RetrogeneDB ID: retro_tbel_3309

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_136893:85991..86688(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDK1
• Ensembl ID: ENSTBEG00000017549
• Aliases: None
• Description: cyclin-dependent kinase 1 [Source:HGNC Symbol;Acc:1722]

Sequence

>retro_tbel_3309
CTTCAAGATGAGCTCATGCAGGATTTCAGGTTGTATCTCATCTTTGAATTTTTTTTCCATGGATCTCAAGAAATACTTGA
ATTCTATCTCTTCTGGTCAGTTCATGGCCTCTTCACTTGTTAAGGGTTATTTGTACCAAATCCTACAAGGGATTGTGTTT
TGTCACTCTAGAAGAGTTCTTCACAGAGACTTAAAACCTCAAAACTTATTAATCGATGGCAAAGGAACAATTAAACTGGC
TTATTTTGGCCTTGCCAGAGCTTTTGGAATACCAATTAGAGTATACATCCATGAGGTGGTGATGCCCGGTACAGCTCTCC
AGAAGTATTGCTGGGGTCAGCCCGTTACGCAACTCCAGTTGACATTTGGAGTATAGGGACCATATTTGCAGAATTAGCCA
CCAAGAAACCACTTTTCCATGGGGATTCAGAAATTGACTAGCTCTTCAGAATTTTCGGAGCTTTGGGCACCCCCAATAAC
AAAGTGTGGCCAGAAGTGGAATCTTTACAGGACTATAAGAATACATTTCCTAAGTGGAAGCCAGGAAGTCTAGCATCCCA
TGTAAAAAAGCTTGGATGAAAATAGTTTAAATCTACTCTCGAAAATGTTAGTCTCTGATCCTGCCAAACGAATTTCTGGC
AAAATGCCCCTGAATCATCCTTATTTTAATGATTCGGACAATCAGATTAAGAAGATG

Alignment

ORF - retro_tbel_3309 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.96 %
• Parental protein coverage: 78.11 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LQDVLMQDSRLYLIFEFLS-MDLKKYLDSIPPGQFMDSSLVKSYLYQILQGIVFCHSRRVLHRDLKPQNL
          LQD.LMQD.RLYLIFE....MDLKKYL.SI..GQFM.SSLVK.YLYQILQGIVFCHSRRVLHRDLKPQNL
Retrocopy LQDELMQDFRLYLIFEXXX>MDLKKYLNSISSGQFMASSLVKGYLYQILQGIVFCHSRRVLHRDLKPQNL

Parental  LIDDKGTIKLADFGLARAFGIPIRVYTHEVMT-LWYRSPEVLLGSARYSTPIDIWSIGTIFAELATKKPL
          LID.KGTIKLA.FGLARAFGIPIRVY.HEV.....Y.SPEVLLGSARY.TP.DIWSIGTIFAELATKKPL
Retrocopy LIDGKGTIKLAYFGLARAFGIPIRVYIHEVVM<ARYSSPEVLLGSARYATPVDIWSIGTIFAELATKKPL

Parental  FHGDSEIDQLFRIFRALGTPNNEVWPEVESLQDYKNTFPKWKPGSLASHVK-NLDENGLDLLSKMLVYDP
          FHGDSEID.LFRIF.ALGTPNN.VWPEVESLQDYKNTFPKWKPGSLASHVK..LDEN.L.LLSKMLV.DP
Retrocopy FHGDSEID*LFRIFGALGTPNNKVWPEVESLQDYKNTFPKWKPGSLASHVK>SLDENSLNLLSKMLVSDP

Parental  AKRISGKMALNHPYFSDLDNQIKKM
          AKRISGKM.LNHPYF.D.DNQIKKM
Retrocopy AKRISGKMPLNHPYFNDSDNQIKKM

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_3309 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3309 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 11 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007001	2 retrocopies	retro_cjac_1846, retro_cjac_671,
Cavia porcellus	ENSCPOG00000005402	3 retrocopies	retro_cpor_1414, retro_cpor_1422, retro_cpor_200,
Dasypus novemcinctus	ENSDNOG00000018590	1 retrocopy	retro_dnov_265,
Equus caballus	ENSECAG00000009716	1 retrocopy	retro_ecab_637,
Felis catus	ENSFCAG00000014972	1 retrocopy	retro_fcat_329,
Microcebus murinus	ENSMICG00000005793	1 retrocopy	retro_mmur_43,
Monodelphis domestica	ENSMODG00000017091	1 retrocopy	retro_mdom_702,
Rattus norvegicus	ENSRNOG00000000632	1 retrocopy	retro_rnor_1638,
Tupaia belangeri	ENSTBEG00000005123	1 retrocopy	retro_tbel_4151,
Tupaia belangeri	ENSTBEG00000017549	3 retrocopies	retro_tbel_3309 , retro_tbel_807, retro_tbel_812,
Tursiops truncatus	ENSTTRG00000001085	2 retrocopies	retro_ttru_1619, retro_ttru_1634,