RetrogeneDB ID: retro_tbel_3961

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_45087:141..1350(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COIL
• Ensembl ID: ENSTBEG00000008882
• Aliases: None
• Description: coilin [Source:HGNC Symbol;Acc:2184]

Sequence

>retro_tbel_3961
GATGATGAAGAGACTAAAAGAAAATCACCAAAGAAAAAGGAGGAGTGCGAATATAAGAAACAGATGAAGAATTCCAAAGC
TCCTAAAGCGCAGGTCGTGAAAGAGTGGGCCCTGCAGAGCTGTAGTCCTCCAAAAGGGTCTGTTAAATACAGTGTGGTTA
AAACCAGAAGGAAAGGTGGCACAGGCGTTTGTTCAAGAGGCAGTCCCCATTCCTCCTCGGAGTCTGACTCTTCTCATGAA
TCAGCCAGTGATGGGACCAGACATGTCACTTTGGGGGTCCAGAATTCCTCAGAGAAACTGTCAACCGAGTCGTCAAAGGA
AGGAATCGCTACAAAAAACACAACTGCTAACAAGCCGACTATCAAAACTGGCTTTAACCCTATCCCCAACAAGAGCAAGA
CCATCCAAACGTCATCTTCTAGTTCTGACTCGAGTTCAGAGTCAGATGACCAGTGCACGACGTCCAAGAGCACTCTGGAG
CGCCCTGTGGGTTTCCTAAAGACAGTAGGCCTCTCTGCAGGAAGAGGCTGTCCGGAGCCGGGGCAGGCTTCACAGACCTC
AAGTGCCATGGGATGGAAATTTTCTGATCCAAACAGTGGCAGGCAGGCTCCTGGACCTCCTCCCAATGTGTCCGTTCCCC
CTAGTTTAGGAAAAGTATGGGGTAGGAGAGAAGACCTTCTTTCTTGGAAGGGAGCTAGGGGTTGGGGCATGCGAGGAAGA
GGTCGAGGACGAGGGAATGGTGTTTCTTGTATCTTGAATAGAAACACTGAATATCAGAAGCAGCAGCAATTGAATGAAAT
GTTAACAGACTCATCTACTATTATCCAGAATCCAGTAGAGGCTCTCAAGAAAGATCACAGTCTGTTATCACTGTTAGCAG
CTGCCCCTCAAGTCGGAGAAAAGATCGCATTTAAGCTTCTGGAACTAACATCCGATTACTCTCCTGATGTCTCTGATTAC
AAGGAAGGAAAAATATTAAGCCACAATCCAGACACCCAGCAAGTAGATATAGAAATTCTTTCATCCTTACCTGCCTTGAA
AGAGCCTGGGAAATTTGATTTGGTTTATCATAACGAAAATGGAACTGAGGTCCTAGAGTATGCTGTGACACAGGAGAGGA
GGTAGATCACTGTTTTTTGGAGAGAGTTGATTGATCCAAGGCTGATTATTGAATCTCCAAGTGACCCACCAAGTACAGAA
CATCCCCGA

Alignment

ORF - retro_tbel_3961 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.09 %
• Parental protein coverage: 69.03 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DDEETKRKSPKKKEKCEYKKQMKNSKAPKAQAVKEWALQSCSPPKGSVKYSVLKTRRKGGTGVCSKGSPR
          DDEETKRKSPKKKE.CEYKKQMKNSKAPKAQ.VKEWALQSCSPPKGSVKYSV.KTRRKGGTGVCS.GSP.
Retrocopy DDEETKRKSPKKKEECEYKKQMKNSKAPKAQVVKEWALQSCSPPKGSVKYSVVKTRRKGGTGVCSRGSPH

Parental  SSSESDSSHESASDGTRHVTLGVQNSSEKLSTELSKEGIATKNTTANKPTIKTGFNPIPSKSKTIQTSSS
          SSSESDSSHESASDGTRHVTLGVQNSSEKLSTE.SKEGIATKNTTANKPTIKTGFNPIP.KSKTIQTSSS
Retrocopy SSSESDSSHESASDGTRHVTLGVQNSSEKLSTESSKEGIATKNTTANKPTIKTGFNPIPNKSKTIQTSSS

Parental  SSDSSSESDDQCTTSKSTPERPAGFLKTVGLSAGRGCPGPGQTSQTPSAVGWKFSDPNSGRQ---PTPPV
          SSDSSSESDDQCTTSKST.ERP.GFLKTVGLSAGRGCP.PGQ.SQT.SA.GWKFSDPNSGRQ...P.P.V
Retrocopy SSDSSSESDDQCTTSKSTLERPVGFLKTVGLSAGRGCPEPGQASQTSSAMGWKFSDPNSGRQAPGPPPNV

Parental  SSPSR--KVWVGEET--SFRGARGGMRRSR---RGNGVSCILNRNTD-QKQQQLNEV-TNSSTIIQNPVE
          S.P....KVW...E...S..GARG...R.R...RGNGVSCILNRNT..QKQQQLNE..T.SSTIIQNPVE
Retrocopy SVPPSLGKVWGRREDLLSWKGARGWGMRGRGRGRGNGVSCILNRNTEYQKQQQLNEMLTDSSTIIQNPVE

Parental  ALKKDYSLLPLLAAAPQVGEKIAFKLLELTSDYSPDVSDYKEGKIISHNPDTQQVDIEILSSLPALKEPG
          ALKKD.SLL.LLAAAPQVGEKIAFKLLELTSDYSPDVSDYKEGKI.SHNPDTQQVDIEILSSLPALKEPG
Retrocopy ALKKDHSLLSLLAAAPQVGEKIAFKLLELTSDYSPDVSDYKEGKILSHNPDTQQVDIEILSSLPALKEPG

Parental  KFDLVYHNENGTEVVEYAVTQERR-ITVFWRELIDPRLIIESPSDPPSTEHPR
          KFDLVYHNENGTEV.EYAVTQERR.ITVFWRELIDPRLIIESPSDPPSTEHPR
Retrocopy KFDLVYHNENGTEVLEYAVTQERR*ITVFWRELIDPRLIIESPSDPPSTEHPR

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_3961 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3961 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 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008740	1 retrocopy	retro_chof_1121,
Callithrix jacchus	ENSCJAG00000013960	1 retrocopy	retro_cjac_2240,
Dasypus novemcinctus	ENSDNOG00000023961	1 retrocopy	retro_dnov_1986,
Echinops telfairi	ENSETEG00000003687	1 retrocopy	retro_etel_1537,
Nomascus leucogenys	ENSNLEG00000008026	1 retrocopy	retro_nleu_1014,
Oryctolagus cuniculus	ENSOCUG00000011345	1 retrocopy	retro_ocun_1798,
Pongo abelii	ENSPPYG00000008248	1 retrocopy	retro_pabe_305,
Tupaia belangeri	ENSTBEG00000008882	4 retrocopies	retro_tbel_2118, retro_tbel_3549, retro_tbel_3961 , retro_tbel_838,