RetrogeneDB ID: retro_itri_1714

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393652.1:757048..757438(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SAR1B
• Ensembl ID: ENSSTOG00000011326
• Aliases: None
• Description: SAR1 homolog B (S. cerevisiae) [Source:HGNC Symbol;Acc:10535]

Sequence

>retro_itri_1714
ATGACTTTTACAACTTTTGATCTGGGTGGACATGTTCAAGCCTGAAGAGTATGGAAAAACTGCCTTCCTGCTGTCAAAGG
CATTGTATTTCTTGTGGATTGTATAGCCCATGAAAGGCTGTTAGAATCGAAAGAAGAATTTGATTTACTAATGACTGATG
ACACCATTGCTAATGTGCCTATACTGATTCTTGGGAATAAGACTGACAGACCTGAAGCCATTAGTGAAGAAAGGTTAAAA
GAAATGTTTGGTTTATATACTCAGACAATAGGAAAGGGCAGTGTATCTTTGAAAGATCTGAATGCCGGACATTTAGAAGT
TTTCATGTGAAATGCGCCCAAAAGACAAGGTTATGGAGAAGGCTTCCGCTGGATGGTACAGTACATTGAT

Alignment

ORF - retro_itri_1714 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.08 %
• Parental protein coverage: 65.66 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTFTTFDLGGHVQARRVWKNYLPAINGIVFLVDCADHERLLESKEELDSLMTDETIANVPILILGNKIDR
          MTFTTFDLGGHVQA.RVWKN.LPA..GIVFLVDC..HERLLESKEE.D.LMTD.TIANVPILILGNK.DR
Retrocopy MTFTTFDLGGHVQA*RVWKNCLPAVKGIVFLVDCIAHERLLESKEEFDLLMTDDTIANVPILILGNKTDR

Parental  PEAISEERLREMFGLYGQTTGKGGVSLKELNARPLEVFMCSVLKRQGYGEGFRWMAQYID
          PEAISEERL.EMFGLY.QT.GKG.VSLK.LNA..LEVFM....KRQGYGEGFRWM.QYID
Retrocopy PEAISEERLKEMFGLYTQTIGKGSVSLKDLNAGHLEVFM*NAPKRQGYGEGFRWMVQYID

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_1714 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1714 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 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000013784	3 retrocopies	retro_dnov_1584, retro_dnov_1804, retro_dnov_919,
Loxodonta africana	ENSLAFG00000001021	1 retrocopy	retro_lafr_1043,
Otolemur garnettii	ENSOGAG00000013347	1 retrocopy	retro_ogar_2472,
Ictidomys tridecemlineatus	ENSSTOG00000011326	1 retrocopy	retro_itri_1714 ,
Ictidomys tridecemlineatus	ENSSTOG00000012780	2 retrocopies	retro_itri_1191, retro_itri_590,