RetrogeneDB ID: retro_itri_1727

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393680.1:399522..400140(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ABHD4
• Ensembl ID: ENSSTOG00000023335
• Aliases: None
• Description: abhydrolase domain containing 4 [Source:HGNC Symbol;Acc:20154]

Sequence

>retro_itri_1727
GGGATCCCCAGCATGATCCTCCTAGGGCACAGTTTGGGAGGATTCCTGGCCACCTCTTACTCTATCAAGTACCCTGAAAG
AGTTAAATACCTTATCCTGGTGGACCCTTGGGGCTTTCCCCTCCCAACTGACCCAGGTGAGATCCGTGCACCTCCCACCT
GGGTCAAGGCTATGGCTTCTGTCCTGGGGCGTTCCAATCCCCTGGCTATTCTTCGAGTAGCTGAGCCCTGGGAGCCTGGC
CTGGTACAGCGATTTTGGCCAGACTTCAAGTGTAAATTTTCAGACTTCTTTGAAGATGATACTATATCAGAGTATATCTA
CCACTGCAATGCACAGGATCCCAGTGGTGAAACAGCATTCAAAGCCATGACGGAGTCCTTTGGCTGGGCCCGGCGCCCCA
TGTTGGAGGGAATTCACTTAATTCGAAAAGATGTACCCATCACCATGATCTATGGGGCCAACACCTGGATAGATACTAGC
ATGGCAAAAAAAGTGAAGATGCAGCGGCCAGATTCCTATGTCCGAGACATGGAGATTGAGGGTGCATCGCATCATGTCTA
TGCTGACCAGCCGCACATCTTTAATGCTGTAATGGAAGAGATCTGTGACTCAGTGGAT

Alignment

ORF - retro_itri_1727 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.27 %
• Parental protein coverage: 58.31 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GIPSMILLGHSLGGFLATSYSIKYPERVKHLILVDPWGFPLRPTDPSEIRAPPTWVKAVASVLGRSNPLA
          GIPSMILLGHSLGGFLATSYSIKYPERVK.LILVDPWGFPL.PTDP.EIRAPPTWVKA.ASVLGRSNPLA
Retrocopy GIPSMILLGHSLGGFLATSYSIKYPERVKYLILVDPWGFPL-PTDPGEIRAPPTWVKAMASVLGRSNPLA

Parental  VLRVAGPWGPGLVQRFRPDFKRKFADFFEDDTISEYIYHCNAQNPSGETAFKAMMESFGWARRPMLERIH
          .LRVA.PW.PGLVQRF.PDFK.KF.DFFEDDTISEYIYHCNAQ.PSGETAFKAM.ESFGWARRPMLE.IH
Retrocopy ILRVAEPWEPGLVQRFWPDFKCKFSDFFEDDTISEYIYHCNAQDPSGETAFKAMTESFGWARRPMLEGIH

Parental  LIRKDVPITMIYGANTWIDTSTGKKVKMQRPDSYVRDMEIEGASHHVYADQPHIFNAVVEEICDSVD
          LIRKDVPITMIYGANTWIDTS..KKVKMQRPDSYVRDMEIEGASHHVYADQPHIFNAV.EEICDSVD
Retrocopy LIRKDVPITMIYGANTWIDTSMAKKVKMQRPDSYVRDMEIEGASHHVYADQPHIFNAVMEEICDSVD

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_1727 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1727 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.

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000009441	1 retrocopy	retro_mmul_545,
Ictidomys tridecemlineatus	ENSSTOG00000023335	1 retrocopy	retro_itri_1727 ,