RetrogeneDB ID: retro_itri_877

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393337.1:9902351..9902914(+)
• 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_877
AGATCAGAGGATGAACCACTACTGCGAGAGAACTCCGCCACTTTGCCATGTTTGCTGTCAATCACCATGATATTTGGCAA
ATGTATAAGAAAGCCGAGGCGTCCTTCTGGACAGCGGAGGAGGTGGATCTTTCCAAGGACAGTCAGCACCGGCAGGCCCT
GAAGCCTGAGGAATGATATTTTATATCACATGTTCTAGCTTTCTTTGAAGCACGTGATGGCATAGCAAGTGAAAATCTGG
TGCAGCGATTTAGCCAAGAGGTTCAAATTATAGAAGCCGGCTGTTTCTGTGGCTTCCAAGTTGCTATGGAAAACATACAT
TCTGAAATATATGGTCTCCTTATTGACATTTACATTAAAAATTCCTAAGACAGGGAATTTCTCTCCAGTGCCATTGAAAT
GATGCCTTGGGTGAAGAAGAAAGCAGACTGTGCCTTGTGTTGGACTGGGGACAAAGAAGCTACCTACAGAAAACGTGTTG
TAGTCTTGGCCACTACGGGAGAAATCTTCTTTTCTGGCTCATTTGCATCAATATTTTGGCTCATAAGAACTGATGCCTGG
CCT

Alignment

ORF - retro_itri_877 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.32 %
• Parental protein coverage: 53.56 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KANEEPLLRKSS-RRFVIFPIQYPDIWKMYKQAQASFWTAEEVDLSKDLPHWNKLKSDEKYFISHILAFF
          ....EPLLR..S.R.F..F.....DIW.MYK.A.ASFWTAEEVDLSKD..H...LK..E.YFISH.LAFF
Retrocopy RSEDEPLLRENS<RHFAMFAVNHHDIWQMYKKAEASFWTAEEVDLSKDSQHRQALKPEE*YFISHVLAFF

Parental  AASDGIVNENLVERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIRDPKKREFLFNAIETMPYVK
          .A.DGI..ENLV.RFSQEVQ..EA.CF.GFQ...EN.HSE.Y.LLID.YI.....REFL..AIE.MP.VK
Retrocopy EARDGIASENLVQRFSQEVQIIEAGCFCGFQVAMENIHSEIYGLLIDIYIKNS*DREFLSSAIEMMPWVK

Parental  KKADWALRWIADRKSTFGERVVAFAAVEGIFFSGSFAAIFWLKKRGLMP
          KKAD.AL.W..D...T...RVV..A....IFFSGSFA.IFWL......P
Retrocopy KKADCALCWTGDKEATYRKRVVVLATTGEIFFSGSFASIFWLIRTDAWP

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_877 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_877 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,