLQAMMLRMAGQEIPEE...VEEF
Retrocopy EEDEFVHHDDGERDNNEEKKSDPSVQFANMPGKSRK<KKKNMKELTPLQAMMLRMAGQEIPEE*WAVEEF

Parental  SEDDDEDDSDDSEAEKQSQKQHKEESHSDGTSTASSQQQAPPQSVPPSQIQAPPMPGPPPLGPPPAPPL
          S.D.DEDDSDDSEAEKQS.KQ.KEESH.DGTSTASS.QQAPP.S.PPSQIQAPPMPGPPPLGPPPA.PL
Retrocopy SADGDEDDSDDSEAEKQS*KQNKEESHADGTSTASS*QQAPPRSAPPSQIQAPPMPGPPPLGPPPALPL

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	0.02 RPM	48.89 RPM
SRP007412_cerebellum	0.00 RPM	84.85 RPM
SRP007412_heart	0.03 RPM	43.34 RPM
SRP007412_kidney	0.00 RPM	47.88 RPM
SRP007412_liver	0.00 RPM	37.64 RPM
SRP007412_testis	0.11 RPM	377.48 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3136 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3136 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3136 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014759	1 retrocopy	retro_btau_20,
Canis familiaris	ENSCAFG00000012926	2 retrocopies	retro_cfam_1369, retro_cfam_1911,
Callithrix jacchus	ENSCJAG00000021611	1 retrocopy	retro_cjac_1737,
Homo sapiens	ENSG00000084463	2 retrocopies	retro_hsap_1878, retro_hsap_4719,
Gorilla gorilla	ENSGGOG00000004448	3 retrocopies	retro_ggor_1375, retro_ggor_1711, retro_ggor_2932,
Macropus eugenii	ENSMEUG00000013971	1 retrocopy	retro_meug_1952,
Myotis lucifugus	ENSMLUG00000015216	1 retrocopy	retro_mluc_1074,
Macaca mulatta	ENSMMUG00000019299	1 retrocopy	retro_mmul_1329,
Monodelphis domestica	ENSMODG00000017949	1 retrocopy	retro_mdom_143,
Mustela putorius furo	ENSMPUG00000011619	1 retrocopy	retro_mputfur_280,
Mus musculus	ENSMUSG00000030216	1 retrocopy	retro_mmus_2740,
Nomascus leucogenys	ENSNLEG00000003926	1 retrocopy	retro_nleu_2651,
Oryctolagus cuniculus	ENSOCUG00000017177	1 retrocopy	retro_ocun_974,
Otolemur garnettii	ENSOGAG00000010518	1 retrocopy	retro_ogar_207,
Ochotona princeps	ENSOPRG00000015008	3 retrocopies	retro_opri_107, retro_opri_1159, retro_opri_678,
Pongo abelii	ENSPPYG00000004323	3 retrocopies	retro_pabe_1558, retro_pabe_2099, retro_pabe_3663,
Pan troglodytes	ENSPTRG00000004724	3 retrocopies	retro_ptro_1260, retro_ptro_1637, retro_ptro_3136 ,
Rattus norvegicus	ENSRNOG00000005505	3 retrocopies	retro_rnor_1287, retro_rnor_2726, retro_rnor_741,
Rattus norvegicus	ENSRNOG00000049593	1 retrocopy	retro_rnor_740,
Sorex araneus	ENSSARG00000007085	1 retrocopy	retro_sara_753,
Sarcophilus harrisii	ENSSHAG00000016649	1 retrocopy	retro_shar_81,
Tupaia belangeri	ENSTBEG00000003394	1 retrocopy	retro_tbel_2213,