RetrogeneDB ID: retro_itri_659

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393309.1:522435..522870(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARL8A
• Ensembl ID: ENSSTOG00000013990
• Aliases: None
• Description: ADP-ribosylation factor-like 8A [Source:HGNC Symbol;Acc:25192]

Sequence

>retro_itri_659
AGCTGTCAGTTCAATGAGGACATGATCCCCACCGTGGGTTTCAACATGAGCAAAATCACCAAAGGGAACGTGACCATCAA
GCTCTGGGACATTGGGAGACAGCCCCGTTTCCACAGCATGTGGGAGCGCTACTGCCAGATAGTGAGTGCCATAGTGTATA
TGGTAGATGCTTCAGACCAGGAGAAGATAGAGGCCTCCAAAAATGAACTCCACAACTCACTGGACAAACCTCAGTTGCAG
GGCATCCCGGTCTTAGTCCTGGGTAACAAGCAAGACCTCCCAGGGGCACTGGATGACAAGGAACTGATAGAAAAAATGAA
TCTGTCTGCCATCCAGGACTGAGAAGTTTGCTGCTACTCCATCTCCTGCAAAGAGAAGGACAACACTGACATCACCCTAT
TGTGGCTTATTCAAAACTCAAAGTCACAGAGAAGC

Alignment

ORF - retro_itri_659 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.97 %
• Parental protein coverage: 77.96 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SGQFNEDMIPTVGFNMRKITKGNVTIKLWDIGGQPRFRSMWERYCRGVSAIVYMVDAADQEKIEASKNEL
          S.QFNEDMIPTVGFNM.KITKGNVTIKLWDIG.QPRF.SMWERYC..VSAIVYMVDA.DQEKIEASKNEL
Retrocopy SCQFNEDMIPTVGFNMSKITKGNVTIKLWDIGRQPRFHSMWERYCQIVSAIVYMVDASDQEKIEASKNEL

Parental  HNLLDKPQLQGIPVLVLGNKRDLPGALDEKELIEKMNLSAIQDREICCYSISCKEKDNIDITLQWLIQHS
          HN.LDKPQLQGIPVLVLGNK.DLPGALD.KELIEKMNLSAIQD.E.CCYSISCKEKDN.DITL.WLIQ.S
Retrocopy HNSLDKPQLQGIPVLVLGNKQDLPGALDDKELIEKMNLSAIQD*EVCCYSISCKEKDNTDITLLWLIQNS

Parental  KSRRS
          KS.RS
Retrocopy KSQRS

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_659 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_659 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Meleagris gallopavo	ENSMGAG00000001081	1 retrocopy	retro_mgal_18,
Oryctolagus cuniculus	ENSOCUG00000023009	1 retrocopy	retro_ocun_1404,
Ictidomys tridecemlineatus	ENSSTOG00000004295	1 retrocopy	retro_itri_175,
Ictidomys tridecemlineatus	ENSSTOG00000009288	3 retrocopies	retro_itri_1754, retro_itri_273, retro_itri_363,
Ictidomys tridecemlineatus	ENSSTOG00000013990	1 retrocopy	retro_itri_659 ,
Ictidomys tridecemlineatus	ENSSTOG00000019470	2 retrocopies	retro_itri_1439, retro_itri_1614,
Ictidomys tridecemlineatus	ENSSTOG00000019768	1 retrocopy	retro_itri_883,