RetrogeneDB ID: retro_tbel_4274

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_74416:1..988(-)
• 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_4274
GAGTGGGATAGTAGAGAAAGCTGGGGCCATAAAAGCTACCGAGAAAGTCACAAAAGGAAGAGGCAATCCCACAGTAGTAC
ACAGGAGAATAGACACTGTAAACCACATCACCAATTTAAAAAATCTGATTGTCATTATTTAGAAGCATGGTCCTTGAATG
AGAGAGAGTATCGGGACTGGAGATATGTTGATGAATACAGGAATGATTACTGCAAAGGCTATGTTCCTAGGCATTATCAC
AGAGACATTGAAAACAGTTACCAAATCCACTGCAGTAAATCCTCAGTCCGAAGCAGGAGAAGCAGTCCTAAAAGGAAGCG
TAATAGACACTGTTCAAATCATCAGCCACGTTTGAAGAGCCACCGAAGGAAAAGATCCAGGAGTATAGAGGATGATGAGG
GTCACCTGATCTGTCAAAGTGGAGACGTTCTAAGAGCAAGATATGAAATCGTGGACACTTTGGGTGAAGGGGCCTTTGGT
AAAGTTGTAGAATGCATTGATCATGCCATGGATGGCATGCATGTAGCTGTGAAAATTGTAAAAAATGTAGGCTGTTACCG
TGAAGCAGCTCTTTCAGAAATCCAAGTATTGGGGCATTTAAATAGTAGTGATCCCAATAGTGTCTTCCGATGTGTCCAGA
TGCTAGAATGGTTTGATCATCATGGTCACGTTTGTATTGTGTTGGAACTGCTGGGACTTAGTACTTAAGATTTCATTAAA
GAAAACAGCTTTCTGCCATTTCAAATTGACCACATCAGGCAGATGGCATATCAGATCTGCCAATCAATAAACTTTTTGCA
TCATAATAAATTAACCCATACAGATCTGAAGCCCGAAAATATTTTATTTGTGAAGTCTGACTATGTAGTCAAATACAATT
CTAAAATGAAACGTGATGAACGCACACTACAAAACACAGATACCAAAGTTGTTGACTTTGGAAGTGCAATGTATGATGAT
GAACATCACAGTACCTTGGTGTCTACA

Alignment

ORF - retro_tbel_4274 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.74 %
• Parental protein coverage: 67.34 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ERGSRGSY-HEHYRSRKHKRRRSRSWSSSSDRTRRRRREDSYHVRSRSSYDDRSS--DRRVYDRRYCGSY
          E..SR.S..H..YR...HKR.R....S.SS....R..........S...Y....S...R...D.RY...Y
Retrocopy EWDSRESWGHKSYRE-SHKRKRQ---SHSSTQENRHCKPHHQFKKSDCHYLEAWSLNEREYRDWRYVDEY

Parental  RRNDYSRDRGEAYYDTDYRHSYEYHRENSSYRSQRSSRRKHRRRRRHSRTFSRSSSQHSSRRAKSVEDDA
          R.NDY........Y..D...SY..H...SS.RS.RSS....R.R.RH..........H...R..S.EDD.
Retrocopy R-NDYCKGYVPRHYHRDIENSYQIHCSKSSVRSRRSSPK--RKRNRHCSNHQPRLKSHRRKRSRSIEDD-

Parental  EGHLIYHVGDWLQERYEIVSTLGEGTFGRVVQCVDHRRGGARVALKIIKNVEKYKEAARLEINVLEKINE
          EGHLI...GD.L..RYEIV.TLGEG.FG.VV.C.DH...G..VA.KI.KNV..Y.EAA..EI.VL...N.
Retrocopy EGHLICQSGDVLRARYEIVDTLGEGAFGKVVECIDHAMDGMHVAVKIVKNVGCYREAALSEIQVLGHLNS

Parental  KDPDNKNLCVQMFDWFDYHGHMCISFELLGLSTFDFLKDNNYLPYPIHQVRHMAFQLCQAVKFLHDNKLT
          .DP.....CVQM..WFD.HGH.CI..ELLGLST.DF.K.N..LP..I...R.MA.Q.CQ...FLH.NKLT
Retrocopy SDPNSVFRCVQMLEWFDHHGHVCIVLELLGLST*DFIKENSFLPFQIDHIRQMAYQICQSINFLHHNKLT

Parental  HTDLKPENILFVNSDYELTYNLEKKRDERSVKSTAVRVVDFGSATFDHEHHSTIVST
          HTDLKPENILFV.SDY...YN...KRDER....T...VVDFGSA..D.EHHST.VST
Retrocopy HTDLKPENILFVKSDYVVKYNSKMKRDERTLQNTDTKVVDFGSAMYDDEHHSTLVST

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_4274 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4274 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 ,