RetrogeneDB ID: retro_tbel_3549

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_144436:38301..39507(-)
• 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_3549
GATGATGAAGAGACTAAAAGAAAATCACCAAAGAAAAAGGAGAAGTGCGAATATAAGAAACAGATGAAGAATTCCAAAGC
TCCTAAAGCGCAGGCCGTGAAAGAGTGGGCCCTGCAGAGCTGTAGTCCTCCAAAAGGGTCTGTTAAATACAGTGTGGTTA
AAACCAGAAGGAAAGGTGGCACAGGCGTTTGTTCAAAAGGCAGTCCCCATTCCTCCTCGGAGTCTGACTCTTCTCATGAA
TCAGCCAGTGATGGGACGAGACATGTCACTTTGGGGGTCCAGAATTCCTCAGAGAAACTGTCAACCGAGTTGTCAAAGGA
AGGAATCGCTACAAAAAACACAACTGCTAACAAGCCGACTATCAAAACTGGCTTTAACCCTATCCCCAACAAGAACAAGA
CCATCCAAACGTCATCTTCTAGTTCGGACTCGAGTTCAGAGTCAGATGACCAGTGCACGACGTCCAAGAGCACTCTGGAG
CGCCCTGTGGGTTTCCTAAAGACAGTAGGCCTCTCTGCAGGAAGAGGCTGTCCGGGGCCGGGGCAGGCTTCACAGACTCC
AAGTGCTGTGGGATGGAAATTTTCTGATCCAAACAGTGGCAGGCAGGCTCCTGGACCTCCTCCCAATGTGTCCGTTCCCC
CTAGTTTAGGAAAAGTATGGGGTAGGAGAGAAGACCTTCTTTCTTGGAAGGGAGCTAGGGGTCGGGGCATGCGAGGAAGA
GGTCGAGGACAAGGGAATGATGTTTCTTGTATCTTGAATAGAAACACTGAATATCAGAAGCAGCAGCAATTGAATGAAAT
GTTAACAAACTCATCTACTATTATCCAGAATCCAGTAGAGGCTCTCAAGAAAGATCACAGTCTGTTATCGCTGTTAGCAG
CTGCCCCTCAAGTCGGAGAAAAGATCGCATTTAAGCTTCTGGAACTAACATCCGATTACTCTCCTGATGTCTCTGATTAC
AAGGAAGGAAAAATATTAAGCCACAATCCAGACACCCAGCAAGTAGATATAGAAATTCTTTCATCCGTACCTGCCTTGAA
AGAGCCTGGGAAATTTGATTTGGTTTATCATAACGAAAATGGAACTGAGGTCGTAGAGTATGCTGTGACACAGGAGAGGA
GGATCACTGTTTTTTGGAGAGAGTTAATTGATCCAAGGCTGATTATTGAATCTCCAAGTGACCCAACAAGTACAGAACAT
CCCCGA

Alignment

ORF - retro_tbel_3549 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.8 %
• Parental protein coverage: 69.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DDEETKRKSPKKKEKCEYKKQMKNSKAPKAQAVKEWALQSCSPPKGSVKYSVLKTRRKGGTGVCSKGSPR
          DDEETKRKSPKKKEKCEYKKQMKNSKAPKAQAVKEWALQSCSPPKGSVKYSV.KTRRKGGTGVCSKGSP.
Retrocopy DDEETKRKSPKKKEKCEYKKQMKNSKAPKAQAVKEWALQSCSPPKGSVKYSVVKTRRKGGTGVCSKGSPH

Parental  SSSESDSSHESASDGTRHVTLGVQNSSEKLSTELSKEGIATKNTTANKPTIKTGFNPIPSKSKTIQTSSS
          SSSESDSSHESASDGTRHVTLGVQNSSEKLSTELSKEGIATKNTTANKPTIKTGFNPIP.K.KTIQTSSS
Retrocopy SSSESDSSHESASDGTRHVTLGVQNSSEKLSTELSKEGIATKNTTANKPTIKTGFNPIPNKNKTIQTSSS

Parental  SSDSSSESDDQCTTSKSTPERPAGFLKTVGLSAGRGCPGPGQTSQTPSAVGWKFSDPNSGRQ---PTPPV
          SSDSSSESDDQCTTSKST.ERP.GFLKTVGLSAGRGCPGPGQ.SQTPSAVGWKFSDPNSGRQ...P.P.V
Retrocopy SSDSSSESDDQCTTSKSTLERPVGFLKTVGLSAGRGCPGPGQASQTPSAVGWKFSDPNSGRQAPGPPPNV

Parental  SSPSR--KVWVGEET--SFRGARG-GMRRSRRGNG--VSCILNRNTD-QKQQQLNEV-TNSSTIIQNPVE
          S.P....KVW...E...S..GARG.GMR...RG.G..VSCILNRNT..QKQQQLNE..TNSSTIIQNPVE
Retrocopy SVPPSLGKVWGRREDLLSWKGARGRGMRGRGRGQGNDVSCILNRNTEYQKQQQLNEMLTNSSTIIQNPVE

Parental  ALKKDYSLLPLLAAAPQVGEKIAFKLLELTSDYSPDVSDYKEGKIISHNPDTQQVDIEILSSLPALKEPG
          ALKKD.SLL.LLAAAPQVGEKIAFKLLELTSDYSPDVSDYKEGKI.SHNPDTQQVDIEILSS.PALKEPG
Retrocopy ALKKDHSLLSLLAAAPQVGEKIAFKLLELTSDYSPDVSDYKEGKILSHNPDTQQVDIEILSSVPALKEPG

Parental  KFDLVYHNENGTEVVEYAVTQERRITVFWRELIDPRLIIESPSDPPSTEHPR
          KFDLVYHNENGTEVVEYAVTQERRITVFWRELIDPRLIIESPSDP.STEHPR
Retrocopy KFDLVYHNENGTEVVEYAVTQERRITVFWRELIDPRLIIESPSDPTSTEHPR

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_3549 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3549 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,