RetrogeneDB ID: retro_itri_1778

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393765.1:119274..119698(+)
• 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_1778
CAAGCCAAGAGGATGGCCACGGTGTTCATGTGTGGCATGGAATACCTGCTGTTCACCAGCAGACCCTTCCTGTGGAACCT
GACAGTGTACACGCTCTTGAGATGGCTTACAGAGCAGCTGCTGGCTTGCCACCAGGTGCTGTGGACATGTGCAGGCTGCA
GATGTGTACCAGATGACAGAGGACAGGCACTGCCAGGTGCACCTTCTGGATGACAGAAGGCTGGAGCTTCTGGTTCAGCC
CAAACTTCTGTCAAGAGAGCTCCTGGATCTGATGGCTTCACACTTCAACCTGAAAAAAAAAAAGTACTTTTTGTTCATAG
ATGACACTGGTCAGCAGAACTGGCTGCAGTTGGACCACCGAGTTCTGGACCATGACTTGCCCAAGAAGCCAGGCCCAGCC
GCCTTGCACCTTGCCATCAAGTTC

Alignment

ORF - retro_itri_1778 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.66 %
• Parental protein coverage: 53.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RARRMASVFTCGVEDLLFAGSRFVWNLTVTTLRRWSSERLRACHQVLRT-WCGLR-DVYQMTEGRHCQVH
          .A.RMA.VF.CG.E.LLF....F.WNLTV.TL.RW..E.L.ACHQVL.T..C.L..DVYQMTE.RHCQVH
Retrocopy QAKRMATVFMCGMEYLLFTSRPFLWNLTVYTLLRWLTEQLLACHQVLWT<MCRLQ<DVYQMTEDRHCQVH

Parental  LLDDRRLELLVQPKLLSRELLDLVASHFNLKEKEYFGITFTDDTGQQNWLQLDHRVLDHDLPKKPGPAAL
          LLDDRRLELLVQPKLLSRELLDL.ASHFNL....YF...F.DDTGQQNWLQLDHRVLDHDLPKKPGPAAL
Retrocopy LLDDRRLELLVQPKLLSRELLDLMASHFNLXXXXYF--LFIDDTGQQNWLQLDHRVLDHDLPKKPGPAAL

Parental  QFAVRF
          ..A..F
Retrocopy HLAIKF

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_1778 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1778 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,