RetrogeneDB ID: retro_itri_1786

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393773.1:92633..92956(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GOLT1B
• Ensembl ID: ENSSTOG00000006352
• Aliases: None
• Description: golgi transport 1B [Source:HGNC Symbol;Acc:20175]

Sequence

>retro_itri_1786
GACAAAGTACTACTGGCCTTTGGAAATGTTTTGTTTGTGACTGGCTAGGCTTTTATAATCAGTTTAGAAAGCACATTCAG
ATTCTTTTCCCAAAAACATAAAATGAAAGCTACAGGATTTTTCCTAGGTGGTATATTTGTAGTTCTTATTGGTTGGCCTT
TGAGAGGCAGGATATTTGAAAATTACGGATTTTTTAACTTGTTCAGGGGCTTCTTTTCTGTGTGGTTGGCTTTATTAGAA
GAATGCCTATTCTTGGATTCCTCTTAAATTTACCTGGAATTAGATCATGTATAGATAAAGTTGGAAAAAGCAACAATATT
GTT

Alignment

ORF - retro_itri_1786 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.82 %
• Parental protein coverage: 78.26 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DKALLAIGNVLFVAGLAFVIGLERTFRFFFQKHKMKATGFFLGGVFVVLIGWPLIGMIFEIYGFFLLFRG
          DK.LLA.GNVLFV.G.AF.I.LE.TFRFF.QKHKMKATGFFLGG.FVVLIGWPL.G.IFE.YGFF.LFRG
Retrocopy DKVLLAFGNVLFVTG*AFIISLESTFRFFSQKHKMKATGFFLGGIFVVLIGWPLRGRIFENYGFFNLFRG

Parental  FFPV-VVGFIRRVPVLGSLLNLPGIRSFVDKVGESNNMV
          FF.V.VVGFIRR.P.LG.LLNLPGIRS..DKVG.SNN.V
Retrocopy FFSV<VVGFIRRMPILGFLLNLPGIRSCIDKVGKSNNIV

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_1786 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1786 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016231	1 retrocopy	retro_amel_604,
Canis familiaris	ENSCAFG00000012256	1 retrocopy	retro_cfam_1835,
Dasypus novemcinctus	ENSDNOG00000013576	2 retrocopies	retro_dnov_158, retro_dnov_1730,
Felis catus	ENSFCAG00000028655	1 retrocopy	retro_fcat_1782,
Oryctolagus cuniculus	ENSOCUG00000008797	1 retrocopy	retro_ocun_1706,
Otolemur garnettii	ENSOGAG00000004756	1 retrocopy	retro_ogar_3234,
Ictidomys tridecemlineatus	ENSSTOG00000006352	1 retrocopy	retro_itri_1786 ,