RetrogeneDB ID: retro_itri_1067

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393366.1:6542793..6543176(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ENOPH1
• Ensembl ID: ENSSTOG00000013987
• Aliases: None
• Description: enolase-phosphatase 1 [Source:HGNC Symbol;Acc:24599]

Sequence

>retro_itri_1067
TTTGAAGATGTCATCCCAACAGTCAGGAAGTGAAAAGAAGCGGGAATGAAGGTGTTTATCTATCCTTCTGGAAGTGCAGA
GGCTCAGAAGCTATTATTTGGGCATTCTACAGAGGGAAATATTCTTGAGCTTTTTGATTGTCACTTTGATACCAAGATTG
GACACAAAGTGGAGAGTGAGAGTTATAGAAAGTTTGCAAACAGCATTGGATGCTCAACCAACATCTTGTTTCCAACAGAT
GTGACTTTAAAAGCCAGTGCTGCTGAGGAAGCAGATGAGCATATAGCTTGGGTGTTGACACTGGTAAGGCAGGATTAACA
GATGATGAGAAAACTTCCTATAGCCTCATCACATCCTTCAACAGACTATACCTGCCTTATTCA

Alignment

ORF - retro_itri_1067 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80. %
• Parental protein coverage: 54.66 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FEDVVPAVRKWREDGMKVYIYSSGSVEAQKLLFGHSTEGNILELFDGHFDTKIGHKVESESYKKIANSIG
          FEDV.P.VRK..E.GMKV.IY.SGS.EAQKLLFGHSTEGNILELFD.HFDTKIGHKVESESY.K.ANSIG
Retrocopy FEDVIPTVRK*KEAGMKVFIYPSGSAEAQKLLFGHSTEGNILELFDCHFDTKIGHKVESESYRKFANSIG

Parental  CSTNNILFLTDITLEASAAEEAGVHVAVV-VRPGNAGLTDDEKTSYSLITSFSELYLPSS
          CST.NILF.TD.TL.ASAAEEA..H.A.V.V..G.AGLTDDEKTSYSLITSF..LYLP.S
Retrocopy CST-NILFPTDVTLKASAAEEADEHIAWV<VDTGKAGLTDDEKTSYSLITSFNRLYLPYS

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_1067 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1067 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 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003283	4 retrocopies	retro_chof_2150, retro_chof_470, retro_chof_486, retro_chof_596,
Equus caballus	ENSECAG00000019612	1 retrocopy	retro_ecab_164,
Erinaceus europaeus	ENSEEUG00000004274	1 retrocopy	retro_eeur_563,
Loxodonta africana	ENSLAFG00000008619	1 retrocopy	retro_lafr_1158,
Macropus eugenii	ENSMEUG00000011458	1 retrocopy	retro_meug_1125,
Ictidomys tridecemlineatus	ENSSTOG00000013987	2 retrocopies	retro_itri_1067 , retro_itri_1587,
Tursiops truncatus	ENSTTRG00000001800	1 retrocopy	retro_ttru_1231,