RetrogeneDB ID: retro_tbel_1285

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_4328:297942..298876(-)
• Located in intron of: None

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_1285
ATGAGTCTACCATCATCAGATACTGAAGAAAAAAGCAGAAGCAAGAGAAAAAAGAAACACAGCAGACTGTCATCTTCAAG
CAGTTCTTCAGGTAGGAGAACATACAGCCAAAAAAATGGTGGAAAGAAATCAAGATGAAAGTAAAGATTTTGGCGCAGAG
ATGTCCAACCTCATTCACATTCTTAAGATAGAAGATGCAGGCATCAATCAAGCAGTAGTTCTTCTTATGGCTCTAGAATA
AAACAAAGTCAAAGTCGTTCAAAGGGTTGAGGGAAATCCTATAGATTTCAGAGGTCTAGATCAAGAAGCAGAACAAGAAG
GTCCAGGTTAAGACCTTGTCCACATTTCCATAGTCAAAGCAGTGAGAGATCAAGGCACAGGAGAACCCATAGTCACTCTC
GGCATAGAGAATGGCATAAAGGCAGAGACAAAGAGTAAAGAGAAAAGGAGGATAAAGGCAAGGACAAGGAATTACATAAT
ATCAAATATGGGAATCTGGAAATATCAAAGCTGGATTAGAACATCTGCTGCCAGCTGAAAAGGCCAAAGCCAGACTATGG
CTGGTTCTTGAAGCTGCTGCAAAAGCTGATGAAGCGTTAAAAGCCAAAGAAAGAAATGAGAAAAAAGCAAAGAGAAGAAA
AGAGGAATACCAAGCCACCCTGGTAGAACAAGTGAAAAGAGTAAAAGAAATTGAAGTTATTGAAAGTGATTGTTTTGTTT
AGCAGATTCTTTTGTTTATATCAAGTAAAGAAGTCAAAAGACACTAGAATCTAGTGAAGTGAAACATGCAGCTTCAGCGT
CTGGACCAGCATCAGTAGTTGTTGAGCCACCCAGTACTGAAAAAGAAACAGACTCTAGTAGCATCCCTAGTGCTACCAAG
TACCAAGACGACAATTCTTTGGCCCATCCAAAGTTGTTTATTGAGAAAGCTGAA

Alignment

ORF - retro_tbel_1285 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.16 %
• Parental protein coverage: 94.53 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MGRRSSDTEEESRSKRKKKHRRRSSSSSSSGSRTYSRKKGGRKSRSKSRSWSRDLQPRSHSYDRRRRHRS
          M...SSDT...........H.R.SSSSSSSG.RTYS.K.GG.KSR.K.R.W.RD.QP.SHS.DRR.RH.S
Retrocopy MSLPSSDTXXXXXXXXXXXHSRLSSSSSSSGRRTYSQKNGGKKSR*K*RFWRRDVQPHSHS*DRRCRHQS

Parental  SSSSSYGSRRKRSRSRSRGRGKSYRVQRSRSKSRTRRSRSRPRPRSHSRSSERSSHRRTRSRSRDRERRK
          SSSSSYGSR.K.S.SRS.G.GKSYR.QRSRS.SRTRRSR.RP.P..HS.SSERS.HRRT.S.SR.RE..K
Retrocopy SSSSSYGSRIKQSQSRSKG*GKSYRFQRSRSRSRTRRSRLRPCPHFHSQSSERSRHRRTHSHSRHREWHK

Parental  GRDKEKREKEKDKGKDKELHNIKRG-ESGNIKAGLEHLPPAEQAKARLQLVLEAAAKADEALKAKERNEE
          GRDKE.REKE.DKGKDKELHNIK.G.ESGNIKAGLEHL.PAE.AKARL.LVLEAAAKADEA.........
Retrocopy GRDKE*REKE-DKGKDKELHNIKYG<ESGNIKAGLEHLLPAEKAKARLWLVLEAAAKADEAXXXXXXXXX

Parental  EAKRRKEEDQATLVEQVKRVKEIEAIESDSFVQQ--TFRSSKEVK-KTVEPSEVKHAASASGPASVVADP
          .......E.QATLVEQVKRVKEIE.IESD.FV.Q...F.SSKEVK.KT.E.SEVKHAASASGPASVV..P
Retrocopy XXXXXXXEYQATLVEQVKRVKEIEVIESDCFV*QILLFISSKEVK<KTLESSEVKHAASASGPASVVVEP

Parental  PSTEKEIDPSSIPTTIKYQDDNSLAHPNSVLQAAE
          PSTEKE.D.SSIP...KYQDDNSLAHP......AE
Retrocopy PSTEKETDSSSIPSATKYQDDNSLAHPKLFIEKAE

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_1285 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1285 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 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,