RetrogeneDB ID: retro_tbel_1400

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_460:356262..356747(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC25A38
• Ensembl ID: ENSTBEG00000015842
• Aliases: None
• Description: solute carrier family 25, member 38 [Source:HGNC Symbol;Acc:26054]

Sequence

>retro_tbel_1400
TGCAGGGGTCGCCTATCACTTTGATCAAGACACTCTAGAAGAGGGTGATACAGCTATGAGAGCATGTATGCAGCCCTGAG
AAGCATCTTTCCCCGTGAAGGGCACCGGGGCCTCATTTGCAGCCTGACAGTGATTTGTGTTCATAATGGGCCCTTTTCAG
GAATCTATCTGATGTTTTACAACTAGATCCAAACATTGTGACCAGTTGGATACAGCCCGTATTCCACTTTTAAATTTCAG
GTGTGAGATATTTGCTGGTATTCTGGCCTCATCAGTAACCCAGCCTGCAGATGTTAGCAAAACTCATATCCATCTCTACC
CATGAAATTTCAGTGTCTTAGCTAAGCAGTGACACTCATTTTCAAAGATTATGAACTGCATGGCTTCTTCCAGTGCAGTG
TCCCCAGGCTCTCCACAGAACTTGGATGACAGTGATGGCATGGACAATCTGTGAAGAGATGATGACCACGATGGGCCCAA
AATCC

Alignment

ORF - retro_tbel_1400 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.31 %
• Parental protein coverage: 58.72 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  CMSPITVIKTRYESGRYGYESIYAALRSIYRSEGHRGLFCGLTATLLRDAPFSGIYLMFYN-QTKHIVPH
          C.............G.Y.YES.YAALRSI...EGHRGL.C.LT.......PFSGIYLMFYN...KH....
Retrocopy CRGRLSL*SRHSRRG*YSYESMYAALRSIFPREGHRGLICSLTVICVHNGPFSGIYLMFYN>RSKHC---

Parental  DQLDTTLIPVVNFSCGIFAGILASLVTQPADVIKTHMQL-SPRKFQWIGQAVTLIFKDYGLRGFFQGSVP
          DQLDT..IP..NF.C.IFAGILAS.VTQPADV.KTH..L..P.KFQ....AVTLIFKDY.L.GFFQ.SVP
Retrocopy DQLDTARIPLLNFRCEIFAGILASSVTQPADVSKTHIHL<LPMKFQCLS*AVTLIFKDYELHGFFQCSVP

Parental  R-ALRRTLMAAMAWTVYEEMMAKMGLKS
          R.AL.RT.M..MAWT..EEMM..MG.KS
Retrocopy R<ALHRTWMTVMAWTICEEMMTTMGPKS

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_1400 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1400 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000144659	1 retrocopy	retro_hsap_266,
Gorilla gorilla	ENSGGOG00000013530	1 retrocopy	retro_ggor_315,
Nomascus leucogenys	ENSNLEG00000005614	1 retrocopy	retro_nleu_868,
Pan troglodytes	ENSPTRG00000014772	1 retrocopy	retro_ptro_223,
Rattus norvegicus	ENSRNOG00000018552	1 retrocopy	retro_rnor_2942,
Tupaia belangeri	ENSTBEG00000015842	1 retrocopy	retro_tbel_1400 ,