RetrogeneDB ID: retro_itri_724

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393314.1:8142565..8143359(+)
• 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_724
TCCCAGCTGGGGGGATTGAAGCTCCCTGTCAACAAGGTTCTGAGCAGCCATTTCCAGGTGGCTCACACTGTGCACATGAG
TGCCCTGGGCTTGCCTGGCTATCACCTCCATGCAGCCTATGCAGGGGATTGGCAGCTCAGCCCCACAGAGGTGTTCCCCA
CTGTGGTAGGGGATATGGACAGCAGCAGAAGTCTCAACGCCCAGGTCCTACTTCTGTTGGCAGAGCAGCTCCAAGCTAAG
GCCATCCTCCAGACACTACAGGCCAAGTTCCTGACATGGCAGTTTGATGGCGAGTATCGAGATGACTACACAGCCACTCT
GACCCTAGGAAATCCTAATCCAATTGAGGAATCGGTGATCATGGCTGCTCACTTTCTGCAGAGCCTCACTCATCGACTGG
TGCTGGGAGGAGAGCTAGTTTATCACCAGCGGCCAGGCGAAGAGGGGGCCATCTTGACTCTGGCTGGGAAGTACTAGGCT
GTACACTGGGTGGCTACATGGAATGTGGGATCTGGTGGGGCCCATGCAAGCTATTACCACAGGGCAAATGAACAGGTTCA
GGTTGGAATGGAGTTTGAGGCAAACATAAGGCTACAAGACACAACCTTCTCCTTTGCTTACCACCTGACTTTGCCCCAGC
CAACATGGTGTTTAGAGGCTTGGTGGATAGTAACTGATGCATAGGTGCTGTGCTGGAGAAGATGATGCCCCCATTGCCCG
TCACCTTGGCCCTTGGAGCCTTCCTTAATCACTGGTGCAACAGATTCCGTTGTAGCTTCAGCATCACTGTGGGC

Alignment

ORF - retro_itri_724 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.14 %
• Parental protein coverage: 86.36 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AQMEGVKLVVNKVLSSHFQVAHTVHMSALGLPGYHLHAAYAGDWQLSPTEVFPTVVGDMDSSGSLNAQVL
          .Q..G.KL.VNKVLSSHFQVAHTVHMSALGLPGYHLHAAYAGDWQLSPTEVFPTVVGDMDSS.SLNAQVL
Retrocopy SQLGGLKLPVNKVLSSHFQVAHTVHMSALGLPGYHLHAAYAGDWQLSPTEVFPTVVGDMDSSRSLNAQVL

Parental  LLLAERLRAKAVFQTQQAKFLTWQFDGEYRGDDYTATLTLGNPDLIGESVIMVAHFLQSLTHRLVLGGEL
          LLLAE.L.AKA..QT.QAKFLTWQFDGEYR.DDYTATLTLGNP..I.ESVIM.AHFLQSLTHRLVLGGEL
Retrocopy LLLAEQLQAKAILQTLQAKFLTWQFDGEYR-DDYTATLTLGNPNPIEESVIMAAHFLQSLTHRLVLGGEL

Parental  VYHRRPGEEGAILTLAGKYSAVHWVATLNVGSGGAHASYYHRANEQVQVGVEFEANTRLQDTTFSFGYHL
          VYH.RPGEEGAILTLAGKY.AVHWVAT.NVGSGGAHASYYHRANEQVQVG.EFEAN.RLQDTTFSF.YHL
Retrocopy VYHQRPGEEGAILTLAGKY*AVHWVATWNVGSGGAHASYYHRANEQVQVGMEFEANIRLQDTTFSFAYHL

Parental  TLPQ-ANMVFRGLVDSNWCVGAVLEKKMPPLPVTLALGAFLNHWRNRFHCGFSITVG
          TLPQ.ANMVFRGLVDSN.C.GAVLEK.MPPLPVTLALGAFLNHW.NRF.C.FSITVG
Retrocopy TLPQ<ANMVFRGLVDSN*CIGAVLEKMMPPLPVTLALGAFLNHWCNRFRCSFSITVG

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_724 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_724 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,