RetrogeneDB ID:

retro_hsap_2019

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:19:58556956..58558134(+)
Located in intron of:ENSG00000152467
Retrocopy
information
Ensembl ID:ENSG00000268660
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:LETM1
Ensembl ID:ENSG00000168924
Aliases:None
Description:leucine zipper-EF-hand containing transmembrane protein 1 [Source:HGNC Symbol;Acc:6556]


Retrocopy-Parental alignment summary:






>retro_hsap_2019
AGCTTCCTGCGCTTCCAGCTCACGATGCGGCTGCGCTCCATAAAGGCAGAGGACAAGCTGTTTGCTGAGGAAGGGGTGGA
CAGCCTGAACGTCAAGGAGCTGCAGGCGGCATGTCGGGCACGAGGCATGCGGGCCCTGGGCGTCAGGGAAAACCACCTGA
GGGGCCAGCTGAAGCAGTGGCTGGACCTGCACCTGCATCAGGAGATCCCCACATCGCTGCTCATCCTGTCCCGGACCATG
TAGCTCCCGGACACCCTCTTGCCAGCCGACCAGCTCAAGTCCACACTGCAGACTCTCCCAGAGATTGTGGCAAAGGAAGC
ACAGGTGAAAGTGGCCGAGGTGGAGGGCAAGCAGGTGGACAAGGCCAAGCTAGAGGCCACACTGCAGGAGAAGGCGACCA
TGCAGTAGGAGCACCGCGAGAAGGAGCTGCAGAAGCATTCGGAGGTGGCGAAGGATGTTGAACCCGAATGTGTGGAAGGC
GCTCCCCAAAGGCCAGGGGCCCAGCCCCAGCCAGAAGTGCCTGACACTGTCCTGCAGTCAGAGACCATGAAGGACACTGC
CCCCGTGCTAGAGGGCTTGAAGGAGGAAGAGATGACTAAGGAGGAGATCAGCATCCTCAGCAATGCCTGCTCTAAGCTGC
AGGAACAGAAGAAGTCACTCACCAGGAAGAAGGAGGAGCTGGAGCTGCTGAAGGAGGACATGCAGGACTACAGCGAGGAC
TTGCAGGAGCTCAAGAAGGAACTTTCAAAGACTGGTGAAGAAAAATACATGGAAGGATCTAAAGCCAGCAAGAGATTGAC
AAAAAGGGTGCAGCAGATAATCGGGCAGATCAACGGCTTGATCTCGCAGCTGGAGATGGACCAGTGGGCCAGCAAGCTGG
CCCCGGCCAAGGGCGTGCCCATGGGGGAGAACGTCATCAGTGTTGCCGAGCTCATCAACGCCATGAAGCAAGTCAAGCAC
ATTCCCAAAAGCAAGCTCACCAGCCTGGCCGCAGCACTGAATGAAAATAAGGATGGCAAGGTCAACGTCGACCACCTCAT
CAAGGTGATTGAGCTGGTGGACAAAGAAGATGTTCACGTCTCCACCAGTCAGGTGGCCGAGATTGTAGCAACACTGGAAA
AAGAGGAGAAAGGGTGGAGAAGGAGAAGGTGGAGAAGGAGGTTGCAGAGGTGAAGAGC

ORF - retro_hsap_2019 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.47 %
Parental protein coverage: 53.86 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalNFLRFQLTMRLRSIKADDKLIAEEGVDSLNVKELQAACRARGMRALGVTEDRLRGQLKQWLDLHLHQEIP
.FLRFQLTMRLRSIKA.DKL.AEEGVDSLNVKELQAACRARGMRALGV.E..LRGQLKQWLDLHLHQEIP
RetrocopySFLRFQLTMRLRSIKAEDKLFAEEGVDSLNVKELQAACRARGMRALGVRENHLRGQLKQWLDLHLHQEIP
ParentalTSLLILSRAMYLPDTLSPADQLKSTLQTLPEIVAKEAQVKVAEVEGEQVDNKAKLEATLQEEAAIQQEHR
TSLLILSR.M.LPDTL.PADQLKSTLQTLPEIVAKEAQVKVAEVEG.QVD.KAKLEATLQE.A..Q.EHR
RetrocopyTSLLILSRTM*LPDTLLPADQLKSTLQTLPEIVAKEAQVKVAEVEGKQVD-KAKLEATLQEKATMQ*EHR
ParentalEKELQKRSEVAKDFEPERVVAAPQRPGTEPQPEMPDTVLQSETLKDTAPVLEGLKEEEITKEEIDILSDA
EKELQK.SEVAKD.EPE.V..APQRPG..PQPE.PDTVLQSET.KDTAPVLEGLKEEE.TKEEI.ILS.A
RetrocopyEKELQKHSEVAKDVEPECVEGAPQRPGAQPQPEVPDTVLQSETMKDTAPVLEGLKEEEMTKEEISILSNA
ParentalCSKLQEQKKSLTKEKEELELLKEDVQDYSEDLQEIKKELSKTGEEKYVEESKASKRLTKRVQQMIGQIDG
CSKLQEQKKSLT..KEELELLKED.QDYSEDLQE.KKELSKTGEEKY.E.SKASKRLTKRVQQ.IGQI.G
RetrocopyCSKLQEQKKSLTRKKEELELLKEDMQDYSEDLQELKKELSKTGEEKYMEGSKASKRLTKRVQQIIGQING
ParentalLISQLEMDQQAGKLAPANGMPTGENVISVAELINAMKQVKHIPESKLTSLAAALDENKDGKVNIDDLVKV
LISQLEMDQ.A.KLAPA.G.P.GENVISVAELINAMKQVKHIP.SKLTSLAAAL.ENKDGKVN.D.L.KV
RetrocopyLISQLEMDQWASKLAPAKGVPMGENVISVAELINAMKQVKHIPKSKLTSLAAALNENKDGKVNVDHLIKV
ParentalIELVDKEDVHISTSQVAEIVATLEKEEK-VEEKEKAKEKAEKEVAEVKS
IELVDKEDVH.STSQVAEIVATLEKEEK...EKEK.....EKEVAEVKS
RetrocopyIELVDKEDVHVSTSQVAEIVATLEKEEK<RVEKEK----VEKEVAEVKS

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 52 .48 RPM
bodymap2_adrenal 0 .00 RPM 37 .46 RPM
bodymap2_brain 0 .35 RPM 31 .50 RPM
bodymap2_breast 0 .00 RPM 60 .74 RPM
bodymap2_colon 0 .00 RPM 17 .94 RPM
bodymap2_heart 0 .22 RPM 34 .43 RPM
bodymap2_kidney 0 .08 RPM 57 .33 RPM
bodymap2_liver 0 .00 RPM 27 .67 RPM
bodymap2_lung 0 .00 RPM 24 .53 RPM
bodymap2_lymph_node 0 .00 RPM 30 .30 RPM
bodymap2_ovary 0 .21 RPM 40 .02 RPM
bodymap2_prostate 0 .00 RPM 22 .22 RPM
bodymap2_skeletal_muscle 0 .00 RPM 36 .50 RPM
bodymap2_testis 1 .11 RPM 37 .73 RPM
bodymap2_thyroid 0 .02 RPM 43 .42 RPM
bodymap2_white_blood_cells 0 .00 RPM 33 .39 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2019 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2019 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2019 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2019 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2019 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pongo abelii retro_pabe_1655
Parental genes homology:
Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000018591 retrocopy
retro_cjac_1529,
Homo sapiens ENSG00000168924 1 retrocopy
retro_hsap_2019 ,
Gorilla gorilla ENSGGOG000000029232 retrocopies
retro_ggor_1158, retro_ggor_1159,
Nomascus leucogenys ENSNLEG000000000672 retrocopies
retro_nleu_1752, retro_nleu_2731,
Otolemur garnettii ENSOGAG000000148831 retrocopy
retro_ogar_20,
Pongo abelii ENSPPYG000000145331 retrocopy
retro_pabe_1655,
Ictidomys tridecemlineatus ENSSTOG000000141671 retrocopy
retro_itri_160,

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 = 0.06 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 .03 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .02 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 .02 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .06 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 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .04 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 .03 RPM
YRI_NA19114 0 .00 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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