RetrogeneDB ID: retro_ptro_501

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 10:76389663..76391008(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IMPDH2
• Ensembl ID: ENSPTRG00000014908
• Aliases: None
• Description: Inosine-5'-monophosphate dehydrogenase [Source:UniProtKB/TrEMBL;Acc:H2R178]

Sequence

>retro_ptro_501
TCTCCTCCCCTATGGACACTGACAGAGGCTGACATGGCAATCGGGATGGCTCTGATGGGAGGTATTGGTTTCATTCACCA
CAACTGCACCCCAGAGTTCGAGGCCAATGAGGTGCGGAAGGTCAAGAAGTTTGAACAGGGCTTCATCACGGACCCTGTGG
TGCTGAGCCCCTTGCACACCGTGGGTGATGTGCTTGGAGGCCAAGATGCTGCATGGCTTCTCTGGTATCCCCCTCACTGA
GACGGGCACCATGGGCAGCAAGCTGGTGGGCATCATCACCTCCCGAGACGTCGACTTTCTTGCTAAGAAGGAGCACACCA
CCTTCATCAGTGAGGTGATGACGCCAAGGATGGAACTGGTGGTGGCTGACGTTGAAAGGTGTGACGTTGAAAGAGGCAAA
TGAGATCCTGCAGCGTAGCAAGAAAGGGAAGCTGCCTATCGTCAGTGATCGCGATGAGCTGGTGGCCATCATTGCCCGCA
CTGACCTGAAGAAGAATCGAGACTACCCTCTGGCCTCCAAGGATTCCCACAAACAGCTGCTGTGCGGGGCAGCTGTGGGC
ACCCGTGAGGATGACAAATGCCACCTGGACCTGCTCACCCAGGTGGGTGTCAACGTTGTAGTCTTGGACTCATCCCAAGG
GAGCTCGGTGTATCAGATCACCATGGTGCATTACATCAAACAGAAGTACCCCCACCTCCAGGTGATTGGGGGGAACGTGG
TGACAGCAGCCCAGGCCAAGAACCTGATGGACGCTCGTGTGGACGGGCTGCATGTGGGCATGGGCTACGGCTCCATCTGC
ATTACCCAGGAAGTGATGGCCTGCGGTTGGCCCCAGGGCACTGCTGTGTACAAGGTGGCCAAGTATGCCCAGTGCTTTGG
TGTGCCCATCATAGTCGATGGTGGCATCCAGACTGTGGGGCACGTGGTCAAGGCCCTGGCCCTTGGAGCCTCCACAGTGA
TGATGGGCTTCTGCTGGCCATCACCACGGAGGCACCTGGTGAGTACTTCTTCTTAGAAAGGGTGCAGCTCAAGAAGTACC
AGGGCATGGGCTCACTGGATGCCATGGAGAAGAGCAGCAGCAGCCAGAAACGATACTTCAGCAAGGGGGATAAGGTGAAG
ATCGCACAGGGTGTCTCGGGCTCCATCCAGGACAAAGGGTCCATTCAGAAGTTCATGCCCTACCTCATAGCGGGCATCCA
GCACAGCTGCCAGGATATCGGGGCCCGCAGCCTGTCTGTCCTTTGGTCCATGATGTACTCAGGGGAGCTCAAGTTTGAGA
AGCAGACCATGTCGGCCCAGATCAAGGGTGGTGTCCATGGCCTGCACTCGTATGAGAAGCAGCTG

Alignment

ORF - retro_ptro_501 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.28 %
• Parental protein coverage: 86.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SSPMDTVTEAGMAIAMALTGGIGFIHHNCTPEFQANEVRKVKKYEQGFITDPVVLSPKDRVRDVF-EAKA
          S.P..T.TEA.MAI.MAL.GGIGFIHHNCTPEF.ANEVRKVKK.EQGFITDPVVLSP...V.DV..EAK.
Retrocopy SPPLWTLTEADMAIGMALMGGIGFIHHNCTPEFEANEVRKVKKFEQGFITDPVVLSPLHTVGDVL>EAKM

Parental  RHGFCGIPITDTGRMGSRLVGIISSRDIDFL-KEEEHDCFLEEIMTKREDLV-VAPAGITLKEANEILQR
          .HGF.GIP.T.TG.MGS.LVGII.SRD.DFL.K.E......E......E..V.....G.TLKEANEILQR
Retrocopy LHGFSGIPLTETGTMGSKLVGIITSRDVDFLAKKEHTTFISEVMTPRMELVV>LTLKGVTLKEANEILQR

Parental  SKKGKLPIVNEDDELVAIIARTDLKKNRDYPLASKDAKKQLLCGAAIGTHEDDKYRLDLLAQAGVDVVVL
          SKKGKLPIV...DELVAIIARTDLKKNRDYPLASKD..KQLLCGAA.GT.EDDK..LDLL.Q.GV.VVVL
Retrocopy SKKGKLPIVSDRDELVAIIARTDLKKNRDYPLASKDSHKQLLCGAAVGTREDDKCHLDLLTQVGVNVVVL

Parental  DSSQGNSIFQINMIKYIKDKYPNLQVIGGNVVTAAQAKNLIDAGVDALRVGMGSGSICITQEVLACGRPQ
          DSSQG.S..QI.M..YIK.KYP.LQVIGGNVVTAAQAKNL.DA.VD.L.VGMG.GSICITQEV.ACG.PQ
Retrocopy DSSQGSSVYQITMVHYIKQKYPHLQVIGGNVVTAAQAKNLMDARVDGLHVGMGYGSICITQEVMACGWPQ

Parental  ATAVYKVSEYARRFGVPVIADGGIQNVGHIAKALALGASTVMM-GSLLAATTEAPGEYFFSDGIRLKKYR
          .TAVYKV..YA..FGVP.I.DGGIQ.VGH..KALALGASTVMM.G.LLA.TTEAPGEYFF.....LKKY.
Retrocopy GTAVYKVAKYAQCFGVPIIVDGGIQTVGHVVKALALGASTVMM<GLLLAITTEAPGEYFFLERVQLKKYQ

Parental  GMGSLDAMDKHLSSQNRYFSEADKIKVAQGVSGAVQDKGSIHKFVPYLIAGIQHSCQDIGAKSLTQVRAM
          GMGSLDAM.K..SSQ.RYFS..DK.K.AQGVSG..QDKGSI.KF.PYLIAGIQHSCQDIGA.SL.....M
Retrocopy GMGSLDAMEKSSSSQKRYFSKGDKVKIAQGVSGSIQDKGSIQKFMPYLIAGIQHSCQDIGARSLSVLWSM

Parental  MYSGELKFEKRTSSAQVEGGVHSLHSYEKRL
          MYSGELKFEK.T.SAQ..GGVH.LHSYEK.L
Retrocopy MYSGELKFEKQTMSAQIKGGVHGLHSYEKQL

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	0.09 RPM	40.50 RPM
SRP007412_cerebellum	0.25 RPM	53.74 RPM
SRP007412_heart	0.15 RPM	30.69 RPM
SRP007412_kidney	0.55 RPM	65.75 RPM
SRP007412_liver	0.36 RPM	36.11 RPM
SRP007412_testis	5.37 RPM	15.07 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_501 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_501 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_501 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_697
Gorilla gorilla	retro_ggor_594
Pongo abelii	retro_pabe_528

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000009844	1 retrocopy	retro_fcat_1377,
Homo sapiens	ENSG00000178035	1 retrocopy	retro_hsap_697,
Gorilla gorilla	ENSGGOG00000013245	1 retrocopy	retro_ggor_594,
Mus musculus	ENSMUSG00000062867	1 retrocopy	retro_mmus_3158,
Nomascus leucogenys	ENSNLEG00000006743	7 retrocopies	retro_nleu_1126, retro_nleu_1371, retro_nleu_1378, retro_nleu_1591, retro_nleu_2183, retro_nleu_2188, retro_nleu_359,
Pongo abelii	ENSPPYG00000013884	1 retrocopy	retro_pabe_528,
Pan troglodytes	ENSPTRG00000014908	1 retrocopy	retro_ptro_501 ,
Pan troglodytes	ENSPTRG00000019660	7 retrocopies	retro_ptro_1087, retro_ptro_1724, retro_ptro_1758, retro_ptro_2575, retro_ptro_2719, retro_ptro_2886, retro_ptro_3198,
Rattus norvegicus	ENSRNOG00000031965	1 retrocopy	retro_rnor_1523,
Tursiops truncatus	ENSTTRG00000017349	2 retrocopies	retro_ttru_1148, retro_ttru_1665,