RetrogeneDB ID: retro_itri_1008

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393358.1:6033442..6033772(+)
• Located in intron of: ENSSTOG00000002257

Retrocopy information

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

Parental gene information

• Parental gene symbol: EMC4
• Ensembl ID: ENSSTOG00000000516
• Aliases: None
• Description: ER membrane protein complex subunit 4 [Source:HGNC Symbol;Acc:28032]

Sequence

>retro_itri_1008
ATAACAGCCCAGGGGGGCTTGGTGGCCACCTGAGGCCAATGGTTGAAGTGGCCCATTGAGCTGAGTGGGCCTGGAGGAGG
TAGCAGGGACAGAAGTAACCACAGCAGTAGCCAGGAAGACTCACTAGACCCAGTTGGTTACTTGGACAAGCAAGTACCTA
ATACCAGAGTGCAGGAGATAGACTGGATCCTAGTGGAGAAGTACTATTGGGTCATCGCCTTGGGCCCCTCCAAACAGATT
CCCATGGACCTCTTCATCATGCACACAGCAGGAAATACTATCTCCATCTTCCCTGATGTGATGGTATGCATGGCAGCCTG
GCAACCCATT

Alignment

ORF - retro_itri_1008 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.55 %
• Parental protein coverage: 60.11 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTAQGGLVANRGRRFKWAIELSGPGGGSRGRSDRGSSQGDSLYPVGYLDKQVPDTSVQETDRILVEKRCW
          .TAQGGLVA..G...KW.IELSGPGGGSR.RS...SSQ.DSL.PVGYLDKQVP.T.VQE.D.ILVEK..W
Retrocopy ITAQGGLVAT*GQWLKWPIELSGPGGGSRDRSNHSSSQEDSLDPVGYLDKQVPNTRVQEIDWILVEKYYW

Parental  DIALGPLKQIPMNLFIMYMAGNTISIFPTMMVCMMAWRPI
          .IALGP.KQIPM.LFIM..AGNTISIFP..MVCM.AW.PI
Retrocopy VIALGPSKQIPMDLFIMHTAGNTISIFPDVMVCMAAWQPI

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_1008 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1008 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 11 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005576	2 retrocopies	retro_chof_1859, retro_chof_254,
Dipodomys ordii	ENSDORG00000008407	2 retrocopies	retro_dord_387, retro_dord_581,
Echinops telfairi	ENSETEG00000001688	1 retrocopy	retro_etel_1631,
Felis catus	ENSFCAG00000001736	1 retrocopy	retro_fcat_759,
Macropus eugenii	ENSMEUG00000004615	1 retrocopy	retro_meug_1129,
Microcebus murinus	ENSMICG00000003864	2 retrocopies	retro_mmur_1313, retro_mmur_180,
Oryctolagus cuniculus	ENSOCUG00000006160	4 retrocopies	retro_ocun_1686, retro_ocun_395, retro_ocun_719, retro_ocun_817,
Ochotona princeps	ENSOPRG00000009190	1 retrocopy	retro_opri_605,
Pteropus vampyrus	ENSPVAG00000003824	1 retrocopy	retro_pvam_386,
Rattus norvegicus	ENSRNOG00000005719	1 retrocopy	retro_rnor_897,
Ictidomys tridecemlineatus	ENSSTOG00000000516	1 retrocopy	retro_itri_1008 ,