RetrogeneDB ID:

retro_hsap_4275

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:9:80765450..80766109(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000233457
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SYNGR2
Ensembl ID:ENSG00000108639
Aliases:None
Description:synaptogyrin 2 [Source:HGNC Symbol;Acc:11499]


Retrocopy-Parental alignment summary:






>retro_hsap_4275
ATGGAGAGCGGGGCCTATGGCGCTGCCAAAGGCGGGCGGCTCCTTCCACCTGCGGGCGCTTCCTGACGCAACCGCAGGTG
GTGGTGAGCGCTGCGTGCAGGGTCTTCGCCTTGATCGTGTTCTCCTGCATCTATGACAAGGGCTACAGCAAGTCTAAGCA
GAGGTACTGCGTTTTCAACCATAACGAGGACGCCTTCCGCTACCGCAATGCCATCAGGGTGCTGGCCTTCCAGGCCTCGG
CCTCCTTGGTGGTCGACGTTTATTTTCCCCAGATCATTAATGCCACTGACCGCAAGTACCTGGTCGTGGGTGACCTGCTC
TTCTCAGCTCTCTGAGCCTTCCTGTGGTTTGTTGGTTTCTACTTCCTCACTAACCAGTGGGCGGCCACCCAACCGGAGGA
CGTGCTGGTGGGGGCCAACTCCGCGCAGGCAGCCATCACCTTCAGCTTCTTTTCCATCTTCTCCTGGGGCGTGCTGGCCT
TCCTGGCCTACCGGCACTACAAGGCTGGCGTGGACTTCATCCAGAACTACGTCGACTCCACCCTGGACCCCAACACTGCC
TACGCCTCCTACCCAGGTGCATCTGTGGACAACTACCAGCATCTGCCCTTCACCCAGAATGCGGAGACCACTGAGGGCTA
CCAGCCGCCCCCTGTGTAC

ORF - retro_hsap_4275 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 81.42 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMESGAYGAAK-AGGSFDLR-RFLTQPQVVARAVCLVFALIVFSCIYGEGYSNAHESKQMYCVFNRNEDAC
MESGAYGAAK.AGGSF.LR.RFLTQPQVV..A.C.VFALIVFSCIY..GYS....SKQ.YCVFN.NEDA.
RetrocopyMESGAYGAAK>AGGSFHLR>RFLTQPQVVVSAACRVFALIVFSCIYDKGYS---KSKQRYCVFNHNEDAF
ParentalRYGSAIGVLAFLASAFFLVVDAYFPQISNATDRKYLVIGDLLFSALWTFLWFVGFCFLTNQWAVTNPKDV
RY..AI.VLAF.ASA..LVVD.YFPQI.NATDRKYLV.GDLLFSAL..FLWFVGF.FLTNQWA.T.P.DV
RetrocopyRYRNAIRVLAFQASAS-LVVDVYFPQIINATDRKYLVVGDLLFSAL*AFLWFVGFYFLTNQWAATQPEDV
ParentalLVGADSVRAAITFSFFSIFSWGVLASLAYQRYKAGVDDFIQNYVDPTPDPNTAYASYPGASVDNYQQPPF
LVGA.S..AAITFSFFSIFSWGVLA.LAY..YKAGV.DFIQNYVD.T.DPNTAYASYPGASVDNYQ..PF
RetrocopyLVGANSAQAAITFSFFSIFSWGVLAFLAYRHYKAGV-DFIQNYVDSTLDPNTAYASYPGASVDNYQHLPF
ParentalTQNAETTEGYQPPPVY
TQNAETTEGYQPPPVY
RetrocopyTQNAETTEGYQPPPVY

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 .71 RPM
bodymap2_adrenal 0 .00 RPM 71 .75 RPM
bodymap2_brain 0 .00 RPM 11 .11 RPM
bodymap2_breast 0 .00 RPM 34 .88 RPM
bodymap2_colon 0 .00 RPM 33 .64 RPM
bodymap2_heart 0 .00 RPM 37 .99 RPM
bodymap2_kidney 0 .00 RPM 45 .06 RPM
bodymap2_liver 0 .00 RPM 33 .67 RPM
bodymap2_lung 0 .00 RPM 142 .88 RPM
bodymap2_lymph_node 0 .00 RPM 76 .18 RPM
bodymap2_ovary 0 .00 RPM 26 .54 RPM
bodymap2_prostate 0 .00 RPM 54 .92 RPM
bodymap2_skeletal_muscle 0 .00 RPM 178 .02 RPM
bodymap2_testis 0 .02 RPM 18 .89 RPM
bodymap2_thyroid 0 .00 RPM 34 .48 RPM
bodymap2_white_blood_cells 0 .00 RPM 92 .10 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4275 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4275 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4275 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4275 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4275 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000108639 2 retrocopies
retro_hsap_1472, retro_hsap_4275 ,
Macaca mulatta ENSMMUG000000218641 retrocopy
retro_mmul_1200,
Pongo abelii ENSPPYG000000086842 retrocopies
retro_pabe_1220, retro_pabe_3487,
Ictidomys tridecemlineatus ENSSTOG000000068341 retrocopy
retro_itri_705,

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 = 0.05 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .03 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 .05 RPM
FIN_HG00277 0 .04 RPM
FIN_HG00315 0 .03 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .04 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 .04 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .05 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .05 RPM
GBR_HG00142 0 .03 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .03 RPM
TSI_NA20513 0 .02 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 .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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