RetrogeneDB ID: retro_itri_1744

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393709.1:32486..32782(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000012736
• Aliases: None
• Description: None

Sequence

>retro_itri_1744
AAGATCAACAAGATGATGGAAAAACTCAAGACTCATGTGAAAGCCCAGAACAGCTCAACTAGCCATGATAAAATGGGTTT
TAAGTGTTGCTTTCTACATATTGCAAGCTGCCTTGATGAAGTCACTCATTTGGAAGTATTATACTGTCCACTGTGACTGT
TGTGCTGAGGAAATAAACAACACCACTAGACTGCCTGGTAGACTTCCCTACAAAAATAGCAGGTGGCGTTGGAATTACTA
GTTGGATTTTATTCTGTAACTAGTTGTGGCAACACTTCCTACTTCATCCTTTCAGC

Alignment

ORF - retro_itri_1744 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73. %
• Parental protein coverage: 55.75 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KINKMTDKLKTHVKA-RTAQLAKIKWVMSVAFYILQAALMISLIWKYYSV-PVAVVPSKWITPLDRLVAF
          KINKM..KLKTHVKA.RTAQLA.IKWV.SVAFYILQAALM.SLIWKYY.V..V.VV..K..TPLD.LV.F
Retrocopy KINKMMEKLKTHVKA>RTAQLAMIKWVLSVAFYILQAALMKSLIWKYYTV>TVTVVLRK*TTPLDCLVDF

Parental  PTRVAGGVGITCWILVCNKV-VAIVLHPFS
          PT..AGGVGIT.WIL.CN.......LHPFS
Retrocopy PTKIAGGVGITSWILFCN*LWQHFLLHPFS

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_1744 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1744 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 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005714	2 retrocopies	retro_cjac_2153, retro_cjac_3208,
Dasypus novemcinctus	ENSDNOG00000024987	1 retrocopy	retro_dnov_1496,
Homo sapiens	ENSG00000182093	1 retrocopy	retro_hsap_3080,
Gorilla gorilla	ENSGGOG00000013144	1 retrocopy	retro_ggor_2116,
Microcebus murinus	ENSMICG00000015808	1 retrocopy	retro_mmur_1275,
Macaca mulatta	ENSMMUG00000020654	2 retrocopies	retro_mmul_1966, retro_mmul_853,
Mus musculus	ENSMUSG00000023147	1 retrocopy	retro_mmus_1452,
Nomascus leucogenys	ENSNLEG00000013146	1 retrocopy	retro_nleu_2014,
Otolemur garnettii	ENSOGAG00000026761	1 retrocopy	retro_ogar_2691,
Pongo abelii	ENSPPYG00000011427	1 retrocopy	retro_pabe_2552,
Pan troglodytes	ENSPTRG00000013915	1 retrocopy	retro_ptro_2078,
Ictidomys tridecemlineatus	ENSSTOG00000012736	1 retrocopy	retro_itri_1744 ,
Tursiops truncatus	ENSTTRG00000015373	1 retrocopy	retro_ttru_1711,