RetrogeneDB ID: retro_itri_240

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393281.1:12586363..12586588(+)
• Located in intron of: ENSSTOG00000000280

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL17
• Ensembl ID: ENSSTOG00000003313
• Aliases: None
• Description: mitochondrial ribosomal protein L17 [Source:HGNC Symbol;Acc:14053]

Sequence

>retro_itri_240
AATGAATAAATCCAGGTGTCATGGGTGCGTGTGGACAAGATGAGGGGCTACAGTGAGGAGTTCATTGACTAGGGGAAGCT
GAGAGACACCAACAAATGAGCTATGAGCATGGCTGACTTCTGGCTCACGGAAAAGGACTCGATCCCAAAGCAGTTTCAAG
TACTGACACCTCAATTTCAATATCAGAATGGGGGATACACAAGAACGCTGCTGCAGATCCCAAAC

Alignment

ORF - retro_itri_240 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72. %
• Parental protein coverage: 60.66 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HERIEASWARVDEMRGYAEKLIDYGKLGDTNERAMRMADFWLTEKDLIPKLFQVLAPRFQDQNGGYTR-M
          .E.I..SW.RVD.MRGY.E..ID.GKL.DTN..AM.MADFWLTEKD.IPK.FQVL.P.FQ.QNGGYTR..
Retrocopy NE*IQVSWVRVDKMRGYSEEFID*GKLRDTNK*AMSMADFWLTEKDSIPKQFQVLTPQFQYQNGGYTRTL

Parental  LQIPN
          LQIPN
Retrocopy LQIPN

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_240 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_240 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 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000027536	1 retrocopy	retro_cpor_1430,
Macropus eugenii	ENSMEUG00000013588	1 retrocopy	retro_meug_1822,
Myotis lucifugus	ENSMLUG00000001144	2 retrocopies	retro_mluc_2368, retro_mluc_679,
Mustela putorius furo	ENSMPUG00000005449	1 retrocopy	retro_mputfur_125,
Rattus norvegicus	ENSRNOG00000019497	1 retrocopy	retro_rnor_1979,
Sus scrofa	ENSSSCG00000024693	1 retrocopy	retro_sscr_217,
Ictidomys tridecemlineatus	ENSSTOG00000003313	3 retrocopies	retro_itri_1019, retro_itri_1156, retro_itri_240 ,