RetrogeneDB ID: retro_ptro_2595

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:3525114..3526983(-)
• Located in intron of: ENSPTRG00000018877

Retrocopy information

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

Parental gene information

• Parental gene symbol: PAPOLA
• Ensembl ID: ENSPTRG00000006704
• Aliases: None
• Description: None

Sequence

>retro_ptro_2595
ATGCCGTTTCCGGTGACAACCCAGGGACCACCGCAGCCGGCGCCGCCGCCGAAGCGCTACGGCGTCTTCTCGCCTATCAG
TCTAGCGGTCCCCAAGGAGACGGACTGCCTCCTCACCCAGAGGCTAATAGAAACCCTCAGGCCCTTCGGGGTCTTCGAAG
AGGAAGAGGAACTGCAGCGCAGGATTTTAGTTTTGGAAAAATTAAATAATCTGGTAAAGGAATGGATACGCGAAATCAGT
GAAAGCAAGAGTCTTCCCCAGTCTGTAATTGAAAACGTTGGAGGAAAGATTTTTACGTTTGGCTCTTACAGATTAGGAGT
ACATACGAAAGGCGCAGATATTGACGCCTTGTGCGTTGCACCAAGTCATGTGGATCGAAGCGACTTTTTCACCTCATTCT
ATGCTAAACTGAAACTACAGGAGGAAGTAAAAGATTTAAGGGCTGTCGAGGAGGCATTTGTGCCAGTTATCAAACTGTGT
TTTGATGGGATAGAGATTGATATTTTATTTGCAAGATTAGCACTACAGACTATTCCAGAAGATTTGGACTTAAGAGATGA
CAGTCTACTTAAAAATTTAGACATTAGATGCATAAGAAGCCTTAATGGTTGCCGGGTAACCGATGAAATTTTACATCTAG
TGCCAAACATTGACAACTTCAGGCTGACTCTGAGAGCCATCAAACTGTGGGCCAAGTGCCACAATATCTATTCCAATATA
TTAGGTTTCCTCGGAGGTGTTTCCTGGGCCATGCTAGTAGCAAGAACTTGTCAGCTTTATCCAAATGCAGTAGCGTCAAC
TCTTGTACGGAAATTCTTCTTGGTATTTTCAGAATGGGAATGGCCAAACCCAGTGTTACTGAAGGAGCCTGAAGAACGGA
ATCTTAATTTGCCTGTATGGGACCCAAGAGTAAATCCCAGTGATAGGTACCATCTTATGCCTATCATCACACCAGCATAC
CCACAGCAGAACTCCACATACAACGTGTCTATTTCAACCAGGATGGTCATGATTGAGGAGTTTAAACAGGGGCTTGCTAT
CACACACGAGATTTTGCTAAGTAAGGCAGAGTGGTCCAAACTCTTTGAAGCTCCAAGCTTCTTTCAAAAGTACAAGCATT
ATATTGTACTTCTGGCAAGTGCATCAACAGAAAAACAACATTTAGAATGGGTGGGCTTGGTGGAATCAAAGATCCGAATC
CTGGTTGGGAGCTTGGAGAAGAATGAATTTATTACACTGGCACATGTGAATCCACAGTCATTTCCAGCACCCAAAGAAAA
TCCTGATATGGAAGAATTTTGTACAATGTGGGTGATTGGGTTAGGGCTAAAAAAGCCAGAAAACTCTGAAATTCTCAGCA
TTGATCTCACCTATGATATCCAGTCTTTCACAGATACTGTTTATAGGCAAGCAGTGAATAGTAAGATGTTTGAGATGGGT
ATGAAAATTACTGCAATGCATTTAAGAAGAAAGGAACTTCACCAGCTGCTGCCTCATCATGTGCTTCAGGACAAGAAAGC
ACACTCAACAGAAGGTAGAAGATTGACAGATTTGAACGACAGCAGCTTTGACTTGTCTGCAGGCTGTGAAAACAGCATGT
CTGTGCCTTCATCTACTAGCACTATGAAGACAGGCCCATTGATTAGCAGTTCTCAGGGTAGAAACAGTCCTGCCTTGGCT
GTAGTGACAGCATCTGTGGCTAACATACAGGCTACTGAAATTTCCTTGCAACAGGTGAATACCAATGAAAGTTCAGGGGT
TGCATTAAACGAAAGTATTCCTCACGCTGTCTCTCAGCCTGCCATTTCTCCATCACCAAAGGCCATGGTCGCCAGAGTTC
TTTCTTCAACATGTCTCATAAGCCATCCA

Alignment

ORF - retro_ptro_2595 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.08 %
• Parental protein coverage: 83.89 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPFPVTTQGSQQTQPPQKHYGITSPISLAAPKETDCVLTQKLIETLKPFGVFEEEEELQRRILILGKLNN
          MPFPVTTQG..Q..PP.K.YG..SPISLA.PKETDC.LTQ.LIETL.PFGVFEEEEELQRRIL.L.KLNN
Retrocopy MPFPVTTQGPPQPAPPPKRYGVFSPISLAVPKETDCLLTQRLIETLRPFGVFEEEEELQRRILVLEKLNN

Parental  LVKEWIREISESKNLPQSVIENVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDRSDFFTSFYDKLKLQ
          LVKEWIREISESK.LPQSVIENVGGKIFTFGSYRLGVHTKGADIDALCVAP.HVDRSDFFTSFY.KLKLQ
Retrocopy LVKEWIREISESKSLPQSVIENVGGKIFTFGSYRLGVHTKGADIDALCVAPSHVDRSDFFTSFYAKLKLQ

Parental  EEVKDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRCIRSLNGCRVTDEI
          EEVKDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRCIRSLNGCRVTDEI
Retrocopy EEVKDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRCIRSLNGCRVTDEI

Parental  LHLVPNIDNFRLTLRAIKLWAKRHNIYSNILGFLGGVSWAMLVARTCQLYPNAIASTLVHKFFLVFSKWE
          LHLVPNIDNFRLTLRAIKLWAK.HNIYSNILGFLGGVSWAMLVARTCQLYPNA.ASTLV.KFFLVFS.WE
Retrocopy LHLVPNIDNFRLTLRAIKLWAKCHNIYSNILGFLGGVSWAMLVARTCQLYPNAVASTLVRKFFLVFSEWE

Parental  WPNPVLLKQPEECNLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVSVSTRMVMVEEFKQGLAITDE
          WPNPVLLK.PEE.NLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVS.STRMVM.EEFKQGLAIT.E
Retrocopy WPNPVLLKEPEERNLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVSISTRMVMIEEFKQGLAITHE

Parental  ILLSKAEWSKLFEAPNFFQKYKHYIVLLASAPTEKQRLEWVGLVESKIRILVGSLEKNEFITLAHVNPQS
          ILLSKAEWSKLFEAP.FFQKYKHYIVLLASA.TEKQ.LEWVGLVESKIRILVGSLEKNEFITLAHVNPQS
Retrocopy ILLSKAEWSKLFEAPSFFQKYKHYIVLLASASTEKQHLEWVGLVESKIRILVGSLEKNEFITLAHVNPQS

Parental  FPAPKENPDKEEFRTMWVIGLVFKKTENSENLSVDLTYDIQSFTDTVYRQAINSKMFEVDMKIAAMHVKR
          FPAPKENPD.EEF.TMWVIGL..KK.ENSE.LS.DLTYDIQSFTDTVYRQA.NSKMFE..MKI.AMH..R
Retrocopy FPAPKENPDMEEFCTMWVIGLGLKKPENSEILSIDLTYDIQSFTDTVYRQAVNSKMFEMGMKITAMHLRR

Parental  KQLHQLLPNHVLQKKKKHSTEGVKLTALNDSSLDLSMDSDNSMSVPSPTSATKTSPLNSSGSSQGRNSPA
          K.LHQLLP.HVLQ.KK.HSTEG..LT.LNDSS.DLS....NSMSVPS.TS..KT.PL.S..SSQGRNSPA
Retrocopy KELHQLLPHHVLQDKKAHSTEGRRLTDLNDSSFDLSAGCENSMSVPSSTSTMKTGPLIS--SSQGRNSPA

Parental  PAVTAASVTNIQATEVSVPQVNSSESSGGTSSESIPQTATQPAISPPPKPTVSRVVSSTRLVNPP
          .AV..ASV.NIQATE.S..QVN..ESSG....ESIP....QPAISP.PK..V.RV.SST.L...P
Retrocopy LAVVTASVANIQATEISLQQVNTNESSGVALNESIPHAVSQPAISPSPKAMVARVLSSTCLISHP

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	0.04 RPM	50.12 RPM
SRP007412_cerebellum	0.11 RPM	56.89 RPM
SRP007412_heart	0.03 RPM	81.81 RPM
SRP007412_kidney	0.03 RPM	99.90 RPM
SRP007412_liver	0.00 RPM	68.41 RPM
SRP007412_testis	126.78 RPM	220.67 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2595 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2595 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2595 has 9 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_30
Gorilla gorilla	retro_ggor_202
Pongo abelii	retro_pabe_3113
Macaca mulatta	retro_mmul_1675
Callithrix jacchus	retro_cjac_1763
Mus musculus	retro_mmus_37
Rattus norvegicus	retro_rnor_863
Bos taurus	retro_btau_1078
Canis familiaris	retro_cfam_1783

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014142	1 retrocopy	retro_amel_517,
Bos taurus	ENSBTAG00000004054	1 retrocopy	retro_btau_1078,
Canis familiaris	ENSCAFG00000017783	1 retrocopy	retro_cfam_1783,
Callithrix jacchus	ENSCJAG00000006512	2 retrocopies	retro_cjac_1763, retro_cjac_543,
Homo sapiens	ENSG00000090060	1 retrocopy	retro_hsap_30,
Gorilla gorilla	ENSGGOG00000006287	1 retrocopy	retro_ggor_202,
Myotis lucifugus	ENSMLUG00000010922	1 retrocopy	retro_mluc_1396,
Macaca mulatta	ENSMMUG00000018610	1 retrocopy	retro_mmul_1675,
Monodelphis domestica	ENSMODG00000012887	2 retrocopies	retro_mdom_1714, retro_mdom_1916,
Mustela putorius furo	ENSMPUG00000003054	1 retrocopy	retro_mputfur_1375,
Mus musculus	ENSMUSG00000021111	1 retrocopy	retro_mmus_37,
Nomascus leucogenys	ENSNLEG00000000625	1 retrocopy	retro_nleu_2771,
Otolemur garnettii	ENSOGAG00000004611	1 retrocopy	retro_ogar_987,
Pongo abelii	ENSPPYG00000006128	1 retrocopy	retro_pabe_3113,
Pan troglodytes	ENSPTRG00000006704	1 retrocopy	retro_ptro_2595 ,
Pteropus vampyrus	ENSPVAG00000013925	1 retrocopy	retro_pvam_360,
Vicugna pacos	ENSVPAG00000006464	1 retrocopy	retro_vpac_378,