RetrogeneDB ID: retro_tbel_840

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_3130:229292..229882(-)
• Located in intron of: ENSTBEG00000010697

Retrocopy information

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

Parental gene information

• Parental gene symbol: RSRC1
• Ensembl ID: ENSTBEG00000001973
• Aliases: None
• Description: arginine/serine-rich coiled-coil 1 [Source:HGNC Symbol;Acc:24152]

Sequence

>retro_tbel_840
ATGGGACATGGGTCATCAGATACTGAAGAAGAAAGCAGAAGCAAGAGAAAAAAGAAACACCAAAGATGGTCATCTTCAAG
CAGTTCTTTAGATAGCAGCACATACAGCTGAAAAAAAGTGGAAGGAAATCAAGATCAAAGTCAAGATCTTGGTCCAGAGA
TTTCCAGCCTCATTCACATTCTTATTATAGAATACACAGGCATTGACCAAACAGTATCTCTTCTTATGGTTCTAGAAGGA
AGCGAAGTCAAAGTTGCTCAAAGAAATGAGGGAAATCCTATAGAGCTCAGAGGTCTAGATCAAAAAGCAGAACAGGAAGG
TTCAGGTTGAGACCTTGTCCATGTTCCCATAGTTGAAGCAGTGAGAGAACAAGTCACAGGAGAACCCATAGTTCACTCTT
GGGACAGAGAACAGTGTAAGGCAGAGACAAAGAGAAAAGAGAAAAGGAAAAGGATAAAGGCATGGATGAGGGATTGCACA
ACATCAGATAGGGGGAATCTGGAAACAGCAAAGCTGGATTAGAACATCTACTGCCAGCTAGACAGGCCAATGCTAGACTA
CAATGAGTTCTTGAAGTGGCTGTAAAAGCT

Alignment

ORF - retro_tbel_840 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.5 %
• Parental protein coverage: 59.88 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MGRRSSDTEEESRSKRKKKHRRRSSSSSSSGSRTYS-RKKGGRKSRSKSRSWSRDLQPRSHSYDRRRRHR
          MG..SSDTEEESRSKRKKKH.R.SSSSSS..S.TYS..KK.GRKSRSKSRSWSRD.QP.SHSY.R..RH.
Retrocopy MGHGSSDTEEESRSKRKKKHQRWSSSSSSLDSSTYS<LKKSGRKSRSKSRSWSRDFQPHSHSYYRIHRH*

Parental  SSSSSSYGSRRKRSRSRSRGRGKSYRVQRSRSKSRTRRSRSRPRPRSHSRSSERSSHRRTRS-RSRDRER
          ..S.SSYGSRRKRS.S.S...GKSYR.QRSRSKSRT.R.R.RP.P.SHS.SSER.SHRRT.S..S.DRE.
Retrocopy PNSISSYGSRRKRSQSCSKK*GKSYRAQRSRSKSRTGRFRLRPCPCSHS*SSERTSHRRTHS>HSWDREQ

Parental  RK-GRDKEKREKEKDKGKDKELHNIKRGESGNIKAGLEHLPPAEQAKARLQLVLEAAAKA
          .K.GRDKEKREKEKDKG.D..LHNI..GESGN.KAGLEHL.PA.QA.ARLQ.VLE.A.KA
Retrocopy CK<GRDKEKREKEKDKGMDEGLHNIR*GESGNSKAGLEHLLPARQANARLQ*VLEVAVKA

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_840 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_840 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 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004797	1 retrocopy	retro_cjac_553,
Cavia porcellus	ENSCPOG00000000876	2 retrocopies	retro_cpor_618, retro_cpor_671,
Echinops telfairi	ENSETEG00000017217	1 retrocopy	retro_etel_1555,
Homo sapiens	ENSG00000174891	1 retrocopy	retro_hsap_4281,
Mus musculus	ENSMUSG00000034544	1 retrocopy	retro_mmus_666,
Nomascus leucogenys	ENSNLEG00000004137	1 retrocopy	retro_nleu_2851,
Rattus norvegicus	ENSRNOG00000012639	2 retrocopies	retro_rnor_2454, retro_rnor_577,
Tupaia belangeri	ENSTBEG00000001973	13 retrocopies	retro_tbel_1285, retro_tbel_1372, retro_tbel_2078, retro_tbel_2400, retro_tbel_2545, retro_tbel_3145, retro_tbel_3313, retro_tbel_3748, retro_tbel_3834, retro_tbel_4317, retro_tbel_4458, retro_tbel_4494, retro_tbel_840 ,