RetrogeneDB ID: retro_pabe_3102

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7:135608423..135609962(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IMPDH1
• Ensembl ID: ENSPPYG00000017976
• Aliases: None
• Description: IMP (inosine 5'-monophosphate) dehydrogenase 1 [Source:HGNC Symbol;Acc:6052]

Sequence

>retro_pabe_3102
CGCGGCAGCATGGCAGACTACCTGATCAGAGGTGGCACCGGCTACATGTCCAAGGACGGGCTCACGGCGCAGCAGCTCTT
CACCGGTGCAGCAGCTTGCGACGGCCTCACCTACAACAACTTCCTGATTCTCCCAGGATTCATAGACTTCATAGCTGATG
AGGTGGACCTGACCTCAGCCCTGACCTGGAAGATCACGCTGAAGACGCCACTGATCTCCTCCCCCATGGACACTGTGACA
GAAGCTGACATGGCCATCGCGATGGCTCTGATGGGAGGTATTGGTTTCATTCACCACAACTGCACCCCAGAGTTCCAGGC
CAACGAGGTGCGGAAGGTCAAGAAGTTTGAACGGGGCTTTTTCATGGACCCCGTGGTACTGAGCCCCTCACACACTATGG
GTGATGTGCTGGAGGCCAAGATGCGGCATGGCTTCTCTGGCAACCCCATCACTGAGACAGGCACCATGGGCAGCAAGCTG
CTGGACATTGTCACCTCCCGAGACATAACTTTCTTGCTGAGAAGGACCACATCACCCTCCTCAGTGAGGTGATGACACCA
AGGATTGAGCTGGTGGTGGCTCCAGCAGGTGTGATGTTGAAAGAGGCAAATGAGATCCTGCAGCCATAGCAAGAAAGGGA
AGCTGCCTGTCGTCAATGATCGCAATGAGCTGGTGGCCATCATCGCCCACACCAACATGAAGAAGAACTGAGACTACCCT
CTGGCCTCCAAGGATTCCCACAAGCAGCTGCTGTGCGGGGCAGCTGTGGGCACCCGTGAGGATGACAAATACCGCCTGGA
CCTGCTCACCCAGGTGGGCGTTGACGTCATAGTCTTGGACTTGTCCCAAGGGAACTCATTGTATCAGATGCCCATGGTGT
ATTACATCAAACAGAAGTACCCCCACCTCCAGGTGATTGGGGGGAACATGGTGACAGCAGCCCAGGCCAAGAACCTGATT
GACGCTGGTGTGGAAGCGCTCTGCGTGGGCATGGGCTGCAGCTCCATCTGCATCACCCAGGAAGTGATGGCCTACAGTCA
GCCCCAGGGCACTGCTGTGTACAAGGTGGCCGAGTATGCCCGGCATTTTGGTGTGCCTATCATAGCCGATGGCGGCATCC
AGACCATGGGGCACGTGGTCAAGGCCCTGGCCCTTGGAGCCTCCACAGTGATGATGGGCTCCCTACTGGCCGCCACCACG
GAGGTCCCCAGCGAGTACTTCTTCTCTGACGAGGTGTGGCTCAAGAAGTACCGGGGCATGGGCTCACTGGATGTCCTGGA
GAAGAGCAGCAGCAGCCAGAAACAATACTTCATCAAGGGGTATAATGTGAAGATCACGCAGGGTGTCTCCGGCTCCATCC
AGGACAAAGGGTCCATTTAGAAGTTCATGCCCTACCTCATAGTGGGCATCCAGCATGGCTGCCAGGATACTGGGGCCCAC
AACCTGTCTGTCCTTTGGTCCATGATTTACTCAGGAGAGCGCAAGTTTGAGAAGTGGACCATGTTGGCCCAGATCAAGGG
TGGCGTCCAAGGCCTGTAC

Alignment

ORF - retro_pabe_3102 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.05 %
• Parental protein coverage: 86.15 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RASMADYLISGGTGYVPEDGLTEQKNF---ASADGLTYNDFLILPGFIDFIADEVDLTSALTRKITLKTP
          R.SMADYLI.GGTGY...DGLT.Q..F...A..DGLTYN.FLILPGFIDFIADEVDLTSALT.KITLKTP
Retrocopy RGSMADYLIRGGTGYMSKDGLTAQQLFTGAAACDGLTYNNFLILPGFIDFIADEVDLTSALTWKITLKTP

Parental  LISSPMDTVTEADMAIAMALMGGIGFIHHNCTPEFQANEVRKVKKFEQGFITDPVVLSPSHTVGDVLEAK
          LISSPMDTVTEADMAIAMALMGGIGFIHHNCTPEFQANEVRKVKKFE.GF..DPVVLSPSHT.GDVLEAK
Retrocopy LISSPMDTVTEADMAIAMALMGGIGFIHHNCTPEFQANEVRKVKKFERGFFMDPVVLSPSHTMGDVLEAK

Parental  MRHGFSGIPITETGTMGSKLVGIVTSRDI-DFLAEKDHTTLLSEVMTPRIELVVAPAGVTLKEANEILQ-
          MRHGFSG.PITETGTMGSKL..IVTSRDI..FLAEKDH.TLLSEVMTPRIELVVAPAGV.LKEANEILQ.
Retrocopy MRHGFSGNPITETGTMGSKLLDIVTSRDI<NFLAEKDHITLLSEVMTPRIELVVAPAGVMLKEANEILQ>

Parental  RSKKGKLPIVNDRDELVAIIARTDLKKNRDYPLASKDSQKQLLCGAAVGTREDDKYRLDLLTQAGVDVIV
          .SKKGKLP.VNDR.ELVAIIA.T..KKN.DYPLASKDS.KQLLCGAAVGTREDDKYRLDLLTQ.GVDVIV
Retrocopy HSKKGKLPVVNDRNELVAIIAHTNMKKN*DYPLASKDSHKQLLCGAAVGTREDDKYRLDLLTQVGVDVIV

Parental  LDSSQGNSVYQIAMVHYIKQKYPHLQVIGGNVVTAAQAKNLIDAGVDGLRVGMGCGSICITQEVMACGRP
          LD.SQGNS.YQ..MV.YIKQKYPHLQVIGGN.VTAAQAKNLIDAGV..L.VGMGC.SICITQEVMA...P
Retrocopy LDLSQGNSLYQMPMVYYIKQKYPHLQVIGGNMVTAAQAKNLIDAGVEALCVGMGCSSICITQEVMAYSQP

Parental  QGTAVYKVAEYARRFGVPIIADGGIQTVGHVVKALALGASTVMMGSLLAATTEAPGEYFFSDGVRLKKYR
          QGTAVYKVAEYAR.FGVPIIADGGIQT.GHVVKALALGASTVMMGSLLAATTE.P.EYFFSD.V.LKKYR
Retrocopy QGTAVYKVAEYARHFGVPIIADGGIQTMGHVVKALALGASTVMMGSLLAATTEVPSEYFFSDEVWLKKYR

Parental  GMGSLDAMEKSSSSQKRYFSEGDKVKIAQGVSGSIQDKGSIQKFVPYLIAGIQHGCQDIGARSLSVLRSM
          GMGSLD..EKSSSSQK.YF..G..VKI.QGVSGSIQDKGSI.KF.PYLI.GIQHGCQD.GA..LSVL.SM
Retrocopy GMGSLDVLEKSSSSQKQYFIKGYNVKITQGVSGSIQDKGSI*KFMPYLIVGIQHGCQDTGAHNLSVLWSM

Parental  MYSGELKFEKRTMSAQIEGGVHGLH
          .YSGE.KFEK.TM.AQI.GGV.GL.
Retrocopy IYSGERKFEKWTMLAQIKGGVQGLY

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	0.00 RPM	16.92 RPM
SRP007412_cerebellum	0.00 RPM	9.12 RPM
SRP007412_heart	0.03 RPM	3.31 RPM
SRP007412_kidney	0.00 RPM	8.88 RPM
SRP007412_liver	0.00 RPM	5.17 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3102 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3102 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3102 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3797
Pan troglodytes	retro_ptro_2575

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017770	1 retrocopy	retro_cjac_2045,
Homo sapiens	ENSG00000106348	7 retrocopies	retro_hsap_2360, retro_hsap_2368, retro_hsap_2608, retro_hsap_3797, retro_hsap_4005, retro_hsap_4247, retro_hsap_4808,
Gorilla gorilla	ENSGGOG00000003963	6 retrocopies	retro_ggor_1790, retro_ggor_1798, retro_ggor_1827, retro_ggor_2551, retro_ggor_2688, retro_ggor_2993,
Macropus eugenii	ENSMEUG00000016082	2 retrocopies	retro_meug_2095, retro_meug_542,
Macaca mulatta	ENSMMUG00000014509	2 retrocopies	retro_mmul_1551, retro_mmul_317,
Nomascus leucogenys	ENSNLEG00000012341	1 retrocopy	retro_nleu_2508,
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	ENSPTRG00000019660	7 retrocopies	retro_ptro_1087, retro_ptro_1724, retro_ptro_1758, retro_ptro_2575, retro_ptro_2719, retro_ptro_2886, retro_ptro_3198,