RetrogeneDB ID:

retro_hsap_4152

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:9:35010870..35011260(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000233148
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SYF2
Ensembl ID:ENSG00000117614
Aliases:None
Description:SYF2 homolog, RNA splicing factor (S. cerevisiae) [Source:HGNC Symbol;Acc:19824]


Retrocopy-Parental alignment summary:






>retro_hsap_4152
AAACTACCTGCAAACTGGGAAGTTAATAAGGCTCATTTCAAATGGGAATTGCAGGAAGAAGGAGAAAAAAAAAAGAATGT
TCACAAAAAGACTATGAGAAAAGATACAGAAAGATGGGAGAGGAAAAGGAAAAACTCCAATCTGGGATTTTTACATTATG
CCACTTCCCAGTTACACCAGTATCATTTGTTGACCAAGCAGATCAAACCTGACATAGAAATATATTAAAAACTAAGAGAA
AAATATGGAGAGGAGTTCTATACAACATCTAACAGCCTTCTTCATGGAACATATTTGCCTTCCACAGAGAAAACTGATAG
GACAGAAAAGCAAATTGAAAACTGAGATGAATATAGCTGGAGACACCCTTAGGATGATGATGCAGATATC

ORF - retro_hsap_4152 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 54.74 %
Parental protein coverage: 56.38 %
Number of stop codons detected: 3
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalKARLEWELKEEEKKKECAARGEDYEKVKLLEISAEDAERWERKKKRKNPDLGFSDYAAAQLRQYHRLTKQ
K....WE......K.E....G.....V........D.ERWERK..RKN..LGF..YA..QL.QYH.LTKQ
RetrocopyKLPANWEVNKAHFKWELQEEGXXXXNVHK-KTMRKDTERWERK--RKNSNLGFLHYATSQLHQYHLLTKQ
ParentalIKPDMETYERLREKHGEEFFPTSNSLLHGTHVPSTEEIDRMVIDLEKQIEKRDKYSRRRPYNDDADI
IKPD.E.Y..LREK.GEEF..TSNSLLHGT..PSTE..DR.....EKQIE..D.YS.R.P..DDADI
RetrocopyIKPDIEIY*KLREKYGEEFYTTSNSLLHGTYLPSTEKTDR----TEKQIEN*DEYSWRHP*DDDADI

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 63 .53 RPM
bodymap2_adrenal 0 .12 RPM 53 .61 RPM
bodymap2_brain 0 .05 RPM 37 .18 RPM
bodymap2_breast 0 .00 RPM 46 .54 RPM
bodymap2_colon 0 .00 RPM 107 .86 RPM
bodymap2_heart 0 .15 RPM 25 .61 RPM
bodymap2_kidney 0 .04 RPM 48 .41 RPM
bodymap2_liver 0 .09 RPM 17 .32 RPM
bodymap2_lung 0 .00 RPM 38 .38 RPM
bodymap2_lymph_node 0 .00 RPM 41 .83 RPM
bodymap2_ovary 0 .04 RPM 61 .59 RPM
bodymap2_prostate 0 .00 RPM 72 .35 RPM
bodymap2_skeletal_muscle 0 .00 RPM 47 .38 RPM
bodymap2_testis 0 .02 RPM 71 .10 RPM
bodymap2_thyroid 0 .00 RPM 85 .64 RPM
bodymap2_white_blood_cells 0 .00 RPM 64 .64 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4152 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4152 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4152 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4152 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4152 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Callithrix jacchus retro_cjac_467
Parental genes homology:
Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000101151 retrocopy
retro_amel_566,
Bos taurus ENSBTAG000000016511 retrocopy
retro_btau_478,
Choloepus hoffmanni ENSCHOG000000052731 retrocopy
retro_chof_2034,
Callithrix jacchus ENSCJAG000000185591 retrocopy
retro_cjac_467,
Homo sapiens ENSG00000117614 1 retrocopy
retro_hsap_4152 ,
Monodelphis domestica ENSMODG000000139511 retrocopy
retro_mdom_899,
Oryctolagus cuniculus ENSOCUG000000130501 retrocopy
retro_ocun_1522,
Sarcophilus harrisii ENSSHAG000000071521 retrocopy
retro_shar_15,

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 = 0.09 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .03 RPM
CEU_NA12004 0 .04 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .02 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .09 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 .03 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .05 RPM
GBR_HG00131 0 .03 RPM
GBR_HG00133 0 .02 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .03 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .02 RPM
TSI_NA20518 0 .03 RPM
TSI_NA20532 0 .03 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .03 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .02 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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