RetrogeneDB ID:

retro_hsap_4898

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:X:124460748..124461870(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000213489
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:FBLIM1
Ensembl ID:ENSG00000162458
Aliases:FBLIM1, CAL, FBLP-1, FBLP1
Description:filamin binding LIM protein 1 [Source:HGNC Symbol;Acc:24686]


Retrocopy-Parental alignment summary:






>retro_hsap_4898
ATGGCCTCAAAGCCTGAGAAGAGTGTGGCATCGTCTGTCTTTATCACCCTTGCACCCCTGTGCCACGATTTAGCTGTGGT
TGAGGAAGGGGGCAGGCGGTTTGTGAGGCCTGATGTGGCCTCCCCTGGGAGGCTCCTGCCCCCATGAAGGCACCCGGAGC
TGGCTTAGCGGGAAAGCCCAGCCCCTGGGCACCCCCTGGCAGGGCTGCAGCCACAGTGCCAGCTGCACCTCTGCAGCTCT
CCAATGGAGGATGCTCACCCCCTCCTCCTGTCCTGGATGGTGAGGACGCACTTCCTGACCTGGACCTCGTCCCACCCCCT
CCACTGCCCCCTCCGGTGCTCCTGTCTTCTGAAGAAGAGGCTCCTGCTCCAATGGGGGCCTCACTCATTGCAGACTTAGA
GCGGTTGCACCTGCCCTCGCCCCCACCCCGACCACAGGCCCCAGTGGAGGGACCTTCAGTCCAGCCTGGGCCCAGTCCCC
TCGGGCCTGGGGAGGAAGAGCTTCCGCCTTCCCCAGCAGAGCCTGTTGAGAGAGAGTCGTCCACAGACATCTGTGCCTTC
TGCCACAAAACCGTGTCCCCCGCAAGAGCTGGCTGTGGAGGCCATAAAGAGGCAGTACCATGCCCAGTGCTTCACGTGGC
ACACCTGCCACCGCCAGCTAGCTGGGCAGAGCTTCTACCAGGATGGGCGACCCCTCTGCAAACCCTGCTACCAGGACACA
CTGGAGAAGTGCGGCAAGTGTGGCCAGGTGGTCCGGGAGCACATCATCAGGGCCCTGGGCCAGGCCTTCCACCCCTCCTG
CTTCATGTGTGTGACCTGTGCCCGGTGCATCCAGGATGAGAGCTCTGCCCTGGGCAGCCAAAACGAGATGTACTGCCTAG
ACGAATTCTACAAGAAATTTGCTCCCGTATGCAGCATCTGTGAGAATCCCATTATTCCTCGGGATGGGAAAGATGCCTTC
AAAATCAAGTGCATGGGAAGAAACTTCCATGTAAATTGCTACAGGTGTGAGGACTGCAGGATCCTCCTGTCTGTGGAGCC
CAGGAACCAAGGCTGCTACCCCCTGGACAACCATCTCTTCTGCAAGCAGTGCCACGTGAAGCAGAGTGCTGCTGGGTGCT
GC

ORF - retro_hsap_4898 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.82 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMASKPEKRVASSVFITLAPPRRDVAVAEEVR-QAVCEARRGRPWEAPAPMKTPEAGLAGRPSPWTTPGRA
MASKPEK.VASSVFITLAP...D.AV.EE...QAVCEA..G.PWEAPAPMK.P.AGLAG.PSPW..PGRA
RetrocopyMASKPEKSVASSVFITLAPLCHDLAVVEEGG<QAVCEA*CGLPWEAPAPMKAPGAGLAGKPSPWAPPGRA
ParentalAATVPAAPMQLFNGGCPPPPPVLDGEDVLPDLDLLPPPPPPPPVLLPSEEEAPAPMGASLIADLEQLHLS
AATVPAAP.QL.NGGC.PPPPVLDGED.LPDLDL.PPPP.PPPVLL.SEEEAPAPMGASLIADLE.LHL.
RetrocopyAATVPAAPLQLSNGGCSPPPPVLDGEDALPDLDLVPPPPLPPPVLLSSEEEAPAPMGASLIADLERLHLP
ParentalPPPPPPQAPAEGPSVQPGP--LRPMEEELPPPPAEPVEKGASTDICAFCHKTVSP-RELAVEAMKRQYHA
.PPP.PQAP.EGPSVQPGP..L.P.EEELPP.PAEPVE...STDICAFCHKTVSP..ELAVEA.KRQYHA
RetrocopySPPPRPQAPVEGPSVQPGPSPLGPGEEELPPSPAEPVERESSTDICAFCHKTVSP>QELAVEAIKRQYHA
ParentalQCFTCRTCRRQLAGQSFYQKDGRPLCEPCYQDTLERCGKCGEVVRDHIIRALGQAFHPSCFTCVTCARCI
QCFT..TC.RQLAGQSFYQ.DGRPLC.PCYQDTLE.CGKCG.VVR.HIIRALGQAFHPSCF.CVTCARCI
RetrocopyQCFTWHTCHRQLAGQSFYQ-DGRPLCKPCYQDTLEKCGKCGQVVREHIIRALGQAFHPSCFMCVTCARCI
ParentalGDESFALGSQNEVYCLDDFYRKFAPVCSICENPIIPRDGKDAFKIECMGRNFHENCYRCEDCRILLSVEP
.DES.ALGSQNE.YCLD.FY.KFAPVCSICENPIIPRDGKDAFKI.CMGRNFH.NCYRCEDCRILLSVEP
RetrocopyQDESSALGSQNEMYCLDEFYKKFAPVCSICENPIIPRDGKDAFKIKCMGRNFHVNCYRCEDCRILLSVEP
ParentalTDQGCYPLNNHLFCKPCHVKRSAAGCC
..QGCYPL.NHLFCK.CHVK.SAAGCC
RetrocopyRNQGCYPLDNHLFCKQCHVKQSAAGCC

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 37 .23 RPM
bodymap2_adrenal 0 .00 RPM 132 .36 RPM
bodymap2_brain 0 .00 RPM 3 .94 RPM
bodymap2_breast 0 .00 RPM 19 .90 RPM
bodymap2_colon 0 .00 RPM 45 .92 RPM
bodymap2_heart 0 .00 RPM 44 .97 RPM
bodymap2_kidney 0 .00 RPM 38 .84 RPM
bodymap2_liver 0 .00 RPM 1 .61 RPM
bodymap2_lung 0 .00 RPM 64 .43 RPM
bodymap2_lymph_node 0 .00 RPM 89 .50 RPM
bodymap2_ovary 0 .00 RPM 106 .99 RPM
bodymap2_prostate 0 .00 RPM 56 .03 RPM
bodymap2_skeletal_muscle 0 .00 RPM 2 .53 RPM
bodymap2_testis 0 .00 RPM 124 .56 RPM
bodymap2_thyroid 0 .00 RPM 18 .91 RPM
bodymap2_white_blood_cells 0 .00 RPM 0 .10 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4898 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4898 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4898 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4898 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4898 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_3266
Gorilla gorilla retro_ggor_3058
Pongo abelii retro_pabe_3809
Macaca mulatta retro_mmul_2635
Parental genes homology:
Parental genes homology involve 7 parental genes, and 12 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000187251 retrocopy
retro_btau_1013,
Homo sapiens ENSG00000162458 2 retrocopies
retro_hsap_4898 , retro_hsap_778,
Gorilla gorilla ENSGGOG000000151902 retrocopies
retro_ggor_3058, retro_ggor_645,
Macaca mulatta ENSMMUG000000322432 retrocopies
retro_mmul_1095, retro_mmul_2635,
Pongo abelii ENSPPYG000000018372 retrocopies
retro_pabe_3809, retro_pabe_751,
Pan troglodytes ENSPTRG000000002082 retrocopies
retro_ptro_3266, retro_ptro_544,
Pteropus vampyrus ENSPVAG000000090001 retrocopy
retro_pvam_415,

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 ) 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 .00 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .00 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 .00 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 .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 .00 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 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .00 RPM

Indel association:

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



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