RetrogeneDB ID: retro_itri_735

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393314.1:11932608..11932853(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000005297
• Aliases: None
• Description: None

Sequence

>retro_itri_735
GCGGTTCTGCAGCTCTGGCACAGCCATCCACCAATCCAATCCAAGTTCTCAAAGTGGCAGTTGCAGAACTGGAAAGTGTT
TTCCAATTAACTCAGTACTCTAATGTGACCACCAGAAAGGGGCTTGCAAGATGCATCAACGTGACTGAAACCAGAGTGCA
GGCTTAGCTTAACAAAAGGAGAGCTCAACATAGGAATCATCAGAGGAAGTTAATGCTTGGAGATGCACCATCTGGTTTGC
AGGAC

Alignment

ORF - retro_itri_735 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.04 %
• Parental protein coverage: 52.56 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AVPQPGGTRPRIQYKFSKWQLQ-ELESVFQVTQYPDVATRRELARCMNVSEARVQAWFKYRRAKHRKTLR
          AV.Q.....P.IQ.KFSKWQLQ.ELESVFQ.TQY..V.TR..LARC.NV.E.RVQA....RRA.HR...R
Retrocopy AVLQLWHSHPPIQSKFSKWQLQ<ELESVFQLTQYSNVTTRKGLARCINVTETRVQA*LNKRRAQHRNHQR

Parental  ETSLRNAPHPTQD
          ...L..AP...QD
Retrocopy KLMLGDAPSGLQD

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_735 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_735 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Otolemur garnettii	ENSOGAG00000030871	2 retrocopies	retro_ogar_306, retro_ogar_384,
Otolemur garnettii	ENSOGAG00000030942	1 retrocopy	retro_ogar_337,
Pteropus vampyrus	ENSPVAG00000009422	1 retrocopy	retro_pvam_753,
Ictidomys tridecemlineatus	ENSSTOG00000005297	1 retrocopy	retro_itri_735 ,
Tupaia belangeri	ENSTBEG00000002729	1 retrocopy	retro_tbel_3738,