RetrogeneDB ID:

retro_hsap_4278

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:9:84701074..84703683(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000230360
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:DDX10
Ensembl ID:ENSG00000178105
Aliases:DDX10, HRH-J8
Description:DEAD (Asp-Glu-Ala-Asp) box polypeptide 10 [Source:HGNC Symbol;Acc:2735]


Retrocopy-Parental alignment summary:






>retro_hsap_4278
ATGGGCAAAACTGCGGACTCTCCGGGTTCGGGAGCCCGACCCGACCCGGTGCGGAGCTTCAATCGCTGGAAGAAAAAACA
CAGCCACGGGCAGAACAAAAAGAATCAGTTGAGGAAGCAACTGAAGAAACCCGAATGGCAGGTCGAGCGCGAGGGTAACA
GCCGCCTCATGCAGAACTATGAGAAGATAAATGTAAATGAAATTACAAGATTTTCAGATTTTTCCTTGTCCAAAAAAACA
TTGAAAGGTTTGCAAGAAGCTCAGTACCGTTTGGTAACTGAGATACAGAAGCAGACCATTGGATTGGCTTTGCAAGGTAG
AGATGTACCTGGAGTGGCCAAAACTGGATCTGGCAAGACTTTGGCTTTCCTTGTTCCAGTGCTAGAAGCCTTATATCGTC
TGCAATAGACCTCAACAGATGGGCTGGGGGTTCTCATAATATCACCTATGAGAGAACTGACCTATCAGACCTTTGAGGTT
CTCCAAAAGGTAGGAAAGAATCATGACTTCTCAGCTGGTCTCATCATTGGTGGAAAGTATCTGAAACACGAAGCTGAGAG
GATCAACAACATAAATATACTCGTGTGCGCACCAGGTCGGCTTCTTCAACACATGGATGAAACGGTGTCTTTTCATGCTA
CTGCTCTCCTAATGTTAGTTCTTGATGAAGCATATAGAATCTTGGATGTGGGCTTTGCTGATACCATGAATGCTATTATT
GAAAATCTCCCCAAGAAACGTCAGACTTTACTTTTCTCAGCAACACAAACTATATCTGTAAAGGACCTTGCACGCTTGAG
TTTGAAAAACACTGAGTATGTCTGGGTTCATGAAAAATGCAAAATATAGCACCCCTGCCACTTTGGAACAGAACTACATA
GTCTGTGAGCAGCAGCAAAAAATAAGTGTGCTGTATTCCTTTTTGAGAAGGCACCTGAAGAAGAAGAGCATTGTATTTTT
TTCCAGTTGCTAAAAGGTCTGATATCTGTACCGAGTGTTTTGCCAGCTACGTCCTGGTATTTCTATCCTTGCCCTCCATG
GTCGATAGCAGCAAATGAGAAGAATGGAAGTCTATAATGAGTTTGTCCGTAAGAGAGCTGCAGTACTCTTTGCTAGTGAT
GTTGCAGCCAGGGGGCTGGATTTCCCGGCTGTGAATTGGGCTCTTCAGTTTGATTGTCCTGAGGATGCCAACACATATAT
TCACAGAGCAGGTAGAACTGCCAGGTACAAAGAGGATGGTGAAGCTTTATTAATTTTGCTTGCCTCAGAAAAAGCTATAG
TGCAGCAGCTTCTTCAGAAGAAAGTACCTATAAAGGAAATCAAAATCAATCCAGAAAAACTTATAGATATCCAGAAAAAA
TTGGAATCTTTTTCAGCTGAAGATCAAGATTTAAAAGAAAGAGCTCAAAGGTGTTTCATCTCCGATATATGATTGGTATA
TCTGATGAAGGATAAAGAAGTATTTGATGTGAGCAAGTTACCTATACCTGAATATGCCCTGTCTCTTGGGCTTGCTGTGG
CACCATGCATAAGATTTCTTCAGAAAATGCAGAAACAACCCACCAAAGAATTGGTAATGAGCCAAGCCAATAAAGTAACT
GAGCCAAGGGCTCCCTCCCTCACCAATGACAAAGTGGAAGAATTTAGAGCCTTCTTCAATGAGAAAATGTCCATCCTTCA
GAAAGGTGGAAAAAGACTCAAAGGGACAGAGCACAGACTGGCTAATGATACTAGTGATGAAGAACAGGAGGAAGAGGAAG
ATAATGAAGAAGAAATGGAAGAGAAACTGGCAAAAGCAAAAGGATCTCAAGCTCCATCTCTTCCTAACACCAGTGAAGCA
AAGAAGATCAAGGAAGTTCCTATGCAGTTCCTGGACAGAGATGAGGAGGAAGAAGATGCTGATTTCTTGAAGGTGAAGTG
GCACAATGTGTTTGGATTTGACTTTAAAGAGGAGAAAACATTACAGAAGAAAGAACCTTCTAAATCCAGCATCAAGAAAA
AAGTGACCAAAGTTGCAGAAGCAAAAAAAGTAATGAAGAGAAATTTTAAAGCGAATAAGAAGATAACATGTACTGATGAA
GGGGAGTTGGTTCAACAGTGGCCACAAATGCAGAAATCTGCCATCAAGGATGCTGAGGAAGATGATGACACGGGTGGTAT
CAACTTAGATAAAGCAAAGGGAAGACTTCAGAAAGAGGACAAATTTGACAAAGAAGAATATAGGAAGAAAATTAAGGCAA
AGCATTGGGAGAAAAGACTGAAAGAAAGGGAAGCCAGAAGAGAAGCCAACACGAGACAAGCAAAGGCCAAAGATGAAGAG
GAAGACTTTCTGGATTGGAGTGATGATGATGATGATGGATTTGATCCAAGCACACTCCTAGATCCAGATAAGTACAGAAG
CTCTGAAGATTCAGATAGTGAAGATATGGAAAATAAAATGTGATACCAAGAAGAAGCAGGGAATGAAAAAGAGGAAGAAC
AGTGAAGTGGAAGATGTAGGACCAACAAGTCATAACAGAAAGAAGGCCACGTGGGACACTTTAGAGCCTTTGGATACTGG
CCTGTCTTTAGCAGAGGATGAAGAGCTGGTGTTACATCTGCTAAGAAGT

ORF - retro_hsap_4278 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.17 %
Parental protein coverage: 99.77 %
Number of stop codons detected: 5
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMGKTANSPGSGARPDPVRSFNRWKKKHSHRQNKKKQLRKQLKKPEWQVERESISRLMQNYEKINVNEITR
MGKTA.SPGSGARPDPVRSFNRWKKKHSH.QNKK.QLRKQLKKPEWQVERE..SRLMQNYEKINVNEITR
RetrocopyMGKTADSPGSGARPDPVRSFNRWKKKHSHGQNKKNQLRKQLKKPEWQVEREGNSRLMQNYEKINVNEITR
ParentalFSDFPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPVLEALYRLQWTSTD
FSDF.LSKKTLKGLQEAQYRLVTEIQKQTIGLALQG.DV.G.AKTGSGKTLAFLVPVLEALYRLQ.TSTD
RetrocopyFSDFSLSKKTLKGLQEAQYRLVTEIQKQTIGLALQGRDVPGVAKTGSGKTLAFLVPVLEALYRLQ*TSTD
ParentalGLGVLIISPTRELAYQTFEVLRKVGKNHDFSAGLIIGGKDLKHEAERINNINILVCTPGRLLQHMDETVS
GLGVLIISP.REL.YQTFEVL.KVGKNHDFSAGLIIGGK.LKHEAERINNINILVC.PGRLLQHMDETVS
RetrocopyGLGVLIISPMRELTYQTFEVLQKVGKNHDFSAGLIIGGKYLKHEAERINNINILVCAPGRLLQHMDETVS
ParentalFHATDLQMLVLDEADRILDMGFADTMNAVIENLPKKRQTLLFSATQTKSVKDLARLSLKNPEYVWVHEK-
FHAT.L.MLVLDEA.RILD.GFADTMNA.IENLPKKRQTLLFSATQT.SVKDLARLSLKN.EYVWVHEK.
RetrocopyFHATALLMLVLDEAYRILDVGFADTMNAIIENLPKKRQTLLFSATQTISVKDLARLSLKNTEYVWVHEK>
ParentalAKYSTPATLEQNYIVCELQQKISVLYSFLRSHLKKKSIVFFSSCKEVQYLYRVFCRLRPGVSILALHGRQ
AKYSTPATLEQNYIVCE.QQKISVLYSFLR.HLKKKSIVFFSSC..V.YLYRVFC.LRPG.SILALHGR.
RetrocopyAKYSTPATLEQNYIVCEQQQKISVLYSFLRRHLKKKSIVFFSSC*KV*YLYRVFCQLRPGISILALHGR*
ParentalQQMRRMEVYNEFVRKRAAVLFATDIAARGLDFPAVNWVLQFDCPEDANTYIHRAGRTARYKEDGEALLIL
QQMRRMEVYNEFVRKRAAVLFA.D.AARGLDFPAVNW.LQFDCPEDANTYIHRAGRTARYKEDGEALLIL
RetrocopyQQMRRMEVYNEFVRKRAAVLFASDVAARGLDFPAVNWALQFDCPEDANTYIHRAGRTARYKEDGEALLIL
ParentalLPSEKAMVQQLLQKKVPVKEIKINPEKLIDVQKKLESILAQDQDLKERAQRCFVSYVRSVYLMKDKEVFD
L.SEKA.VQQLLQKKVP.KEIKINPEKLID.QKKLES..A.DQDLKERAQRCF.S....VYLMKDKEVFD
RetrocopyLASEKAIVQQLLQKKVPIKEIKINPEKLIDIQKKLESFSAEDQDLKERAQRCFISDI*LVYLMKDKEVFD
ParentalVSKLPIPEYALSLGLAVAPRVRFLQKMQKQPTKELVRSQADKVIEPRAPSLTNDEVEEFRAYFNEKMSIL
VSKLPIPEYALSLGLAVAP..RFLQKMQKQPTKELV.SQA.KV.EPRAPSLTND.VEEFRA.FNEKMSIL
RetrocopyVSKLPIPEYALSLGLAVAPCIRFLQKMQKQPTKELVMSQANKVTEPRAPSLTNDKVEEFRAFFNEKMSIL
ParentalQKGGKRLEGTEHRQDNDTGNEEQEEEEDDEEEMEEKLAKAKGSQAPSLPNTSEAQKIKEVPTQFLDRDEE
QKGGKRL.GTEHR..NDT..EEQEEEED.EEEMEEKLAKAKGSQAPSLPNTSEA.KIKEVP.QFLDRDEE
RetrocopyQKGGKRLKGTEHRLANDTSDEEQEEEEDNEEEMEEKLAKAKGSQAPSLPNTSEAKKIKEVPMQFLDRDEE
ParentalEEDADFLKVKRHNVFGLDLKDEKTLQKKEPSKSSIKKKMTKVAEAKKVMKRNFKVNKKITFTDEGELVQQ
EEDADFLKVK.HNVFG.D.K.EKTLQKKEPSKSSIKKK.TKVAEAKKVMKRNFK.NKKIT.TDEGELVQQ
RetrocopyEEDADFLKVKWHNVFGFDFKEEKTLQKKEPSKSSIKKKVTKVAEAKKVMKRNFKANKKITCTDEGELVQQ
ParentalWPQMQKSAIKDAEEDDDTGGINLHKAKERLQEEDKFDKEEYRKKIKAKHREKRLKEREARREANKRQAKA
WPQMQKSAIKDAEEDDDTGGINL.KAK.RLQ.EDKFDKEEYRKKIKAKH.EKRLKEREARREAN.RQAKA
RetrocopyWPQMQKSAIKDAEEDDDTGGINLDKAKGRLQKEDKFDKEEYRKKIKAKHWEKRLKEREARREANTRQAKA
ParentalKDEEEAFLDWSDDDDDDDDGFDPSTLPDPDKYRSSEDSDSEDMENKI-SDTKKKQGMKKRSNSEVEDVGP
KDEEE.FLDWSDDDDD...GFDPSTL.DPDKYRSSEDSDSEDMENK.....KK.QGMKKR.NSEVEDVGP
RetrocopyKDEEEDFLDWSDDDDD---GFDPSTLLDPDKYRSSEDSDSEDMENKM>DTKKK-QGMKKRKNSEVEDVGP
ParentalTSHNRKKARWDTLEPLDTGLSLAEDEELVLHLLRS
TSHNRKKA.WDTLEPLDTGLSLAEDEELVLHLLRS
RetrocopyTSHNRKKATWDTLEPLDTGLSLAEDEELVLHLLRS

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 20 .10 RPM
bodymap2_adrenal 0 .00 RPM 26 .22 RPM
bodymap2_brain 0 .00 RPM 20 .44 RPM
bodymap2_breast 0 .02 RPM 16 .15 RPM
bodymap2_colon 0 .00 RPM 27 .50 RPM
bodymap2_heart 0 .00 RPM 9 .18 RPM
bodymap2_kidney 0 .00 RPM 22 .67 RPM
bodymap2_liver 0 .00 RPM 12 .36 RPM
bodymap2_lung 0 .00 RPM 17 .44 RPM
bodymap2_lymph_node 0 .00 RPM 18 .86 RPM
bodymap2_ovary 0 .02 RPM 41 .37 RPM
bodymap2_prostate 0 .00 RPM 28 .92 RPM
bodymap2_skeletal_muscle 0 .00 RPM 15 .99 RPM
bodymap2_testis 0 .00 RPM 63 .46 RPM
bodymap2_thyroid 0 .00 RPM 29 .32 RPM
bodymap2_white_blood_cells 0 .00 RPM 19 .16 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4278 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4278 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4278 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4278 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4278 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2901
Gorilla gorilla retro_ggor_2862
Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000178105 1 retrocopy
retro_hsap_4278 ,
Gorilla gorilla ENSGGOG000000002711 retrocopy
retro_ggor_2862,
Pongo abelii ENSPPYG000000038491 retrocopy
retro_pabe_3489,
Pan troglodytes ENSPTRG000000042561 retrocopy
retro_ptro_2901,

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 = 0.07 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .04 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .05 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .03 RPM
FIN_HG00277 0 .04 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 .02 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 .02 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .07 RPM
TSI_NA20538 0 .05 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .03 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .03 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 .02 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).



Copyright © RetrogeneDB 2014-2017