RetrogeneDB ID: retro_itri_1782

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393765.1:457438..457872(-)
• 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_1782
GCTGGAGCCAAGAGCATGGCCTCGGTGTTCATGTGCTGCATGGAGGACCTGTTGTTAACCAGCAGCCCCTTCGTATGGAA
CCTGACAGTGTCCATGCTGTGGAGATGGTCTACGGAGCCGTGGCGGCGGGCTTACCACTAGGTTCTGCGGACTTCTGCGG
GCTGCGGAAGTATACCAGATGACAGAGGACAGGCACTACAGGTGCAGCTCTTTGATGACAGAAGGCTGGAGCTGCTGGTT
CAGTGCAAAGTTCTGTCAAAAATTCTGCTGGACCTTGTGGCTTCACATTTCAACCTGAAACAAAAAGAGTGCTTTGGAAT
AATGTTCATAGATGACACTGATCAGCAGAACTGACTGCAGTTGGACCACGAGTTCTGGACCATGATCTGCCCAAAAAGCC
GGGCCCAGCTGCCTTGCATCTTGCCATCAGGTTC

Alignment

ORF - retro_itri_1782 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.0 %
• Parental protein coverage: 53.9 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  ARARRMASVFTCGVEDLLFAGSRFVWNLTVTTLRRWSSER-LRACHQVLRT-WCGLR-DVYQMTEGRH-C
          A.A..MASVF.C..EDLL...S.FVWNLTV..L.RWS.E...RA.H.VLRT..CGLR..VYQMTE.RH..
Retrocopy AGAKSMASVFMCCMEDLLLTSSPFVWNLTVSMLWRWSTEPWRRAYH*VLRT<FCGLR<EVYQMTEDRH<L

Parental  QVHLLDDRRLELLVQPKLLSRELLDLVASHFNLKEKEYFGITFTDDTGQQNWLQLDH-RVLDHDLPKKPG
          QV.L.DDRRLELLVQ.K.LS..LLDLVASHFNLK.KE.FGI.F.DDT.QQN.LQLDH.RVLDHDLPKKPG
Retrocopy QVQLFDDRRLELLVQCKVLSKILLDLVASHFNLKQKECFGIMFIDDTDQQN*LQLDH<RVLDHDLPKKPG

Parental  PAALQFAVRF
          PAAL..A.RF
Retrocopy PAALHLAIRF

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_1782 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1782 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,