RetrogeneDB ID: retro_itri_164

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393531.1:174280..175069(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000028170
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000004006
• Aliases: None
• Description: None

Sequence

>retro_itri_164
ATGTCGGCGCAGCCGGGGCTCTGGCCCGAGGTCCAGGACACCTGCACCTCTCTGGGGCTTATGTTGTCGATTGTGCTGTT
CGTGGGTCTGGGCCGCATGAGTGCTCGGCAGCAACTGCACAGGCCCCTGGCCCACGCCTTCGCTTTGGAGTTTCTGGCCA
CCTTCCAGCTCTGCTGCTGCACCCATGAGCTACAACTGCTTAGTGCGCAGGACTCCGCGCACCCCACCTGGACGCTGACG
CTAATCTACTTCTTTTCGTTGGTGCATGGCCTGACTCTGGTGGGCACTTCCGGCAATCCGTGCGGCGTGATGATGCAGAT
GATGCTGGGGGGAATGTCCCCCGAGATGGGTGCAGTGAGGCTGTCGTCTCAGCTAGTTAGCGCTCTGTGCAGCAGGTACT
GTGTAAGCGCCCTGTGGAACCTGGGTCTGACCAAGTATCACTTCAGCGAGAGGAACTTGGCTTGCAAGAATCCCATCAAT
TCCGATTTACCCCAAGCGATCATCACAGAGGCCATCTGCTCCTTTATCTTCCACAGCGCTCTGCTGCAGTTCCAGGAGGT
CCGAACCAAGCTTCGTATCCACCTGCTGGCTGCACTCATCACCTTTTTGGCCTACGCAGGAAGTATAACAGGAGCTGTAT
TTAATCCAGCATTGGCACTTTCACTTCATTTCATGTGTTTTGATGAAGCTTTCCTTCAATTTTTTATAGTGTATTGGCTG
GCTCCTTCTGTAGGTATATTGTTGATGATTTTAATGTTCAGTTTTTTCCTTCCATGGCTGCATAACAAC

Alignment

ORF - retro_itri_164 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.97 %
• Parental protein coverage: 97.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QDSAHPTWTLTLIYFFSLVHGLTLVGTSGNPCGVMMQMMLGGMSPEMGAVRLSSQLVSALCSRYCVSALW
          QDSAHPTWTLTLIYFFSLVHGLTLVGTSGNPCGVMMQMMLGGMSPEMGAVRLSSQLVSALCSRYCVSALW
Retrocopy QDSAHPTWTLTLIYFFSLVHGLTLVGTSGNPCGVMMQMMLGGMSPEMGAVRLSSQLVSALCSRYCVSALW

Parental  NLGLTKYHFSERNLACKNPINSDLPQAIITEAICSFIFHSALLQFQEVRTKLRIHLLAALITFLAYAGGS
          NLGLTKYHFSERNLACKNPINSDLPQAIITEAICSFIFHSALLQFQEVRTKLRIHLLAALITFLAYAG.S
Retrocopy NLGLTKYHFSERNLACKNPINSDLPQAIITEAICSFIFHSALLQFQEVRTKLRIHLLAALITFLAYAG-S

Parental  ITGAVFNPALALSLHFMCFDEAFPQFFIVYWLAPSVGILLMILMFSFFLPWLHNN
          ITGAVFNPALALSLHFMCFDEAF.QFFIVYWLAPSVGILLMILMFSFFLPWLHNN
Retrocopy ITGAVFNPALALSLHFMCFDEAFLQFFIVYWLAPSVGILLMILMFSFFLPWLHNN

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_164 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_164 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Ictidomys tridecemlineatus	ENSSTOG00000004006	2 retrocopies	retro_itri_164 , retro_itri_295,