RetrogeneDB ID:

retro_hsap_968

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:12:13154710..13155761(+)
Located in intron of:ENSG00000255621
Retrocopy
information
Ensembl ID:ENSG00000183935
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:HTR7
Ensembl ID:ENSG00000148680
Aliases:HTR7, 5-HT7
Description:5-hydroxytryptamine (serotonin) receptor 7, adenylate cyclase-coupled [Source:HGNC Symbol;Acc:5302]


Retrocopy-Parental alignment summary:






>retro_hsap_968
CTCTCTGCGATCGCGGGCAACTGCCTGGTGGTATCTCCGTGTGCTTCGTCAAGAAGCTCCGCCAGCCCTCCAACTACCTG
ATCGTGTCCATGGCGCTGGCCAACCTCTCGGTGGCCATGGCGGTCATGCCCTTCATCAGTGTCACCGACCTCATCGGGGG
CAAGTGGATCTTTGGACACTTTTTCTGTAACGTCTTCTCCATGAATGTCATGTGCTGCACGGCCTGGATCTTGACCTTGT
ACGTGATCAGCATCGACAGGTACCTTGGGATCATGAAGCCTCTCACGTACCCTATGAGGCAGAAGGGGAAATGCATGACG
AAGATGATTCTTTCTGTCTGCCTTCTTTCCGCCTTTGTCACTTTACCTACCATTTTTGGTCGGGCTCAGAATGTAAACGA
TGATAAGGTGTGCTTGGTCAGTCAAGACTTTGGCTACACGATTTACTCCACCGCAGTGGCATCCTAATCCCCATGTGCGT
CATGCTTTTCATGTACTAACAGATTTACAAGGCCGCCAGGAAAAGCGCGGCCTAACACAGGTTACCTGGCTTCCCTCGAG
TGGAGCCAGACAGCAGTAGTCACCCTGAATGGCACAGTGAAGTTCCAGGAGGTGGAAGAGTGTGCAAACCTTTCGAGACT
CCTCAAGCATGAAAGGAAAAAATATCTCCATCTTTAAGCGGAAACAGAAAGCAGCGACTACCTTGGGGATCATCGTCTGG
GCCTCCACCATGTGCTGGCCGCCCTTTTTCCTCCTGACAGCCAGACCCTTCTGTCTATGGCACTGCCTGCAGCTGCATCC
CACTGTGGGTGGAGAGGATATTTCCATGGCTGGGCTATGCAAACTCTCTCATTAACCCTTTTATTTATGCCTTCTTCAAC
TGGGACCTGAGGACCACCTATTGCAGCCGGCTCCAGTGCCAGTACCAGAATATCAACCAGACACTCTCAGCTGCAGGCAT
GCATGAAGCCCTGAAGCTTGCTGAGAGGCCAGAGAGACCTGAGTTTGTCCTACAAAACTCTGACTACTGTAGAAAAAAAA
GTCATGATTCA

ORF - retro_hsap_968 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.4 %
Parental protein coverage: 79.33 %
Number of stop codons detected: 2
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalLLTIAGNCLVV-ISVCFVKKLRQPSNYLIVSLALADLSVAVAVMPFVSVTDLIGGKWIFGHFFCNVFIAM
L..IAGNCLVV.ISVCFVKKLRQPSNYLIVS.ALA.LSVA.AVMPF.SVTDLIGGKWIFGHFFCNVF..M
RetrocopyLSAIAGNCLVV<ISVCFVKKLRQPSNYLIVSMALANLSVAMAVMPFISVTDLIGGKWIFGHFFCNVF-SM
ParentalDVMCCTASIMTLCVISIDRYLGITRPLTYPVRQNGKCMAKMILSVWLLSASITLPPLFGWAQNVNDDKVC
.VMCCTA.I.TL.VISIDRYLGI..PLTYP.RQ.GKCM.KMILSV.LLSA..TLP..FG.AQNVNDDKVC
RetrocopyNVMCCTAWILTLYVISIDRYLGIMKPLTYPMRQKGKCMTKMILSVCLLSAFVTLPTIFGRAQNVNDDKVC
ParentalLISQDFGYTIYSTAVA-FYIPMSVMLFMYYQIYKAARKSAAKHKFPGFPRVEPDS-VIALNGIVKLQKEV
L.SQDFGYTIYSTAVA...IPM.VMLFMY.QIYKAARKSAA.H..PGFPRVEPDS.V..LNG.VK.Q.EV
RetrocopyLVSQDFGYTIYSTAVA<ILIPMCVMLFMY*QIYKAARKSAA*HRLPGFPRVEPDS>VVTLNGTVKFQ-EV
ParentalEECANLSRLLKHERK-NISIFKREQKAATTLGIIVGAFTVCWLPFFLLSTARPF-ICGTSCSCIPLWVER
EECANLSRLLKHERK.NISIFKR.QKAATTLGIIV.A.T.CW.PFFLL.TARPF...GT.CSCIPLWVER
RetrocopyEECANLSRLLKHERK>NISIFKRKQKAATTLGIIVWASTMCWPPFFLL-TARPF>VYGTACSCIPLWVER
ParentalTFLWLGYANSLINPFIYAFFNRDLRTTYRSLLQCQYRNINRKLSAAGMHEALKLAERPERPEFVLQNADY
.F.WLGYANSLINPFIYAFFN.DLRTTY.S.LQCQY.NIN..LSAAGMHEALKLAERPERPEFVLQN.DY
RetrocopyIFPWLGYANSLINPFIYAFFNWDLRTTYCSRLQCQYQNINQTLSAAGMHEALKLAERPERPEFVLQNSDY
ParentalCRKKGHDS
C....HDS
RetrocopyCXXXXHDS

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 1 .97 RPM 0 .18 RPM
bodymap2_adrenal 2 .31 RPM 0 .66 RPM
bodymap2_brain 0 .59 RPM 2 .53 RPM
bodymap2_breast 0 .70 RPM 0 .35 RPM
bodymap2_colon 0 .19 RPM 0 .31 RPM
bodymap2_heart 0 .31 RPM 0 .26 RPM
bodymap2_kidney 0 .76 RPM 0 .27 RPM
bodymap2_liver 0 .85 RPM 0 .17 RPM
bodymap2_lung 0 .02 RPM 0 .26 RPM
bodymap2_lymph_node 0 .58 RPM 0 .35 RPM
bodymap2_ovary 1 .20 RPM 0 .48 RPM
bodymap2_prostate 0 .83 RPM 2 .11 RPM
bodymap2_skeletal_muscle 0 .00 RPM 0 .00 RPM
bodymap2_testis 0 .94 RPM 18 .23 RPM
bodymap2_thyroid 2 .69 RPM 0 .85 RPM
bodymap2_white_blood_cells 0 .33 RPM 0 .98 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_968 in 9 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF002CFW POLR2A 12:13154177..13154384
ENCFF002CFX POLR2A 12:13154073..13154407
ENCFF002CGN POLR2A 12:13154011..13154475
ENCFF002CLM POLR2A 12:13153195..13153735
ENCFF002CLM POLR2A 12:13153566..13154106
ENCFF002CRK POLR2A 12:13153194..13153718
ENCFF002CSY POLR2A 12:13153241..13153745
ENCFF002CZW POLR2A 12:13153115..13153865
ENCFF002DAV POLR2A 12:13153196..13153740
ENCFF002DBO POLR2A 12:13154091..13154475

EST - click to see more details

No EST(s) were mapped for retro_hsap_968 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_968 retrocopy 5' end.

Lab - click to see more details

retro_hsap_968 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_968 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000148680 1 retrocopy
retro_hsap_968 ,

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 = 0.18 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 .02 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 .18 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .06 RPM
FIN_HG00349 0 .06 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .03 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .06 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .06 RPM
GBR_HG00133 0 .07 RPM
GBR_HG00134 0 .04 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .02 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .03 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .06 RPM
TSI_NA20771 0 .03 RPM
TSI_NA20786 0 .03 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .03 RPM
YRI_NA18916 0 .04 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .03 RPM
YRI_NA19114 0 .03 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .02 RPM

Indel association:

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





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