RetrogeneDB ID: retro_itri_1255

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393415.1:2675435..2676152(+)
• Located in intron of: ENSSTOG00000008633

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF128
• Ensembl ID: ENSSTOG00000022922
• Aliases: None
• Description: ring finger protein 128, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:21153]

Sequence

>retro_itri_1255
TGGCTGGCACTCATTGAACGGGGCGGTTGTACCTTCACACAGAAAATTAAGGTGGCAACTGAGAAGGGAGCCAGTGGAGT
GATCATCTATAACTTTCCGGGAACTGGCAATCAGGTTTTCCCCATGTCTCATCAGGCATTTGAAGACACCATTGTAGTGA
TGATTGGTAACTTAAAAGGCACAGAAATTTTGCATTTAATTCAGAAGGGATTTCATGTTACAGCCATGGTTGCGGTGGGG
AGAAAACACATCATCTGGATGAATCACTACTTTGTCTCCTTTATGATCGTCACAACCGCGACTTTAGCATATTTCATCTT
TTATCACATAAGAAGACTTTGGGTAGCAAGGATTCAGCACAGGAGATGGCAGCGATTAACAACAGACCTCAAGAAAGCTT
TTGGCCAACTCCAACTTAGGGTATTAAAAGAGGGGGATGAGGAATTAAATCCAAATGGAGATAGCTGTGTAGTTTGTTTT
GAACCCTATAAGCCTAATGATACGATTCGTATTCTGACTTGTAAACACTTTTTCCACAAGAATTGCATTGACCCCTGGAT
TCTAGCCCATGGCACGTGCCCCATGTGCAAATGTGACATTCTTAAAGCTTTGGGAATTCATGTGGATATTGAAGATGGAA
CAGAATCTTTGCAAGTTCTAATGTCAAACGAAATACCAGAAACCCTATCACCTAGGGACGAGGAGACAAATCATGAG

Alignment

ORF - retro_itri_1255 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.14 %
• Parental protein coverage: 57.24 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  WLALIQRGGGCTFADKIHLAYERGASGAVIFNFPGTRNEVIPMSHPGAGDIVAIMIGNLKGTKILQSIQK
          WLALI.RGG.CTF..KI..A.E.GASG..I.NFPGT.N.V.PMSH....D....MIGNLKGT.IL..IQK
Retrocopy WLALIERGG-CTFTQKIKVATEKGASGVIIYNFPGTGNQVFPMSHQAFEDTIVVMIGNLKGTEILHLIQK

Parental  GIQVTMVIEVGKKHGPWVNHYSIFFVSVSFFIITAATVGYFIFYSARRLRNARAQSRKQRQLKADAKKAI
          G..VT....VG.KH..W.NHY...F..V.....TA...........RRL..AR.Q.R....L..D.KKA.
Retrocopy GFHVTAMVAVGRKHIIWMNHYFVSFMIVT----TATLAYFIFYH-IRRLWVARIQHRRWQRLTTDLKKAF

Parental  GRLQLRTLKQGDKEIGPDGDSCAVCIELYKPNDLVRILTCNHIFHKTCVDPWLLEHRTCPMCKCDILKAL
          G.LQLR.LK.GD.E..P.GDSC.VC.E.YKPND..RILTC.H.FHK.C.DPW.L.H.TCPMCKCDILKAL
Retrocopy GQLQLRVLKEGDEELNPNGDSCVVCFEPYKPNDTIRILTCKHFFHKNCIDPWILAHGTCPMCKCDILKAL

Parental  GIEVDVEDGSVSLQVPVSNDASNSASPHEEDNRSE
          GI.VD.EDG..SLQV..SN......SP..E....E
Retrocopy GIHVDIEDGTESLQVLMSNEIPETLSPRDEETNHE

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_1255 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1255 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 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000022920	1 retrocopy	retro_btau_1358,
Loxodonta africana	ENSLAFG00000002816	1 retrocopy	retro_lafr_946,
Macropus eugenii	ENSMEUG00000001567	1 retrocopy	retro_meug_1139,
Mustela putorius furo	ENSMPUG00000003695	1 retrocopy	retro_mputfur_340,
Oryctolagus cuniculus	ENSOCUG00000012328	1 retrocopy	retro_ocun_37,
Pan troglodytes	ENSPTRG00000022151	1 retrocopy	retro_ptro_2651,
Sus scrofa	ENSSSCG00000012551	1 retrocopy	retro_sscr_597,
Ictidomys tridecemlineatus	ENSSTOG00000022922	2 retrocopies	retro_itri_1254, retro_itri_1255 ,
Tursiops truncatus	ENSTTRG00000007536	1 retrocopy	retro_ttru_6,