RetrogeneDB ID:

retro_hsap_2012

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:19:53982603..53983342(+)
Located in intron of:ENSG00000198346
Retrocopy
information
Ensembl ID:ENSG00000250731
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:TPM3
Ensembl ID:ENSG00000143549
Aliases:TPM3, CAPM1, CFTD, HEL-189, HEL-S-82p, NEM1, OK/SW-cl.5, TM-5, TM3, TM30, TM30nm, TM5, TPMsk3, TRK, hscp30
Description:tropomyosin 3 [Source:HGNC Symbol;Acc:12012]


Retrocopy-Parental alignment summary:






>retro_hsap_2012
ATGGCTGGGATCACCACCATCGAGGCAGTGAAGCGCAAGATCCAGGTTCTGCAGCTGCAGGCAGATGATGAGGAGTGAGC
TGAGCACCTCCAGTGAGAAGCTGAGAGAGAAAGGTGGGCCCGGGAACAGGCTGAGGCTGAAGTGGCCTCCGTGAACGGTA
GGATCCAGCTGGTTGAAGAGGAGCTGGACTGTGCTCAGGAGCGCCTGGCCACTGCCCTGCAAAAGCTGGAAGAAGCGGGA
AAAGCTGCTGATGAGAGTGAGAGAGATACAAAGGTTATTGAAATCTGGGCCTTAAAAGATGAAGAAGATGGAACTCCAGG
AAATCCAACTCAAAGAAGCTAAGCACATTGCAGATGAGGCAGATGGGAAGTATGAAGAGGTGGCTCGTAAGTTGGTGATC
ATTGAAAGAGACATGGAATGCACAGAAGAATGAGCTGAGCTGGCAGAGTCCCGTTGCTGAGAGATGGATGAGCAGATCAG
ACTGATGGACCAGAACCTGAAGTGTCTGAGTGCAGCTGAAGAAAAGTACCCTCAAAAAGAAGACAAATGTGAGGAAGAGA
TGAAGATTCTTACTGATAATCTCGAGGAGGCAGAGACCCATGCTGAGTTGGCTGAGAGATCAGTAGCCAAGCTGGAAAAG
ACAATTGATGACTTGGAAGATAAACTGAAATGCACCAAAGAGGAACACCTCTGTACACAAAGGATGCTGGACCAGACTCT
GCTTGACCTGAATGAGATG

ORF - retro_hsap_2012 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86. %
Parental protein coverage: 100. %
Number of stop codons detected: 4
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMAGITTIEAVKRKIQVLQQQADDAEERAERLQREVEGERRAREQAEAEVASLNRRIQLVEEELDRAQERL
MAGITTIEAVKRKIQVLQ.QADD.EE.AE.LQ.E.E.ER.AREQAEAEVAS.N.RIQLVEEELD.AQERL
RetrocopyMAGITTIEAVKRKIQVLQLQADD-EE*AEHLQ*EAERERWAREQAEAEVASVNGRIQLVEEELDCAQERL
ParentalATALQKLEEAEKAADESERGMKVIE-NRALK-DEEKMELQEIQLKEAKHIAEEADRKYEEVARKLVIIEG
ATALQKLEEA.KAADESER..KVIE.N..LK....KMELQEIQLKEAKHIA.EAD.KYEEVARKLVIIE.
RetrocopyATALQKLEEAGKAADESERDTKVIE<NLGLK<KMKKMELQEIQLKEAKHIADEADGKYEEVARKLVIIER
ParentalDLERTEERAELAESRCREMDEQIRLMDQNLKCLSAAEEKYSQKEDKYEEEIKILTDKLKEAETRAEFAER
D.E.TEE.AELAESRC.EMDEQIRLMDQNLKCLSAAEEKY.QKEDK.EEE.KILTD.L.EAET.AE.AER
RetrocopyDMECTEE*AELAESRC*EMDEQIRLMDQNLKCLSAAEEKYPQKEDKCEEEMKILTDNLEEAETHAELAER
ParentalSVAKLEKTIDDLEDKLKCTKEEHLCTQRMLDQTLLDLNEM
SVAKLEKTIDDLEDKLKCTKEEHLCTQRMLDQTLLDLNEM
RetrocopySVAKLEKTIDDLEDKLKCTKEEHLCTQRMLDQTLLDLNEM

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 .30 RPM 404 .93 RPM
bodymap2_adrenal 2 .64 RPM 369 .51 RPM
bodymap2_brain 0 .47 RPM 214 .17 RPM
bodymap2_breast 0 .56 RPM 275 .26 RPM
bodymap2_colon 0 .25 RPM 177 .60 RPM
bodymap2_heart 0 .07 RPM 174 .40 RPM
bodymap2_kidney 0 .19 RPM 210 .94 RPM
bodymap2_liver 0 .06 RPM 92 .56 RPM
bodymap2_lung 0 .00 RPM 466 .61 RPM
bodymap2_lymph_node 0 .15 RPM 264 .49 RPM
bodymap2_ovary 0 .50 RPM 156 .91 RPM
bodymap2_prostate 0 .07 RPM 137 .16 RPM
bodymap2_skeletal_muscle 0 .00 RPM 495 .87 RPM
bodymap2_testis 0 .40 RPM 238 .91 RPM
bodymap2_thyroid 1 .05 RPM 446 .09 RPM
bodymap2_white_blood_cells 0 .49 RPM 781 .04 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2012 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2012 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2012 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2012 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2012 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 14 parental genes, and 45 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000118772 retrocopies
retro_amel_1017, retro_amel_1212,
Bos taurus ENSBTAG000000332173 retrocopies
retro_btau_1166, retro_btau_210, retro_btau_933,
Canis familiaris ENSCAFG000000173114 retrocopies
retro_cfam_1278, retro_cfam_1678, retro_cfam_2089, retro_cfam_983,
Cavia porcellus ENSCPOG000000072791 retrocopy
retro_cpor_150,
Dasypus novemcinctus ENSDNOG000000191567 retrocopies
retro_dnov_1322, retro_dnov_1767, retro_dnov_329, retro_dnov_451, retro_dnov_848, retro_dnov_878, retro_dnov_944,
Equus caballus ENSECAG000000109421 retrocopy
retro_ecab_390,
Felis catus ENSFCAG000000125961 retrocopy
retro_fcat_1441,
Homo sapiens ENSG00000143549 9 retrocopies
retro_hsap_1482, retro_hsap_1639, retro_hsap_2001, retro_hsap_2011, retro_hsap_2012 , retro_hsap_2237, retro_hsap_2395, retro_hsap_3711, retro_hsap_3893,
Homo sapiens ENSG000001674602 retrocopies
retro_hsap_2623, retro_hsap_3969,
Myotis lucifugus ENSMLUG000000133311 retrocopy
retro_mluc_1038,
Macaca mulatta ENSMMUG0000001080510 retrocopies
retro_mmul_1019, retro_mmul_1240, retro_mmul_1384, retro_mmul_1385, retro_mmul_1703, retro_mmul_1829, retro_mmul_2128, retro_mmul_2354, retro_mmul_314, retro_mmul_880,
Mustela putorius furoENSMPUG000000078751 retrocopy
retro_mputfur_604,
Mus musculus ENSMUSG000000279401 retrocopy
retro_mmus_21,
Oryctolagus cuniculus ENSOCUG000000118212 retrocopies
retro_ocun_699, retro_ocun_8,

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 = 1.48 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .86 RPM
CEU_NA11843 0 .34 RPM
CEU_NA11930 1 .14 RPM
CEU_NA12004 0 .80 RPM
CEU_NA12400 0 .53 RPM
CEU_NA12751 0 .56 RPM
CEU_NA12760 0 .31 RPM
CEU_NA12827 0 .94 RPM
CEU_NA12872 1 .03 RPM
CEU_NA12873 0 .80 RPM
FIN_HG00183 0 .80 RPM
FIN_HG00277 1 .48 RPM
FIN_HG00315 0 .55 RPM
FIN_HG00321 0 .33 RPM
FIN_HG00328 1 .04 RPM
FIN_HG00338 0 .81 RPM
FIN_HG00349 1 .05 RPM
FIN_HG00375 0 .24 RPM
FIN_HG00377 0 .83 RPM
FIN_HG00378 0 .76 RPM
GBR_HG00099 0 .78 RPM
GBR_HG00111 0 .88 RPM
GBR_HG00114 1 .18 RPM
GBR_HG00119 1 .27 RPM
GBR_HG00131 1 .01 RPM
GBR_HG00133 1 .21 RPM
GBR_HG00134 0 .81 RPM
GBR_HG00137 0 .47 RPM
GBR_HG00142 0 .72 RPM
GBR_HG00143 0 .77 RPM
TSI_NA20512 0 .90 RPM
TSI_NA20513 0 .51 RPM
TSI_NA20518 0 .44 RPM
TSI_NA20532 0 .48 RPM
TSI_NA20538 0 .83 RPM
TSI_NA20756 0 .90 RPM
TSI_NA20765 1 .28 RPM
TSI_NA20771 0 .62 RPM
TSI_NA20786 0 .71 RPM
TSI_NA20798 1 .28 RPM
YRI_NA18870 0 .61 RPM
YRI_NA18907 0 .14 RPM
YRI_NA18916 0 .25 RPM
YRI_NA19093 0 .57 RPM
YRI_NA19099 1 .01 RPM
YRI_NA19114 0 .52 RPM
YRI_NA19118 0 .41 RPM
YRI_NA19213 0 .67 RPM
YRI_NA19214 0 .98 RPM
YRI_NA19223 0 .76 RPM

Indel association:

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





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