RetrogeneDB ID: retro_rnor_1523

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:118529346..118530440(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Impdh2
• Ensembl ID: ENSRNOG00000031965
• Aliases: Impdh2, IMPD 2, IMPDH 2
• Description: Inosine-5'-monophosphate dehydrogenase 2 [Source:UniProtKB/Swiss-Prot;Acc:E9PU28]

Sequence

>retro_rnor_1523
GGGCTCACCGCGCAGCAGCTCTTCACCAATGCGGAAGGCCTCACCTACCACGATTTCCTGATCCTTCCAGGATTCATAGA
CTTATGGCAGATGAAGCGGACCTGACATCAGCCCTGACCCGGAAGACCACACTGAAGACACCACTGATCTCGTCTCCCAT
GGATACTGTGACAGAGGCTGACATGGCCATTGCAATGGCTCTCATGGGAGGAATTGGTTTCATTCACTTTAACTGTACCC
CAGAGTTCCAGGCCAATGAAGAGCGGAAGGTCAAGAAGTTTGAGCAAGTCTTCATCACAGACCCTGTGGTCCTGAGCCCT
TCACATACCGTGAGTGATGTTTTCAATGCCAAAATACAACATGGCTTCTCTGGTATCCCTATCCCCGCTATGGGCACCAT
CGGAGCAAGCTGGTGAGCATCGTTACCTCCTGAGACATCGACTTCCTTGCTGAGAAGGACCACACCACCCTCCTCAGTGA
GGTGATGACGCCGAGGACCGAGCTGATGGTGGCTCCAGCAGGTGTGACATTGAAAGAGGCAAATGAGATTTTATAGCGCA
GCAAGAAGGGAAGCTGCCCATAGTCAACGATCAAGGCGAGCTGGTAGCCATCATTGCACGCACAGACCTGAAAAAGAACA
GAGACTACCCTCTGGCCTCCAAGGACTTCCACAAGTATCTGTTGTGTGGGACATCTGTGGACACCCATGAGGATAGCAAA
TACCATGTGGATCTGCTCACTCAGTCCAGCGCTGACTTCATAGTGCTAGATTCATCCCAGGGGAACTCGGTATATCAGAT
CGCCATGGTGCGCTATATCAAGCAGAAGTATCCCCACCTCCAAGTGACTGGGGAAACGTAGTGACAGCGGCCCAGGTCAA
GAATACTAGTGTGGATGGGCTTCCCGTGTGCCTGGGCTATGGTTCCATCTGCATCACTCAGGAATTGATGGCCTGTGGTC
GACCCCAGGGCACTGCTGTCTACAAGGTGGGTGAGTATGCCCGGCGCTTTGGGGTGCTGGTAATAGCTGATGGTGGTATC
CAGACCGTGGGCCATGTGGTCAAAGCCCTGGCACTCGGAGCCTCTACAGTGCTG

Alignment

ORF - retro_rnor_1523 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.65 %
• Parental protein coverage: 71.79 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GLTAQQLFNCGDGLTYNDFLILPGYIDF-TADQVDLTSALTKKITLKTPLVSSPMDTVTEAGMAIAMALT
          GLTAQQLF....GLTY.DFLILPG.ID...AD..DLTSALT.K.TLKTPL.SSPMDTVTEA.MAIAMAL.
Retrocopy GLTAQQLFTNAEGLTYHDFLILPGFIDL<MADEADLTSALTRKTTLKTPLISSPMDTVTEADMAIAMALM

Parental  GGIGFIHHNCTPEFQANEVRKVKKYEQGFITDPVVLSPKDRVRDVFEAKARHGFCGIPITDTGRMG-SRL
          GGIGFIH.NCTPEFQANE.RKVKK.EQ.FITDPVVLSP...V.DVF.AK..HGF.GIPI...G..G.S.L
Retrocopy GGIGFIHFNCTPEFQANEERKVKKFEQVFITDPVVLSPSHTVSDVFNAKIQHGFSGIPIPAMGTIG<SKL

Parental  VGIISSRDIDFLKEEEHDRFLEEIMTKREDLVVAPAGVTLKEANEILQRSKK-GKLPIVNESDELVAIIA
          V.I..S.DIDFL.E..H...L.E.MT.R..L.VAPAGVTLKEANEIL.RSKK.GKLPIVN...ELVAIIA
Retrocopy VSIVTS*DIDFLAEKDHTTLLSEVMTPRTELMVAPAGVTLKEANEIL*RSKK<GKLPIVNDQGELVAIIA

Parental  RTDLKKNRDYPLASKDTKKQLLCGAAIGTHEDDKYRLDLLALAGVDVVVLDSSQGNSIFQINMIKYIKEK
          RTDLKKNRDYPLASKD..K.LLCG....THED.KY..DLL.....D..VLDSSQGNS..QI.M..YIK.K
Retrocopy RTDLKKNRDYPLASKDFHKYLLCGTSVDTHEDSKYHVDLLTQSSADFIVLDSSQGNSVYQIAMVRYIKQK

Parental  YPNLQVIG-GNVVTAAQAKNLIDAGVDALRVGMGSGSICITQEVLACGRPQATAVYKVSEYARRFGVPVI
          YP.LQV.G.GNVVTAAQ.KN.....VD.L.V..G.GSICITQE..ACGRPQ.TAVYKV.EYARRFGV.VI
Retrocopy YPHLQVTG<GNVVTAAQVKN---TSVDGLPVCLGYGSICITQELMACGRPQGTAVYKVGEYARRFGVLVI

Parental  ADGGIQNVGHIAKALALGASTVM
          ADGGIQ.VGH..KALALGASTV.
Retrocopy ADGGIQTVGHVVKALALGASTVL

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
SRP017611_brain	0.00 RPM	31.63 RPM
SRP017611_kidney	0.00 RPM	36.85 RPM
SRP017611_liver	0.00 RPM	27.30 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1523 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1523 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1523 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 16 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,
Rattus norvegicus	ENSRNOG00000031965	1 retrocopy	retro_rnor_1523 ,
Tursiops truncatus	ENSTTRG00000017349	2 retrocopies	retro_ttru_1148, retro_ttru_1665,