RetrogeneDB ID: retro_tbel_760

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_2964:80951..81378(-)
• Located in intron of: ENSTBEG00000008753

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTIF3
• Ensembl ID: ENSTBEG00000012276
• Aliases: None
• Description: mitochondrial translational initiation factor 3 [Source:HGNC Symbol;Acc:29788]

Sequence

>retro_tbel_760
GAGCGAACTATACATGTTTCTGATGAAAATGGCAATTTGTTGGGAAACATGCACTGAGTTGATGTGATTAGAACTCATGG
ATGAGAGAGAACTGAAACTGGTTCAGAAAGCCAGCACAGAGCATCCAGAGTAACACCTCATGACTGGGCTCCAGATTCAC
CAAGCACGACTGTGGCTTCGGGAGCAGAAGGTTAGACCCAAAACTAGACCAATCCTGATAAAGGAAGTAACATTTTCTTC
AAATACTGGACAACACGATTTGGACACAAAAAGTAAACAGATTCAGCCGTGGGTTGAGAAAAAAATACCAGTTCAAATTG
GTATAAAGAAAGGGAAAAATGTAGATGATTCAGAAGAGAAAGTGGAGGCAATATTTAATCGAATACTCCTGACTATGCCT
GGAATTGATACTCTCTCATCAAGGCCA

Alignment

ORF - retro_tbel_760 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.29 %
• Parental protein coverage: 52.35 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ERIIHVFDEKGNDLGNMHRADVIR-LMDERELRLVQRNASTEPPEYQLMTGLQIHQERLRLREQEKARPK
          ER.IHV.DE.GN.LGNMH..DVIR.LMDEREL.LVQ..ASTE.PE..LMTGLQIHQ.RL.LREQ.K.RPK
Retrocopy ERTIHVSDENGNLLGNMH*VDVIR>LMDERELKLVQK-ASTEHPE*HLMTGLQIHQARLWLREQ-KVRPK

Parental  TGPTLIKELTFSSTDERQHDLDTKSKQILQWIEKKYQVQITIKKGKNIDEPEKKTEAIFNQILQTMPGIA
          T.P.LIKE.TFSS....QHDLDTKSKQI..W.EKK..VQI.IKKGKN.D..E.K.EAIFN.IL.TMPGI.
Retrocopy TRPILIKEVTFSS-NTGQHDLDTKSKQIQPWVEKKIPVQIGIKKGKNVDDSEEKVEAIFNRILLTMPGID

Parental  TFSSRP
          T.SSRP
Retrocopy TLSSRP

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_760 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_760 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004404	1 retrocopy	retro_chof_466,
Homo sapiens	ENSG00000122033	1 retrocopy	retro_hsap_3284,
Gorilla gorilla	ENSGGOG00000008409	1 retrocopy	retro_ggor_1318,
Nomascus leucogenys	ENSNLEG00000000343	1 retrocopy	retro_nleu_1350,
Oryctolagus cuniculus	ENSOCUG00000011721	1 retrocopy	retro_ocun_533,
Pongo abelii	ENSPPYG00000005236	1 retrocopy	retro_pabe_2713,
Pan troglodytes	ENSPTRG00000005732	1 retrocopy	retro_ptro_2221,
Tupaia belangeri	ENSTBEG00000012276	3 retrocopies	retro_tbel_4048, retro_tbel_4602, retro_tbel_760 ,