RetrogeneDB ID: retro_ggor_594

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 10:90513272..90514615(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGGOG00000025920
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: IMPDH2
• Ensembl ID: ENSGGOG00000013245
• Aliases: None
• Description: Inosine-5'-monophosphate dehydrogenase [Source:UniProtKB/TrEMBL;Acc:G3RBQ8]

Sequence

>retro_ggor_594
TCTCCTCCCCTATAGACACTGACAGAGGCTGACGTGGCAATCGGGATGGCTCTGATGGGAGGTATTGTTTCATTTACCAC
AACTGCACCCCAGAGTTCGAGGCCAATGAGGTGCGGAAGGTCAAGAAGTTTGAACAGGGCTTCATCACGGACCCTGTGGT
GCTGAGCCCCTTGCACACCGTGGGTGATGTGCTTGGAGGCCAAGATGCTGCATGGCTTCTCTGGTATCCCCCTCACTGAG
ACGGGCACCATGGGCAGCAAGCTGGTGGGCATCATCACCTCCCGAGACGTCGACTTTCTTGCTAAGAAGGAGCACACCAC
CTTCCTCAGTGAGGTGATGACGCCAAGGATGGAACTGGTGGTGGCTGACGCTGAAAGGTGTGACGTTGAAAGAGGCAAAT
GAGATCCTGCAGCGTAGCAAGAAAGAGAAGCTGCCTATTGTCAGTGATCGCGATGAGCTGGTGGCCATCATTGCCCGCAC
TGACCTGAAGAAGAATCAAGACTACCCTCTGGCCTCCAAGGATTCCCACAAACAGCTGCTGTGCGGGGCAGCTGTGGGCA
CCCGTGAGGATGACAAATGCCACCTGGACCTGCTCACCCAGGCGGGTGTCAACGTCGTAGTCTTGGACTCATCCCAAGGG
AGCTCGGTGTATCAGATCACCATGGTGCATTACATCAAACAGAAGTACCCCCACCTCCAGGTGATTGGGGAGAACGTGGT
GACAGCAGCCCAGGCCAAGAACCTGATGGACGCTCGTGTGGACGGGCTGCATGTGGGCATGGGCTACGGCTCCATCTGCA
TTACCCAGGAAGTGATGGCCTGCGGTTGGCCCCAGGGCACTGCTGTGTATAAGGTGGCTGAGTATGCCCAGTGCTTTGGT
GTGCCCATCATAGTCGATGGTGGCATCCAGACTGTGGGGTATGTGGTCAAGGCCCTGGCCCTTGGAGCCTCCACAGTGAT
GATGGGCTCCTGCTGGCCACCACCACGGAGGCACCTGGTGAGTACTTCTTCTTAGAAAGGGTACAGCTCAACAAGTACCA
GGGCATGGGCTCACTGGATGCCATGGAGAAGAGCAGTACAGCCAGAAACAATACTTCAGCAAGGGGGATAAGGTGAAGGT
CGCACAGGGTGTCTCCGGCTCCATCCAGGACAAAGGGTCCATTCAGAAGTTCGTGCCCTACCTCATAGCGGGCATCCAGC
ACAGCTGCCAGGATATCGGGGCCCGCAGCCTGTCTGTCCTTCGGTCCATGATGTACTCAGGGGAGCTCAAGTTTGAGAAG
CAGACCATGTCAGCCCAGATCAAGGGTGGTGTCCATGGCCTGCACTTGTATGAGAAGCAGCTG

Alignment

ORF - retro_ggor_594 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.85 %
• Parental protein coverage: 86.8 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  SSPMDTVTEAGMAIAMALTGGIG-FIHHNCTPEFQANEVRKVKKYEQGFITDPVVLSPKDRVRDVF-EAK
          S.P..T.TEA..AI.MAL.GGI..FI.HNCTPEF.ANEVRKVKK.EQGFITDPVVLSP...V.DV..EAK
Retrocopy SPPL*TLTEADVAIGMALMGGIV<FIYHNCTPEFEANEVRKVKKFEQGFITDPVVLSPLHTVGDVL>EAK

Parental  ARHGFCGIPITDTGRMGSRLVGIISSRDIDFL-KEEEHDCFLEEIMTKREDLV-VAPAGITLKEANEILQ
          ..HGF.GIP.T.TG.MGS.LVGII.SRD.DFL.K.E......E......E..V.....G.TLKEANEILQ
Retrocopy MLHGFSGIPLTETGTMGSKLVGIITSRDVDFLAKKEHTTFLSEVMTPRMELVV>LTLKGVTLKEANEILQ

Parental  RSKKGKLPIVNEDDELVAIIARTDLKKNRDYPLASKDAKKQLLCGAAIGTHEDDKYRLDLLAQAGVDVVV
          RSKK.KLPIV...DELVAIIARTDLKKN.DYPLASKD..KQLLCGAA.GT.EDDK..LDLL.QAGV.VVV
Retrocopy RSKKEKLPIVSDRDELVAIIARTDLKKNQDYPLASKDSHKQLLCGAAVGTREDDKCHLDLLTQAGVNVVV

Parental  LDSSQGNSIFQINMIKYIKDKYPNLQVIGGNVVTAAQAKNLIDAGVDALRVGMGSGSICITQEVLACGRP
          LDSSQG.S..QI.M..YIK.KYP.LQVIG.NVVTAAQAKNL.DA.VD.L.VGMG.GSICITQEV.ACG.P
Retrocopy LDSSQGSSVYQITMVHYIKQKYPHLQVIGENVVTAAQAKNLMDARVDGLHVGMGYGSICITQEVMACGWP

Parental  QATAVYKVSEYARRFGVPVIADGGIQNVGHIAKALALGASTVMMGS-LLAATTEAPGEYFFSDGIRLKKY
          Q.TAVYKV.EYA..FGVP.I.DGGIQ.VG...KALALGASTVMMGS.LLA.TTEAPGEYFF.....L.KY
Retrocopy QGTAVYKVAEYAQCFGVPIIVDGGIQTVGYVVKALALGASTVMMGS<LLATTTEAPGEYFFLERVQLNKY

Parental  RGMGSLDAMDKHLS-SQNRYFSEADKIKVAQGVSGAVQDKGSIHKFVPYLIAGIQHSCQDIGAKSLTQVR
          .GMGSLDAM.K....SQ..YFS..DK.KVAQGVSG..QDKGSI.KFVPYLIAGIQHSCQDIGA.SL...R
Retrocopy QGMGSLDAMEKSST<SQKQYFSKGDKVKVAQGVSGSIQDKGSIQKFVPYLIAGIQHSCQDIGARSLSVLR

Parental  AMMYSGELKFEKRTSSAQVEGGVHSLHSYEKRL
          .MMYSGELKFEK.T.SAQ..GGVH.LH.YEK.L
Retrocopy SMMYSGELKFEKQTMSAQIKGGVHGLHLYEKQL

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	0.14 RPM	30.98 RPM
SRP007412_cerebellum	0.12 RPM	35.14 RPM
SRP007412_heart	0.41 RPM	20.70 RPM
SRP007412_kidney	0.29 RPM	43.87 RPM
SRP007412_liver	0.26 RPM	39.75 RPM
SRP007412_testis	8.91 RPM	28.28 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_594 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_594 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_697
Pan troglodytes	retro_ptro_501
Pongo abelii	retro_pabe_528

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 22 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	ENSGGOG00000003963	6 retrocopies	retro_ggor_1790, retro_ggor_1798, retro_ggor_1827, retro_ggor_2551, retro_ggor_2688, retro_ggor_2993,
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,
Rattus norvegicus	ENSRNOG00000031965	1 retrocopy	retro_rnor_1523,
Tursiops truncatus	ENSTTRG00000017349	2 retrocopies	retro_ttru_1148, retro_ttru_1665,