RetrogeneDB ID:

retro_hsap_1859

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:17:66130651..66131745(-)
Located in intron of:ENSG00000267023
Retrocopy
information
Ensembl ID:ENSG00000267352
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SH3GL1
Ensembl ID:ENSG00000141985
Aliases:SH3GL1, CNSA1, EEN, SH3D2B, SH3P8
Description:SH3-domain GRB2-like 1 [Source:HGNC Symbol;Acc:10830]


Retrocopy-Parental alignment summary:






>retro_hsap_1859
ATGTCGGTTGCCGGGCTGAAGAAGCAGTTCTACAAGGCGAGCCAACTGGTCAGTGAGAAGGTCGGAGGGGCTGAGGGGAC
CAAGCTGGATGATGACTTCGAAGAGATGGAGAAGGTGGATGTCATCAGCAAGGCGGTGACGTAAGTACTGTCCAGGACCA
TCGAGTACCCGCAGCCCAACCCAGCCTCGCAGGCTAAACTGACCATGCTCAACACCGCGTGCAAGATCCGGGGCCAGGTG
AAGAACCCCGGCTACCTGCAGTCAGGGGGGCTCCTGGGCGAGTGCCTGATCCGCCATGGGAAGGAGCTGCGCGACGAGTC
CAACTTCAGCGATGCACTGCTGGATGCCGGCGAGCCCATGAAGCACCTGGCAGAGGTGAAGGACTCCCTGGACATAGAGG
TCAAGCATAACTTCATTGACCCCCTCCAGAACCTATGTGAGAAAGACCTGAAGGAGATCCAGCACCACCTGCAGAAGCTG
GAGGGCCGCCGCCTGGACTTTGACTAAAAGAAGCGGCAGGGCAAGATCCCCGAAGAGGAGCTGCACCAGGCGCTGGAGAA
GTTTGAGGAGTCCAAGGAGGTGGCAGAAACCAGCATGCACAACCTCCTGGAGACCGACATCCAGTAGGTGAGTCAACTCC
CGGCCTTGGCAGAGGCGCAGCTGGACTACCACCGGCAGGCCGTGCAGATCCTGGACCAGCTGGCCCAGAAGTTCAAGTGC
AGGATCCGGGAAGCTTCCTCACGACCCAGGCGGGAGTATAAGCCCAAGCCCCGGGAGTGCTTTGACCTCGGAAAGCCTGA
GCAGTCCAACCGGGGCTTCCCCTGCACCACAGTCCCCAAGATCGCAGCTTCGTCCTCTTTCCGATCTTACGACAAGTCCA
TCTGGACTCCTAGCAGGAGCATGCCGCCCCTAGACCAGCCGAGCTGCAAGGGCTGTATGACTTGGAGCCGGAGAAAGATA
GGGAGCTGGGCTTCCATGAGGGCGATGTCTTCATGCTGATCAACCAGATGAACGAGAACTGATACGAGGGCATGCTGGAC
GGCCAGTCGGGCTTCTTCCTGCTCAGCTATGTGGACGTGCTCGTGCCTCTGCCC

ORF - retro_hsap_1859 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.33 %
Parental protein coverage: 99.73 %
Number of stop codons detected: 4
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMSVAGLKKQFYKASQLVSEKVGGAEGTKLDDDFKEMEKKVDVTSKAVTEVLARTIEYLQPNPASRAKLTM
MSVAGLKKQFYKASQLVSEKVGGAEGTKLDDDF.EMEK.VDV.SKAVT.VL.RTIEY.QPNPAS.AKLTM
RetrocopyMSVAGLKKQFYKASQLVSEKVGGAEGTKLDDDFEEMEK-VDVISKAVT*VLSRTIEYPQPNPASQAKLTM
ParentalLNTVSKIRGQVKNPGYPQSEGLLGECMIRHGKELGGESNFGDALLDAGESMKRLAEVKDSLDIEVKQNFI
LNT..KIRGQVKNPGY.QS.GLLGEC.IRHGKEL..ESNF.DALLDAGE.MK.LAEVKDSLDIEVK.NFI
RetrocopyLNTACKIRGQVKNPGYLQSGGLLGECLIRHGKELRDESNFSDALLDAGEPMKHLAEVKDSLDIEVKHNFI
ParentalDPLQNLCEKDLKEIQHHLKKLEGRRLDFDYKKKRQGKIPDEELRQALEKFEESKEVAETSMHNLLETDIE
DPLQNLCEKDLKEIQHHL.KLEGRRLDFD.KK.RQGKIP.EEL.QALEKFEESKEVAETSMHNLLETDI.
RetrocopyDPLQNLCEKDLKEIQHHLQKLEGRRLDFD*KK-RQGKIPEEELHQALEKFEESKEVAETSMHNLLETDIQ
ParentalQVSQLSALVDAQLDYHRQAVQILDELAEKLKRRMREASSRPKREYKPKPREPFDLGEPEQSNGGFPCTTA
.VSQL.AL..AQLDYHRQAVQILD.LA.K.K.R.REASSRP.REYKPKPRE.FDLG.PEQSN.GFPCTT.
Retrocopy*VSQLPALAEAQLDYHRQAVQILDQLAQKFKCRIREASSRPRREYKPKPRECFDLGKPEQSNRGFPCTTV
ParentalPKIAASSSFRSSDKPIRTPSRSMPPLDQPSCK-ALYDFEPENDGELGFHEGDVITLTNQIDENWYEGMLD
PKIAASSSFRS.DK.I.TPSRSMPPLDQPSCK..LYD.EPE.D.ELGFHEGDV..L.NQ..EN.YEGMLD
RetrocopyPKIAASSSFRSYDKSIWTPSRSMPPLDQPSCK<GLYDLEPEKDRELGFHEGDVFMLINQMNEN*YEGMLD
ParentalGQSGFFPLSYVEVLVPLP
GQSGFF.LSYV.VLVPLP
RetrocopyGQSGFFLLSYVDVLVPLP

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 2 .03 RPM 61 .30 RPM
bodymap2_adrenal 5 .32 RPM 44 .54 RPM
bodymap2_brain 1 .69 RPM 14 .81 RPM
bodymap2_breast 3 .25 RPM 32 .30 RPM
bodymap2_colon 1 .70 RPM 39 .72 RPM
bodymap2_heart 0 .92 RPM 7 .38 RPM
bodymap2_kidney 3 .12 RPM 19 .61 RPM
bodymap2_liver 1 .39 RPM 12 .63 RPM
bodymap2_lung 2 .62 RPM 33 .98 RPM
bodymap2_lymph_node 5 .35 RPM 28 .95 RPM
bodymap2_ovary 3 .20 RPM 59 .89 RPM
bodymap2_prostate 1 .13 RPM 36 .20 RPM
bodymap2_skeletal_muscle 2 .04 RPM 12 .70 RPM
bodymap2_testis 1 .23 RPM 41 .36 RPM
bodymap2_thyroid 3 .13 RPM 31 .96 RPM
bodymap2_white_blood_cells 1 .36 RPM 20 .04 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_1859 in 1 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF002DBP POLR2A 17:66131427..66131757

EST - click to see more details

2 EST(s) were mapped to retro_hsap_1859 retrocopy
EST ID Start End Identity Match Mis-match Score
AA078809 66130923 66131376 97.8 445 5 438
CN272201 66130658 66130882 100 224 0 224

TSS - click to see more details

No TSS is located nearby retro_hsap_1859 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1859 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1859 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_2151
Pongo abelii retro_pabe_1516
Parental genes homology:
Parental genes homology involve 6 parental genes, and 16 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000141985 3 retrocopies
retro_hsap_1742, retro_hsap_1745, retro_hsap_1859 ,
Gorilla gorilla ENSGGOG000000081983 retrocopies
retro_ggor_2151, retro_ggor_2258, retro_ggor_675,
Macaca mulatta ENSMMUG000000002731 retrocopy
retro_mmul_1264,
Monodelphis domestica ENSMODG000000009311 retrocopy
retro_mdom_1530,
Nomascus leucogenys ENSNLEG000000031222 retrocopies
retro_nleu_2914, retro_nleu_3075,
Pongo abelii ENSPPYG000000094056 retrocopies
retro_pabe_1488, retro_pabe_1516, retro_pabe_1530, retro_pabe_1542, retro_pabe_1700, retro_pabe_3542,

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 = 1.1 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .09 RPM
CEU_NA11843 0 .63 RPM
CEU_NA11930 0 .20 RPM
CEU_NA12004 0 .11 RPM
CEU_NA12400 0 .28 RPM
CEU_NA12751 0 .39 RPM
CEU_NA12760 0 .49 RPM
CEU_NA12827 0 .61 RPM
CEU_NA12872 0 .24 RPM
CEU_NA12873 0 .06 RPM
FIN_HG00183 0 .22 RPM
FIN_HG00277 0 .11 RPM
FIN_HG00315 0 .17 RPM
FIN_HG00321 0 .24 RPM
FIN_HG00328 0 .28 RPM
FIN_HG00338 0 .19 RPM
FIN_HG00349 0 .06 RPM
FIN_HG00375 0 .27 RPM
FIN_HG00377 0 .05 RPM
FIN_HG00378 0 .59 RPM
GBR_HG00099 0 .20 RPM
GBR_HG00111 0 .47 RPM
GBR_HG00114 0 .16 RPM
GBR_HG00119 0 .14 RPM
GBR_HG00131 0 .49 RPM
GBR_HG00133 0 .55 RPM
GBR_HG00134 0 .33 RPM
GBR_HG00137 0 .30 RPM
GBR_HG00142 0 .31 RPM
GBR_HG00143 0 .13 RPM
TSI_NA20512 0 .17 RPM
TSI_NA20513 0 .02 RPM
TSI_NA20518 0 .17 RPM
TSI_NA20532 0 .34 RPM
TSI_NA20538 0 .14 RPM
TSI_NA20756 0 .06 RPM
TSI_NA20765 0 .12 RPM
TSI_NA20771 0 .20 RPM
TSI_NA20786 0 .16 RPM
TSI_NA20798 0 .31 RPM
YRI_NA18870 0 .44 RPM
YRI_NA18907 0 .35 RPM
YRI_NA18916 0 .11 RPM
YRI_NA19093 0 .18 RPM
YRI_NA19099 0 .03 RPM
YRI_NA19114 0 .18 RPM
YRI_NA19118 1 .10 RPM
YRI_NA19213 0 .12 RPM
YRI_NA19214 0 .15 RPM
YRI_NA19223 0 .52 RPM

Indel association:

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



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