RetrogeneDB ID: retro_itri_1704

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393647.1:207748..208438(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP1R8
• Ensembl ID: ENSSTOG00000004381
• Aliases: None
• Description: protein phosphatase 1, regulatory subunit 8 [Source:HGNC Symbol;Acc:9296]

Sequence

>retro_itri_1704
GCACTTTCACAAAGGCACACACTGCACAAGAAACCTCAGACGTTGCCATCAGCTGTGAAAGGAGAGGAAAAGATGAATGA
AGATTATGAACTCAAGGACCCATTGGGACTTCCAGAGAAAGAGACTGAGCTTGATAACCTGACAGAGCTCAACACTGTCC
ACAAGAAGTGGATTTCTATCCTCACATTAAGGAAGGAAATATGGACATTCAGAGACCAGAGCAGAAAAGGAAGAACTCAT
GGGTGACTTTCAGTGAGATGATAAGATCATCAACTCAGATGATGTGGATCCCTCAGTTGAGCAATTCCGGAACATGGTGC
AAATTGCAGTAGTCCCAGTGAAGAAAAAGTGAGTGGAGGGCCCTGGATCCCTGGCCTGGAGGAATGAGGGAGCAGGCACA
TGCAGAATTTTGCCTTTAGTGGGGGATTCTATGGGGGATTTCCCCCAACACAGTGAAGCAGGCTCCCAGCCGCATGGCAT
TCACGGGACAGCACTTGTGGGTGGCTTGCCCATGCCATACCCAAACCTTGCTCCTGATGTGGACTTGACTCCCATCGTGC
CATCAGCAGTGAAAATGAACCACGCACCAACTCCTGCAGTCTATAACCCTGAAGCTGTTCATGAGCCAAAGAAGAAAAAA
TATGCAGAGGGACTTGGCTGAGCAAGAAGCCCACACCTTTCTTTCTTATG

Alignment

ORF - retro_itri_1704 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.9 %
• Parental protein coverage: 66.38 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  ASTRAYTLREKPQTLPSAVKGDEKMSGEDDELKGLLGLPEEETELDNLTEFNTAHNKRISTLT-IEEGNL
          A.....TL..KPQTLPSAVKG.EKM..ED.ELK..LGLPE.ETELDNLTE.NT.H.K.IS.LT.I.EGN.
Retrocopy ALSQRHTLHKKPQTLPSAVKGEEKMN-EDYELKDPLGLPEKETELDNLTELNTVHKKWISILT<IKEGNM

Parental  DIQRPKRKRKNSRVTFSE-DDEIINPEDVDPSVGRFRNMVQTAVVPVKKKRVEGPGSL-GLEESGSRRMQ
          DIQRP..KRKNS.VTFSE.DD.IIN..DVDPSV..FRNMVQ.AVVPVKKK.VEGPGSL.GLEE.GSR.MQ
Retrocopy DIQRPEQKRKNSWVTFSE<DDKIINSDDVDPSVEQFRNMVQIAVVPVKKK*VEGPGSL<GLEE*GSRHMQ

Parental  NFAFSG-GLYGGLPPT-HSEAGSQPHGIHGTALIGGLPMPYPNLAPDVDLTPVVPSAVNMNPTPNPAVYN
          NFAFSG.G...G..P..HSEAGSQPHGIHGTAL.GGLPMPYPNLAPDVDLTP.VPSAV.MN..P.PAVYN
Retrocopy NFAFSG<GILWGISPN<HSEAGSQPHGIHGTALVGGLPMPYPNLAPDVDLTPIVPSAVKMNHAPTPAVYN

Parental  PEAVNEPKKKKYA-KEAWPGKKPTPSLLI
          PEAV.EPKKKKYA....W..KKPTP..L.
Retrocopy PEAVHEPKKKKYA<RGTWLSKKPTPFFLM

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_1704 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1704 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.

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012023	1 retrocopy	retro_cfam_334,
Homo sapiens	ENSG00000117751	1 retrocopy	retro_hsap_380,
Gorilla gorilla	ENSGGOG00000012062	1 retrocopy	retro_ggor_387,
Loxodonta africana	ENSLAFG00000017834	1 retrocopy	retro_lafr_1173,
Macaca mulatta	ENSMMUG00000006933	1 retrocopy	retro_mmul_491,
Pan troglodytes	ENSPTRG00000000417	1 retrocopy	retro_ptro_296,
Ictidomys tridecemlineatus	ENSSTOG00000004381	2 retrocopies	retro_itri_1611, retro_itri_1704 ,