RetrogeneDB ID: retro_tbel_4449

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_83928:4610..5341(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CMBL
• Ensembl ID: ENSTBEG00000001698
• Aliases: None
• Description: carboxymethylenebutenolidase homolog (Pseudomonas) [Source:HGNC Symbol;Acc:25090]

Sequence

>retro_tbel_4449
ATGGCTAACGAGGCTTATCTCTGCCCCTGTGACATCGGCCACCAAACGGAGTATGGCGGCATGGAGCAGGCAGTTCAAGT
CGAGCACATCAAGGCTTATGTCACCCGGTCCCCTGTGGACGCAGGCAAAGCTGTGATTGTCATCCAGGACATATTCGACC
AGCAGTCGCCCAACACTAGGGACGTGGCAGACATGACCGCCGGAAACGGATACACGACCATTGTGCCAGACTTCTTCGGA
GGGCAGGAGCCGTGGGACCCCTCTGGTGACTGGCCCACCTTCCCTGAGTGGTTGAAAACGAGAAACGCCAGGAAGATCCA
TAAAGAGATTAAAGCGGTCTTGAAGTATCTGAAACAGCAGTTGTCACGCCCAGAAAACTGGCGGCGTGGGCTTCTGCTGG
GGCGGAACTGCTGTCCATCACCCGAAGACGGCATCCTCAGAATTCTAGGCAGGGTGTCTGTCTATGGCATCGCCAAGGAT
TCTGAAGATGTTCAAGTTTAAAGAACCCCACGTGATTCATTTTTGCTGAAAACGATGCAGTGATTCCACTTGAGCAGGTC
TCTTTGCTGACGCAGAAACTGAAAGACCACTGCAAAGCTGAATATCAAATTAAAACCTTTTCCGGGCAAACACACGGGTT
CGTGCATCGAAGAAGAGAAGATTGCTCACCTGAAGACAAGCCCTCCATAGACGAGGTGAGAAGGAACTTAATCGAATGGC
CTAACAAATAC

Alignment

ORF - retro_tbel_4449 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.45 %
• Parental protein coverage: 99.59 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MANEAYPCPCDIGHRMEYGGMGQEVQVEHIKAYVTRSPVDAGKAVIVIQDIFGWQLPNTRYMADMIAGNG
          MANEAY.CPCDIGH..EYGGM.Q.VQVEHIKAYVTRSPVDAGKAVIVIQDIF..Q.PNTR..ADM.AGNG
Retrocopy MANEAYLCPCDIGHQTEYGGMEQAVQVEHIKAYVTRSPVDAGKAVIVIQDIFDQQSPNTRDVADMTAGNG

Parental  YTTIVPDFFVGQEPWDPSGDWSTFPEWLKTRNARKIHKEINAVLKYLKQQ-CHAQKIGVVGFCWGGTAVH
          YTTIVPDFF.GQEPWDPSGDW.TFPEWLKTRNARKIHKEI.AVLKYLKQQ.CHAQK.G.VGFCWGGTAVH
Retrocopy YTTIVPDFFGGQEPWDPSGDWPTFPEWLKTRNARKIHKEIKAVLKYLKQQ>CHAQKTGGVGFCWGGTAVH

Parental  HLMMASSEFKAG-VSVYGIVKDSEDVY-SLKNPTLFIFAENDAVIPLEQVSLLTQKLKDHCKVEYQIKTF
          H...ASSEF.AG.VSVYGI.KDSEDV..SLKNPT.FIFAENDAVIPLEQVSLLTQKLKDHCK.EYQIKTF
Retrocopy HPKTASSEF*AG<VSVYGIAKDSEDVQ<SLKNPT*FIFAENDAVIPLEQVSLLTQKLKDHCKAEYQIKTF

Parental  SGQTHGFVHRKREDCSPEDKPYIDEARRNLIEWLNKY
          SGQTHGFVHR.REDCSPEDKP.IDE.RRNLIEW.NKY
Retrocopy SGQTHGFVHRRREDCSPEDKPSIDEVRRNLIEWPNKY

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_4449 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4449 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009759	1 retrocopy	retro_chof_2582,
Callithrix jacchus	ENSCJAG00000009079	1 retrocopy	retro_cjac_613,
Dasypus novemcinctus	ENSDNOG00000024697	2 retrocopies	retro_dnov_1840, retro_dnov_2561,
Microcebus murinus	ENSMICG00000000533	1 retrocopy	retro_mmur_1038,
Otolemur garnettii	ENSOGAG00000016909	1 retrocopy	retro_ogar_2398,
Tupaia belangeri	ENSTBEG00000001698	1 retrocopy	retro_tbel_4449 ,