RetrogeneDB ID: retro_itri_968

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393352.1:8568576..8569179(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000012288
• Aliases: None
• Description: None

Sequence

>retro_itri_968
AAAGCTTATGATAAAGCTGTGGCTTCCTTCAAGCATGCTCTAAAGAATGGTGACATTCGTGAAACTTCAGATAAACCAAA
GGGCAAATCTAGGTGAAAACCTCTTAAGAAGAATAAAAGCCGGAAGACTGTTTCGACCTCCCTGAAACAGTGGAAAGCTG
GTGACAAGTGTTCTGCCATTTGGTCAGAAGATGGCTATATTTACCAGCTACCATTGCTTCAGTTGATTTTTAAGAGAGAA
AACTGTATCGTGATTTACACTGGATATGGAAATAGAGAAAAATCTGTCGGATCTGCTTTCCCCAACCTCTGAAGTAGGTA
ATAATATAGAACAGAAAGCTCAGGAGAATGAAAATGAAAGTCAAGTTTCTGAAGATGAAAGTGAAAACTCCTCTAGATCT
CCTGGAAATAAATCAAATAACATCAAGTCAAAAGCAATTCCATGGAACTATTTCCTTATTCCACTACTACCAATGCCAGG
GTCAGGATTGGGACCAGGAAAGCCAGGCCTAAAATTCAGTAGCCCACCACCACCTTCACCACCACTTCATGTTGGTTACC
TACATTTCCTTCAGGCCCATCAATAATTCTCCACCCCATCCCC

Alignment

ORF - retro_itri_968 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.29 %
• Parental protein coverage: 71.13 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KAYDKAVASFKHALKNGDICETSDKPKGTPRRKPVKKNKSQKKNTTTPVKQWKVGDKCSAIWSEDGCIY-
          KAYDKAVASFKHALKNGDI.ETSDKPKG..R.KP.KKNKS..K...T..KQWK.GDKCSAIWSEDG.IY.
Retrocopy KAYDKAVASFKHALKNGDIRETSDKPKGKSR*KPLKKNKS-RKTVSTSLKQWKAGDKCSAIWSEDGYIY<

Parental  PATIASVD-FKRETCIVIYTGYGNREEQNLSDLLSPTSEVANNIEQNTQENENESQVSTDESENSSRSPG
          PATIASVD.F.RE......T......E.NLSDLLSPTSEV.NNIEQ..QENENESQVS.DESENSSRSPG
Retrocopy PATIASVD<FLREKTVS*FT-LDMEIEKNLSDLLSPTSEVGNNIEQKAQENENESQVSEDESENSSRSPG

Parental  NKPNNIKSKATPWDCFLPPPPPMPGSGLGPGKPGLKFSGPPPPPPPPHFL-SCWLPPFPSGPPIIPPPPP
          NK.NNIKSKA.PW..FL.P..PMPGSGLGPGKPGLKFS....PPPP...L.SCWLP.FPSGP.II..P.P
Retrocopy NKSNNIKSKAIPWNYFLIPLLPMPGSGLGPGKPGLKFSS---PPPPSPPL<SCWLPTFPSGPSIILHPIP

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_968 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_968 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 13 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000012328	1 retrocopy	retro_cpor_988,
Dasypus novemcinctus	ENSDNOG00000007283	4 retrocopies	retro_dnov_1239, retro_dnov_1613, retro_dnov_1637, retro_dnov_2175,
Echinops telfairi	ENSETEG00000001406	2 retrocopies	retro_etel_1549, retro_etel_2012,
Homo sapiens	ENSG00000205571	1 retrocopy	retro_hsap_4140,
Gorilla gorilla	ENSGGOG00000026704	1 retrocopy	retro_ggor_2780,
Myotis lucifugus	ENSMLUG00000010603	1 retrocopy	retro_mluc_1623,
Macaca mulatta	ENSMMUG00000020214	1 retrocopy	retro_mmul_216,
Nomascus leucogenys	ENSNLEG00000004454	1 retrocopy	retro_nleu_1054,
Oryctolagus cuniculus	ENSOCUG00000017097	1 retrocopy	retro_ocun_617,
Pan troglodytes	ENSPTRG00000016955	1 retrocopy	retro_ptro_2813,
Sus scrofa	ENSSSCG00000016970	1 retrocopy	retro_sscr_654,
Ictidomys tridecemlineatus	ENSSTOG00000012288	1 retrocopy	retro_itri_968 ,
Tupaia belangeri	ENSTBEG00000002399	1 retrocopy	retro_tbel_1033,