RetrogeneDB ID: retro_itri_140

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393605.1:677221..677914(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000005976
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000004511
• Aliases: None
• Description: None

Sequence

>retro_itri_140
ATGGCGGGCTCTTGGTCATTGGATCATCACAGAGGGTGTATCTCCACTTGCTGCGCAGGTGACCTCAAGGATAAGAGGAA
CGACTCGTCGCTGTTGGGCAGGAGGCTCTCGGAGGACTCGGGCCGCCACCGGCTGCTGGAGAAGTGGGCGATCATGTGGA
ACTCCGTGAGCACAGACGCGACCGAGGCCAGCACCGACAAGTTTCCCAAGGAGGCGGCCCCGGCGGAGCCCCCGCTGGTG
TTCCTGTGCTCCGGCTTCCGGCGTCCGCTGGGCGACTCGCTGAGCTGGGATACCAGCCAGGAGGACACCAACTGCATCCT
GCTGCGCTGTGTTTCCTGTAATGTTTCTGTGGATAAAGAGCAGAAGCTTTCCAAACGTAAAGATGAAAATGGTTGCATTC
TCAAGACCCTGTACTGTGCGGGTTGCTCCCTCCATCTTGGCTATGTGTTCAGGTGCACTCCCAAGAATCTGGATTATAAG
AGAGACTTGTTTTGCCTCAGTGTTGAAGCCATTGAAAGTTATACTTTAGGGTCCTCTGAAAAACAAATTTTGCCAGAAGA
TAAAGAGCTTTTTAATCTTGAAAGCCGAGTTGAAATAGAAAAGTCTCTAAAACAGATGGAAGATGTCTTGAAAGCATTGC
AAACGAAGCTGTGGGAGGTTGAATCAAAATTGTCCTTTATGAGCTGCAAAAAA

Alignment

ORF - retro_itri_140 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.65 %
• Parental protein coverage: 99.57 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGSWSLGRHRGCISTCCAGDLKDKRNDSSPLGRRLSEDSGRHRLLEKWASMWNSVSTDATEASTDRFPE
          MAGSWSL..HRGCISTCCAGDLKDKRNDSS.LGRRLSEDSGRHRLLEKWA.MWNSVSTDATEASTD.FP.
Retrocopy MAGSWSLDHHRGCISTCCAGDLKDKRNDSSLLGRRLSEDSGRHRLLEKWAIMWNSVSTDATEASTDKFPK

Parental  EAAPAEPPLVFLCSGCRRPLGDSLSWVTSQEDTNCILLRCVSCNVSVDKEQKLSKRKDENGCILETLYCA
          EAAPAEPPLVFLCSG.RRPLGDSLSW.TSQEDTNCILLRCVSCNVSVDKEQKLSKRKDENGCIL.TLYCA
Retrocopy EAAPAEPPLVFLCSGFRRPLGDSLSWDTSQEDTNCILLRCVSCNVSVDKEQKLSKRKDENGCILKTLYCA

Parental  GCSLHLGYVFRCTPKNLDYKRDLFCLSVEAIESYTLGSSEKQIMPEDKELFNLESRVEIEKSLKQMEDVL
          GCSLHLGYVFRCTPKNLDYKRDLFCLSVEAIESYTLGSSEKQI.PEDKELFNLESRVEIEKSLKQMEDVL
Retrocopy GCSLHLGYVFRCTPKNLDYKRDLFCLSVEAIESYTLGSSEKQILPEDKELFNLESRVEIEKSLKQMEDVL

Parental  KALQTKLWEVESKLSFMSCK
          KALQTKLWEVESKLSFMSCK
Retrocopy KALQTKLWEVESKLSFMSCK

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_140 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_140 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009090	1 retrocopy	retro_cjac_682,
Ictidomys tridecemlineatus	ENSSTOG00000004511	1 retrocopy	retro_itri_140 ,