RetrogeneDB ID: retro_itri_1254

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393415.1:2671959..2672616(+)
• 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_1254
TCTTGGCTGGCCCTCATTGAACGGGGAGGCTGTACTTTTACACATAAAATCAACGTGGCAGCAGAAAAGGGAGCAAATGG
GGTGATCATCTATAACTATCCAGGTACGGGCAACAAAGTGTTTCCTATGTCTCACCAGGGAACAGAAAACATAGTTGCAG
TGATGATAGGCAACCTAAAAGGCATGGAACTTTTGCACTTGATTCAGAAAGGAGTCTATGTGACCATCATCATTGAAGTG
GGGAGAATGCACATGCCATGGCTAAGCCACTATGTCATGTCTCTGTTTACCTTCCTGGCAGCCACAGTTGCCTACCTTTT
CTTGTACTGTGCCTGGAGACCTAGAGCACCCAATTCTTCCACCATAAGACGAAGACAGATAAAGGCTGATGTGAAGAAAG
CTATTGGTCAGCTTCAACTTCGAGTGCTCAAAGAAGGGGATAAGGAGCTAGATCCAAATGAGGACAACTGCGTTGTTTGT
TTTGACATATACAAACCTCAAGATGTAGTACGTATTTTAACTTGCAAGCATTTTTTCCATAAGACATGCATTGACCCCTG
GCTTTTAGCCCATAGGACATGCCCCATGTGCAAATGTGACATTCTGAAAACTTAGAAACCTAGAGCCTCTTCTGAAGATA
TAGCCAGATCTTTTCAA

Alignment

ORF - retro_itri_1254 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.89 %
• Parental protein coverage: 52.57 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SWLALIQRGGGCTFADKIHLAYERGASGAVIFNFPGTRNEVIPMSHPGAGDIVAIMIGNLKGTKILQSIQ
          SWLALI.RGG.CTF..KI..A.E.GA.G..I.N.PGT.N.V.PMSH.G...IVA.MIGNLKG...L..IQ
Retrocopy SWLALIERGG-CTFTHKINVAAEKGANGVIIYNYPGTGNKVFPMSHQGTENIVAVMIGNLKGMELLHLIQ

Parental  KGIQVTMVIEVGKKHGPWVNHYSIFFVSVSFFIITAATVGYFIFYSARRLRNARAQSRKQRQLKADAKKA
          KG..VT..IEVG..H.PW..HY....V...F....A.....F..Y.A.R.R.........RQ.KAD.KKA
Retrocopy KGVYVTIIIEVGRMHMPWLSHY----VMSLFTFLAATVAYLFL-YCAWRPRAPNSSTIRRRQIKADVKKA

Parental  IGRLQLRTLKQGDKEIGPDGDSCAVCIELYKPNDLVRILTCNHIFHKTCVDPWLLEHRTCPMCKCDILKA
          IG.LQLR.LK.GDKE..P..D.C.VC...YKP.D.VRILTC.H.FHKTC.DPWLL.HRTCPMCKCDILK.
Retrocopy IGQLQLRVLKEGDKELDPNEDNCVVCFDIYKPQDVVRILTCKHFFHKTCIDPWLLAHRTCPMCKCDILKT

Parental  LGIEVDVEDGSVSLQ
          .......ED...S.Q
Retrocopy *KPRASSEDIARSFQ

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_1254 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1254 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 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,