RetrogeneDB ID: retro_itri_984

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393355.1:2754941..2755208(-)
• Located in intron of: ENSSTOG00000021805

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS25
• Ensembl ID: ENSSTOG00000027997
• Aliases: None
• Description: mitochondrial ribosomal protein S25 [Source:HGNC Symbol;Acc:14511]

Sequence

>retro_itri_984
CTGCAATACCTGGGTCCAAGTGACACAGTGGTCAGGGACTTGGTGCAGGCCACGATAGTGAATTATAACATGCACAGGGA
GCTCAGTTGGCACCAAAAAAACTTGTCTTTCAACATACCTCAGATCCAATAGAAAAACCATTGGGTGCAGATTATGATGC
TTAAGAACATGACACCATCACCCCTCATGTGATTCTATTTAGATTATGGAGAGCAGATCCTGGTGGATGTAGAGATCAAG
AGCAGTAAGGAGATCACAGAGCACATT

Alignment

ORF - retro_itri_984 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60. %
• Parental protein coverage: 52.02 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LQYLAQGTVVFKDSVKVMTVNYNTHGELGEGARKFVFFNIPQIQYKNPWVQIMMFKNMTPTPFLRFYLDS
          LQYL.....V..D.V....VNYN.H.EL.....K...FNIPQIQ.KN.WVQIMM.KNMTP.P...FYLD.
Retrocopy LQYLGPSDTVVRDLVQATIVNYNMHRELS-WHQKNLSFNIPQIQ*KNHWVQIMMLKNMTPSPLM*FYLDY

Parental  GEQVLVDVETKTNKEIVEHV
          GEQ.LVDVE.K..KEI.EH.
Retrocopy GEQILVDVEIKSSKEITEHI

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_984 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_984 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 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017160	1 retrocopy	retro_cjac_3303,
Homo sapiens	ENSG00000131368	1 retrocopy	retro_hsap_1127,
Gorilla gorilla	ENSGGOG00000011005	1 retrocopy	retro_ggor_880,
Latimeria chalumnae	ENSLACG00000009006	1 retrocopy	retro_lcha_49,
Macaca mulatta	ENSMMUG00000005157	2 retrocopies	retro_mmul_1946, retro_mmul_874,
Nomascus leucogenys	ENSNLEG00000005218	1 retrocopy	retro_nleu_184,
Pongo abelii	ENSPPYG00000013409	1 retrocopy	retro_pabe_932,
Pelodiscus sinensis	ENSPSIG00000008882	1 retrocopy	retro_psin_36,
Pan troglodytes	ENSPTRG00000014658	1 retrocopy	retro_ptro_678,
Rattus norvegicus	ENSRNOG00000010912	1 retrocopy	retro_rnor_1184,
Ictidomys tridecemlineatus	ENSSTOG00000027997	1 retrocopy	retro_itri_984 ,