RetrogeneDB ID: retro_itri_511

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393297.1:11263139..11264074(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000012187
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NADK
• Ensembl ID: ENSSTOG00000012783
• Aliases: None
• Description: NAD kinase [Source:HGNC Symbol;Acc:29831]

Sequence

>retro_itri_511
CTGGAAGAGAACAACATGATCATGTACATGGAAAAGAAGGTGCTGGAAGACCTTGCTATAGTGAGTGACAAAACTTCGGG
TTCATGAAGAAGAGGTTCTTCACTTTCTGGGAAGATTATTATGACATCTCCAACCAGGTCGACTTCATCATCTGTCTGGG
GGTGACGGGATCCTGCTCTGTGCCTCCTCGCTCTTCCAGGGAGAGTGCCTCTGGTTATGGCGTTCTACCTGGGCTCCCTG
AGCTTCCTGACCCTGTTCAACCTCAAGAACTTTCAGTCCCAAGTAACCCAGGTGATAGTAGGGAATGCAGCTATTGTTCT
TCGGAGTGGGCTGAGGGTCAGGGTGGTGAAGGAGCTCAGAGGCAAGAAGAGGACCACCCATAATGCGTTCAGTGAGAATG
GCCTGCCAGCCCCAGGCCTGGACACAGAGATTGGGAAGCAGCCCATGCAGTACCAGATGTTGAACGAAGTGATGACTGAT
AGAGGTCCCTCCTCATACCTGTCCAACATGAATGTCTACCTGGACAGACACCTCATGACCACGGTGCAGGGCAATGCAGT
GATTGTGTCCACCCGGACCAGCGGCATAGTTTATGCAGCTGCAGCGGGAGCCTCCATGATCCACCCCAAAGTGCCGGCCA
TTATGCTCACACCCATCTGCTCACACTTGCCGTCCTGCTCGCCCAAGGTGGTCCCTGCAGGGGTCGAGCTGAAGATCATG
GTGTCACCAGAAGCCAGGAACACTGCATGGGTGTCCTTGGATACATGGAAGCCTCAGGAAGTCTGCCATGGAAACAGCAT
CACCGTCACTGCCTCCTGCCACCTGCTGCCCTCCATTTGTGTGCGGGGCCAGGTGAGCGACTGGTTTAAGAGCCTGGCTC
AGTGTCTGCACTGGACATGAGGAAGAAGCCAGCCCTCATGGAGGATGAGGAGGAT

Alignment

ORF - retro_itri_511 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.84 %
• Parental protein coverage: 53.31 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LQENNMIVYVEKKVLEDPAIACD-DNFGPVKKKFCTFREDYDDISNQIDFIICLG-GDGTLLYASSLFQG
          L.ENNMI.Y.EKKVLED.AI..D..NFG..KK.F.TF.EDY.DISNQ.DFIICLG.GDG.LL.ASSLFQG
Retrocopy LEENNMIMYMEKKVLEDLAIVSD<QNFGFMKKRFFTFWEDYYDISNQVDFIICLG<GDGILLCASSLFQG

Parental  S-VPPVMAFHLGSLGFLTPFNFENFQSQVTQVIEGNAAIVLRSRLKVRVVKELRGKRMTVHNGLSENGLP
          ..VP.VMAF.LGSL.FLT.FN..NFQSQVTQVI.GNAAIVLRS.L.VRVVKELRGK..T.HN..SENGLP
Retrocopy E<VPLVMAFYLGSLSFLTLFNLKNFQSQVTQVIVGNAAIVLRSGLRVRVVKELRGKKRTTHNAFSENGLP

Parental  APGLDPEVGKQAMQYQVLNEVVIDRGPSSYLSNVDVYLDGHLITTVQGDGVIVSTPTGSTAYAAAAGASM
          APGLD.E.GKQ.MQYQ.LNEV..DRGPSSYLSN..VYLD.HL.TTVQG..VIVST.T....YAAAAGASM
Retrocopy APGLDTEIGKQPMQYQMLNEVMTDRGPSSYLSNMNVYLDRHLMTTVQGNAVIVSTRTSGIVYAAAAGASM

Parental  IHPNVPAIMLTPICPHSLSFRPIVVPAGVELKIMLSPEARNTAWVSLDGRKRQEIRHGDSITITTSRYPL
          IHP.VPAIMLTPIC.H..S..P.VVPAGVELKIM.SPEARNTAWVSLD..K.QE..HG.SIT.T.S...L
Retrocopy IHPKVPAIMLTPICSHLPSCSPKVVPAGVELKIMVSPEARNTAWVSLDTWKPQEVCHGNSITVTASCHLL

Parental  PSICVRDPVSDWFESLAQCLHW-NVRKKQAHFAEDEED
          PSICVR..VSDWF.SLAQCLHW...RKK.A...EDEED
Retrocopy PSICVRGQVSDWFKSLAQCLHW<DMRKKPA-LMEDEED

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_511 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_511 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000022883	1 retrocopy	retro_ecab_140,
Ictidomys tridecemlineatus	ENSSTOG00000012783	1 retrocopy	retro_itri_511 ,