RetrogeneDB ID: retro_itri_126

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393392.1:1292865..1293420(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000024053
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000011829
• Aliases: None
• Description: None

Sequence

>retro_itri_126
ATGCCGAAACCAAAGGAGCAGGATCAGCAACAGCAGCAGCCACCACTGCCCGAGCAGGAAGAGACTGGAGATGAGGAGGA
TGAGAGTCCCATCCGACCACCCAGCCTTCTGGACCCTCCCCGCAAGGACAATGGAAAGCCTGATGACCCCAAACCAGCTC
TTCCCAAAGGTCCTCCAGAATCAAGGGGACTGATGATTCCACCACTGATGAGTCTCCCACCTCCTCCCTGGAGCAGAGGC
CCAATCTGGGGAGGCCTCAGCCTCAGGTCTGGCCCATATGGTCATGGTTGGTGGGGGTTCAGTGCTGAACCCCCTTTTCT
GGGGCCAGTCCATGGGGGTCCCTCCAGAGAAAGCTTCCACAAAGAGCAGAGAAACTCTCGAAGGCTCAAAAGCTGGTCTC
TTATCAAGAATACCTGCCCGCCTAAGGATGGCCCCCAGGTTATGGAAGACAAATCTGACCGCCCCGTCTGTCGACACTTT
TCCAAAAAAGGCCACTGTAGATATGAAGACCTCTGTGCCTTCTACCACCCAGGTGTCAATGGACCTCCTCTGTGA

Alignment

ORF - retro_itri_126 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.57 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPKRKKQNQQQQPPPQQPPLPEREETGDEEDESLIGPPSLLGPPPMANGKPGDPKSALHRGPPGSRGLMI
          MPK.K.Q.QQQ....QQPPLPE.EETGDEEDES.I.PPSLL.PP...NGKP.DPK.AL..GPP.SRGLMI
Retrocopy MPKPKEQDQQQ----QQPPLPEQEETGDEEDESPIRPPSLLDPPRKDNGKPDDPKPALPKGPPESRGLMI

Parental  PPLLSLPPPPRGRGPIRGGLGPRSGPYGRGWWGVSAEPPFLGPGHGGPSRESFHKEQRNPRRLKSWSLIK
          PPL.SLPPPP..RGPI.GGL..RSGPYG.GWWG.SAEPPFLGP.HGGPSRESFHKEQRN.RRLKSWSLIK
Retrocopy PPLMSLPPPPWSRGPIWGGLSLRSGPYGHGWWGFSAEPPFLGPVHGGPSRESFHKEQRNSRRLKSWSLIK

Parental  NTCPPKDGPQVMEDKSDRPVCRHFSKKGHCRYEDLCAFYHPGVNGPPL
          NTCPPKDGPQVMEDKSDRPVCRHFSKKGHCRYEDLCAFYHPGVNGPPL
Retrocopy NTCPPKDGPQVMEDKSDRPVCRHFSKKGHCRYEDLCAFYHPGVNGPPL

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_126 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_126 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 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000022770	1 retrocopy	retro_cpor_775,
Felis catus	ENSFCAG00000025918	2 retrocopies	retro_fcat_1094, retro_fcat_1698,
Gorilla gorilla	ENSGGOG00000014604	1 retrocopy	retro_ggor_1915,
Myotis lucifugus	ENSMLUG00000008758	1 retrocopy	retro_mluc_1567,
Macaca mulatta	ENSMMUG00000013893	1 retrocopy	retro_mmul_1431,
Nomascus leucogenys	ENSNLEG00000005104	1 retrocopy	retro_nleu_1548,
Otolemur garnettii	ENSOGAG00000004430	2 retrocopies	retro_ogar_1030, retro_ogar_1324,
Pongo abelii	ENSPPYG00000016409	1 retrocopy	retro_pabe_2279,
Pan troglodytes	ENSPTRG00000017929	1 retrocopy	retro_ptro_1861,
Sorex araneus	ENSSARG00000002747	2 retrocopies	retro_sara_143, retro_sara_9,
Ictidomys tridecemlineatus	ENSSTOG00000011829	1 retrocopy	retro_itri_126 ,
Tarsius syrichta	ENSTSYG00000000166	2 retrocopies	retro_tsyr_308, retro_tsyr_841,