RetrogeneDB ID: retro_itri_1443

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393488.1:1736112..1736511(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF138
• Ensembl ID: ENSSTOG00000002293
• Aliases: None
• Description: ring finger protein 138, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:17765]

Sequence

>retro_itri_1443
CCACTGTGCCCTGAGGTGCTAGAAACACTCTGTAGAGGATGACCTGGCAGCACTTCTTTTGTAACAAAAATGTGTCCTAC
TGAGATACGAGAGCGTGTACTAAATCATCATATCTGCCATCAAACTAGTACCAGAAGAAAGAAGTCATGTCTTGAGTGAA
CCTTACACATTGAAAATGTCACGAGGGAGTTTTCTAGTAGCTGTGGATGCTGTAAAAACAGATTAAATTCTAGCGCAAGA
GATATCATTACAAATCTTATAAAAAAGATCAAGATGAATACAGTGCAGCCTCTATAATTCCTACTTCTCAGATCTCTCAA
GGTTCAGCAGGGAACATTAAACAGGAGTGAAACTTTCACATCTGACAGCATGGGAAACTCTCCAGGGAATACTCAGTCT

Alignment

ORF - retro_itri_1443 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.09 %
• Parental protein coverage: 54.51 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  PVCQEVLKTPVR-TAACQHVFCR-KCFLTAMRESGIHCPLCRGNVTRRERACPERALDLENIMRKFSGSC
          P.C.EVL.T..R.....QH.FC..K...T..RE.......C....TRR...C.E..L..EN..R.FS.SC
Retrocopy PLCPEVLETLCR<RMTWQHFFCN>KMCPTEIRERVLNHHICHQTSTRRKKSCLE*TLHIENVTREFSSSC

Parental  RCCA-KQIKFYRMRHHYKSCKKYQDEYGVSSIIPNFQISQDSVGN-SNRSETSTSDNTETYQENTSS
          .CC..KQIKF.R.R.HYKS.KK.QDEY...SIIP..QISQ.S.GN..NRSET.TSD.......NT.S
Retrocopy GCCK<KQIKF*RKRYHYKSYKKDQDEYSAASIIPTSQISQGSAGN>LNRSETFTSDSMGNSPGNTQS

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_1443 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1443 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 15 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020160	1 retrocopy	retro_btau_322,
Choloepus hoffmanni	ENSCHOG00000012689	6 retrocopies	retro_chof_1043, retro_chof_1242, retro_chof_1931, retro_chof_418, retro_chof_714, retro_chof_793,
Callithrix jacchus	ENSCJAG00000020875	1 retrocopy	retro_cjac_2325,
Felis catus	ENSFCAG00000014180	2 retrocopies	retro_fcat_1383, retro_fcat_379,
Homo sapiens	ENSG00000134758	1 retrocopy	retro_hsap_3319,
Gorilla gorilla	ENSGGOG00000027857	1 retrocopy	retro_ggor_1302,
Loxodonta africana	ENSLAFG00000003811	1 retrocopy	retro_lafr_408,
Monodelphis domestica	ENSMODG00000010850	4 retrocopies	retro_mdom_1468, retro_mdom_387, retro_mdom_708, retro_mdom_725,
Mustela putorius furo	ENSMPUG00000006982	1 retrocopy	retro_mputfur_276,
Nomascus leucogenys	ENSNLEG00000006401	1 retrocopy	retro_nleu_1665,
Pongo abelii	ENSPPYG00000009094	1 retrocopy	retro_pabe_2734,
Pan troglodytes	ENSPTRG00000009956	1 retrocopy	retro_ptro_2155,
Pteropus vampyrus	ENSPVAG00000003778	2 retrocopies	retro_pvam_1316, retro_pvam_1379,
Rattus norvegicus	ENSRNOG00000015645	3 retrocopies	retro_rnor_2316, retro_rnor_808, retro_rnor_965,
Ictidomys tridecemlineatus	ENSSTOG00000002293	2 retrocopies	retro_itri_1443 , retro_itri_576,