RetrogeneDB ID: retro_itri_538

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393300.1:349739..350527(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COPS7A
• Ensembl ID: ENSSTOG00000027250
• Aliases: None
• Description: COP9 signalosome subunit 7A [Source:HGNC Symbol;Acc:16758]

Sequence

>retro_itri_538
ATGAGTGCGGAGGTGAAGGTGACAGGGCAGAACCAGGAGCAATTTCTGCTCCTGGCCAAGTCGGCCAAGGGGGCAGCGCT
GGCCACACTCATCCACCAGGTGATGGAGGCCCCTGGTGTCAACGTGTTTGGGGAACTGCTGGATATGCCCAATGTTAGAG
AGCTGTCTGAAAGTGACTTTGCTTCCACATTCCGGCTGCTCACAGTGTTTGCTTATGGAACATATGCCGACTACTTAGCT
GAAGCCAGGAATCTTCCTCCACTCACTGAAGCTCAGAAGAATAAACTTCGACACCTCTCAGTTGTCACCCTGGCTGCTAA
AGTCAAGTGCATCCCATATGCAGTGTTGCTAGAAGCCCTTGCTCTGCATAATGTGCGGCAGCTAGAAGACCTGGTGATTG
AGGCTGTATGTGCTGATGTGCTTTGCGGCTCACTGGAACAACGCAATCAGCGTCTAGAGGTTGACTACAGCATTGGACGG
GACATCCAGCGCCAAGACCTTAGTGCCATTGCCCGAACCCTGCAGGAGTGGTGTGTAGGCTGTGAGGTTGTGCTGTCAGG
TATCAAGGAGCAAGTGAGCCATCCAACCAGCACAAGGAGCAGCAGCTGGGCCTAAAGCAGCAGATTGAAAGTGAGGTTGC
CAACCTTAAAAAAACCACTAAAGTTACAACAGCAGCAGCTGCTGCAGCCACATCTCAGGACCCCAAGCAACACCTGACTG
AACTGAGGGACCCAGCTCCAGGCATCAACCAGTGCCAGCCCAGCAAGAAGGCCTCAAAAGGGAAGGGG

Alignment

ORF - retro_itri_538 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.32 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSAEVKVTGQNQEQFLLLAKSAKGAALATLIHQVLEAPGVYVFGELLDMPNVRELAESDFASTFRLLTVF
          MSAEVKVTGQNQEQFLLLAKSAKGAALATLIHQV.EAPGV.VFGELLDMPNVREL.ESDFASTFRLLTVF
Retrocopy MSAEVKVTGQNQEQFLLLAKSAKGAALATLIHQVMEAPGVNVFGELLDMPNVRELSESDFASTFRLLTVF

Parental  AYGTYADYLAEARNLPPLTEAQKNKLRHLSVVTLAAKVKCIPYAVLLEALALRNVRQLEDLVIEAVYADV
          AYGTYADYLAEARNLPPLTEAQKNKLRHLSVVTLAAKVKCIPYAVLLEALAL.NVRQLEDLVIEAV.ADV
Retrocopy AYGTYADYLAEARNLPPLTEAQKNKLRHLSVVTLAAKVKCIPYAVLLEALALHNVRQLEDLVIEAVCADV

Parental  LRGSLDQRNQRLEVDYSIGRDIQRQDLSAIARTLQEWCVGCEVVLSGIEEQVSR-ANQHKEQQLGLKQQI
          L.GSL.QRNQRLEVDYSIGRDIQRQDLSAIARTLQEWCVGCEVVLSGI.EQVS...NQHKEQQLGLKQQI
Retrocopy LCGSLEQRNQRLEVDYSIGRDIQRQDLSAIARTLQEWCVGCEVVLSGIKEQVSH<SNQHKEQQLGLKQQI

Parental  ESEVANLKKTIKVTTAAAAAATSQDPEQHLTELRDPAPGTNQRQPSKKASKGKG
          ESEVANLKKT.KVTTAAAAAATSQDP.QHLTELRDPAPG.NQ.QPSKKASKGKG
Retrocopy ESEVANLKKTTKVTTAAAAAATSQDPKQHLTELRDPAPGINQCQPSKKASKGKG

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_538 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_538 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000004634	1 retrocopy	retro_lafr_297,
Macropus eugenii	ENSMEUG00000010451	1 retrocopy	retro_meug_724,
Microcebus murinus	ENSMICG00000013661	1 retrocopy	retro_mmur_1458,
Oryctolagus cuniculus	ENSOCUG00000011187	1 retrocopy	retro_ocun_1086,
Ictidomys tridecemlineatus	ENSSTOG00000027250	1 retrocopy	retro_itri_538 ,