RetrogeneDB ID: retro_itri_1555

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393538.1:2180331..2180881(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RRM2B
• Ensembl ID: ENSSTOG00000008543
• Aliases: None
• Description: ribonucleotide reductase M2 B (TP53 inducible) [Source:HGNC Symbol;Acc:17296]

Sequence

>retro_itri_1555
CTGAGTGAGAACCCTCACTGCTTTGTCTTCTTTCCTATCAGATACCATGATATTTGGCAGATTTCTAAGAAGGCTGAAGG
TTCCTTTTTGACATATGGGGAGGTGGCTATTTCCAAGGACATTCTGCACTAGGAAGCCCTGAAATCTGAGGAATGATATT
TTATGTCTCATATTATGAATTTCTTTGCAGCAAGTGATGGCATAGTAAATGAAAATTTGGTGGAGTGATTAAGCCAGGAA
GTTCAAATTACAGAAGTTCACTGTTTCTATGACTTCCAAATTGCCATGAAAAACTACATTGTGAAATGTATAGTCTCCTT
ATTGACACTTAAAAGATTTCAAAGAAAGGGAATTTCTCTTCAATGCCATTGAAACAATGCCTTATGTAAAGAAAAAAGCA
AATTAGGTCTTGCATTGGATTGGGGACAAAGAAGCTACCTACAGAGAATGTGTTGTAGCCTTTGTGGCTGTGGAAGGAAA
CTTCTTCTATGTTTCTTTTGAATCAATATTCTAGTTCAAGAAACAGGGATTGATGCCTGGCCTAAGTTTC

Alignment

ORF - retro_itri_1555 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.5 %
• Parental protein coverage: 52.71 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LRKSSRRFVIFPIQYPDIWKMYKQAQASFWTAEEVDLSKDLPHWNKLKSDEKYFISHILAFFAASDGIVN
          L......FV.FPI.Y.DIW...K.A..SF.T..EV..SKD..H...LKS.E.YF.SHI..FFAASDGIVN
Retrocopy LSENPHCFVFFPIRYHDIWQISKKAEGSFLTYGEVAISKDILH*EALKSEE*YFMSHIMNFFAASDGIVN

Parental  ENLVERFSQEVQVPEARCFYGFQILIEN-VHSEMYSLLIDTYIRDPKKREF-LFNAIETMPYVKKKADWA
          ENLVE..SQEVQ..E..CFY.FQI...N..H.EMYSLLIDT.....KK..F.LFNAIETMPYVKKKA...
Retrocopy ENLVE*LSQEVQITEVHCFYDFQIAMKN<LHCEMYSLLIDT-*KISKKGNF<LFNAIETMPYVKKKAN*V

Parental  LRWIADRKSTFGERVVAFAAVEGIFFSGSFAAIFWLKKRGLMPGLTF
          L.WI.D...T..E.VVAF.AVEG.FF..SF..IF..KK.GLMPGL.F
Retrocopy LHWIGDKEATYRECVVAFVAVEGNFFYVSFESIF*FKKQGLMPGLSF

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_1555 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1555 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 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012265	4 retrocopies	retro_chof_1118, retro_chof_1233, retro_chof_277, retro_chof_692,
Callithrix jacchus	ENSCJAG00000015923	1 retrocopy	retro_cjac_4130,
Echinops telfairi	ENSETEG00000020338	1 retrocopy	retro_etel_1219,
Gorilla gorilla	ENSGGOG00000003053	1 retrocopy	retro_ggor_3001,
Mus musculus	ENSMUSG00000022292	1 retrocopy	retro_mmus_988,
Otolemur garnettii	ENSOGAG00000004487	1 retrocopy	retro_ogar_2602,
Pan troglodytes	ENSPTRG00000020481	1 retrocopy	retro_ptro_3204,
Ictidomys tridecemlineatus	ENSSTOG00000008543	2 retrocopies	retro_itri_1555 , retro_itri_877,
Tupaia belangeri	ENSTBEG00000008855	1 retrocopy	retro_tbel_3693,