RetrogeneDB ID: retro_itri_1781

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393765.1:296881..297318(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000025976
• Aliases: None
• Description: None

Sequence

>retro_itri_1781
CCGGCTGGAGCCAAGAGCATGGCCTCGGTTTTCATATGCTGCATGGAGGACCTGTTGTTAACCAGAAGCCCCTTCCTATA
AAACCTGACAGTGTCCATGCTGTGGAGATGGTCTACGGAGCCACGGCAGCGGGCTTGCCACCAGGTTCTGCGGACTTGTG
TGGGCTGCGGAAGTATACCAGATGACAGAGGACAGGCACCACAGGTGCAGCTCCTGGATGACAGAAGGCTGGAGCTGCTG
GTTCAGCCCAAAGTTCTGTCAAAAATGCTGCTGGACCTTGTGGCTTCACACTTCAACCTGAAATAAAAGGAGTACTTTGG
AATAATGTTCATAGATGACACTAATCAGCAGAACTTACTGCAGTTGGACCACGAGTTCTGGACCATGATCTGCCCAAAAA
GCCGGGCCCAGCCGCCTTGCATCTTGCCATCAGGTTC

Alignment

ORF - retro_itri_1781 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.83 %
• Parental protein coverage: 54.28 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  PARARRMASVFTCGVEDLLFAGSRFVWNLTVTTLRRWSSE-RLRACHQVLRT-WCGLR-DVYQMTEGRH-
          PA.A..MASVF.C..EDLL...S.F..NLTV..L.RWS.E.R.RACHQVLRT..CGLR..VYQMTE.RH.
Retrocopy PAGAKSMASVFICCMEDLLLTRSPFL*NLTVSMLWRWSTEPRQRACHQVLRT<LCGLR<EVYQMTEDRH<

Parental  CQVHLLDDRRLELLVQPKLLSRELLDLVASHFNLKEKEYFGITFTDDTGQQNWLQLDH-RVLDHDLPKKP
          .QV.LLDDRRLELLVQPK.LS..LLDLVASHFNLK.KEYFGI.F.DDT.QQN.LQLDH.RVLDHDLPKKP
Retrocopy PQVQLLDDRRLELLVQPKVLSKMLLDLVASHFNLK*KEYFGIMFIDDTNQQNLLQLDH<RVLDHDLPKKP

Parental  GPAALQFAVRF
          GPAAL..A.RF
Retrocopy GPAALHLAIRF

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_1781 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1781 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 1 parental gene, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ictidomys tridecemlineatus	ENSSTOG00000025976	6 retrocopies	retro_itri_1757, retro_itri_1759, retro_itri_1778, retro_itri_1781 , retro_itri_1782, retro_itri_186,