RetrogeneDB ID:

retro_hsap_3985

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:8:94861788..94862305(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000254387
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:MYL12B
Ensembl ID:ENSG00000118680
Aliases:MYL12B, MLC-B, MRLC2
Description:myosin, light chain 12B, regulatory [Source:HGNC Symbol;Acc:29827]


Retrocopy-Parental alignment summary:






>retro_hsap_3985
ATGTCAAGCAAAAGAGCAAACACCAAGACCACCAAGAAGTGCCCTCAGCACACGACATCCAATATGTTTGCTGTGTTTGA
TCAGTCACAGATTCAGGAGTTCAAAGAGGCCTTCAACATGATTGATCAGAACAGAGATGGTTTCATCGACAAGGAAGATT
TGCAGGATATGCTTGCTTCATCCGGGAAGAGTCCAACTGATTGGTATCTGGATGCCATGATGAATGAGGCTCCAGGCCCA
ATCAGTTTCACCGTGTTCCTCACCATGTTTGGTGAGAAGTTAAATGGCACAGATCCTGAAGATGTCATCAGACATGCTTT
TGCTTGCTTTGATGAAGAAGCAACTGGCACCATTCAGGAAGATTACCTGTGAGAGCTGCTGACAACCATGGGGGGATGGG
TTCATGGATGAGGAAGTGGATGAGCTGTATAGAGAAGATCCTATTGACAAAAAGGGAAATTTCAATTATATTGAGTTCAC
ATGCATCCTAAAACATGGAGCAAAAGACGAAGATGAC

ORF - retro_hsap_3985 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.86 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMSSKKAKTKTTKKRPQRATSNVFAMFDQSQIQEFKEAFNMIDQNRDGFIDKEDLHDMLASLGKNPTDAYL
MSSK.A.TKTTKK.PQ..TSN.FA.FDQSQIQEFKEAFNMIDQNRDGFIDKEDL.DMLAS.GK.PTD.YL
RetrocopyMSSKRANTKTTKKCPQHTTSNMFAVFDQSQIQEFKEAFNMIDQNRDGFIDKEDLQDMLASSGKSPTDWYL
ParentalDAMMNEAPGPINFTMFLTMFGEKLNGTDPEDVIRNAFACFDEEATGTIQEDYLRELLTTM-GDRFTDEEV
DAMMNEAPGPI.FT.FLTMFGEKLNGTDPEDVIR.AFACFDEEATGTIQEDYL.ELLTTM.GD.F.DEEV
RetrocopyDAMMNEAPGPISFTVFLTMFGEKLNGTDPEDVIRHAFACFDEEATGTIQEDYL*ELLTTM>GDGFMDEEV
ParentalDELYREAPIDKKGNFNYIEFTRILKHGAKDKDD
DELYRE.PIDKKGNFNYIEFT.ILKHGAKD.DD
RetrocopyDELYREDPIDKKGNFNYIEFTCILKHGAKDEDD

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 210 .77 RPM
bodymap2_adrenal 0 .00 RPM 316 .66 RPM
bodymap2_brain 0 .00 RPM 110 .24 RPM
bodymap2_breast 0 .00 RPM 231 .99 RPM
bodymap2_colon 0 .00 RPM 189 .86 RPM
bodymap2_heart 0 .04 RPM 107 .72 RPM
bodymap2_kidney 0 .00 RPM 376 .01 RPM
bodymap2_liver 0 .00 RPM 150 .36 RPM
bodymap2_lung 0 .09 RPM 444 .32 RPM
bodymap2_lymph_node 0 .00 RPM 198 .85 RPM
bodymap2_ovary 0 .29 RPM 235 .68 RPM
bodymap2_prostate 0 .00 RPM 213 .23 RPM
bodymap2_skeletal_muscle 0 .00 RPM 92 .61 RPM
bodymap2_testis 0 .00 RPM 234 .78 RPM
bodymap2_thyroid 0 .00 RPM 322 .07 RPM
bodymap2_white_blood_cells 0 .00 RPM 279 .67 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3985 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3985 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3985 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3985 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3985 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2705
Gorilla gorilla retro_ggor_2675
Parental genes homology:
Parental genes homology involve 19 parental genes, and 45 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000126651 retrocopy
retro_amel_1847,
Canis familiaris ENSCAFG000000321681 retrocopy
retro_cfam_1224,
Dasypus novemcinctus ENSDNOG000000070042 retrocopies
retro_dnov_463, retro_dnov_953,
Dipodomys ordii ENSDORG000000075621 retrocopy
retro_dord_531,
Erinaceus europaeus ENSEEUG000000069851 retrocopy
retro_eeur_311,
Felis catus ENSFCAG000000228711 retrocopy
retro_fcat_2019,
Homo sapiens ENSG000001013351 retrocopy
retro_hsap_956,
Homo sapiens ENSG00000118680 4 retrocopies
retro_hsap_1487, retro_hsap_3129, retro_hsap_3451, retro_hsap_3985 ,
Gorilla gorilla ENSGGOG000000040514 retrocopies
retro_ggor_1139, retro_ggor_1140, retro_ggor_2330, retro_ggor_2675,
Myotis lucifugus ENSMLUG000000051892 retrocopies
retro_mluc_706, retro_mluc_947,
Monodelphis domestica ENSMODG000000214641 retrocopy
retro_mdom_987,
Mustela putorius furoENSMPUG000000050111 retrocopy
retro_mputfur_294,
Mus musculus ENSMUSG000000348682 retrocopies
retro_mmus_1483, retro_mmus_1539,
Nomascus leucogenys ENSNLEG000000069073 retrocopies
retro_nleu_1709, retro_nleu_1906, retro_nleu_2250,
Otolemur garnettii ENSOGAG000000297772 retrocopies
retro_ogar_2409, retro_ogar_857,
Pongo abelii ENSPPYG000000090323 retrocopies
retro_pabe_1236, retro_pabe_2585, retro_pabe_3026,
Pan troglodytes ENSPTRG000000098364 retrocopies
retro_ptro_1006, retro_ptro_2118, retro_ptro_2340, retro_ptro_2705,
Rattus norvegicus ENSRNOG000000157332 retrocopies
retro_rnor_1614, retro_rnor_2718,
Tarsius syrichta ENSTSYG000000104189 retrocopies
retro_tsyr_1034, retro_tsyr_1265, retro_tsyr_1320, retro_tsyr_1464, retro_tsyr_1961, retro_tsyr_2054, retro_tsyr_277, retro_tsyr_391, retro_tsyr_751,

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 = 0.04 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .03 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .04 RPM
CEU_NA12751 0 .00 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 .00 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .03 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .02 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 .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 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .03 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 .02 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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