RetrogeneDB ID: retro_itri_375

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393287.1:14038820..14039480(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX47
• Ensembl ID: ENSSTOG00000027266
• Aliases: None
• Description: DEAD (Asp-Glu-Ala-Asp) box polypeptide 47 [Source:HGNC Symbol;Acc:18682]

Sequence

>retro_itri_375
TTCTCTGCTAACATTACCCCGAAGGTACAAAAACTTCGGAGAGCAACTCTGAAGAATTCTGTAAAATCCTGTGAATTTAC
TGTTTCCTCTAAATACCAGAGGTTGGAAACTTACAGCAATGTTATCTTATTATTCCCTCTAAATTCCAGGATGCATACCT
GGTTTATATTGTCAAGGAATTGGCTGGAAACCCCATGATATTCTGCAGCACCTGTATTAATACTCAGAGAACAGCTTTGC
TGCTTTGAAATCTTGGATTTACTGCTACCCCCTCTGTGGACAGATGAGTCAGAGCAAGTGCCTAGGATTGCTGAATAAGG
TTAAGGCCGAGGCTTGCTCCGTTCTTCTGGCAACTGATGTTGCCAGCAGAGGTTTGGACATCCCTTATGTGGATTCGGTG
GTCACCTCGGACATCTGCCTCATTCCAGTGATTACGTCTATGGTATAGGTGGAACAGCCACTGCTGGGCACTCTGGAAAG
GTGAGAGCTTTTGTCACACAGTATGATGGCAACTCTTCCAGCACATACAACATTTAATTGGGGAAAAAACTGCTTGTCTT
TCCAACACAGGATGACGAGATTATGAAGTTGATAGAACAAGTGACTTAAGACCAAGGATTTGCCCTGATGGAGTTAAGGG
AACATGGAGCAAAGAAGAAA

Alignment

ORF - retro_itri_375 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.04 %
• Parental protein coverage: 51.41 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  FSATMTKKVQKLQRAALKNPVKCA---VSSKYQTVE-KLQQYYLFIPSKFKDTYLVYILNELAGNSFMIF
          FSA..T.KVQKL.RA.LKN.VK.....VSSKYQ..E..LQQ.YL.IPSKF.D.YLVYI..ELAGN..MIF
Retrocopy FSANITPKVQKLRRATLKNSVKSCEFTVSSKYQRLE<NLQQCYLIIPSKFQDAYLVYIVKELAGNP-MIF

Parental  CSTCNNTQRTALLLRNLGFTAIP-LHGQMSQSKRLGSLNKFKAKARSILLATDVASRGLDIPHVDVVVNF
          CSTC.NTQRTALLL.NLGFTA.P.L.GQMSQSK.LG.LNK.KA.A.S.LLATDVASRGLDIP.VD.VV..
Retrocopy CSTCINTQRTALLL*NLGFTATP<LCGQMSQSKCLGLLNKVKAEACSVLLATDVASRGLDIPYVDSVVTS

Parental  DIPT-HSKDYIHRVGRTARAGRSGKAITFVTQYDV-ELFQRIEHLIG-KKLPVFPTQDDEVMMLTERVTE
          DI...HS.DY....G.TA.AG.SGK...FVTQYD...LFQ.I.HLIG.KKL.VFPTQDDE.M.L.E.VT.
Retrocopy DICL<HSSDYVYGIGGTATAGHSGKVRAFVTQYDG<QLFQHIQHLIG>KKLLVFPTQDDEIMKLIEQVT*

Parental  AQRFARMELREHGEKKK
          .Q.FA.MELREHG.KKK
Retrocopy DQGFALMELREHGAKKK

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_375 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_375 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Otolemur garnettii	ENSOGAG00000003748	2 retrocopies	retro_ogar_2780, retro_ogar_802,
Ictidomys tridecemlineatus	ENSSTOG00000027266	1 retrocopy	retro_itri_375 ,
Tupaia belangeri	ENSTBEG00000013697	1 retrocopy	retro_tbel_2420,