RetrogeneDB ID: retro_itri_629

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393308.1:2268863..2269165(+)
• Located in intron of: ENSSTOG00000003831

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: CST7
• Ensembl ID: ENSSTOG00000005896
• Aliases: None
• Description: cystatin F (leukocystatin) [Source:HGNC Symbol;Acc:2479]

Sequence

>retro_itri_629
AAAACACTCAAGAACAATGTTGAAAAGTTCAACAACTACACCTAGGACAGTGTTTTTCTTCAAGGAGTCTCACGTCAGCA
TAGCCCTGGTGGAGATATAAAATGCCTGAAACACATGTGGAGGTGGAATTTGGCAGACCCACCTGCAGGACAATCAAGGA
CCCTTGTCTGAACAGTTGTGACTTCCAAACCAACTACACTGCAAAGTGGTCTTTGAGTTGCTCCTCTGAGGTCTGGGCCA
TTCCCCAGCTCCTGAGGTTTGAGGAACCCGTTCTCCATTACCAATGACCACAGCTGAGACAA

Alignment

ORF - retro_itri_629 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.96 %
• Parental protein coverage: 64.74 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KAARHSVEKFNNCTND-IFLFKESYISRALVQV-VKGLKYM-LEVEIGRTTCRKTTHHPLDNCDFQTNPD
          K.....VEKFNN.T.D..F.FKES..S.ALV....K.LK.M..EVE.GR.TCR......L..CDFQTN..
Retrocopy KTLKNNVEKFNNYT*D>VFFFKESHVSIALVEI<IKCLKHM<VEVEFGRPTCRTIKDPCLNSCDFQTNYT

Parental  LKRILSCYTEVWVIPWLRKFEVPIIRCQPEDLEQ
          .K..LSC..EVW.IP.L..FE.P....Q...L.Q
Retrocopy AKWSLSCSSEVWAIPQLLRFEEPVLHYQ*PQLRQ

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_629 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_629 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 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Ictidomys tridecemlineatus	ENSSTOG00000005896	1 retrocopy	retro_itri_629 ,