RetrogeneDB ID:

retro_hsap_4901

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:X:130929681..130930157(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000241418
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:FAM195A
Ensembl ID:ENSG00000172366
Aliases:FAM195A, C16orf14, c349E10.1
Description:family with sequence similarity 195, member A [Source:HGNC Symbol;Acc:14142]


Retrocopy-Parental alignment summary:






>retro_hsap_4901
ATGTACACCATCATCAACGGGCCCAGCAAGTTGGTCGCGCAGCGCCGCACAGGTCTCACGCAGCAGCAGGTGAAGGGCCA
GCTCCAGGAGCTCCTGAAAAGCCGGCAGCCCGCGCCGCCGACCTTGCAGCCCCAGCGGGCGCAGCCCTTCGCGCAGCCGC
TGGGACCCTGGCCCCTGTCGAGTGCAGGGCCAAGGCTTGTGTTCAATCGTGTGAATCGCCGGCGGGACCCCTCCAAGTCC
CCATCCCTCCAGGGGACCCAGGAGACCTACACACTGGCCCACAAGGAGAATGTCCGCTTTGTGTCCGAAGCCTGGCAGCA
GGTGCGGCAGCAGCTGGATGGTGGCCCAGCCGGTGAGGGCGGGACAAGGCCTGTGCAGTGGAGAGGATCCCCAATCCCCG
GCTGCAGAACTTCGTGCCCATTGACTTGGACGAGTGGTGGGCGCAGCACTTCCTGGCTAGAATCACCAGCTGTTCC

ORF - retro_hsap_4901 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.61 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMYTITKGPSKLVAQRRTGPTQQQVEGRLGELLKCRQPAPPTSQPPRAQPFAQPPGPWPLSSPGPRLVFNR
MYTI..GPSKLVAQRRTG.TQQQV.G.L.ELLK.RQPAPPT.QP.RAQPFAQP.GPWPLSS.GPRLVFNR
RetrocopyMYTIINGPSKLVAQRRTGLTQQQVKGQLQELLKSRQPAPPTLQPQRAQPFAQPLGPWPLSSAGPRLVFNR
ParentalVNGRRAPSTSPSFEGTQETYTVAHEENVRFVSEAWQQVQQQLDGGPAGEGGPRPVQYVERTPNP-RLQNF
VN.RR.PS.SPS..GTQETYT.AH.ENVRFVSEAWQQV.QQLDGGPAGEGG.RPVQ.....P.P.RLQNF
RetrocopyVNRRRDPSKSPSLQGTQETYTLAHKENVRFVSEAWQQVRQQLDGGPAGEGGTRPVQW-RGSPIP<RLQNF
ParentalVPIDLDEWWAQQFLARITSCS
VPIDLDEWWAQ.FLARITSCS
RetrocopyVPIDLDEWWAQHFLARITSCS

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 2 .09 RPM
bodymap2_adrenal 0 .00 RPM 6 .37 RPM
bodymap2_brain 0 .00 RPM 2 .88 RPM
bodymap2_breast 0 .14 RPM 5 .45 RPM
bodymap2_colon 0 .00 RPM 8 .93 RPM
bodymap2_heart 0 .00 RPM 13 .44 RPM
bodymap2_kidney 0 .00 RPM 15 .18 RPM
bodymap2_liver 0 .00 RPM 13 .44 RPM
bodymap2_lung 0 .23 RPM 4 .25 RPM
bodymap2_lymph_node 0 .00 RPM 8 .68 RPM
bodymap2_ovary 0 .00 RPM 4 .40 RPM
bodymap2_prostate 0 .00 RPM 6 .15 RPM
bodymap2_skeletal_muscle 0 .00 RPM 8 .82 RPM
bodymap2_testis 0 .02 RPM 9 .33 RPM
bodymap2_thyroid 0 .00 RPM 6 .52 RPM
bodymap2_white_blood_cells 0 .02 RPM 2 .76 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4901 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4901 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4901 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4901 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4901 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_3268
Parental genes homology:
Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000119791 retrocopy
retro_cjac_932,
Homo sapiens ENSG00000172366 1 retrocopy
retro_hsap_4901 ,
Gorilla gorilla ENSGGOG000000137841 retrocopy
retro_ggor_43,
Nomascus leucogenys ENSNLEG000000081171 retrocopy
retro_nleu_1269,
Pan troglodytes ENSPTRG000000075481 retrocopy
retro_ptro_3268,
Sus scrofa ENSSSCG000000079951 retrocopy
retro_sscr_433,

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 = 1.27 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .43 RPM
CEU_NA11843 0 .65 RPM
CEU_NA11930 0 .46 RPM
CEU_NA12004 0 .49 RPM
CEU_NA12400 0 .46 RPM
CEU_NA12751 0 .29 RPM
CEU_NA12760 0 .85 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .63 RPM
CEU_NA12873 0 .73 RPM
FIN_HG00183 0 .66 RPM
FIN_HG00277 0 .52 RPM
FIN_HG00315 0 .36 RPM
FIN_HG00321 0 .57 RPM
FIN_HG00328 0 .17 RPM
FIN_HG00338 0 .53 RPM
FIN_HG00349 0 .43 RPM
FIN_HG00375 0 .15 RPM
FIN_HG00377 0 .15 RPM
FIN_HG00378 0 .21 RPM
GBR_HG00099 0 .58 RPM
GBR_HG00111 0 .47 RPM
GBR_HG00114 0 .34 RPM
GBR_HG00119 0 .91 RPM
GBR_HG00131 0 .23 RPM
GBR_HG00133 0 .36 RPM
GBR_HG00134 1 .27 RPM
GBR_HG00137 0 .55 RPM
GBR_HG00142 0 .92 RPM
GBR_HG00143 0 .48 RPM
TSI_NA20512 0 .34 RPM
TSI_NA20513 0 .97 RPM
TSI_NA20518 0 .33 RPM
TSI_NA20532 0 .54 RPM
TSI_NA20538 0 .28 RPM
TSI_NA20756 0 .17 RPM
TSI_NA20765 0 .44 RPM
TSI_NA20771 0 .26 RPM
TSI_NA20786 0 .47 RPM
TSI_NA20798 0 .50 RPM
YRI_NA18870 0 .71 RPM
YRI_NA18907 0 .52 RPM
YRI_NA18916 0 .82 RPM
YRI_NA19093 0 .39 RPM
YRI_NA19099 0 .21 RPM
YRI_NA19114 0 .03 RPM
YRI_NA19118 0 .60 RPM
YRI_NA19213 0 .10 RPM
YRI_NA19214 0 .57 RPM
YRI_NA19223 0 .64 RPM

Indel association:

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



Copyright © RetrogeneDB 2014-2017