RetrogeneDB ID: retro_tbel_17

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_82888:329..1286(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTBEG00000002228
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: CSNK1G1
• Ensembl ID: ENSTBEG00000003013
• Aliases: None
• Description: casein kinase 1, gamma 1 [Source:HGNC Symbol;Acc:2454]

Sequence

>retro_tbel_17
ATGGCCAGCAGCTGCAAGGCTGGATTTATTGTCGGAGGGAAATATAAGCTGGTACGGAAGATCGGGTCTGGCTCCTTCGG
GGACATTTATCTGGCGATTAACATCACCAACGGCGAGGAGGTGGCCGTGAAGCTGGAATCTCAGAAGGCCAGGCATCCCC
AGCTGCTGTACGAGAGCAAACTCTATAAGATTCTTCAAGGTGGGGTTGGCATCCCCCACATACGCTGGTACGGTCAGGAG
AAGGACTGCAGCGTGCTGGTCATGGATCTTCTGGGACCCAGCCTCGAAGACCTCTTCAATTTCTGTTTAAGAAGGTTCTC
GATGAAAACCGTGCTAATGTTAGCTGACCAGATGATCAGTAGAATTGAATACGTGCATTCGAAGAATTTCATACACCGAG
ACCTTAAACCAGATAACTTCCTCATGGGGATTGGACGGCATTGTAATAAATTATTCCTTATTGATTTTGGTTTGGCCAAA
AAGTACAGAGACAACAGGACAAGGCAACATATACCATACAGAGAGGATAAGAACCTCACTGGCACCGCCCGGTACGCTAG
CATCAACGCGCACCTTGGTATTGAACAGAGTCGCCGAGATGACATGGAATCGTTAGGATACGTGTTGATGTATTTTAATA
GAACCAGCCTGCCGTGGCAAGGGCTAAAGGCTGCAACCAAAAAACAAAAATATGAGAAGATTAGTGAAAAGAAGATGTCT
ACTCCCGTTGAAGTGTTATGTAAGGGGTTCCCTGCTGAATTCGCTATGTACTTAAACTATTGCCGTGGGCTGCGTTTCGA
GGAAGTCCCAGATTACATGTATCTGCGGCAACTATTCCGCATTCTTTTCAGGACTTTGAACCACCAGTATGATTACACGT
TTGATTGGATCATTTTAAAGCAGAAAGCGGCACAGCAGGCAGCCACTTCCAGTGGGCCAGGTCAGCAGGCCCAGACC

Alignment

ORF - retro_tbel_17 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.5 %
• Parental protein coverage: 70.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SSTSSGVLMVGPNFRVGKKIGCGNFGELRLXXXXXXXXXXXXXXEPIKSRAPQLHLEYRFYKQLGSAGEG
          .S.......VG.......KIG.G.FG...L..............E..K.R.PQL..E...YK.L...G.G
Retrocopy ASSCKAGFIVGGKYKLVRKIGSGSFGDIYLAINITNGEEVAVKLESQKARHPQLLYESKLYKIL-QGGVG

Parental  LPQVYYFGPCGKYNAMVLELLGPSLEDLFDLCDRTFTLKTVLMIAIQLLSRMEYVHSKNLIYRDVKPENF
          .P.....G........V..LLGPSLEDLF..C.R.F..KTVLM.A.Q..SR.EYVHSKN.I.RD.KP.NF
Retrocopy IPHIRWYGQEKDCSVLVMDLLGPSLEDLFNFCLRRFSMKTVLMLADQMISRIEYVHSKNFIHRDLKPDNF

Parental  L--IGRQGNKKEHVIHIIDFGLAKEYIDPETKKHIPYREHKSLTGTARYMSINTHLGKEQSRRDDLEALG
          L..IGR..NK.......IDFGLAK.Y.D..T..HIPYRE.K.LTGTARY.SIN.HLG.EQSRRDD.E.LG
Retrocopy LMGIGRHCNK----LFLIDFGLAKKYRDNRTRQHIPYREDKNLTGTARYASINAHLGIEQSRRDDMESLG

Parental  HMFMYFLRGSLPWQGLKADTLKERYQKFGDTKRNTPIEALCENFPEEMATYLRYVRRLDFFEKPDYEYLR
          ...MYF.R.SLPWQGLKA.T.K..Y.K....K..TP.E.LC..FP.E.A.YL.Y.R.L.F.E.PDY.YLR
Retrocopy YVLMYFNRTSLPWQGLKAATKKQKYEKISEKKMSTPVEVLCKGFPAEFAMYLNYCRGLRFEEVPDYMYLR

Parental  TLFTDLFERKGYTFDYAYDWV
          .LF..LF.......DY..DW.
Retrocopy QLFRILFRTLNHQYDYTFDWI

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_17 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_17 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 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010080	3 retrocopies	retro_chof_1577, retro_chof_2058, retro_chof_216,
Dasypus novemcinctus	ENSDNOG00000018857	1 retrocopy	retro_dnov_2386,
Rattus norvegicus	ENSRNOG00000016620	1 retrocopy	retro_rnor_2267,
Tupaia belangeri	ENSTBEG00000003013	1 retrocopy	retro_tbel_17 ,