RetrogeneDB ID: retro_hsap_540

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 1:248099314..248100329(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000226191
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CLK3
• Ensembl ID: ENSG00000179335
• Aliases: CLK3, PHCLK3, PHCLK3/152
• Description: CDC-like kinase 3 [Source:HGNC Symbol;Acc:2071]

Sequence

>retro_hsap_540
GTCGGTGATTGGCCCCAAGAGCAATAAAGACAAGTGGGAACCTGGGCCAAGGCGCCTGTGGCAAGGGGGTGAGTGCTTGG
ACCCTGCCAGAAGGACGTCTCGGGTTGCCGGAGGGTCATCTGCAATGTGGGCAAGCACCGGGAGGCGGCACCGCCAAAAC
TCAACGCTCTCGAAAAAAATAAACGAGAAGGACTAAGAGAACCAGCTGCTGTGCGTCTTGGGGTGTGACTGGTTCACCCT
CCGCGGTCCATGCATATCACCTTTGAGCTCCTGGGCAGGAAAACCCTTGAGTTCCCGAAGGAGAATAACATCCAGCCATT
CCCCTCCCACATGTCTGGCACATGGCCCACCAGCTCTGCCACACCCTTAGATTTCTGCACGAGAACCGGCTGACCCACGC
ACACCTGAAAACCGAGAACATCCTGCATGTGGATTCTGAGTTAAACACCGTCTACAGCGAGCACAGGAGCGATGAGAAGT
CAGTGAGGAGCACCAGCGTCCGAGTGGCTGACTTCCCCAATGCCACCTCTGACCGTGGGCACCACATCGCCATGGTGACC
ACGGTCACTGTCGCCTGCCTGAACTGATCCTTGATCTGGGCTGGACACGCCCCTGCCATGTCCAGGGCATGGGCTACCTT
CTCTTTAAGTACTACCAGGTTTCACACTCTTCCAGACCTGTGAAAACCAAGAGCGCCTGGTGATGTTGAAGACCCTACGG
CTCATCCCATTACGCGTGATCTCCTGTACCAAGAAGCAGAAATATTTCTACAAATGGGGCCTAGTTTGGGATGAGAACAG
CTCTGACAGCCCATATGTGAAGAACTGCAAACGTCTGAAGAGTGACATGCTCCAAGACTCTCTGGAGCACGTGCAGCTGT
TTGACCTGATGCGGAGGGTGGTAAAATTGGACGCTGCCCAGCACATCACTCTGGCTGAGACTCTTCTGCACCCCGTCTTT
GCTGGCCTGGCAACCTCAGTCGTGGTCCTTCCACACAAGCCACAACCCAAGCAGA

Alignment

ORF - retro_hsap_540 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.92 %
• Parental protein coverage: 53.76 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 9

Retrocopy - Parental Gene Alignment:

Parental  IGDWLQERYEIVG-NLGEGTFGKVV-ECLDHARGKSQVA-LKIIRNVGKYREAARLEINVL-KKIKEKDK
          .GDW.QE....VG.NLG.G..GK.V.ECLD.AR..S.VA....I.NVGK.REAA....N.L.KKI.EKD.
Retrocopy VGDWPQEQ*RQVG<NLGQGACGKGV<ECLDPARRTSRVA<RRVICNVGKHREAAPPKLNAL>KKINEKD*

Parental  ENKFLCVLMSDWFNFHG-HMCIAFELLGKNTFEFLKENNFQPYP-LPHVRHMAYQLCHALRFLHENQLTH
          EN..LCVL..DWF...G..M.I.FELLG..T.EF.KENN.QP.P.LPHV.HMA.QLCH.LRFLHEN.LTH
Retrocopy ENQLLCVLGCDWFTLRG<SMHITFELLGRKTLEFPKENNIQPFP<LPHVWHMAHQLCHTLRFLHENRLTH

Parental  TDLKPENILFVNSEFETLYNEHKSCEEKSVKNTSIRVADFGSATFDHEHHTTIVAT-RHYRPPEVILELG
          ..LK.ENIL.V.SE..T.Y.EH.S..EKSV..TS.RVADF..AT.D..HH...V.T..H.R.PE.IL.LG
Retrocopy AHLKTENILHVDSELNTVYSEHRS-DEKSVRSTSVRVADFPNATSDRGHHIAMVTT<GHCRLPELILDLG

Parental  WAQPCDVWSIGCILFEYYR-GFTLFQTHENREHLVMMEKILGPIPSHMIHRTRKQKYFYKGGLVWDENSS
          W..PC.V...G..LF.YY..GFTLFQT.EN.E.LVM..K.L..IP...I..T.KQKYFYK.GLVWDENSS
Retrocopy WTRPCHVQGMGYLLFKYYQ<GFTLFQTCENQERLVML-KTLRLIPLRVISCTKKQKYFYKWGLVWDENSS

Parental  DGRYVKENCKPLKSYMLQDSLEHVQLFDLMRRMLEFDPAQRITLAEALLHPFFAGLT-PEERSFHTSRNP
          D..YVK.NCK.LKS.MLQDSLEHVQLFDLMRR....D.AQ.ITLAE.LLHP.FAGL..P...SFHTS.NP
Retrocopy DSPYVK-NCKRLKSDMLQDSLEHVQLFDLMRRVVKLDAAQHITLAETLLHPVFAGLA>PQSWSFHTSHNP

Parental  SR
          SR
Retrocopy SR

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
bodymap2_adipose	0.00 RPM	22.82 RPM
bodymap2_adrenal	0.00 RPM	36.25 RPM
bodymap2_brain	0.05 RPM	12.89 RPM
bodymap2_breast	0.00 RPM	19.96 RPM
bodymap2_colon	0.00 RPM	24.56 RPM
bodymap2_heart	0.00 RPM	13.50 RPM
bodymap2_kidney	0.00 RPM	17.21 RPM
bodymap2_liver	0.00 RPM	9.06 RPM
bodymap2_lung	0.00 RPM	41.54 RPM
bodymap2_lymph_node	0.00 RPM	48.75 RPM
bodymap2_ovary	0.00 RPM	19.78 RPM
bodymap2_prostate	0.00 RPM	35.11 RPM
bodymap2_skeletal_muscle	0.00 RPM	26.23 RPM
bodymap2_testis	0.09 RPM	33.31 RPM
bodymap2_thyroid	0.00 RPM	27.98 RPM
bodymap2_white_blood_cells	0.16 RPM	37.03 RPM

ChIP-Seq

RNA Polymerase II actvity may be related with retro_hsap_540 in 2 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF002CHO	POLR2A	1:248100376..248100618
ENCFF002CZY	POLR2A	1:248100268..248100784

EST

No EST(s) were mapped for retro_hsap_540 retrocopy.

TSS

No TSS is located nearby retro_hsap_540 retrocopy 5' end.

Lab

retro_hsap_540 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_540 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_405

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000112739	1 retrocopy	retro_hsap_4212,
Homo sapiens	ENSG00000176444	1 retrocopy	retro_hsap_3827,
Homo sapiens	ENSG00000179335	1 retrocopy	retro_hsap_540 ,
Macaca mulatta	ENSMMUG00000011069	1 retrocopy	retro_mmul_457,
Pan troglodytes	ENSPTRG00000007278	1 retrocopy	retro_ptro_405,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.00 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.00 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.00 RPM
FIN_HG00338	0.00 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.00 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.03 RPM
GBR_HG00111	0.00 RPM
GBR_HG00114	0.00 RPM
GBR_HG00119	0.00 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.00 RPM
GBR_HG00134	0.00 RPM
GBR_HG00137	0.03 RPM
GBR_HG00142	0.00 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.02 RPM
TSI_NA20518	0.06 RPM
TSI_NA20532	0.00 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.00 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.02 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.02 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.02 RPM
YRI_NA19223	0.02 RPM

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Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).