RetrogeneDB ID: retro_itri_1610

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393571.1:1591317..1591967(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000020241
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MEST
• Ensembl ID: ENSSTOG00000020977
• Aliases: None
• Description: mesoderm specific transcript [Source:HGNC Symbol;Acc:7028]

Sequence

>retro_itri_1610
AGGATGAGGGAATGGTGGGTCCAGGTAGGGCTACTGGCCCCCGCCCCTGCTGGCCGAGTACCTGCACATCCCACCCCCTC
AGCTCTTTCCTGCTCTGCACTCATGGAAGACTTCTGGCAAGTTTTTCACCTACAAGGGACTGCGCATCTTCTACCAGGAC
TCCGTGGGTGGAGTTGGCAGTCCTGAGATAGTTGTGCTTTTACATGGCTTTCCCACTTCCAGCTATGACTGGTACAAGAT
TTGGGAAGGTCTGACCCCGAGGTTTCATCGAGTGATTGCCCTTGACTTCTTAGGCTTTGGCTTCAGTGACAAACCCAGAC
CACACCACTATTCCAAATTTGAGCTGGCCAGCATCATGGAGGCGCTTTTGCGCCATCTAGGACTCCAGAACCGTAGGATC
AACCTGTTGTCTCACGAATATGGAGACATTGTTGCTCAGGAGCTGCTGTATAGGCACAAGCAAAATCGATGTGTCCGGCT
TACCATAAAGAGTCTCTGTCTGTCAAATGGAGGTATCTATCCTGAGACTCATCCGGCCTCTCCTTCTCCAAAAGCTACTT
AAAGATGGAGGTGTGCTGTCACCCATCCTCACGAGGTTGATGAACTTCTTTGTATTTTCTCGAGGTCTTACTCCAGTCTT
TGGACCATAC

Alignment

ORF - retro_itri_1610 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.12 %
• Parental protein coverage: 64.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RMREWWVQVGLLAV-PLLAAYLHIPPPQLSPALHSWKTSGKFFTYKGLRIFYQDSVGVVGSPEIVVLLHG
          RMREWWVQVGLLA..PLLA.YLHIPPPQL.PALHSWKTSGKFFTYKGLRIFYQDSVG.VGSPEIVVLLHG
Retrocopy RMREWWVQVGLLAP>PLLAEYLHIPPPQLFPALHSWKTSGKFFTYKGLRIFYQDSVGGVGSPEIVVLLHG

Parental  FPTSSYDWYKIWEGLTLRFHRVIALDFLGFGFSDKPRPHHYSIFEQASIVEALLRHLGLQNRRINLLSHD
          FPTSSYDWYKIWEGLT.RFHRVIALDFLGFGFSDKPRPHHYS.FE.ASI.EALLRHLGLQNRRINLLSH.
Retrocopy FPTSSYDWYKIWEGLTPRFHRVIALDFLGFGFSDKPRPHHYSKFELASIMEALLRHLGLQNRRINLLSHE

Parental  YGDIVAQELLYRYKQNRSGRLTIKSLCLSNGGIFPETH-RPLLLQKLLKDGGVLSPILTRLMNFFVFSRG
          YGDIVAQELLYR.KQNR..RLTIKSLCLSNGGI.PETH.RPLLLQKLLKDGGVLSPILTRLMNFFVFSRG
Retrocopy YGDIVAQELLYRHKQNRCVRLTIKSLCLSNGGIYPETH>RPLLLQKLLKDGGVLSPILTRLMNFFVFSRG

Parental  LTPVFGPY
          LTPVFGPY
Retrocopy LTPVFGPY

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_1610 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1610 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 14 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005659	2 retrocopies	retro_amel_1177, retro_amel_1874,
Callithrix jacchus	ENSCJAG00000010760	2 retrocopies	retro_cjac_1563, retro_cjac_3931,
Felis catus	ENSFCAG00000022984	5 retrocopies	retro_fcat_1067, retro_fcat_1645, retro_fcat_1693, retro_fcat_2004, retro_fcat_326,
Loxodonta africana	ENSLAFG00000006066	3 retrocopies	retro_lafr_578, retro_lafr_584, retro_lafr_748,
Macropus eugenii	ENSMEUG00000008227	1 retrocopy	retro_meug_885,
Microcebus murinus	ENSMICG00000006129	1 retrocopy	retro_mmur_1091,
Macaca mulatta	ENSMMUG00000009499	2 retrocopies	retro_mmul_1936, retro_mmul_94,
Nomascus leucogenys	ENSNLEG00000012841	3 retrocopies	retro_nleu_1065, retro_nleu_515, retro_nleu_790,
Otolemur garnettii	ENSOGAG00000009224	1 retrocopy	retro_ogar_3464,
Pongo abelii	ENSPPYG00000018006	4 retrocopies	retro_pabe_2337, retro_pabe_2510, retro_pabe_2511, retro_pabe_866,
Pan troglodytes	ENSPTRG00000019698	2 retrocopies	retro_ptro_1769, retro_ptro_2045,
Sorex araneus	ENSSARG00000000502	1 retrocopy	retro_sara_352,
Ictidomys tridecemlineatus	ENSSTOG00000020977	2 retrocopies	retro_itri_1210, retro_itri_1610 ,
Tursiops truncatus	ENSTTRG00000004934	4 retrocopies	retro_ttru_1026, retro_ttru_1115, retro_ttru_1133, retro_ttru_1907,