RetrogeneDB ID: retro_tbel_2448

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_110754:2095..2762(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTRF1L
• Ensembl ID: ENSTBEG00000003131
• Aliases: None
• Description: mitochondrial translational release factor 1-like [Source:HGNC Symbol;Acc:21051]

Sequence

>retro_tbel_2448
ACAGAAGAAAATAATTTTATTTTAGAGGTCACTGTAGGAGTTGGGGGTCAAGAGGCAATGTTATTTACTTCAGAGATATT
TGATACATATAAACAATATGCTGCATTTAAAAGATGGGATTTTGAAACCCTGGAGTATTTCCAAGTGAAATAGGTGGCCT
TAGACATGCATTTGCAATCATTGAGTGTTCAGAAGCTTATAAGTAAATGAAGTTTGAAGGAGGTGTGCACAGAGTACAAA
GAGTGCCAAAGAAAGAGAAGTAAAGCTGCATACACACTGAGCATTATGACAGTAGCAATATTACCCCAACCTACTGAGAT
TAACATGGTGATTAATCCTAAAGATTTGAGATATGATACTGAACAAGCCAGTGGAGCTGGGAGACAGCATGTAAATACCA
CAGACAGTGCTATCCAGATAGCTCATCTTCCAGCAGATGTTTCTGAATGCCAGCAAGAAAGATCTCAGCTGAAAAAGAGA
GAGATGGCAATGAAAAAGTGACATGCAAAACTGTACTCCATGCATCTAGAAGAAGAAACAAGTAAAAGATACAATACTAG
AAAGATTCAGAGTTCAACTAAAGGAAAGTCAGAGAAAATAAGAACATAACATTTTCCACAGAAACAGGTGCACAGATCAC
AGAATAAACAAGTCACTACATGATCTG

Alignment

ORF - retro_tbel_2448 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.97 %
• Parental protein coverage: 58.68 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TDENDLILEVTAGVGGQEAMLFTSEIFDMYQQYAAFKRWNFETLEYF-PSEIGGLRHASASIGGSEAYKH
          T.EN..ILEVT.GVGGQEAMLFTSEIFD.Y.QYAAFKRW.FETLEYF.PSEIGGLRHA.A.I..SEAYK.
Retrocopy TEENNFILEVTVGVGGQEAMLFTSEIFDTYKQYAAFKRWDFETLEYF<PSEIGGLRHAFAIIECSEAYK*

Parental  MKFEGGVHRVQRVPKTEKQGRIHT-STMTVAILPQPTEINLVINPKDLRIDTKRASGAGGQHVNTTDSAV
          MKFEGGVHRVQRVPK.EK...IHT.S.MTVAILPQPTEIN.VINPKDLR.DT..ASGAG.QHVNTTDSA.
Retrocopy MKFEGGVHRVQRVPKKEK*SCIHT>SIMTVAILPQPTEINMVINPKDLRYDTEQASGAGRQHVNTTDSAI

Parental  RIVHLPTGVVSECQQERSQLKNREMAMKKLRAKLYSMQLEEETSKRYNARKIQIGTRGRSEKIRTYNFPQ
          .I.HLP...VSECQQERSQLK.REMAMKK..AKLYSM.LEEETSKRYN.RKIQ..T.G.SEKIRT..FPQ
Retrocopy QIAHLPAD-VSECQQERSQLKKREMAMKK*HAKLYSMHLEEETSKRYNTRKIQSSTKGKSEKIRT*HFPQ

Parental  -NRVTDHRINKSLHDL
          .NR.TDHRINKSLHDL
Retrocopy >NRCTDHRINKSLHDL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tupaia belangeri was not studied using RNA-Seq expression data.

ChIP-Seq

Tupaia belangeri was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_tbel_2448 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2448 was not experimentally validated.

Homology

Retrocopy orthology:

Tupaia belangeri 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,