RetrogeneDB ID: retro_tbel_2078

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_926:500255..500829(+)
• Located in intron of: ENSTBEG00000012260

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_2078
ATGGGACTATGGTCATCAGATATGGAAGAAAAGAGCAGAAGCAAGAAAAGAAAGAAACATCACAGACCATCATCTTCAAG
CAGTTCTTCAGGTAGTAGAACATACAGCCAAAAAAATGGTGGAAAGAAGTCAAGATCAAAGTAGAAATTTTGGTCCATAG
ATCCCCAACCTTGTTCACAGTCTTATGATAGAAGATGCAGGCATCAATCAAGCAGTAGTTCTTCTTGTGGCTCTAGAAGA
AAAAAAGTCAAAGTCATTCAAAGGGACAAAGGAAATCCTATAGGGTTCAGAGGTCTAGATCAAAAAGCAGAACAAGAAAG
TTCAGGTTGAGATCTTGTCCACATTCCCATAGTCAAAGCAGTGAGAGATCAAGTCACAGGAGAACCTGTAGTTGCTCTCG
GCATAGAGACTGGCATAAGGGCATAGACAAAGAGAAAAGGAGAAGGAGAAAGGCAAGGACAAGGAATTACATAACATCAA
ATGTGGAGAATCTGGAAACATCAAAGCTGGATTAGAACATCTGCTGACAGCTGAACAGGCCAAAGCCAGACTATGGCTGG
TTCTTGAAGCTGCT

Alignment

ORF - retro_tbel_2078 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75. %
• Parental protein coverage: 58.97 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MGRRSSDTEEESRSKRKKKHRRRSSSSSSSGSRTYSRKKGGRKSRSKSRSWSRDLQPRSHSYDRRRRHRS
          MG..SSD.EE.SRSK..KKH.R.SSSSSSSGSRTYS.K.GG.KSRSK...WS.D.QP.S.SYDRR.RH.S
Retrocopy MGLWSSDMEEKSRSKKRKKHHRPSSSSSSSGSRTYSQKNGGKKSRSK*KFWSIDPQPCSQSYDRRCRHQS

Parental  SSSSSYGSRR-KRSRSRSRGRGKSYRVQRSRSKSRTRRSRSRPRPRSHSRSSERSSHRRTRSRSRDRERR
          SSSSS.GSRR.K.S.S.S.G..KSYRVQRSRSKSRTR..R.R..P.SHS.SSERSSHRRT.S.SR.R...
Retrocopy SSSSSCGSRR<KKSQSHSKGQRKSYRVQRSRSKSRTRKFRLRSCPHSHSQSSERSSHRRTCSCSRHRDWH

Parental  KGRDKEKR-EKEKDKGKDKELHNIKRGESGNIKAGLEHLPPAEQAKARLQLVLEAA
          KG.DKEKR.EKE..KGKDKELHNIK.GESGNIKAGLEHL..AEQAKARL.LVLEAA
Retrocopy KGIDKEKR<EKE--KGKDKELHNIKCGESGNIKAGLEHLLTAEQAKARLWLVLEAA

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_2078 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2078 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,