RetrogeneDB ID: retro_tbel_4081

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_6584:33173..34289(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CLK2
• Ensembl ID: ENSTBEG00000000216
• Aliases: None
• Description: CDC-like kinase 2 [Source:HGNC Symbol;Acc:2069]

Sequence

>retro_tbel_4081
AATGAGAGAGAGTATCGGGACCGGAGATATGTTGATGAATACAGGAATGATTACTGCGAAGGCTATGTTCCTAGGCATTA
TCACAGAGACATTGAAAGCAGTTACCGAATCCACTGCAGTAAATTCTCAGTCCGAAGCAGGAGAAGCAGTCCTAAAAGGA
AGCGTAATAGACACTGTTCAAGTCATCAGCCACATTTGAAGAGCCACCGAAGGAAAAGATCCAGAAGTATAGAGGATGAT
GAGGGTCACCTGATCTGTCAAAGTGGAGACGTTCTAAGAGCAAGATATGAAATCGTGGACACTTTGGGTGAAGGGGCCTT
TGGTAAAGTTGTAGAATGCATTGATCATGCCATGGATGGTATGCATGTAGCTGTGAAAATTGTAAAAAATGTAGGCCGTT
ACCGTGAAGCAGCTCGTTCAGAAATCCAAGTATTGGAGCATTTAAATAGTAGTGATCCCAATAGTGTCTTCCGATATGTC
CAGATGCTAGAATGGTTTGATCATCATGGTCACGTTTGTATTGTGTTTGAACTGCTGGGACTTAGTACTTAGGATTTCAT
TAAAGAAAATAGCTTTCTGCCATTTCAAATTGACCACATCAGGCAGATGGCATATCAGATCTGCCAATCAATAAACTTTT
TGCATCATAATAAATTAACCCATACAAATCTGAAGCCCAAAAATATTTTATTTGCGAAGTCTGACTATGTAGTCAAATAT
AATTCTAAAATGAAACGTGATGAACACACACTATAAAACACAGATATCGAAGCTGTTGACTTTGGAAGTGCAATGTATGA
TGATGAACATCACAGTACCTTGGTGTCTACACGGCACTACAGAGCTCCCGAGGTCATTTTAGCTTTAGGTTGGTCTCAGC
CCTGTGATGTTTGGAGCATTGGTTGCATCCTTATTGAATATTACCTTGGTTTCGGAGTCTTTCAGACTCATGATAGTAAA
GAGCACTTAGCAATGATGGAACGAATATTAAGACCCATACCAACATACATGATTCCAAAAACAAGGAAACACAAGTATTT
TCACCATAACCAGCTAGATTGGGATGAACATAGTTCTGCTGGTAGATATGTTAGGAGACACTGTAAACCATTAAAG

Alignment

ORF - retro_tbel_4081 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.31 %
• Parental protein coverage: 75.81 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SDRRVYDRRYCGSYRRNDYSRDRGEAYYDTDYRHSYEYHRENSSYRSQRSSRRKHRRRRRHSRTFSRSSS
          ..R...DRRY...YR.NDY........Y..D...SY..H....S.RS.RSS....R.R.RH.........
Retrocopy NEREYRDRRYVDEYR-NDYCEGYVPRHYHRDIESSYRIHCSKFSVRSRRSSPK--RKRNRHCSSHQPHLK

Parental  QHSSRRAKSVEDDAEGHLIYHVGDWLQERYEIVSTLGEGTFGRVVQCVDHRRGGARVALKIIKNVEKYKE
          .H...R..S.EDD.EGHLI...GD.L..RYEIV.TLGEG.FG.VV.C.DH...G..VA.KI.KNV..Y.E
Retrocopy SHRRKRSRSIEDD-EGHLICQSGDVLRARYEIVDTLGEGAFGKVVECIDHAMDGMHVAVKIVKNVGRYRE

Parental  AARLEINVLEKINEKDPDNKNLCVQMFDWFDYHGHMCISFELLGLSTFDFLKDNNYLPYPIHQVRHMAFQ
          AAR.EI.VLE..N..DP......VQM..WFD.HGH.CI.FELLGLST.DF.K.N..LP..I...R.MA.Q
Retrocopy AARSEIQVLEHLNSSDPNSVFRYVQMLEWFDHHGHVCIVFELLGLST*DFIKENSFLPFQIDHIRQMAYQ

Parental  LCQAVKFLHDNKLTHTDLKPENILFVNSDYELTYNLEKKRDERSVKSTAVRVVDFGSATFDHEHHSTIVS
          .CQ...FLH.NKLTHT.LKP.NILF..SDY...YN...KRDE.....T....VDFGSA..D.EHHST.VS
Retrocopy ICQSINFLHHNKLTHTNLKPKNILFAKSDYVVKYNSKMKRDEHTL*NTDIEAVDFGSAMYDDEHHSTLVS

Parental  TRHYRAPEVILELGWSQPCDVWSIGCIIFEYYVGFTLFQTHDNREHLAMMERILGPIPSRMIRKTRKQKY
          TRHYRAPEVIL.LGWSQPCDVWSIGCI..EYY.GF..FQTHD..EHLAMMERIL.PIP..MI.KTRK.KY
Retrocopy TRHYRAPEVILALGWSQPCDVWSIGCILIEYYLGFGVFQTHDSKEHLAMMERILRPIPTYMIPKTRKHKY

Parental  FYRGRLDWDENTSAGRYVRENCKPLR
          F....LDWDE..SAGRYVR..CKPL.
Retrocopy FHHNQLDWDEHSSAGRYVRRHCKPLK

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_4081 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4081 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 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000176444	1 retrocopy	retro_hsap_3827,
Gorilla gorilla	ENSGGOG00000009438	1 retrocopy	retro_ggor_2575,
Macaca mulatta	ENSMMUG00000023141	1 retrocopy	retro_mmul_1627,
Nomascus leucogenys	ENSNLEG00000012062	2 retrocopies	retro_nleu_2126, retro_nleu_3112,
Pan troglodytes	ENSPTRG00000001419	1 retrocopy	retro_ptro_2604,
Tupaia belangeri	ENSTBEG00000000216	2 retrocopies	retro_tbel_4081 , retro_tbel_4274,