RetrogeneDB ID: retro_tbel_1979

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_61:145405..145630(+)
• Located in intron of: ENSTBEG00000005670

Retrocopy information

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

Parental gene information

• Parental gene symbol: CMC2
• Ensembl ID: ENSTBEG00000000038
• Aliases: None
• Description: COX assembly mitochondrial protein 2 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:24447]

Sequence

>retro_tbel_1979
CACTTGCACACTGAAGAATGCAACATCTCAATTAACTTGCTTAAGGAATGTTACAAAAATCACAACATTTTGAAAGCTTT
TGGTCATTGCAACCACATTGATTGGGAGATGCAAAAATGCTTGAAGAATGAATACATGGTAAAGATGGTAAAGAGGACCA
AAAGCACGGAGCATTGCAATGCCGTGAGAAAGAAAAGTTTCAATATTCCAGGGGAATCAGGAAAA

Alignment

ORF - retro_tbel_1979 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.33 %
• Parental protein coverage: 91.14 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HLHTEECNILINLLKECHKNHNILKFFGHCNDLDREMRKCLKNEYIVK---RTKSREHGDAMRKKLFSPP
          HLHTEECNI.INLLKEC.KNHNILK.FGHCN..D.EM.KCLKNEY.VK...RTKS.EH..A.RKK.F..P
Retrocopy HLHTEECNISINLLKECYKNHNILKAFGHCNHIDWEMQKCLKNEYMVKMVKRTKSTEHCNAVRKKSFNIP

Parental  EESEK
          .ES.K
Retrocopy GESGK

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_1979 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1979 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 10 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013929	2 retrocopies	retro_amel_397, retro_amel_681,
Bos taurus	ENSBTAG00000017009	1 retrocopy	retro_btau_109,
Echinops telfairi	ENSETEG00000010422	3 retrocopies	retro_etel_2190, retro_etel_357, retro_etel_816,
Felis catus	ENSFCAG00000004977	1 retrocopy	retro_fcat_193,
Loxodonta africana	ENSLAFG00000004378	2 retrocopies	retro_lafr_311, retro_lafr_896,
Microcebus murinus	ENSMICG00000011915	2 retrocopies	retro_mmur_1149, retro_mmur_701,
Monodelphis domestica	ENSMODG00000025763	1 retrocopy	retro_mdom_1670,
Sorex araneus	ENSSARG00000008906	2 retrocopies	retro_sara_712, retro_sara_84,
Sarcophilus harrisii	ENSSHAG00000001006	1 retrocopy	retro_shar_254,
Tupaia belangeri	ENSTBEG00000000038	3 retrocopies	retro_tbel_1840, retro_tbel_1979 , retro_tbel_2249,