RetrogeneDB ID: retro_pabe_528

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 10:57351284..57352631(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IMPDH2
• Ensembl ID: ENSPPYG00000013884
• Aliases: None
• Description: IMP (inosine 5'-monophosphate) dehydrogenase 2 [Source:HGNC Symbol;Acc:6053]

Sequence

>retro_pabe_528
TCTCCTCCCTTATGGGCACTGACAGAGGCTGATGTGGCAATCGGGATGGCTCTGATGGGAGGTATTGGTTTCATTCACCA
CAACTGCACCCCAGAGTTCCAGGCCAACGAGGTGCAGAAGGTCAAGAAGTTTGAACAGGGCTTCATCATGGACCCCGTGG
TGCTGAGCCCCTCGCACACCGTGGGTGATGTGCTGGAGGCCAAGATGCTGCATGGCTTCTCTGGTATCCCCCTCACTGAG
ACAGGCACCATGGGCAGCAAGCTGGTGGGCATCGTCACCTCCCGAGACATCAACTTTCTTGCTGAGAAGGACCACACCAC
CTTCCTCAGTGAGGTGATGATGCCAACGATGGAACTGGTGGTGGCTGACGTTGAAAGGCGTGACGTTGAAAGAGGCAAAT
GAGATCCTGCAGCATAGCAAGAAAGGGAAGCTGCCTATCGTCAGTGATCACGATGAGCTGGTGGCCATCATTGCCTGCAC
TGACCTGAAGAAGAATCGAGACTACCCTCTGGCCTCCAAGGATTCCCACAAACAGCTGCTGTGCAGGGCAGCTGTGGGCA
CCCGTGAGGATGACAAATACCACCTGGACCTACTCACCCAGGCGGGCATCAACGTCATAGTCTTGGACTCGTCCCAAGGG
AACTTGGTGTATCAGATCACCATGGTGCATTACATCAAACAGAAGTACCCCCACCTCCAGGTGATTGCGGGGAACGTGGT
GACAGCAGCCCAGGCCAAGAACCTGATTGACGCTGGTGTGGACGGGCTGCACGTGAGCATGGGCTACGGCTCCATCTGCA
TCACCCAGGAAGTGATGGCCTGCGGTTGGCCCCAGGGCACTGCTGTGTACAAGGTGGCCGAGTATGCCCAGTGCTTTGGT
GTGCCCATCATAGTTGATGGCGGCATCCAGACCGTGGGGCACGTGGTCAAGGCCCTGGCCCTTGGAGCCTCCACAGTGAT
GATGGGCTTCTGCTGGCCACCACCACGGAGACACCCGGTGAGTACTTCTTCTTAGAAAGGGTGCAGCTCAAGAAGTACCA
GGGCATGGGCTCACTGGATGCCATGGAGAAGAGCAGCAGCAGCCAGAAATGATACTTCAGCGAGGGGGATAAGGTGAAGA
TCGCACAGGGTGTCTCGGGCTCCATCCAGGACAAAGGATCCATTCAGAAGTTCTCGCCCTACCTCATAGCGGGCATCCAG
CACAGCTGCCAGGATATCGGGGCCCGCAGCCTGTCTGTCCTTCGGTCCATGATGTACTCAGGGGAGCTCAAGTTTGAGAA
GCGGACCATGTCAGCCCAGATCAAGGGTGGTGTCCATGGCCTGCACTCTTACGAGAAGCAGCTGTAC

Alignment

ORF - retro_pabe_528 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.84 %
• Parental protein coverage: 87.16 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SSPMDTVTEAGMAIAMALTGGIGFIHHNCTPEFQANEVRKVKKYEQGFITDPVVLSPKDRVRDVFEAKAR
          S.P....TEA..AI.MAL.GGIGFIHHNCTPEFQANEV.KVKK.EQGFI.DPVVLSP...V.DV.EAK..
Retrocopy SPPLWALTEADVAIGMALMGGIGFIHHNCTPEFQANEVQKVKKFEQGFIMDPVVLSPSHTVGDVLEAKML

Parental  HGFCGIPITDTGRMGSRLVGIISSRDIDFLKEEEHDCFL-EEIMTKREDLV-VAPAGITLKEANEILQRS
          HGF.GIP.T.TG.MGS.LVGI..SRDI.FL.E..H..FL.E..M...E..V.....G.TLKEANEILQ.S
Retrocopy HGFSGIPLTETGTMGSKLVGIVTSRDINFLAEKDHTTFLSEVMMPTMELVV>LTLKGVTLKEANEILQHS

Parental  KKGKLPIVNEDDELVAIIARTDLKKNRDYPLASKDAKKQLLCGAAIGTHEDDKYRLDLLAQAGVDVVVLD
          KKGKLPIV...DELVAIIA.TDLKKNRDYPLASKD..KQLLC.AA.GT.EDDKY.LDLL.QAG..V.VLD
Retrocopy KKGKLPIVSDHDELVAIIACTDLKKNRDYPLASKDSHKQLLCRAAVGTREDDKYHLDLLTQAGINVIVLD

Parental  SSQGNSIFQINMIKYIKEKYPNLQVIGGNVVTAAQAKNLIDAGVDALRVGMGSGSICITQEVLACGRPQA
          SSQGN...QI.M..YIK.KYP.LQVI.GNVVTAAQAKNLIDAGVD.L.V.MG.GSICITQEV.ACG.PQ.
Retrocopy SSQGNLVYQITMVHYIKQKYPHLQVIAGNVVTAAQAKNLIDAGVDGLHVSMGYGSICITQEVMACGWPQG

Parental  TAVYKVSEYARRFGVPVIADGGIQNVGHIAKALALGASTVMM-GSLLAATTEAPGEYFFSDGIRLKKYRG
          TAVYKV.EYA..FGVP.I.DGGIQ.VGH..KALALGASTVMM.G.LLA.TTE.PGEYFF.....LKKY.G
Retrocopy TAVYKVAEYAQCFGVPIIVDGGIQTVGHVVKALALGASTVMM<GLLLATTTETPGEYFFLERVQLKKYQG

Parental  MGSLDAMDKHLSSQNRYFSEADKIKVAQGVSGAVQDKGSIHKFVPYLIAGIQHSCQDIGAKSLTQVRAMM
          MGSLDAM.K..SSQ..YFSE.DK.K.AQGVSG..QDKGSI.KF.PYLIAGIQHSCQDIGA.SL...R.MM
Retrocopy MGSLDAMEKSSSSQK*YFSEGDKVKIAQGVSGSIQDKGSIQKFSPYLIAGIQHSCQDIGARSLSVLRSMM

Parental  YSGELKFEKRTSSAQVEGGVHSLHSYEKRLF
          YSGELKFEKRT.SAQ..GGVH.LHSYEK.L.
Retrocopy YSGELKFEKRTMSAQIKGGVHGLHSYEKQLY

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	0.17 RPM	32.01 RPM
SRP007412_cerebellum	0.00 RPM	43.41 RPM
SRP007412_heart	0.06 RPM	18.51 RPM
SRP007412_kidney	0.20 RPM	32.19 RPM
SRP007412_liver	0.09 RPM	25.22 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_528 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_528 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_528 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_697
Pan troglodytes	retro_ptro_501
Gorilla gorilla	retro_ggor_594

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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 ,
Pongo abelii	ENSPPYG00000017976	7 retrocopies	retro_pabe_2133, retro_pabe_2138, retro_pabe_2346, retro_pabe_3102, retro_pabe_3292, retro_pabe_3392, retro_pabe_3736,
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,