RetrogeneDB ID: retro_itri_335

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393284.1:15388127..15388783(-)
• Located in intron of: ENSSTOG00000006690

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTRF1L
• Ensembl ID: ENSSTOG00000009980
• Aliases: None
• Description: mitochondrial translational release factor 1-like [Source:HGNC Symbol;Acc:21051]

Sequence

>retro_itri_335
TGGCATTTTGAAACCTTAGAATACTTTCCAAGTGAAATAGGTGGCCTTAGATATGCATCTACCAGCATTGGCGGTTCAGA
AGCCTATAAACACATAAAATTTGAAGGGGGAGTGCATAGAGTACAGAGAGTGCCAAGGACAGAAAAGCAAGGCCGCATCC
ATACTAGCACAATGGCAGTGGCAATATTATCCCAGCCCACTGAGATTAATATGGTGATTAATCCAAAAGATTTGAGAATT
GATACTAAGCGAGCTAGTGGAGTTGGGGGTCAGCATGTAAATACCACGGACAGTGCTGTCTGGATTGTTCATCTTCCAAC
AGGTGTTGTTTCTGAATGCCAACAAGAGAGGTCTCAACTGAAAAATAGAGATGGCTATGAAAAAATTTGCGTGCAAAGCT
GTACAATATGCGTCTAGAGGAAGAAACAAGTAAAAGATTACAGTGCTAGGAAGATTCAGGTTAGAACTAAAGGAAGATTA
GAGAAAATAAGAACATATTATTTTCCACAGAACCGGGTCACAGATCACAGAATAACAAGTCACTGCATGGTCTTCAGACT
TTTATGCGAGGAGATTATCTACTGGATGAACTTATACAGTCACTGAAGAACTATGCTGATTATGAATCTTTATTAGAAAA
TGTTTCCAAAAAAGCT

Alignment

ORF - retro_itri_335 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.39 %
• Parental protein coverage: 61.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  WNFETLEYFPSEIGGLRHASASIGGSEAYKHMKFEGGVHRVQRVPKTEKQGRIHTSTMTVAILPQPTEIN
          W.FETLEYFPSEIGGLR.AS.SIGGSEAYKH.KFEGGVHRVQRVP.TEKQGRIHTSTM.VAIL.QPTEIN
Retrocopy WHFETLEYFPSEIGGLRYASTSIGGSEAYKHIKFEGGVHRVQRVPRTEKQGRIHTSTMAVAILSQPTEIN

Parental  LVINPKDLRIDTKRASGAGGQHVNTTDSAVRIVHLPTGVVSECQQERSQLKNREMAMK-KLRAKLYNMHL
          .VINPKDLRIDTKRASG.GGQHVNTTDSAV.IVHLPTGVVSECQQERSQLKNR....K..LRAKLYNM.L
Retrocopy MVINPKDLRIDTKRASGVGGQHVNTTDSAVWIVHLPTGVVSECQQERSQLKNRDGYEK<NLRAKLYNMRL

Parental  EEETSKR-YSARKIQVGTKGRSEKIRTYNFPQNRVTDHRI-NKSLHGLETFMQGDYLLDELIQSLKDYAD
          EEETSKR.YSARKIQV.TKGR.EKIRTY.FPQNRVTDHRI.NKSLHGL.TFM.GDYLLDELIQSLK.YAD
Retrocopy EEETSKR>YSARKIQVRTKGRLEKIRTYYFPQNRVTDHRI<NKSLHGLQTFMRGDYLLDELIQSLKNYAD

Parental  YEYLLEIISKKA
          YE.LLE..SKKA
Retrocopy YESLLENVSKKA

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_335 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_335 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012787	1 retrocopy	retro_cjac_1305,
Homo sapiens	ENSG00000112031	1 retrocopy	retro_hsap_3018,
Sarcophilus harrisii	ENSSHAG00000017997	1 retrocopy	retro_shar_129,
Ictidomys tridecemlineatus	ENSSTOG00000009980	1 retrocopy	retro_itri_335 ,
Tupaia belangeri	ENSTBEG00000003131	2 retrocopies	retro_tbel_2448, retro_tbel_4085,