RetrogeneDB ID: retro_itri_963

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393351.1:878353..878839(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS10
• Ensembl ID: ENSSTOG00000013486
• Aliases: None
• Description: ribosomal protein S10 [Source:HGNC Symbol;Acc:10383]

Sequence

>retro_itri_963
ATGTTGTTTCCCAAGAAGAATCAGATTGCCATTTATGAACTTTTTTAAAGGAGGGAATGATGATAGCCAAGAAGGATGTC
TACATGCCCAAGCACCTGGAACTGGCAGATGGGAATGTGCCCAGCCTTCATGTTTTGAAGGCCATGCAGTCTTCAAGTCT
TGAGGCTTTGTAAAGGAACAGTTTGCCTGGAGACATTTCTATTGGTACCTTGTCAATGAGGGCATCCATATCTCTGCAAT
TAACTCTTTTTGCTGCCTGAGATTGTACCTGCCATTCTACATCATAGCTGACCAGAGACTGGTAGGCTTTGCCCCAAAGG
TCTGGAGGGCAAGCAGCCTGCAAGACTCAGGAGAGGTGAGGCCAACAGAGATACCCATGGACAGAGTGCTGTGCCCTCTG
GTGCCAATAAGAAAGTTGGGGCGGGGTCAGCAACTGAATTGCACTTTAGAGGCAGATGGGGTTGTGGACATGGTCAGCTA
CCTCAG

Alignment

ORF - retro_itri_963 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.83 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MLMPKKNRIAIYELL-FKEGVMVAKKDVHMPKHPELADKNVPNLHVMKAMQS-LKSRGYVKEQFAWRHFY
          ML.PKKN.IAIYEL...KEG.M.AKKDV.MPKH.ELAD.NVP.LHV.KAMQS..KS.G.VKEQFAWRHFY
Retrocopy MLFPKKNQIAIYELF<LKEGMMIAKKDVYMPKHLELADGNVPSLHVLKAMQS<FKS*GFVKEQFAWRHFY

Parental  WYLTNEGIQ-YLRDYLHLPPEIVPATLRRSRPETGRPRPKGLEGERPARLTRGEADRDTYRRSAVPPGAD
          WYL.NEGI..YL...L.L.PEIVPA.L..S.PETGR..PKGLEG..PARL.RGEA.RDT...SAVP.GA.
Retrocopy WYLVNEGIH<YLCN*LFLLPEIVPAILHHS*PETGRLCPKGLEGKQPARLRRGEANRDTHGQSAVPSGAN

Parental  KKAEAGAGSATEFQFRGGFGRGRGQPPQ
          KK...GAGSATE..FRG..G.G.GQ.PQ
Retrocopy KK--VGAGSATELHFRGRWGCGHGQLPQ

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_963 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_963 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 60 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015250	4 retrocopies	retro_cjac_215, retro_cjac_296, retro_cjac_325, retro_cjac_63,
Equus caballus	ENSECAG00000006430	1 retrocopy	retro_ecab_198,
Homo sapiens	ENSG00000124614	24 retrocopies	retro_hsap_1509, retro_hsap_1628, retro_hsap_1630, retro_hsap_1657, retro_hsap_1923, retro_hsap_2003, retro_hsap_2113, retro_hsap_229, retro_hsap_2415, retro_hsap_2573, retro_hsap_2574, retro_hsap_2830, retro_hsap_289, retro_hsap_3007, retro_hsap_3170, retro_hsap_3243, retro_hsap_3436, retro_hsap_3454, retro_hsap_3720, retro_hsap_4114, retro_hsap_4190, retro_hsap_460, retro_hsap_869, retro_hsap_992,
Latimeria chalumnae	ENSLACG00000017219	1 retrocopy	retro_lcha_26,
Loxodonta africana	ENSLAFG00000008539	1 retrocopy	retro_lafr_756,
Macaca mulatta	ENSMMUG00000000267	2 retrocopies	retro_mmul_332, retro_mmul_555,
Monodelphis domestica	ENSMODG00000013929	2 retrocopies	retro_mdom_1889, retro_mdom_437,
Mus musculus	ENSMUSG00000052146	9 retrocopies	retro_mmus_1376, retro_mmus_1500, retro_mmus_1831, retro_mmus_2431, retro_mmus_2551, retro_mmus_2708, retro_mmus_3651, retro_mmus_5, retro_mmus_858,
Oryctolagus cuniculus	ENSOCUG00000011373	2 retrocopies	retro_ocun_250, retro_ocun_874,
Pongo abelii	ENSPPYG00000016516	2 retrocopies	retro_pabe_2319, retro_pabe_97,
Rattus norvegicus	ENSRNOG00000000490	4 retrocopies	retro_rnor_169, retro_rnor_224, retro_rnor_359, retro_rnor_74,
Sarcophilus harrisii	ENSSHAG00000000731	3 retrocopies	retro_shar_243, retro_shar_334, retro_shar_724,
Ictidomys tridecemlineatus	ENSSTOG00000013486	5 retrocopies	retro_itri_1448, retro_itri_1515, retro_itri_230, retro_itri_787, retro_itri_963 ,