RetrogeneDB ID: retro_hsap_697

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 10:79540094..79541439(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000213513
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: IMPDH2
• Ensembl ID: ENSG00000178035
• Aliases: IMPDH2, IMPD2, IMPDH-II
• Description: IMP (inosine 5'-monophosphate) dehydrogenase 2 [Source:HGNC Symbol;Acc:6053]

Sequence

>retro_hsap_697
TCTCCTCCCCTGTGGACACTGACAGAGGCTGACATGGCAATCGGGATGGCTCTGATGGGAGGTATTGGTTTCATTCACCA
CAACTGCACCCCAGAGTTCGAGGCCAATGAGGTGCTGAAGGTCAAGAAGTTTGAACAGGGCTTCATCACGGACCCTGTGG
TGCTGAGCCCCTTGCACACCGTGGGTGATGTGCTTGGAGGCCAAGATGCTGCATGGCTTCTCTGGTATCCCCCTCACTGA
GACGGGCACCATGGGCAGCAAGCTGGTGGGCATCATCACCTCCCGAGACGTCGACTTTCTTGCTAAGAAGGAGCACGCCA
CCTTCATCAGTGAGGTGATGACGCCAAGGATGGAACTGGTGGTGGCTGACGTTGAAAGGTGTGACGTTGAAAGAGGCAAA
TGAGATCCTGCAGCGTAACAAGAAAGGGAAGCTGCCTATCGTCAGTGATCGCGATGAGCTGGTGGCCATCATTGCCCGCA
CTGACCTGAAGAAGAATCGAGACTACCCTCTGGCCTCCAAGGATTCCCACAAACAGCTGCTGTGCAGGGCAGCTGTGGGC
ACCCGTGAGGATGACGAATGCCACCTGGACCTGCTCACCCAGGCGGGTGTCAATGTTGTAGTCTTGGACTCATCCCAAGG
GAGCTCGGTGTATCAGATCACCATGGTGCATTACATCAAACAGAAGTACCCCCACCTCCAGGTGATTGGGGGGAACGTGG
TGACAGCAGCCCAGGCCAAGAACCTGATGGACGCTCGTGTGGACGGGCTGCATGTGGGCATGGGCTACGGCTCCATCTGC
ATTACCCAGAAAGTGATGGCCTGCGGTTGGCCCCAGGGCACTGCTGTGTACAAGGTGGCCAAGTATGCCCAGTGCTTTGG
TGTGCCCATCATAGTCGATGGTGGCATCCAGACTGTGGGGCACGTGGTCAAGGCCCTGGCCCTTGGAGCCTCCACAGTGA
TGATGGGCTCCTGCTGGCCACCACCACGGAGGCACCTGGTGAGTACTTCTTCTTAGAAAGGGTGCAGCTCAAGAAGTACC
AGGGCATGGGCTCACTGGATGCCATGGAGAAGAGCAGCAGCAGCCAGAAACGATACTTCAGCAAGGGGGATAAGGTGAAG
ATCGCACAGGGTGTCTCGGGCTCCATCCAGGACAAAGGGTCCATTCAGAAGTTCGTGCCCTACCTCATAGCGGGCATCCA
GCACAGCTGCCAGGATATCGGGGCCCGCAGCCTGTCTGTCCTTTGGTCCATGATGTACTCAGGGGAGCTCAAGTTTGAGA
AGCAGACCATGTCGGCCCAGATCAAGGGTGGTGTCCATGGCCTGCACTCGTATGAGAAGCAGCTG

Alignment

ORF - retro_hsap_697 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.84 %
• 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.ANEV.KVKK.EQGFITDPVVLSP...V.DV..EAK.
Retrocopy SPPLWTLTEADMAIGMALMGGIGFIHHNCTPEFEANEVLKVKKFEQGFITDPVVLSPLHTVGDVL>EAKM

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

Parental  SKKGKLPIVNEDDELVAIIARTDLKKNRDYPLASKDAKKQLLCGAAIGTHEDDKYRLDLLAQAGVDVVVL
          .KKGKLPIV...DELVAIIARTDLKKNRDYPLASKD..KQLLC.AA.GT.EDD...LDLL.QAGV.VVVL
Retrocopy NKKGKLPIVSDRDELVAIIARTDLKKNRDYPLASKDSHKQLLCRAAVGTREDDECHLDLLTQAGVNVVVL

Parental  DSSQGNSIFQINMIKYIKDKYPNLQVIGGNVVTAAQAKNLIDAGVDALRVGMGSGSICITQEVLACGRPQ
          DSSQG.S..QI.M..YIK.KYP.LQVIGGNVVTAAQAKNL.DA.VD.L.VGMG.GSICITQ.V.ACG.PQ
Retrocopy DSSQGSSVYQITMVHYIKQKYPHLQVIGGNVVTAAQAKNLMDARVDGLHVGMGYGSICITQKVMACGWPQ

Parental  ATAVYKVSEYARRFGVPVIADGGIQNVGHIAKALALGASTVMMGS-LLAATTEAPGEYFFSDGIRLKKYR
          .TAVYKV..YA..FGVP.I.DGGIQ.VGH..KALALGASTVMMGS.LLA.TTEAPGEYFF.....LKKY.
Retrocopy GTAVYKVAKYAQCFGVPIIVDGGIQTVGHVVKALALGASTVMMGS<LLATTTEAPGEYFFLERVQLKKYQ

Parental  GMGSLDAMDKHLSSQNRYFSEADKIKVAQGVSGAVQDKGSIHKFVPYLIAGIQHSCQDIGAKSLTQVRAM
          GMGSLDAM.K..SSQ.RYFS..DK.K.AQGVSG..QDKGSI.KFVPYLIAGIQHSCQDIGA.SL.....M
Retrocopy GMGSLDAMEKSSSSQKRYFSKGDKVKIAQGVSGSIQDKGSIQKFVPYLIAGIQHSCQDIGARSLSVLWSM

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
bodymap2_adipose	0.06 RPM	104.98 RPM
bodymap2_adrenal	0.14 RPM	77.95 RPM
bodymap2_brain	0.00 RPM	27.59 RPM
bodymap2_breast	0.08 RPM	80.06 RPM
bodymap2_colon	0.04 RPM	124.21 RPM
bodymap2_heart	0.06 RPM	26.16 RPM
bodymap2_kidney	0.12 RPM	67.42 RPM
bodymap2_liver	0.08 RPM	22.71 RPM
bodymap2_lung	0.00 RPM	80.70 RPM
bodymap2_lymph_node	0.00 RPM	108.07 RPM
bodymap2_ovary	0.04 RPM	223.73 RPM
bodymap2_prostate	0.23 RPM	159.45 RPM
bodymap2_skeletal_muscle	0.00 RPM	160.71 RPM
bodymap2_testis	1.07 RPM	78.22 RPM
bodymap2_thyroid	0.23 RPM	61.28 RPM
bodymap2_white_blood_cells	0.04 RPM	59.48 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_697 was not detected

EST

No EST(s) were mapped for retro_hsap_697 retrocopy.

TSS

No TSS is located nearby retro_hsap_697 retrocopy 5' end.

Lab

retro_hsap_697 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_697 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_501
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	ENSG00000106348	7 retrocopies	retro_hsap_2360, retro_hsap_2368, retro_hsap_2608, retro_hsap_3797, retro_hsap_4005, retro_hsap_4247, retro_hsap_4808,
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,
Rattus norvegicus	ENSRNOG00000031965	1 retrocopy	retro_rnor_1523,
Tursiops truncatus	ENSTTRG00000017349	2 retrocopies	retro_ttru_1148, retro_ttru_1665,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.04 RPM
CEU_NA11843	0.11 RPM
CEU_NA11930	0.03 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.04 RPM
CEU_NA12751	0.10 RPM
CEU_NA12760	0.04 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.03 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.00 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.05 RPM
FIN_HG00338	0.02 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.02 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.04 RPM
GBR_HG00099	0.03 RPM
GBR_HG00111	0.00 RPM
GBR_HG00114	0.05 RPM
GBR_HG00119	0.02 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.00 RPM
GBR_HG00134	0.00 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.08 RPM
GBR_HG00143	0.10 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.02 RPM
TSI_NA20518	0.06 RPM
TSI_NA20532	0.14 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.03 RPM
TSI_NA20765	0.08 RPM
TSI_NA20771	0.03 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.03 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.06 RPM
YRI_NA19093	0.03 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.03 RPM
YRI_NA19118	0.04 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.02 RPM
YRI_NA19223	0.06 RPM

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Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).