RetrogeneDB ID: retro_itri_189

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393279.1:6728943..6729227(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LSM2
• Ensembl ID: ENSSTOG00000013144
• Aliases: None
• Description: LSM2 homolog, U6 small nuclear RNA associated (S. cerevisiae) [Source:HGNC Symbol;Acc:13940]

Sequence

>retro_itri_189
ATGCTCTTCTGCTCCTTTTTTAAGTTCTTTAGGGGAAAGGATGTGGTCATGGAACTCAAGAATGACCTGAGCATCTGTGG
AACCCTCCATTCTGTGGATTAGTATCTCAACATCAAACTAACTGACATTAGTGTTACAGACCCTGAGAAATATCCTCACA
TGTTATCAGTGAAGAACTGCTTCATTCTCGACTCAGTGGTCCATTTTATGCAGTTGCCAGCAGACAAGTGAACACACAGT
TCCTACAGGATGCAGCAAGGAAGGAAGCCCTACAGCAGAAGCAG

Alignment

ORF - retro_itri_189 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.38 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MLFYSFFKSLVGKDVVVELKNDLSICGTLHSVDQYLNIKLTDISVTDPEKYPHMLSVKNCFIRGSVVRYV
          MLF.SFFK...GKDVV.ELKNDLSICGTLHSVD.YLNIKLTDISVTDPEKYPHMLSVKNCFI..SVV...
Retrocopy MLFCSFFKFFRGKDVVMELKNDLSICGTLHSVD*YLNIKLTDISVTDPEKYPHMLSVKNCFILDSVVHFM

Parental  QLPAD-EVDTQLLQDAARKEALQQKQ
          QLPAD..V.TQ.LQDAARKEALQQKQ
Retrocopy QLPAD<QVNTQFLQDAARKEALQQKQ

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_189 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_189 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 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002601	2 retrocopies	retro_cjac_1828, retro_cjac_2088,
Felis catus	ENSFCAG00000004511	1 retrocopy	retro_fcat_309,
Macaca mulatta	ENSMMUG00000006832	3 retrocopies	retro_mmul_1389, retro_mmul_1875, retro_mmul_2099,
Mus musculus	ENSMUSG00000007050	1 retrocopy	retro_mmus_931,
Nomascus leucogenys	ENSNLEG00000006371	1 retrocopy	retro_nleu_960,
Ochotona princeps	ENSOPRG00000003668	2 retrocopies	retro_opri_250, retro_opri_917,
Pongo abelii	ENSPPYG00000016461	1 retrocopy	retro_pabe_2765,
Pan troglodytes	ENSPTRG00000017986	3 retrocopies	retro_ptro_1349, retro_ptro_2063, retro_ptro_2284,
Rattus norvegicus	ENSRNOG00000048725	1 retrocopy	retro_rnor_1463,
Ictidomys tridecemlineatus	ENSSTOG00000013144	1 retrocopy	retro_itri_189 ,