RetrogeneDB ID:

retro_hsap_4651

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:X:9370790..9371888(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000232111
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:CDYL
Ensembl ID:ENSG00000153046
Aliases:CDYL, CDYL1
Description:chromodomain protein, Y-like [Source:HGNC Symbol;Acc:1811]


Retrocopy-Parental alignment summary:






>retro_hsap_4651
ATTGAAAAGATTGTTGACAAAAGGAAAAATTAAAAAGGGAAGACAGAGTATTTGGTTCAGTGAAAAGGCTACAACAGCGA
GGACGACACTTGGGAACCAGAGCAGCACCTCGTGAACTGTCAGGAATACATCCACGACTTCAACAGACACCACACGGAAA
GGCAGAAAGAGAGCACATTGACCAGAACAAACAGGTCCTCTCCCAACAATGCTAGGAAACAAATCTCCAGATCCACAAAC
AGCAGCTTTTCTAAGTCCTCTCCTAAGGCACCAGTGATTGGGAGAGATCACGAATCCAAAAACAGCCAGCTGTTTGCTGC
CAGCCAGCAGTTCAGGAAGAACACAGCTCCGTCTCTCTGCAGCCAGATGAAAATGGACCTAGTGAAGTCAGGTATCAAGA
TCCTCATGCCTAAGAGCCCCATTAAGCAGGACGCAGTGAATGGCTTTCAGAGTGAGAGCTCCAAAAAACTGGACCCCACA
GAGCAGGGTCAGGAGGAATGGTAGTACCCAAAGTGGCAGCGGAAAAGCCAGACAAAGCTTTATTGGGCCCTGGTACTGAG
CAGGCCAGGATGGGGAGCAAGCCTGGATACACCTGCTAGTGCCTCAGGTGCATGGCCCCGTAAGTGCAGCCATGGCCACA
GGCCTACTCGTTAACAGGAAAGCTACATCTACATTCATGGATGCATTAACAGCCAGTGGGACAACCAACATACAGACATC
TGTTACAGCAGTAACTGTCAGCAAAAGGAAATTTATTGACAACAGAAGAGAACAGCCTTTTAACAAACGATTGCATTTCA
GTGTGAGGCAAACAGAAAGTGCCTAAGGATACAGAGTTATTGTGGCCGGGACAAAAGATGGCTTCACCCACATCTTATTC
ACTAGATCAACAGGGAATAACTCAGTAAATACAGCTGTAATGAAAAAAGTCTACCAGCTCTGACAACCACTGCTGATTAC
AGCAAGCTTGTACTGCTCAGCGCCTTTAACAGTGTCTTCTGTTGTGGACTTGACTTTATTTATTTTATGCAGTGTTTGAC
AGATGACAGAAAAAGAGAAAGCATTAAAATGGGAGAACCTATCAGAAACGTCGTGAAT

ORF - retro_hsap_4651 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 76.41 %
Parental protein coverage: 61.87 %
Number of stop codons detected: 3
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalVERIVDKRKNKKGKTEYLVRWKGYDSEDDTWEPEQHLVNCEEYIHDFNRRHTEKQKESTLTRTNRTSPNN
.E.IVDKRKN.KGKTEYLV..KGY.SEDDTWEPEQHLVNC.EYIHDFNR.HTE.QKESTLTRTNR.SPNN
RetrocopyIEKIVDKRKN*KGKTEYLVQ*KGYNSEDDTWEPEQHLVNCQEYIHDFNRHHTERQKESTLTRTNRSSPNN
ParentalARKQISRSTNSNFSKTSPKALVIGKDHESKNSQLFAASQKFRKNTAPSLSSRKNMDLAKSGIKILVPKSP
ARKQISRSTNS.FSK.SPKA.VIG.DHESKNSQLFAASQ.FRKNTAPSL.S...MDL.KSGIKIL.PKSP
RetrocopyARKQISRSTNSSFSKSSPKAPVIGRDHESKNSQLFAASQQFRKNTAPSLCSQMKMDLVKSGIKILMPKSP
ParentalVKSRTAVDGFQSESPEKLDPVEQGQED-TVAPEVAAEKPVGALLGPGAERARMGSRPR-IHPLVPQVPGP
.K...AV.GFQSES..KLDP.EQGQE...V.P.VAAEKP..ALLGPG.E.ARMGS.P..IH.LVPQV.GP
RetrocopyIK-QDAVNGFQSESSKKLDPTEQGQEE<MVVPKVAAEKPDKALLGPGTEQARMGSKPG<IHLLVPQVHGP
ParentalVTAAMATGLAVNGKGTSPFMDALTANGTTNIQTSVTGVTASKRKFIDDRRDQPFDKRLRFSVRQTESAYR
V.AAMATGL.VN.K.TS.FMDALTA.GTTNIQTSVT.VT.SKRKFID.RR.QPF.KRL.FSVRQTESA..
RetrocopyVSAAMATGLLVNRKATSTFMDALTASGTTNIQTSVTAVTVSKRKFIDNRREQPFNKRLHFSVRQTESA*G
ParentalYRDIVVRKQDGFTHILLSTKSSENNSLNPEVMREVQS-ALSTAAADDSKLVLLSAVGSVFCCGLDFIYFI
YR.IV....DGFTHIL..T.S..NNS.N..VM..V...AL.T..AD.SKLVLLSA..SVFCCGLDFIYF.
RetrocopyYRVIVAGTKDGFTHILF-TRSTGNNSVNTAVMKKVYQ<ALTT-TADYSKLVLLSAFNSVFCCGLDFIYFM
ParentalRRLTDDRKRESTKMAEAIRNFVN
..LTDDRKRES.KM.E.IRN.VN
RetrocopyQCLTDDRKRESIKMGEPIRNVVN

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






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
bodymap2_adipose 0 .00 RPM 28 .72 RPM
bodymap2_adrenal 0 .00 RPM 23 .81 RPM
bodymap2_brain 0 .00 RPM 17 .93 RPM
bodymap2_breast 0 .02 RPM 20 .82 RPM
bodymap2_colon 0 .00 RPM 28 .98 RPM
bodymap2_heart 0 .00 RPM 15 .30 RPM
bodymap2_kidney 0 .00 RPM 20 .20 RPM
bodymap2_liver 0 .00 RPM 6 .46 RPM
bodymap2_lung 0 .00 RPM 18 .16 RPM
bodymap2_lymph_node 0 .00 RPM 26 .62 RPM
bodymap2_ovary 0 .00 RPM 23 .69 RPM
bodymap2_prostate 0 .00 RPM 38 .40 RPM
bodymap2_skeletal_muscle 0 .00 RPM 31 .68 RPM
bodymap2_testis 0 .64 RPM 29 .17 RPM
bodymap2_thyroid 0 .00 RPM 26 .21 RPM
bodymap2_white_blood_cells 0 .00 RPM 30 .75 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4651 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4651 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4651 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4651 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4651 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_3090
Parental genes homology:
Parental genes homology involve 5 parental genes, and 10 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000117871 retrocopy
retro_chof_525,
Callithrix jacchus ENSCJAG000000213745 retrocopies
retro_cjac_2675, retro_cjac_3927, retro_cjac_4003, retro_cjac_4228, retro_cjac_4229,
Homo sapiens ENSG00000153046 1 retrocopy
retro_hsap_4651 ,
Otolemur garnettii ENSOGAG000000159202 retrocopies
retro_ogar_2406, retro_ogar_3269,
Pan troglodytes ENSPTRG000000176881 retrocopy
retro_ptro_3090,

Expression level across human populations :
image/svg+xml GBR_HG00142 GBR_HG00099 GBR_HG00114 GBR_HG00143 GBR_HG00131 GBR_HG00137 GBR_HG00133 GBR_HG00119 GBR_HG00111 GBR_HG00134 FIN_HG00378 FIN_HG00338 FIN_HG00349 FIN_HG00375 FIN_HG00315 FIN_HG00277 FIN_HG00328 FIN_HG00321 FIN_HG00377 FIN_HG00183 TSI_NA20756 TSI_NA20538 TSI_NA20798 TSI_NA20532 TSI_NA20765 TSI_NA20518 TSI_NA20513 TSI_NA20512 TSI_NA20771 TSI_NA20786 YRI_NA19114 YRI_NA19099 YRI_NA18870 YRI_NA18907 YRI_NA19223 YRI_NA19214 YRI_NA18916 YRI_NA19093 YRI_NA19118 YRI_NA19213 Toscaniin Italia: Finnish inFinland: British in England and Scotland: Utah Residents (CEPH) with Northernand Western European Ancestry: Yoruba in Ibadan, Nigeria: CEU_NA12760 CEU_NA12827 CEU_NA12872 CEU_NA12751 CEU_NA12873 CEU_NA12400 CEU_NA11930 CEU_NA12004 CEU_NA11831 CEU_NA11843 No expression ( = 0 RPM ) > 0 RPM = 0.31 RPM Legend:


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 .03 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 .00 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .31 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .03 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .05 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 .00 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .00 RPM

Indel association:

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



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