RetrogeneDB ID: retro_tbel_2609

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_113986:154042..154467(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: APOOL
• Ensembl ID: ENSTBEG00000010147
• Aliases: None
• Description: apolipoprotein O-like [Source:HGNC Symbol;Acc:24009]

Sequence

>retro_tbel_2609
GTTTCAGCGAGAAAAGGACCTAGGTTCAAGAGAATTGCTTATCAACTGGACTGGCCACTTTAGGAGCAACTGTTGCTATC
TGTTCAGTCAGTAATAATTGCAAAGGTAACCGGAAAAAAGGCATATGATACAAGTCAGCAAATTTATGAAGCAGTTAGAT
CATTGTGGACAAAAAGAAACCAAAAGCGAATCACTTCCTGAACCTAAAGAAAAAACTAAGCTAGGAAGCTCGGCTGAAAT
AGAAACACCTGCAAAAACAACTCATCTCCTGAAAAGATTCAATGCCTTTGCCAGGAGAACTCAGCTCTGAAATAAAGACC
AAATCAGAATCAATCTCAGGTGCTACACAGTTTATGCCTGACCCCAAGCTCATGGATCACGGGCAATCCCATCCAGAAGA
TGTAGATATGTACAGTACTAGAAGC

Alignment

ORF - retro_tbel_2609 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.56 %
• Parental protein coverage: 53.99 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  VSARKGPRFKRIAYPL-GLATLGATV-CY-PVQSVIIAKVTGKKAYDTSQQIYEAVRSLWTKRNQ-SESL
          VSARKGPRFKRIAY.L.GLATLGATV.CY..VQSVIIAKVTGKKAYDTSQQIYEAVRSLWTKRNQ.SESL
Retrocopy VSARKGPRFKRIAYQL<GLATLGATV<CY<SVQSVIIAKVTGKKAYDTSQQIYEAVRSLWTKRNQ>SESL

Parental  PEPKEKTKLGSSAEIETPAETTHLL-KDSMPLPGELSSEIKTKSESISGATQFMPDPKLMDHGQSHPEDV
          PEPKEKTKLGSSAEIETPA.TTHLL.KDSMPLPGELSSEIKTKSESISGATQFMPDPKLMDHGQSHPEDV
Retrocopy PEPKEKTKLGSSAEIETPAKTTHLL>KDSMPLPGELSSEIKTKSESISGATQFMPDPKLMDHGQSHPEDV

Parental  DMYSTRS
          DMYSTRS
Retrocopy DMYSTRS

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_2609 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2609 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 8 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008249	2 retrocopies	retro_cjac_1783, retro_cjac_2464,
Dipodomys ordii	ENSDORG00000011045	1 retrocopy	retro_dord_373,
Loxodonta africana	ENSLAFG00000008844	1 retrocopy	retro_lafr_1035,
Mustela putorius furo	ENSMPUG00000001899	3 retrocopies	retro_mputfur_606, retro_mputfur_734, retro_mputfur_874,
Sus scrofa	ENSSSCG00000012459	1 retrocopy	retro_sscr_610,
Tupaia belangeri	ENSTBEG00000010147	5 retrocopies	retro_tbel_2037, retro_tbel_2609 , retro_tbel_2840, retro_tbel_3361, retro_tbel_3737,
Tupaia belangeri	ENSTBEG00000014888	6 retrocopies	retro_tbel_1153, retro_tbel_4004, retro_tbel_4261, retro_tbel_4698, retro_tbel_715, retro_tbel_96,
Tursiops truncatus	ENSTTRG00000000429	1 retrocopy	retro_ttru_1337,