RetrogeneDB ID: retro_itri_67

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393294.1:17009435..17009804(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000020260
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: VAMP1
• Ensembl ID: ENSSTOG00000007482
• Aliases: None
• Description: vesicle-associated membrane protein 1 (synaptobrevin 1) [Source:HGNC Symbol;Acc:12642]

Sequence

>retro_itri_67
GCTCCCCGGCCTCCTCAGCCCGCTGCGCAGCTCCGTGGACCCTCGCCCGCTGCCAAAATGTCTGCAGGTGCGCCTGCAGG
TTCCAGTGCTGCCACTGGCAGTAATCGGAGAATTCAACAGACACAAAATCAAGTAGATGAGGTGGTGGACATAATGAGAG
TCAACGTGGACAAGGTGCTAGAAAGAGACCAGAAGCTCTCTGAGCTGGATGACCGTGCAGATGCGTTGCAGGCAGGAGCT
TCTCAATTTGAGACAAGTGCTGCCAAGTTAAAGAGAAAATATTGGTGGAAGAATTGCAAGATGTGGGCAGTAGGGATCAG
CGTTCTGATCATTATCGTCATCATCATCATTGTATGGAGCGTCTCTTAA

Alignment

ORF - retro_itri_67 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.26 %
• Parental protein coverage: 82.91 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GAPPGPPPNTTSNRRLQQTQAQVEEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFESSAAKLKR
          GAP.G....T.SNRR.QQTQ.QV.EVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFE.SAAKLKR
Retrocopy GAPAGSSAATGSNRRIQQTQNQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETSAAKLKR

Parental  KYWWKNCKMMIMLGAICAIIVVVIVIY
          KYWWKNCKM.........IIV..I...
Retrocopy KYWWKNCKMWAVGISVLIIIVIIIIVW

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_67 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_67 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
Echinops telfairi	ENSETEG00000002527	1 retrocopy	retro_etel_259,
Ictidomys tridecemlineatus	ENSSTOG00000007482	1 retrocopy	retro_itri_67 ,