RetrogeneDB ID: retro_tbel_987

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_3507:68021..68676(-)
• Located in intron of: ENSTBEG00000002588

Retrocopy information

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

Parental gene information

• Parental gene symbol: GRSF1
• Ensembl ID: ENSTBEG00000010173
• Aliases: None
• Description: G-rich RNA sequence binding factor 1 [Source:HGNC Symbol;Acc:4610]

Sequence

>retro_tbel_987
TGCAGAATCCACTTCGACAATGGAATACACTTCCTTTTAAAAAGAGATGGGAAACAAAGGGGGTGATGCCTTAACTGAAA
TGGAGTCAGAGCAGGATGCGAATAAAGCCTTAGAGAAACACCGGATGTACATGGGTCAGCGGTATGCGCAAGTCTATGAG
ATAAACAATGAAGATGTGGATGTCTTAATGAAGAGCCTACAGGCCAAATCTTCACCTGTGGCAAACGATGACATGGTATG
TTTGGGAGGACTTCCTTATAGCTGCAATGAGAAAGACATTGTAGACTTTTTTTGTAAGACTGAATATAGTAGACATCACT
TTTGTGATGGACTACAGAGGGGGAAGAAAAACAGGGGAAGCCTATGTGCAGTTTGAAGAGCCAGAAATGAGCAACCAAGC
ACTGTTGAAACACCGGGAAGAAACTGGTAACCCGTATATAGAGGTATTTTCAAGCAGAAGGAATGAAGTTTGAACACATG
TTGGCTCTCATAAGGGAAGGAAAACGGCATCGTCTCCTACCACTAAGTCTATAGCTGAACCAGACGTGTTTTTTTTTTTT
TTTGAACACAAAGTAAATGAGGATGTTCGACCTGTGACAGCTTTTGAAATGAGGAAATAGAATTGCCTAAGAAGATGTCA
GAAAAGCTGCCAGAG

Alignment

ORF - retro_tbel_987 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.03 %
• Parental protein coverage: 70.78 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  CRIRNGENGIHFLLNRDGKRRG-DALIEMESEQDVHKALEKHRMYMGQRYVEVYEINNEDVDALMKSLQV
          CRI....NGIHFLL.RDGK.RG.DAL.EMESEQD..KALEKHRMYMGQRY..VYEINNEDVD.LMKSLQ.
Retrocopy CRI-HFDNGIHFLLKRDGKQRG>DALTEMESEQDANKALEKHRMYMGQRYAQVYEINNEDVDVLMKSLQA

Parental  KSSPVVNDGVVRLRGLPYSCNEKDIVDFFAG-LNIVDITFVMDYRGRRKTGEAYVQFEEPEMANQALLKH
          KSSPV.ND..V.L.GLPYSCNEKDIVDFF...LNIVDITFVMDYRG.RKTGEAYVQFEEPEM.NQALLKH
Retrocopy KSSPVANDDMVCLGGLPYSCNEKDIVDFFCK>LNIVDITFVMDYRGGRKTGEAYVQFEEPEMSNQALLKH

Parental  REEIGNRYIEIFPSRRNEVRTHVGSHKGKKMASSPTAKYITEPDMVFE--EHEVNEDVRPMT-AFESEKE
          REE.GN.YIE.F.SRRNEV.THVGSHKG.K.ASSPT.K.I.EPD......EH.VNEDVRP.T..F..E.E
Retrocopy REETGNPYIEVFSSRRNEV*THVGSHKGRKTASSPTTKSIAEPDVXXXXXEHKVNEDVRPVT<SF*NE-E

Parental  IELPKEMTEKLPE
          IELPK.M.EKLPE
Retrocopy IELPKKMSEKLPE

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_987 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_987 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 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Nomascus leucogenys	ENSNLEG00000007721	1 retrocopy	retro_nleu_1973,
Ictidomys tridecemlineatus	ENSSTOG00000011569	2 retrocopies	retro_itri_1828, retro_itri_523,
Tupaia belangeri	ENSTBEG00000010173	2 retrocopies	retro_tbel_3827, retro_tbel_987 ,
Tarsius syrichta	ENSTSYG00000008487	1 retrocopy	retro_tsyr_770,