RetrogeneDB ID:

retro_hsap_4281

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:9:90759765..90760695(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RSRC1
Ensembl ID:ENSG00000174891
Aliases:RSRC1, SFRS21, SRrp53
Description:arginine/serine-rich coiled-coil 1 [Source:HGNC Symbol;Acc:24152]


Retrocopy-Parental alignment summary:






>retro_hsap_4281
CACTGTAGATGGTCCTCATCGAGGAGTTCTTCAGATAGTAGAATATACAGGTGAAAGAAAGAAGGAAGGAAATCAAGATC
AAAGTCAAAATCTTGGTCCAGAGATCTTCAGCCTTATTCGCATTCTTATGATAGAAGATGCAGGCATCAACCAAGGAGTA
GCTCTCATGGCTCTAGAAGGAAACTAACTCGAAGTCGTTCAAGGGATGGAGAGAAATCCTATGGAGTTAAGAGGTCTAGG
TCAAAAAGCAGAATAAGAAGATCTAGGTCAAGGCCTTGTCTGTGTTCTCACAGTCGGAGCAGTGAAAGGTCCAGCCACAG
AAGAATGCATAGTTGGTCTCGGGATAAAGAACAACGTAAAGTCAGAGATAAAGAGAAAAGGGGAAGGATTAAGGGAAGGA
CAAGGATTACATAACATCAAATCTGGAATCTGGAAACATCAAAGCTGGATTAAACCATCTGCCACCAGCTGAAGAGGCCA
AAGCCAGAATACAGCTGGTTCTTGAAGCTGCTGCAAAAGCTGATGAAGCATTGAAATCCAAAGAAAGAAATGAGGAAGAA
GCAAAGAGAAGAAAGGAGGAAGACCACGCCACCCTGGTAGAACAAGTGAAAAAAGTGAAAGAAATGGAAGCTGTTGAAAG
TGATTCCTTTGTTCAGCAGACATTCAGATCAATTAAGAAGTCAAAAAGTTAGTGGAATCTGGTGAAGCGAAACGTGCAAC
TTCAACATCAGGACCAACATTAGCAGGTGTTGATCCACCCAGTACTGAAAACGAAATACAACTGAGCAGCATCCCTACTT
CTATCAAATACCAAGATGACAATTCCCTGGCCCATCCAAATTTATTTATAGAGAAAGCTGGTGCTGAGCAAAAATGATTC
AGAGGCTAATTGCTCTCTGACAGGAAAGACTAATGGGCAGTCCTGTGGCC

ORF - retro_hsap_4281 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 74.84 %
Parental protein coverage: 94.31 %
Number of stop codons detected: 4
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalHRRRSSSSSSSDSRTYSRKKGGRKSRSKSRSWSRDLQPRSHSYDRRRRHRSSSSSSYGSRRKRSRSRSRG
H.R.SSS.SSSDSR.Y..KK.GRKSRSKS.SWSRDLQP.SHSYDRR.RH...SSS..GSRRK..RSRSR.
RetrocopyHCRWSSSRSSSDSRIYR*KKEGRKSRSKSKSWSRDLQPYSHSYDRRCRHQPRSSS-HGSRRKLTRSRSRD
ParentalRGKSYRVQRSRSKSRTRRSRSRPRLRSHSRSSERSSHRRTRSRSRDRERRKGRDKEK-REKEKDKGKDKE
..KSY.V.RSRSKSR.RRSRSRP.L.SHSRSSERSSHRR..S.SR...........K.REK.KD.GKDK.
RetrocopyGEKSYGVKRSRSKSRIRRSRSRPCLCSHSRSSERSSHRRMHSWSR--DKEQRKVRDK<REKGKD*GKDKD
ParentalLHNIKRGESGNIKAGLEHLPPAEQAKARLQLVLEAAAKADEALKAKERNEEEAKRRKEEDQATLVEQVKR
.......ESGNIKAGL.HLPPAE.AKAR.QLVLEAAAKADEALK.KERNEEEAKRRKEED.ATLVEQVK.
Retrocopy-YITSNLESGNIKAGLNHLPPAEEAKARIQLVLEAAAKADEALKSKERNEEEAKRRKEEDHATLVEQVKK
ParentalVKEIEAIESDSFVQQTFRSSK-EVKKSVEPSEVKQATSTSGPASAVADPPSTEKEIDPTSIPTAIKYQDD
VKE.EA.ESDSFVQQTFRS.K.EVKK.VE..E.K.ATSTSGP..A..DPPSTE.EI...SIPT.IKYQDD
RetrocopyVKEMEAVESDSFVQQTFRSIK<EVKKLVESGEAKRATSTSGPTLAGVDPPSTENEIQLSSIPTSIKYQDD
ParentalNSLAHPNLFIEKADAEEKWFK-RLIALRQERLMGSPVA
NSLAHPNLFIEKA.AE.K.F..RLIAL.QERLMGSPVA
RetrocopyNSLAHPNLFIEKAGAEQK*FR<RLIAL*QERLMGSPVA

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 .02 RPM 27 .13 RPM
bodymap2_adrenal 0 .00 RPM 28 .19 RPM
bodymap2_brain 0 .00 RPM 50 .07 RPM
bodymap2_breast 0 .00 RPM 28 .07 RPM
bodymap2_colon 0 .00 RPM 24 .38 RPM
bodymap2_heart 0 .00 RPM 14 .12 RPM
bodymap2_kidney 0 .00 RPM 25 .77 RPM
bodymap2_liver 0 .00 RPM 10 .06 RPM
bodymap2_lung 0 .00 RPM 12 .45 RPM
bodymap2_lymph_node 0 .00 RPM 25 .36 RPM
bodymap2_ovary 0 .00 RPM 29 .40 RPM
bodymap2_prostate 0 .00 RPM 26 .69 RPM
bodymap2_skeletal_muscle 0 .00 RPM 14 .10 RPM
bodymap2_testis 0 .17 RPM 31 .69 RPM
bodymap2_thyroid 0 .00 RPM 32 .99 RPM
bodymap2_white_blood_cells 0 .00 RPM 22 .33 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4281 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4281 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4281 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4281 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4281 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 8 parental genes, and 22 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000047971 retrocopy
retro_cjac_553,
Cavia porcellus ENSCPOG000000008762 retrocopies
retro_cpor_618, retro_cpor_671,
Echinops telfairi ENSETEG000000172171 retrocopy
retro_etel_1555,
Homo sapiens ENSG00000174891 1 retrocopy
retro_hsap_4281 ,
Mus musculus ENSMUSG000000345441 retrocopy
retro_mmus_666,
Nomascus leucogenys ENSNLEG000000041371 retrocopy
retro_nleu_2851,
Rattus norvegicus ENSRNOG000000126392 retrocopies
retro_rnor_2454, retro_rnor_577,
Tupaia belangeri ENSTBEG0000000197313 retrocopies
retro_tbel_1285, retro_tbel_1372, retro_tbel_2078, retro_tbel_2400, retro_tbel_2545, retro_tbel_3145, retro_tbel_3313, retro_tbel_3748, retro_tbel_3834, retro_tbel_4317, retro_tbel_4458, retro_tbel_4494, retro_tbel_840,

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 = 0.06 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .06 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 .02 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .03 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 .02 RPM

Indel association:

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





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