RetrogeneDB ID:

retro_hsap_3153

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:5:25909611..25911337(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000251593
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:MSN
Ensembl ID:ENSG00000147065
Aliases:MSN, HEL70
Description:moesin [Source:HGNC Symbol;Acc:7373]


Retrocopy-Parental alignment summary:






>retro_hsap_3153
ATGCCCAAAACGATCAGTGTGCGTGTGACCACCATGGACGCAGAGCTGGAGTTTACCATCCAGCCCAACACCACCGGGAA
GCAGCTATTTGACCAGGTGGTGAAAACTATTGGCTTGAGGGAAGTTTGTTTCTTTGGTCTGCAGTACCAGGACACCAAAG
GTTTCTCCACCTGGCTGAAACTCAATTAAGAAGGTGACTGCCCAGGAAGTGCGGAAGGAAAGCCCCCTGCTCTTTAAGTT
CAGTGCCAAGTTCTACCCTGAGGATGTGTCCGACCGAGGAATTGATTCAGGACACCACTCAGCGTCTGTTCCTTCTGCAA
GTGAAAGAGGGCATTCTCAGTGATGATATTTACTGCCGGCCTGAGACTGCTGTGCTGCTGGCCTCCCATGCTGTCCAGTC
TAAGTATGGGAACTTCAGTAAGGAGGTGCATAAGTCTGGCTACCTGGCCGGAGACGAGTTGCTCCCACAGAGAGTCCTGG
AACAGCACAAACTCAGCAAGGACCAGTGGGAGGAGCGGATCCAGGTGTGGCATGAGGAACACCGTGGCATGCTCAGGGAG
GATGCTGTCCTGGAGTATCTGAAGATTGCTCAAGATCTGGAGATGTATGGTGTAAACTACTTCAGCATCAAGAAAAAGAA
AGGCTCAGAGCTGTGGCTGGGGGTGGATGCACTGGGTCTCAACATCTATGAGCAGCATGACAGACTAACTCCCAAGATAG
GCTTTCCTTGGAGTGAAATCAGGAGCATTTCTTTCAATGATAAGAACTTTGTCATCAAGCCCATTGACAAAAGAGCCCCG
GACTTTGTCTTCTATGCTCCCTGGCTGCAGATTAACAAGCGGATCTTGGCCTTGTGCATGGGGAACCGTGAACTATACAT
GCGCCGTCGCAAGCCTGACACCATTGAGGTGCAGCAGATGAAGGCACGGGCCCGGGAGGAGAAGCACCAGAAGCAGATGG
AGCGTGCTATGCTGGAAAATGAGAAGAAGCGTGAAATGGCAGAAAAGCAGAAAGAGAAGATTGAACGGGAGAAGGAGCTG
ATGGGGAGGCTGAAGCAGATCGAGGAACAGACTAAGAAGGCTCAGCAAGAACTGGAAGAACAGACCCGTAGGGCTCTGGA
ACTTGGGAAGGAACGGAAGCATGCCCAGAGCGAGGCTGAAAAGCTGGCCAAGGAGCTTCAAGAAGCTGAAGAGGCCAAGG
AAGTCTTGCTGCAGGCCTCCCGGGACCAGAAAAAGACTCAGGAATAGCTGGCCTTGGAAATGGCAGAGCTGACAGCTCAA
ATCTCTCAGCTGGAACTGGCCCGACAGAAGAAAGAGAGTGAGGCTATGGAGTGGCAGCAGAAGGCCCAGATGGTACAGGA
AGACTTGGAGAAGACCCGTGCTGAGCTGAAGACTGCCATGAGTACATCTCATGTGGCAGAGCCTGCTGAGAATGAGCAGG
ATGAGCAGGATGAGAATGGGGCAGAGGCTAGTGCTGACCTACGGGCTGATGCTATGGCCAAGGACCGCAGTGAGGAGGAA
TGTACCACTGAGGCAGAGAAGAATGAGCGTGTGCAGAAGCACCTGAAGGCCCTCACTTCGGAGCTGGCCAGTGCCCGAGA
TGAGTCCAAGAAGACTGCCAATGACATGATCCATGCTGAGAACATGTGACTGGGCCGAGATAAATACAAGACCCTGTGCC
AGATCGTCAGGGCAGCAACAAGCAGCACATTGACGAATTTGAGTCT

ORF - retro_hsap_3153 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 89.14 %
Parental protein coverage: 99.83 %
Number of stop codons detected: 2
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMPKTISVRVTTMDAELEFAIQPNTTGKQLFDQVVKTIGLREVWFFGLQYQDTKGFSTWLKLN-KKVTAQD
MPKTISVRVTTMDAELEF.IQPNTTGKQLFDQVVKTIGLREV.FFGLQYQDTKGFSTWLKLN.KKVTAQ.
RetrocopyMPKTISVRVTTMDAELEFTIQPNTTGKQLFDQVVKTIGLREVCFFGLQYQDTKGFSTWLKLN>KKVTAQE
ParentalVRKESPLLFKFRAKFYPEDVSE-ELIQDITQRLFFL-QVKEGILNDDIYCPPETAVLLASYAVQSKYGDF
VRKESPLLFKF.AKFYPEDVS..E.....T....FL.QVKEGIL.DDIYC.PETAVLLAS.AVQSKYG.F
RetrocopyVRKESPLLFKFSAKFYPEDVSD>EELIQDTTQRLFLLQVKEGILSDDIYCRPETAVLLASHAVQSKYGNF
ParentalNKEVHKSGYLAGDKLLPQRVLEQHKLNKDQWEERIQVWHEEHRGMLREDAVLEYLKIAQDLEMYGVNYFS
.KEVHKSGYLAGD.LLPQRVLEQHKL.KDQWEERIQVWHEEHRGMLREDAVLEYLKIAQDLEMYGVNYFS
RetrocopySKEVHKSGYLAGDELLPQRVLEQHKLSKDQWEERIQVWHEEHRGMLREDAVLEYLKIAQDLEMYGVNYFS
ParentalIKNKKGSELWLGVDALGLNIYEQNDRLTPKIGFPWSEIRNISFNDKKFVIKPIDKKAPDFVFYAPRLRIN
IK.KKGSELWLGVDALGLNIYEQ.DRLTPKIGFPWSEIR.ISFNDK.FVIKPIDK.APDFVFYAP.L.IN
RetrocopyIKKKKGSELWLGVDALGLNIYEQHDRLTPKIGFPWSEIRSISFNDKNFVIKPIDKRAPDFVFYAPWLQIN
ParentalKRILALCMGNHELYMRRRKPDTIEVQQMKAQAREEKHQKQMERAMLENEKKKREMAEKEKEKIEREKEEL
KRILALCMGN.ELYMRRRKPDTIEVQQMKA.AREEKHQKQMERAMLENE.KKREMAEK.KEKIEREK.EL
RetrocopyKRILALCMGNRELYMRRRKPDTIEVQQMKARAREEKHQKQMERAMLENE-KKREMAEKQKEKIEREK-EL
ParentalMERLKQIEEQTKKAQQELEEQTRRALELEQERKRAQSEAEKLAKERQEAEEAKEALLQASRDQKKTQEQL
M.RLKQIEEQTKKAQQELEEQTRRALEL..ERK.AQSEAEKLAKE.QEAEEAKE.LLQASRDQKKTQE.L
RetrocopyMGRLKQIEEQTKKAQQELEEQTRRALELGKERKHAQSEAEKLAKELQEAEEAKEVLLQASRDQKKTQE*L
ParentalALEMAELTARISQLEMARQKKESEAVEWQQKAQMVQEDLEKTRAELKTAMSTPHVAEPAENEQDEQDENG
ALEMAELTA.ISQLE.ARQKKESEA.EWQQKAQMVQEDLEKTRAELKTAMST.HVAEPAE........NG
RetrocopyALEMAELTAQISQLELARQKKESEAMEWQQKAQMVQEDLEKTRAELKTAMSTSHVAEPAEXXXXXXXXNG
ParentalAEASADLRADAMAKDRSEEERTTEAEKNERVQKHLKALTSELANARDESKKTANDMIHAENMRLGRDKYK
AEASADLRADAMAKDRSEEE.TTEAEKNERVQKHLKALTSELA.ARDESKKTANDMIHAENM.LGRDKYK
RetrocopyAEASADLRADAMAKDRSEEECTTEAEKNERVQKHLKALTSELASARDESKKTANDMIHAENM*LGRDKYK
ParentalTLRQI-RQGNTKQRIDEFES
TL.QI.RQG..KQ.IDEFES
RetrocopyTLCQI<RQGSNKQHIDEFES

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 .12 RPM 1021 .89 RPM
bodymap2_adrenal 0 .08 RPM 692 .03 RPM
bodymap2_brain 0 .02 RPM 137 .50 RPM
bodymap2_breast 0 .06 RPM 514 .56 RPM
bodymap2_colon 0 .04 RPM 497 .24 RPM
bodymap2_heart 0 .02 RPM 201 .08 RPM
bodymap2_kidney 0 .06 RPM 536 .62 RPM
bodymap2_liver 0 .00 RPM 104 .16 RPM
bodymap2_lung 0 .11 RPM 2347 .50 RPM
bodymap2_lymph_node 0 .04 RPM 604 .20 RPM
bodymap2_ovary 0 .04 RPM 382 .97 RPM
bodymap2_prostate 0 .03 RPM 410 .62 RPM
bodymap2_skeletal_muscle 0 .00 RPM 133 .43 RPM
bodymap2_testis 0 .00 RPM 298 .44 RPM
bodymap2_thyroid 0 .06 RPM 496 .66 RPM
bodymap2_white_blood_cells 0 .14 RPM 2206 .79 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3153 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3153 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3153 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3153 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3153 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2281
Gorilla gorilla retro_ggor_1359
Pongo abelii retro_pabe_2623
Parental genes homology:
Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG000001377101 retrocopy
retro_hsap_840,
Homo sapiens ENSG00000147065 1 retrocopy
retro_hsap_3153 ,
Gorilla gorilla ENSGGOG000000018231 retrocopy
retro_ggor_1359,
Macropus eugenii ENSMEUG000000152401 retrocopy
retro_meug_1267,
Oryctolagus cuniculus ENSOCUG000000001491 retrocopy
retro_ocun_1173,
Pongo abelii ENSPPYG000000204191 retrocopy
retro_pabe_2623,
Tursiops truncatus ENSTTRG000000029461 retrocopy
retro_ttru_173,

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 = 0.52 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .11 RPM
CEU_NA11843 0 .17 RPM
CEU_NA11930 0 .33 RPM
CEU_NA12004 0 .08 RPM
CEU_NA12400 0 .32 RPM
CEU_NA12751 0 .29 RPM
CEU_NA12760 0 .09 RPM
CEU_NA12827 0 .19 RPM
CEU_NA12872 0 .30 RPM
CEU_NA12873 0 .19 RPM
FIN_HG00183 0 .08 RPM
FIN_HG00277 0 .07 RPM
FIN_HG00315 0 .08 RPM
FIN_HG00321 0 .18 RPM
FIN_HG00328 0 .19 RPM
FIN_HG00338 0 .21 RPM
FIN_HG00349 0 .37 RPM
FIN_HG00375 0 .22 RPM
FIN_HG00377 0 .30 RPM
FIN_HG00378 0 .25 RPM
GBR_HG00099 0 .32 RPM
GBR_HG00111 0 .13 RPM
GBR_HG00114 0 .18 RPM
GBR_HG00119 0 .24 RPM
GBR_HG00131 0 .14 RPM
GBR_HG00133 0 .14 RPM
GBR_HG00134 0 .28 RPM
GBR_HG00137 0 .16 RPM
GBR_HG00142 0 .17 RPM
GBR_HG00143 0 .32 RPM
TSI_NA20512 0 .08 RPM
TSI_NA20513 0 .17 RPM
TSI_NA20518 0 .28 RPM
TSI_NA20532 0 .17 RPM
TSI_NA20538 0 .14 RPM
TSI_NA20756 0 .47 RPM
TSI_NA20765 0 .19 RPM
TSI_NA20771 0 .40 RPM
TSI_NA20786 0 .18 RPM
TSI_NA20798 0 .03 RPM
YRI_NA18870 0 .44 RPM
YRI_NA18907 0 .14 RPM
YRI_NA18916 0 .15 RPM
YRI_NA19093 0 .36 RPM
YRI_NA19099 0 .40 RPM
YRI_NA19114 0 .29 RPM
YRI_NA19118 0 .23 RPM
YRI_NA19213 0 .19 RPM
YRI_NA19214 0 .52 RPM
YRI_NA19223 0 .18 RPM

Indel association:

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





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