RetrogeneDB ID:

retro_hsap_1030

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:12:76531204..76532392(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000257872
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RTN4IP1
Ensembl ID:ENSG00000130347
Aliases:None
Description:reticulon 4 interacting protein 1 [Source:HGNC Symbol;Acc:18647]


Retrocopy-Parental alignment summary:






>retro_hsap_1030
ATGGAATTTCTGAAGACTTGTGTACTTAGAAGAAATGCGTGTACTGTGGTTTGCTTCTGGAGAAGCAAAGTTGTCCAAAG
GCCTTCCATTAGAAGGATTAGTACTACCTCTCCAAGGAGCACTGTCATGCCTGCTTGGGTGATAGATAAGTATGGGAAGA
ATGAAGTGCTTCGATTGACTCAGAACGTGATGATACCTATCATACGCTAGCCAAATGAAGTCACTGTAAAAGTTCACCCT
GCCAGTGTAAATCCTATAGACGTCAATATGAGAAGTGGTTATGGAGCTACAGCTTTAAATATGAAGCGTAATCCTTTACA
CATGAAAATCAAAGGAGAAGAATTTCCTCTGACTCTGATTCGGGATGTCTCTGGAATGGTGATGGAATGTGGGCTGGATG
TGAAGTACTTCAAGCCTTGAGATAAGGTCTGGGCTGCAGTTCCTCCTTGGAAACAAGGCACTCTTTCAGAGTTTGTTGTA
GTCAGTGGAAATGAGGTCTCTCACAAACCCAAATCACTCACTCATATATCAAGCTGCCTCTTCGCCATATGTGGCTCTCA
CAGCCTCATCTGCCATAAACAAAGTTGGTGACCTGAATGACAAGAATTGCACAGGAAGACGTGTTCTAATCTTAGGCGCT
TCAAGCGGAGTTGGTAGTTTTGCTATACAGGTAATGAAAGCATGGGATGCTCGTGTGACAGCAATTTGCGCTCAAGATGC
CAGTGAGCTTATAAAGAAGCTTGGGGCAGATGATGTAATTGATTACAAATTTGGAAGTGTGGAAGAGCAGTTGAAATCCT
TAAAACCGTTTGATTTCATCCTTGGTAATGTTGGCGGATCCACTGAAACATGGGCTCAGATTTTCTCAAGAAATGGTCAG
GAGCCACCTATGTGACTTTGGTGAGTCCTTTCCTCCTGAACATGGACTGATTGGGCATAGCAGATGGCATGTTACAGGCA
GGAGTCACCATAGTCTCGAAGGCATTAAAGCATTTCTGGAAAGGAGTCCATTATCGCTGGGCGTTTTTTGTGGCCAGTGG
TCCACGTTTAGGTGACATTGCAGAACTGGTGGATGTGGGAAAAATTGGGCCAGTTATTGAACAAACCTTTCCTTTTTCTA
AAGTTCCAGAAGCCTTCCTTAAGGTGGAAAGAGGACACATATGAGGAAAGACTGTAATTAATGTTGTT

ORF - retro_hsap_1030 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.69 %
Parental protein coverage: 100. %
Number of stop codons detected: 4
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMEFLKTCVLRRNACTAVCFWRSKVVQKPSVRRISTTSPRSTVMPAWVIDKYGKNEVLRFTQNMMMPIIHY
MEFLKTCVLRRNACT.VCFWRSKVVQ.PS.RRISTTSPRSTVMPAWVIDKYGKNEVLR.TQN.M.PII..
RetrocopyMEFLKTCVLRRNACTVVCFWRSKVVQRPSIRRISTTSPRSTVMPAWVIDKYGKNEVLRLTQNVMIPIIR*
ParentalPNEVIVKVHAASVNPIDVNMRSGYGATALNMKRDPLHVKIKGEEFPLTLGRDVSGVVMECGLDVKYFKPG
PNEV.VKVH.ASVNPIDVNMRSGYGATALNMKR.PLH.KIKGEEFPLTL.RDVSG.VMECGLDVKYFKP.
RetrocopyPNEVTVKVHPASVNPIDVNMRSGYGATALNMKRNPLHMKIKGEEFPLTLIRDVSGMVMECGLDVKYFKP*
ParentalDEVWAAVPPWKQGTLSEFVVVSGNEVSHKPKSLTHT-QAASLPYVALTAWSAINKVGGLNDKNCTGKRVL
D.VWAAVPPWKQGTLSEFVVVSGNEVSHKPKSLTH..QAAS.PYVALTA.SAINKVG.LNDKNCTG.RVL
RetrocopyDKVWAAVPPWKQGTLSEFVVVSGNEVSHKPKSLTHI>QAASSPYVALTASSAINKVGDLNDKNCTGRRVL
ParentalILGASGGVGTFAIQVMKAWDAHVTAVCSQDASELVRKLGADDVIDYKSGSVEEQLKSLKPFDFILDNVGG
ILGAS.GVG.FAIQVMKAWDA.VTA.C.QDASEL..KLGADDVIDYK.GSVEEQLKSLKPFDFIL.NVGG
RetrocopyILGASSGVGSFAIQVMKAWDARVTAICAQDASELIKKLGADDVIDYKFGSVEEQLKSLKPFDFILGNVGG
ParentalSTETWA-PDFLKKWSGATYVTLVTPFLLNMDRLGIADGMLQTGVTVGSKALKHFWKGVHYRWAFFMASGP
STETWA..DFLKKWSGATYVTLV.PFLLNMD.LGIADGMLQ.GVT..SKALKHFWKGVHYRWAFF.ASGP
RetrocopySTETWA<SDFLKKWSGATYVTLVSPFLLNMD*LGIADGMLQAGVTIVSKALKHFWKGVHYRWAFFVASGP
ParentalCLDDIAELVDAGKIRPVIEQTFPFSKVPEAFLKVERGHARGKTVINVV
.L.DIAELVD.GKI.PVIEQTFPFSKVPEAFLKVERGH..GKTVINVV
RetrocopyRLGDIAELVDVGKIGPVIEQTFPFSKVPEAFLKVERGHI*GKTVINVV

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 2 .60 RPM
bodymap2_adrenal 0 .00 RPM 7 .72 RPM
bodymap2_brain 0 .00 RPM 9 .19 RPM
bodymap2_breast 0 .00 RPM 6 .54 RPM
bodymap2_colon 0 .00 RPM 2 .90 RPM
bodymap2_heart 0 .00 RPM 12 .66 RPM
bodymap2_kidney 0 .00 RPM 10 .86 RPM
bodymap2_liver 0 .00 RPM 7 .99 RPM
bodymap2_lung 0 .00 RPM 1 .74 RPM
bodymap2_lymph_node 0 .00 RPM 3 .23 RPM
bodymap2_ovary 0 .00 RPM 4 .51 RPM
bodymap2_prostate 0 .00 RPM 4 .50 RPM
bodymap2_skeletal_muscle 0 .00 RPM 2 .98 RPM
bodymap2_testis 0 .00 RPM 12 .20 RPM
bodymap2_thyroid 0 .00 RPM 10 .96 RPM
bodymap2_white_blood_cells 0 .00 RPM 6 .67 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1030 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1030 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1030 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1030 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1030 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_705
Gorilla gorilla retro_ggor_814
Pongo abelii retro_pabe_863
Parental genes homology:
Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000130347 1 retrocopy
retro_hsap_1030 ,
Gorilla gorilla ENSGGOG000000082541 retrocopy
retro_ggor_814,
Nomascus leucogenys ENSNLEG000000133491 retrocopy
retro_nleu_908,
Otolemur garnettii ENSOGAG000000127031 retrocopy
retro_ogar_590,
Pongo abelii ENSPPYG000000168821 retrocopy
retro_pabe_863,
Pan troglodytes ENSPTRG000000184611 retrocopy
retro_ptro_705,

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 = 0.08 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 .03 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .08 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 .03 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 .00 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .03 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .03 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .03 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .03 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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