RetrogeneDB ID: retro_itri_254

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393281.1:40152868..40153260(+)
• Located in intron of: ENSSTOG00000014493

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS18B
• Ensembl ID: ENSSTOG00000011853
• Aliases: None
• Description: mitochondrial ribosomal protein S18B [Source:HGNC Symbol;Acc:14516]

Sequence

>retro_itri_254
GGGTGTGTACCCCCACAATGAACTTGATAGACCAGTATTCATTAAGAATAAAAATGCTGTTAATCCTTACTCCCTCTGCT
GGGATCACGAGTTGCAGGTCGACTTTAGGAACCTAAAGCTCTTGAATTGATTTGTCTGCGCCCATGTGGGAATCCTCTTC
CGTGCTCCACATACAAGGAGTCTGTGCAAAGCAGCATGGGAAGTTGATCCAAGACATCCTGAAAGCCAGAGGTCATGGTC
TCTTCAGTTACCACGTTCCCTGGGTGGAATGACAGGACCTTGACTTCAGTACATCTCTTAGATCTGTGACTGCTACACCT
CCCGCCCCTACCCTAATTTCAGGTGGCCCTTGATACCCATGGTATAGCTGGAAACAGCCACAAGAAAGACAA

Alignment

ORF - retro_itri_254 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.91 %
• Parental protein coverage: 66.67 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GGIPPQQTRKTCIR-KNKIAGNPCPICRDHNLYVDFRNVKLLEQFVCAHTGIIFHAPYT-GVCMKQHKKL
          G..PPQ.T..T.I..KNK.A.NP...C.DH.L.VDFRN.KLL..FVCAH.GI.F.AP.T.GVC.KQH.KL
Retrocopy GCVPPQ*T**TSIH>KNKNAVNPYSLCWDHELQVDFRNLKLLN*FVCAHVGILFRAPHT>GVCAKQHGKL

Parental  TQAIQKARDHGLLSYHIPQVEPRDLDFSTSHGAVTSTPPAPTLVSGDPWYPWYTWKQPPERE
          .Q.I.KAR.HGL.SYH.P.VE..DLDFSTS...VT.TPPAPTL.SG.P.YPWY.WKQP.ER.
Retrocopy IQDILKARGHGLFSYHVPWVE*QDLDFSTSLRSVTATPPAPTLISGGP*YPWYSWKQPQERQ

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_254 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_254 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 12 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005581	1 retrocopy	retro_chof_505,
Macropus eugenii	ENSMEUG00000012457	10 retrocopies	retro_meug_1183, retro_meug_2004, retro_meug_2124, retro_meug_215, retro_meug_610, retro_meug_648, retro_meug_696, retro_meug_712, retro_meug_717, retro_meug_734,
Macaca mulatta	ENSMMUG00000006525	1 retrocopy	retro_mmul_900,
Monodelphis domestica	ENSMODG00000015933	1 retrocopy	retro_mdom_426,
Mus musculus	ENSMUSG00000024436	1 retrocopy	retro_mmus_2036,
Nomascus leucogenys	ENSNLEG00000005224	1 retrocopy	retro_nleu_1811,
Oryctolagus cuniculus	ENSOCUG00000002149	2 retrocopies	retro_ocun_1307, retro_ocun_1641,
Pongo abelii	ENSPPYG00000016412	1 retrocopy	retro_pabe_2050,
Pan troglodytes	ENSPTRG00000017932	1 retrocopy	retro_ptro_1648,
Rattus norvegicus	ENSRNOG00000000804	1 retrocopy	retro_rnor_1328,
Ictidomys tridecemlineatus	ENSSTOG00000011853	1 retrocopy	retro_itri_254 ,
Tarsius syrichta	ENSTSYG00000003333	1 retrocopy	retro_tsyr_1769,