RetrogeneDB ID: retro_itri_301

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393283.1:9489405..9489978(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TOMM40L
• Ensembl ID: ENSSTOG00000003800
• Aliases: None
• Description: translocase of outer mitochondrial membrane 40 homolog (yeast)-like [Source:HGNC Symbol;Acc:25756]

Sequence

>retro_itri_301
ATGGGTAATACATTGGGCCTGGCACTGATGGGGACTTTGCCTGCTGTAGCCCCTGCCAAGAGGAACCTCTACTCCACCCT
GGGAGTTTTGATGTGCTGCACCAGCTATGCAAAGGCGTATTCCCAGCACAGATAGAGGGAGTGAAGCTCGTTGTCAACAA
GGTTCTGAGCAGCCATCTCCAGGTGGCTCACACTGTGCACATGAGTGCCCTGGGCTATCACCTCCATGCAGCCCATGCAG
GGGTTTGGCAGCTCAGCCCCACAGAGGTGTTCCCCACTGTGGTAGGGGATATGGACAGCAGTGAAAGTCTCAACGCCCAG
GTCCTACTTCTGTTGGCAGAGTGGCTCTGAGCCAAGACTGCCTTCCAGACACAACAGGTCAAGTTCCTGAGATGGCAGTT
TGAAGGCAAGTATCGGAGGAGATGACTACACAGCCACTCTGACCCTAGGAAATCCTGACCTGATTGGGGGATCGGTGACC
ATGGTTGCTCACTTCCTGCAGAGCCTCACTCATCGACTGGTGCTGGGAGGAGCGCTGGTTCATCATGGGCAGCCAGGCGA
GGAGGGGGCCCTT

Alignment

ORF - retro_itri_301 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.61 %
• Parental protein coverage: 62.99 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MGNTLGLAPMGSMPRRSPRR-EEPLPNPGSFDELHRLCKDVFPAQMEGVKLVVNKVLSSHFQVAHTVHMS
          MGNTLGLA.MG..P...P...EEPL..PGSFD.LH.LCK.VFPAQ.EGVKLVVNKVLSSH.QVAHTVHMS
Retrocopy MGNTLGLALMGTLPAVAPAK<EEPLLHPGSFDVLHQLCKGVFPAQIEGVKLVVNKVLSSHLQVAHTVHMS

Parental  ALGLPGYHLHAAYAGDWQLSPTEVFPTVVGDMDSSGSLNAQVLLLLAERLRAKAVFQTQQAKFLTWQFDG
          AL...GYHLHAA.AG.WQLSPTEVFPTVVGDMDSS.SLNAQVLLLLAE.L.AK..FQTQQ.KFL.WQF.G
Retrocopy AL---GYHLHAAHAGVWQLSPTEVFPTVVGDMDSSESLNAQVLLLLAEWL*AKTAFQTQQVKFLRWQFEG

Parental  EYR-GDDYTATLTLGNPDLIGESVIMVAHFLQSLTHRLVLGGELVYHRRPGEEGAI
          .YR.GDDYTATLTLGNPDLIG.SV.MVAHFLQSLTHRLVLGG.LV.H..PGEEGA.
Retrocopy KYR>GDDYTATLTLGNPDLIGGSVTMVAHFLQSLTHRLVLGGALVHHGQPGEEGAL

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_301 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_301 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
Erinaceus europaeus	ENSEEUG00000004808	1 retrocopy	retro_eeur_472,
Echinops telfairi	ENSETEG00000015755	2 retrocopies	retro_etel_1124, retro_etel_1461,
Gorilla gorilla	ENSGGOG00000005720	2 retrocopies	retro_ggor_1075, retro_ggor_1761,
Otolemur garnettii	ENSOGAG00000013733	1 retrocopy	retro_ogar_2524,
Ictidomys tridecemlineatus	ENSSTOG00000003800	2 retrocopies	retro_itri_301 , retro_itri_724,
Ictidomys tridecemlineatus	ENSSTOG00000009019	1 retrocopy	retro_itri_150,
Drosophila melanogaster	FBgn0016041	1 retrocopy	retro_dmel_74,