RetrogeneDB ID: retro_tbel_4048

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_59370:845..1261(+)
• Located in intron of: None

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_4048
GAGAAGAGACTGGTTCGTAGGAAGGCAAGCACAGAGCCCCCAGAGTACTAGCTCATGACCGAGCTCCAGATTCACCAAGA
GTGACTGCAACTTTGGGAGCAGGAGAAGGCCCGACCCAAAACTGGACCAACCCTGATAAAGGAATTAACATTTTCTTCAA
ATATTGGACAACATGACTTGGACACAAAGAGTAAACAGATTCAGCAGTGGATTGAGGAAAAATACCAAAGTTCAAATTAC
TATAAAGAAAGGGAAGGATGTAGATGAGCCAGAAGAGAAAATGGAGGCAATATTTAATCAGATACTCTAGACTACGCCTG
GAATTGCTACCTTCTCATCCAGGCCACAAGCTGTTAAAGGGAGGAAAAGTTTTGATGTGTGTCCTTTGTCATTTGAGCAA
TAAAAAAGAAAAGGCA

Alignment

ORF - retro_tbel_4048 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.85 %
• Parental protein coverage: 50.18 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ELRLVQRNASTEPPEYQLMTGLQIHQERLRLREQEKARPKTGPTLIKELTFSSTDERQHDLDTKSKQILQ
          E.RLV.R.ASTEPPEY.LMT.LQIHQE.L.L.EQEKARPKTGPTLIKELTFSS....QHDLDTKSKQI.Q
Retrocopy EKRLVRRKASTEPPEY*LMTELQIHQE*LQLWEQEKARPKTGPTLIKELTFSS-NIGQHDLDTKSKQIQQ

Parental  WIEKKYQ-VQITIKKGKNIDEPEKKTEAIFNQILQTMPGIATFSSRPQAV-KGGKAWMCVLRHLSKKEEK
          WIE.KYQ.VQITIKKGK..DEPE.K.EAIFNQIL.T.PGIATFSSRPQAV.KGGK..MCVL.HLS.K.EK
Retrocopy WIEEKYQ>VQITIKKGKDVDEPEEKMEAIFNQIL*TTPGIATFSSRPQAV>KGGKVLMCVLCHLSNKKEK

Parental  A
          A
Retrocopy A

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_4048 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4048 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.

---

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,