RetrogeneDB ID:

retro_hsap_2401

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:2:234774782..234776003(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000224287
Aliases:MSL3P1, MSL3L2
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:MSL3
Ensembl ID:ENSG00000005302
Aliases:MSL3, MSL3L1
Description:male-specific lethal 3 homolog (Drosophila) [Source:HGNC Symbol;Acc:7370]


Retrocopy-Parental alignment summary:






>retro_hsap_2401
TTAAAAGGCCTCTCCATCGAAGAAAAAAATGAAAATGATGAAAACTCATTAAGCAGTTCCTCTGACAGTAGTGAAGACAA
GGATGAAAAAATAAGTGAAGAATGTGATATTGAAGAAAAGACTGAAGTGAAAGAAGAACCGGAGCTTCAAACAAAAAGGG
AAATGGAAGAAAGAACAGTAACTCTAGAAATCCCTGAAGTTCTGAAGAGGCAGCTGGAGGATGATTGTTACTACATTAAT
CGGAGGAAACGGTTAGTGCAACTTCCATGCCACACCAACATCATAACGATTTTGGAATCCTATGTGAAGCATTTTGCTAT
CAGTGCAGCCTTTTCAGCCAATGAGAGGCCTCGTCACCATCACGCTATGCCACATGCCAGCATGAACGTGCCTTATATCC
CAGCAGAAAAGAATATTGACCTTTGTAAGGAGATGGTGGATGGATTAAGAATAACCTTTGATTACACTCTCCCGTTGGTT
TTACTCTATCCCTATGAACAAGCTCAGTATAAAAAGGTGACTGCATCTAAGGTTTTTCTTGCAATTAAGGAAAGTGCCAC
AAATACTAATAGGAGCCAGGAGAAGCTCTCTCCCAGCTTACGTTTGTTGAATCCATCCAGGCCGCAGTCTACAGAGAGTC
AGTCGACCAGCGGTGAACCAGCCACCCCTAAAAGGCGCAAAGCCGAGCCGCAAGCAGTGCAGTCTCTGAGGCGGTCCTCG
CCCCACACCGCCAACTGTGACAGGCTTTCTAAGAGCAGCACCTCACCTCAGCCCAAGCGCTGGCAGCAGGACATGTCCAC
CAGTGTGCCCAAGCTGTTCCTGCACCTGGAAAAGAAGACACCTGTGCATAGCAGATCATCTTCACCTACTCTGACTCCTA
GCCAGGAAGGGAGTCCTGTGTTTGCTGGCTTTGAAGGGAGAAGAACTAATGAAATAAATGAGGTCCTCTCCTGGAAGCTC
GTACCTGACAATTACCCACCAGGTGACCAGCCACCTCCACCCTCTTACATTTACGGGGCGCAACATTTGCTGCGATTGTT
TGTCAAACTTCCAGAAATTCTTGGAAAAATGTCCTTTACTGAGAAGAATCTGAAGGCTTTATTGAAGCACTTTGATCTCT
TTGTGAGGTTTTTAGCAGAATACCACGATGACTTCTTCCCAGAGTCAGCTTACGTCGCTGCCTCTGAGGTGCATTACAGC
ACCAGGAACCCCCAGGCAGTC

ORF - retro_hsap_2401 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.75 %
Parental protein coverage: 80.16 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalLKGLPTEEKDENDENSLSSSSDCSENKDEEISEESDIEEKTEVKEEPELQTRREMEERTITIEIPEVLKK
LKGL..EEK.ENDENSLSSSSD.SE.KDE.ISEE.DIEEKTEVKEEPELQT.REMEERT.T.EIPEVLK.
RetrocopyLKGLSIEEKNENDENSLSSSSDSSEDKDEKISEECDIEEKTEVKEEPELQTKREMEERTVTLEIPEVLKR
ParentalQLEDDCYYINRRKRLVKLPCQTNIITILESYVKHFAINAAFSANERPRHHHVMPHANMNVHYIPAEKNVD
QLEDDCYYINRRKRLV.LPC.TNIITILESYVKHFAI.AAFSANERPRHHH.MPHA.MNV.YIPAEKN.D
RetrocopyQLEDDCYYINRRKRLVQLPCHTNIITILESYVKHFAISAAFSANERPRHHHAMPHASMNVPYIPAEKNID
ParentalLCKEMVDGLRITFDYTLPLVLLYPYEQAQYKKVTSSKFFLPIKESATSTNRSQEELSPSPPLLNPSTPQS
LCKEMVDGLRITFDYTLPLVLLYPYEQAQYKKVT.SK.FL.IKESAT.TNRSQE.LSPS..LLNPS.PQS
RetrocopyLCKEMVDGLRITFDYTLPLVLLYPYEQAQYKKVTASKVFLAIKESATNTNRSQEKLSPSLRLLNPSRPQS
ParentalTESQPTTGEPATPKRRKAEPEALQSLRRSTRHSANCDRLSESSASPQPKRRQQDTSASMPKLFLHLEKKT
TESQ.T.GEPATPKRRKAEP.A.QSLRRS..H.ANCDRLS.SS.SPQPKR.QQD.S.S.PKLFLHLEKKT
RetrocopyTESQSTSGEPATPKRRKAEPQAVQSLRRSSPHTANCDRLSKSSTSPQPKRWQQDMSTSVPKLFLHLEKKT
ParentalPVHSRSSSPIPLTPSKEGSAVFAGFEGRRTNEINEVLSWKLVPDNYPPGDQPPPPSYIYGAQHLLRLFVK
PVHSRSSSP..LTPS.EGS.VFAGFEGRRTNEINEVLSWKLVPDNYPPGDQPPPPSYIYGAQHLLRLFVK
RetrocopyPVHSRSSSP-TLTPSQEGSPVFAGFEGRRTNEINEVLSWKLVPDNYPPGDQPPPPSYIYGAQHLLRLFVK
ParentalLPEILGKMSFSEKNLKALLKHFDLFLRFLAEYHDDFFPESAYVAACEAHYSTKNPRAI
LPEILGKMSF.EKNLKALLKHFDLF.RFLAEYHDDFFPESAYVAA.E.HYST.NP.A.
RetrocopyLPEILGKMSFTEKNLKALLKHFDLFVRFLAEYHDDFFPESAYVAASEVHYSTRNPQAV

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 .44 RPM 20 .45 RPM
bodymap2_adrenal 0 .45 RPM 52 .24 RPM
bodymap2_brain 0 .54 RPM 23 .56 RPM
bodymap2_breast 1 .87 RPM 26 .30 RPM
bodymap2_colon 0 .39 RPM 27 .57 RPM
bodymap2_heart 0 .48 RPM 13 .83 RPM
bodymap2_kidney 1 .03 RPM 21 .88 RPM
bodymap2_liver 1 .42 RPM 9 .89 RPM
bodymap2_lung 0 .60 RPM 24 .05 RPM
bodymap2_lymph_node 0 .24 RPM 83 .35 RPM
bodymap2_ovary 0 .64 RPM 26 .51 RPM
bodymap2_prostate 2 .77 RPM 23 .61 RPM
bodymap2_skeletal_muscle 0 .11 RPM 28 .43 RPM
bodymap2_testis 24 .43 RPM 52 .92 RPM
bodymap2_thyroid 0 .96 RPM 25 .10 RPM
bodymap2_white_blood_cells 1 .52 RPM 83 .73 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_2401 in 36 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF002CFW POLR2A 2:234776792..234777168
ENCFF002CFX POLR2A 2:234776803..234777165
ENCFF002CHO POLR2A 2:234776750..234777173
ENCFF002CIH POLR2A 2:234776840..234776995
ENCFF002CJE POLR2A 2:234776840..234777147
ENCFF002CJZ POLR2A 2:234776808..234777152
ENCFF002CLM POLR2A 2:234776695..234777235
ENCFF002CMI POLR2A 2:234776796..234777188
ENCFF002COJ POLR2A 2:234776763..234777199
ENCFF002CPG POLR2A 2:234776722..234777212
ENCFF002CQA POLR2A 2:234776842..234777064
ENCFF002CQC POLR2A 2:234776761..234777241
ENCFF002CQE POLR2A 2:234776923..234777074
ENCFF002CQG POLR2A 2:234776866..234777030
ENCFF002CQI POLR2A 2:234776762..234777198
ENCFF002CQK POLR2A 2:234776812..234777159
ENCFF002CQM POLR2A 2:234776887..234777132
ENCFF002CQO POLR2A 2:234776796..234777153
ENCFF002CRK POLR2A 2:234776656..234777180
ENCFF002CSY POLR2A 2:234776755..234777155
ENCFF002CXM POLR2A 2:234776709..234777199
ENCFF002CXN POLR2A 2:234776699..234777195
ENCFF002CXO POLR2A 2:234776779..234777203
ENCFF002CXP POLR2A 2:234776745..234777225
ENCFF002CXR POLR2A 2:234776903..234777080
ENCFF002CZC POLR2A 2:234776919..234777077
ENCFF002CZD POLR2A 2:234776744..234777254
ENCFF002CZW POLR2A 2:234776567..234777317
ENCFF002DAE POLR2A 2:234776837..234777147
ENCFF002DAV POLR2A 2:234776673..234777217
ENCFF002DBB POLR2A 2:234776907..234777107
ENCFF002DBE POLR2A 2:234776893..234777041
ENCFF002DBO POLR2A 2:234776833..234777092
ENCFF002DBP POLR2A 2:234776883..234777093
ENCFF002DBQ POLR2A 2:234776780..234777150
ENCFF002DBT POLR2A 2:234776798..234777168

EST - click to see more details

2 EST(s) were mapped to retro_hsap_2401 retrocopy
EST ID Start End Identity Match Mis-match Score
CB119809 234775400 234775714 99.7 313 1 312
CR740463 234774749 234775220 99 469 2 466

TSS - click to see more details

No TSS is located nearby retro_hsap_2401 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2401 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2401 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1751
Gorilla gorilla retro_ggor_1820
Pongo abelii retro_pabe_2166
Parental genes homology:
Parental genes homology involve 12 parental genes, and 24 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000092781 retrocopy
retro_btau_883,
Callithrix jacchus ENSCJAG000000010611 retrocopy
retro_cjac_1490,
Cavia porcellus ENSCPOG000000046925 retrocopies
retro_cpor_1423, retro_cpor_1424, retro_cpor_1425, retro_cpor_1426, retro_cpor_95,
Homo sapiens ENSG00000005302 2 retrocopies
retro_hsap_2401 , retro_hsap_4097,
Gorilla gorilla ENSGGOG000000065822 retrocopies
retro_ggor_1820, retro_ggor_2749,
Macaca mulatta ENSMMUG000000026892 retrocopies
retro_mmul_2362, retro_mmul_972,
Monodelphis domestica ENSMODG000000173501 retrocopy
retro_mdom_1422,
Pongo abelii ENSPPYG000000201232 retrocopies
retro_pabe_2166, retro_pabe_3353,
Pan troglodytes ENSPTRG000000216622 retrocopies
retro_ptro_1751, retro_ptro_2778,
Pteropus vampyrus ENSPVAG000000050001 retrocopy
retro_pvam_203,
Sorex araneus ENSSARG000000084771 retrocopy
retro_sara_139,
Tarsius syrichta ENSTSYG000000127884 retrocopies
retro_tsyr_1079, retro_tsyr_1649, retro_tsyr_1706, retro_tsyr_948,

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 = 6.36 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .11 RPM
CEU_NA11843 2 .30 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 4 .48 RPM
CEU_NA12400 2 .67 RPM
CEU_NA12751 3 .79 RPM
CEU_NA12760 2 .78 RPM
CEU_NA12827 5 .57 RPM
CEU_NA12872 4 .16 RPM
CEU_NA12873 0 .10 RPM
FIN_HG00183 4 .91 RPM
FIN_HG00277 3 .22 RPM
FIN_HG00315 4 .44 RPM
FIN_HG00321 6 .05 RPM
FIN_HG00328 2 .06 RPM
FIN_HG00338 5 .41 RPM
FIN_HG00349 3 .81 RPM
FIN_HG00375 4 .03 RPM
FIN_HG00377 3 .28 RPM
FIN_HG00378 3 .44 RPM
GBR_HG00099 3 .28 RPM
GBR_HG00111 2 .67 RPM
GBR_HG00114 3 .34 RPM
GBR_HG00119 5 .20 RPM
GBR_HG00131 4 .63 RPM
GBR_HG00133 3 .64 RPM
GBR_HG00134 4 .28 RPM
GBR_HG00137 2 .91 RPM
GBR_HG00142 6 .36 RPM
GBR_HG00143 4 .91 RPM
TSI_NA20512 3 .08 RPM
TSI_NA20513 3 .75 RPM
TSI_NA20518 5 .80 RPM
TSI_NA20532 3 .67 RPM
TSI_NA20538 4 .56 RPM
TSI_NA20756 3 .70 RPM
TSI_NA20765 2 .55 RPM
TSI_NA20771 3 .97 RPM
TSI_NA20786 0 .03 RPM
TSI_NA20798 4 .43 RPM
YRI_NA18870 4 .77 RPM
YRI_NA18907 2 .22 RPM
YRI_NA18916 4 .46 RPM
YRI_NA19093 4 .32 RPM
YRI_NA19099 4 .18 RPM
YRI_NA19114 3 .33 RPM
YRI_NA19118 4 .25 RPM
YRI_NA19213 4 .74 RPM
YRI_NA19214 5 .21 RPM
YRI_NA19223 5 .75 RPM

Indel association:

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





Copyright © RetrogeneDB 2014-2017