RetrogeneDB ID: retro_tbel_2400

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_110019:44757..45604(+)
• 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_2400
ATGGGACTACGGTCATAAGATATGAAAGAAAAGAGCAGAAGCAAGAAAAAAAAAAAAGAAACACAGCAGACATCTTCAAA
CAGTTCTTCAGGTAGTAGAACATACAGCCCAAAAAATGGTGGAAAGAAATCAAGATCAAAGTAAATATTTTGGTCCATAG
ACCCCCAACCTCGTTCACATTCTTATGATAGAAGATGCAGGCATCAATCAAGCAGTTCTTCTTATGGCTCTAGAATAAAA
AATGTCGAAGTCGTTCAAAAGGGCGAAGAAAATCCTAGAGTTCAGAGGTCTAAATCAAAAAGCAGAACAAGAAGGTCCAG
GTTGAGACCTTGTCCACATTCCCATAGTCAAAGTAGTGAGAGATCAAGTCACAGGAGAACCCATAGTCGCTCTCAGCATA
GAGAATGGCATAAAGGTAGAGACAAAGAGAAAAAAGGAGAAGGATAAAGGCAAGGACAAGGAATTACATAACATCAAATG
TGGAGAATCTGGAAACATCAAAGCTGGATTAGAACATCTGCCGCCAGCTGAACAGGCCAAAGTCAGACTATGGCTGGTTC
TTGAAGCTGCTGCAAAAGCTGCTGAAGCATTAAAAGCTGAAGAAAGAAATGAGAAAGAAGCAAAGAGAAGAAAAGAGGAA
GACCAAGCCACCCTGGTAGAACAAGTGAAAAGAGTAAAAGAAATTGAAATAATTGAAAGTGATTCTTTTGTTCAGCAGAT
TTTTTTTTTTTTTGTTCAGATCAAGTAAAGAAGTCAAAAGACAGTAGAACCTAGGGAAGTGAAAGATGCAGCTTTGGCGT
CTGAACCAGCATCAGTAATTGCTGACCTGCCCAGTACTGAAAGCAAG

Alignment

ORF - retro_tbel_2400 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.81 %
• Parental protein coverage: 85.71 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGRRSSDTEEESRSKRKKKHRRRSSSSSSSGSRTYSRKKGGRKSRSKSRSWSRDLQPRSHSYDRRRRHRS
          MG.RS.D..E.SRSK.........SS.SSSGSRTYS.K.GG.KSRSK...WS.D.QPRSHSYDRR.RH.S
Retrocopy MGLRS*DMKEKSRSKXXXXETQQTSSNSSSGSRTYSPKNGGKKSRSK*IFWSIDPQPRSHSYDRRCRHQS

Parental  SSSSSYGSRRKRSRSRSRGRGKSYRVQRSRSKSRTRRSRSRPRPRSHSRSSERSSHRRTRSRSRDRERRK
          SSSS.YGSR.K.......G.....RVQRS.SKSRTRRSR.RP.P.SHS.SSERSSHRRT.S..R...R..
Retrocopy SSSS-YGSRIKNVEVVQKGE-ENPRVQRSKSKSRTRRSRLRPCPHSHSQSSERSSHRRTHS--RSQHREW

Parental  GRDKEK-REKEKDKGKDKELHNIKRGESGNIKAGLEHLPPAEQAKARLQLVLEAAAKADEALKAKERNEE
          .....K.R.KEKDKGKDKELHNIK.GESGNIKAGLEHLPPAEQAK.RL.LVLEAAAKA.EAL........
Retrocopy HKGRDK>RKKEKDKGKDKELHNIKCGESGNIKAGLEHLPPAEQAKVRLWLVLEAAAKAAEALXXXXXXXX

Parental  EAKRRKEEDQATLVEQVKRVKEIEAIESDSFVQQTFRSSKEVK----KTVEPSEVKHAASASGPASVVAD
          .........QATLVEQVKRVKEIE.IESDSFVQQ........K....KTVEP.EVK.AA.AS.PASV.AD
Retrocopy XXXXXXXXXQATLVEQVKRVKEIEIIESDSFVQQXXXXXVQIK*RSQKTVEPREVKDAALASEPASVIAD

Parental  PPSTEKE
          .PSTE..
Retrocopy LPSTESK

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_2400 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2400 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,