RetrogeneDB ID: retro_ptro_741

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 12:16696941..16699054(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SUPT16H
• Ensembl ID: ENSPTRG00000006122
• Aliases: None
• Description: None

Sequence

>retro_ptro_741
ATGGCTGTGACTCTGGACAAAGACGCTTATTATCAGTGAGTGAAGAGAGTGTACAGCAATTGGCAGAAAGGAGAAGATGA
GTATGCCAACGTTGAGCCATTGTTGTATCAGTGGGTGTTGATGAAGAAATTGTTTATTCCAAATCAACTGCCTTACAGAC
ATGGCTCTTTGGTTACGAACTAACTGATACTACCATGGTCTTTTGTGATGACAAAATCATCTTTATGGCCAGCAAGAAAA
AAGTGGAGTTTTTGAAACAGATTGCCAACACTAAGGGCAATGAGAATGCTAATGGAGCCCCTGCCATCAGACTGCTGATA
TGAGAAAAGAATGAAAGTAGTAAGAGTAGCTTTGACAAAATGATTGAAGCCATTAAAGAAAGCAAGAATGGCAAGAAGAT
TGGAGTGTTCAGCAAAGACAAATTCCCTGGAGAGTTCATGAAGAGCTGGAATGACTGCCTCAACAAAGAAGGCTTTGACA
AAATAGATATCAGTGCAGTTGTGGCATATACCGTCGCTGTAAAGGAGGATGGGGAGCTCAAATTAACGAAGAAAGCAGCC
GGCATCACTTCTGAAGTCTTCAACAAATTCTTCAAGGAAAGAGTCATGGAAATAGTTGATGCAGATGAGAAAGTTTGACA
CAGCAAACTGGCTGAGTCTGTGGAAAAGGCCGTTGAAGAGAAAAAATACCTTGCTGGGGCAGACCCTTCTACTGTGGAAA
TGTGTTACCCTCCTATCATTCAGAGTGGTGGCAACTATAATCTCAAGTTCAGTGTGGTGAGTGACAAGAATCACATGCAT
TTTGGGGCTAACACTTGTGCCATGGGTATTCGCTTCAAGTCTTACTGCTCCAACCTGTTCGCACTTTGATGGCTGATCCT
TCTCAGGAAGTTCAAGAAAATTACAAGTTTTTACTCCAGCTTCAAGAAGAGCTGCTGAAGGAATTAAGACATGGTGTGAA
GATATGTGATGTATATAATGCTGTCATGGACGTGGTTAAAAAGCAGAAGCCAGAACTCCTGAACAAAATTACCAGAAACC
TAGGATTTGGGGTGGGAATTGAATTCCATGAAAGCTTCCTACTAATCAATAGTAAAAATCAATACAAACTGAAGACAGGA
ATGGTTTTCAGCATCAGTTTGGGATTCTCAGACCTGACTAACAAGGAGGGGGAAAAGCCAGAAGAGAAAACCTATGCCCT
GTTCCTTAGTGACACAGTGCTTATGGATGAGGATGGCCCAGTTACTGTTCTCACTTCTGTGAAGAAGAAAGTGAAGAATG
TGGGGATTTTCCTAAGGAACGAAGACGAGGAAGAGGAGGAGGAGGAGAAAGATGAGGCAGAGGACCTTTTGGAAAGAGGT
TCTCGGGCAGCATTACTTACAGAAAGAACAGGAATGAAATGACTGCAGAAGAGAAGTGAAGAGCACATCAAAAAGAACTA
GCGGCTCAACTCAATGAAGAAGCAAAGAGGCGATTGACTGAACAAAAGGGAGAACAGGAGATTCAGAAAGCTCACAAATC
TAATGTGTCCTATAAACACCCATCTCTGATGCCTAAGGAACCACATATTGGGGAAATGAAGATCTACATCGATAAGAAAT
ATGAGACTGTGATAATGCCTGTGTTTGGCATTGCAACACCTTTTCACATTGCCACAATCAAGAATATAAGTATGTCCGTG
GAAGGAGATTATACTTACTTGCAAATCAACTTTTATTGCCCAGGCAGTGCTCTGGGCAGGAATGAAGGCAACATCTTTCC
TAACCCTGAAGCGACTTTTGTCGAAGAAATTACATACCAAGCGTCATACGATGACCGGGGAACAGACAGTACCAGCCTTG
AACCTTGAGAATGCTTTCCAAATTATTAAAGAAGTACAGAAACGTTATAAAACTCGAGAAGCTGAAGAGAAAGAGAAGGA
GGGCATTGTAAAACAAGACTCACTGGTGATCAATCTAAACTGGAGTAATTCCAAACTGGAAGATCTATACATTCGCCCAA
ATATTGCCCAAAAGAGGCTGCAAGGCTCACTGGAGGCCCGTGTCAATGGCTTCCGCTTCATATCTGTTCGAGGAGACAAA
GTGGATATTTTGTACAATAATATTAAGCATGCT

Alignment

ORF - retro_ptro_741 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.62 %
• Parental protein coverage: 67.53 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MAVTLDKDAYYRRVKRLYSNWRKGEDEYANVD-AIVVSVGVDEEIVYAKSTALQTWLFGYELTDTIMVFC
          MAVTLDKDAYY..VKR.YSNW.KGEDEYANV..AIVVSVGVDEEIVY.KSTALQTWLFGYELTDT.MVFC
Retrocopy MAVTLDKDAYYQ*VKRVYSNWQKGEDEYANVE<AIVVSVGVDEEIVYSKSTALQTWLFGYELTDTTMVFC

Parental  DDKIIFMASKKKVEFLKQIANTKGNENANGAPAITLLIREKNESNKSSFDKMIEAIKESKNGKKIGVFSK
          DDKIIFMASKKKVEFLKQIANTKGNENANGAPAI.LLI.EKNES.KSSFDKMIEAIKESKNGKKIGVFSK
Retrocopy DDKIIFMASKKKVEFLKQIANTKGNENANGAPAIRLLI*EKNESSKSSFDKMIEAIKESKNGKKIGVFSK

Parental  DKFPGEFMKSWNDCLNKEGFDKIDISAVVAYTIAVKEDGELNLMKKAASITSEVFNKFFKERVMEIVDAD
          DKFPGEFMKSWNDCLNKEGFDKIDISAVVAYT.AVKEDGEL.L.KKAA.ITSEVFNKFFKERVMEIVDAD
Retrocopy DKFPGEFMKSWNDCLNKEGFDKIDISAVVAYTVAVKEDGELKLTKKAAGITSEVFNKFFKERVMEIVDAD

Parental  EKVRHSKLAESVEKAIEEKKYLAGADPSTVEMCYPPIIQSGGNYNLKFSVVSDKNHMHFGAITCAMGIRF
          EKV.HSKLAESVEKA.EEKKYLAGADPSTVEMCYPPIIQSGGNYNLKFSVVSDKNHMHFGA.TCAMGIRF
Retrocopy EKV*HSKLAESVEKAVEEKKYLAGADPSTVEMCYPPIIQSGGNYNLKFSVVSDKNHMHFGANTCAMGIRF

Parental  KSYCSNL-VRTLMVDPSQEVQENYNFLLQLQEELLKELRHGVKICDVYNAVMDVVKKQKPELLNKITKNL
          KSYCSNL.VRTLM.DPSQEVQENY.FLLQLQEELLKELRHGVKICDVYNAVMDVVKKQKPELLNKIT.NL
Retrocopy KSYCSNL<VRTLMADPSQEVQENYKFLLQLQEELLKELRHGVKICDVYNAVMDVVKKQKPELLNKITRNL

Parental  GFGMGIEFREGSLVINSKNQYKLKKGMVFSINLGFSDLTNKEGKKPEEKTYALFIGDTVLVDEDGPATVL
          GFG.GIEF.E..L.INSKNQYKLK.GMVFSI.LGFSDLTNKEG.KPEEKTYALF..DTVL.DEDGP.TVL
Retrocopy GFGVGIEFHESFLLINSKNQYKLKTGMVFSISLGFSDLTNKEGEKPEEKTYALFLSDTVLMDEDGPVTVL

Parental  TSVKKKVKNVGIFLKNEDEEEEEEEKDEAEDLLGRGSRAALLTERT-RNEMTAEEKRRAHQKELAAQLNE
          TSVKKKVKNVGIFL.N...............LL.RGSRAALLTERT.RNEMTAEEK.RAHQKELAAQLNE
Retrocopy TSVKKKVKNVGIFLRNXXXXXXXXXXXXXXXLLERGSRAALLTERT<RNEMTAEEK*RAHQKELAAQLNE

Parental  EAKRRLTEQKGEQQIQKARKSNVSYKNPSLMPKEPHIREMKIYIDKKYETVIMPVFGIATPFHIATIKNI
          EAKRRLTEQKGEQ.IQKA.KSNVSYK.PSLMPKEPHI.EMKIYIDKKYETVIMPVFGIATPFHIATIKNI
Retrocopy EAKRRLTEQKGEQEIQKAHKSNVSYKHPSLMPKEPHIGEMKIYIDKKYETVIMPVFGIATPFHIATIKNI

Parental  SMSVEGDYTYLRINFYCPGSALGRNEGNIFPN-PEATFVKEITYRASNIKAPG-EQTVPALNLQNAFRII
          SMSVEGDYTYL.INFYCPGSALGRNEGNIFPN.P...F.....Y..S.I..PG.EQTVPALNL.NAF.II
Retrocopy SMSVEGDYTYLQINFYCPGSALGRNEGNIFPN<P*SDFCRR-NYIPSVIR*PG<EQTVPALNLENAFQII

Parental  KEVQKRYKTREAEEKEKEGIVKQDSLVINLNRSNPKLKDLYIRPNIAQKRMQGSLEAHVNGFRFTSVRGD
          KEVQKRYKTREAEEKEKEGIVKQDSLVINLN.SN.KL.DLYIRPNIAQKR.QGSLEA.VNGFRF.SVRGD
Retrocopy KEVQKRYKTREAEEKEKEGIVKQDSLVINLNWSNSKLEDLYIRPNIAQKRLQGSLEARVNGFRFISVRGD

Parental  KVDILYNNIKHA
          KVDILYNNIKHA
Retrocopy KVDILYNNIKHA

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	0.05 RPM	78.61 RPM
SRP007412_cerebellum	0.07 RPM	169.03 RPM
SRP007412_heart	0.00 RPM	55.81 RPM
SRP007412_kidney	0.08 RPM	75.32 RPM
SRP007412_liver	0.20 RPM	55.81 RPM
SRP007412_testis	0.32 RPM	193.80 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_741 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_741 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_741 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1089
Gorilla gorilla	retro_ggor_857

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000092201	1 retrocopy	retro_hsap_1089,
Gorilla gorilla	ENSGGOG00000002243	1 retrocopy	retro_ggor_857,
Nomascus leucogenys	ENSNLEG00000014392	1 retrocopy	retro_nleu_1624,
Pan troglodytes	ENSPTRG00000006122	1 retrocopy	retro_ptro_741 ,