RetrogeneDB ID:

retro_hsap_2994

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:4:153848597..153849359(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000231841
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:FAM192A
Ensembl ID:ENSG00000172775
Aliases:FAM192A, C16orf94, CDA018, NIP30
Description:family with sequence similarity 192, member A [Source:HGNC Symbol;Acc:29856]


Retrocopy-Parental alignment summary:






>retro_hsap_2994
ATGGATGGAGGGGATGATGGTAACCTTGTTATCAAAAAGAGGTTTGTGTCTGAGGCAGAACTAGATGAATGGTGCAAAAG
GAGGCAAGAAGAATGGGAGAAAGTTCGAAAACCTGAAGATTCAGAAGAATGTCCAGAGGAGGTTTATGACCCTCGATCTC
TATATGAAAGGCTACAGGAACAGAAGGACAGGAAGCAGCAGGAGTATGAGGAACAGTTCAAATTCAAAAACATGGTAAGA
GGCTTAGATGAAGATGAGACCAACTTCCTTGATGAGGTTTCTCGACAGCAGGAACTAATAGAAAAGCAACAAAGAGAAGA
AGAACTGAAAGAACTGAAGGAATACAGAAATAACCTCAAGAAGGTTGGAATTTCTCAAGAGAACAAGAAGGAAGTGGAAA
AGAAACTGACTGTGAAGCCCTTAGAAACCAAGAACAAGTTCTCCCAGGTGAAGCTGTTGGCAGGAGCTGTGAAGCGTAAG
AGCTCAGAGAGTGACAACAGTGTGAAAAGACTGAAACCGGACCCTGAGCCAGATGACAAGAATCAAGAGCCCTCATCCTG
CAAGTCTCTCAGAAACACCTCCCTGAGTGGCTCCTCCATCCACTGCCCCTCTGCTGCAGTCTGTATCAGCATCCTCCCAG
GCCTGTGCACCTACTCTGGGAGCAGCAACTCTGAGTCCAGCGCAGACAGTGAAGGCACCATCAATGCCACCGGAAAGATT
GTCTCCTTTATCTTCCAAACCAATACCTTCCTTGAGGCCCCT

ORF - retro_hsap_2994 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.91 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMDGGDDGNLIIKKRFVSEAELDERRKRRQEEWEKVRKPEDPEECPEEVYDPRSLYERLQEQKDRKQQEYE
MDGGDDGNL.IKKRFVSEAELDE..KRRQEEWEKVRKPED.EECPEEVYDPRSLYERLQEQKDRKQQEYE
RetrocopyMDGGDDGNLVIKKRFVSEAELDEWCKRRQEEWEKVRKPEDSEECPEEVYDPRSLYERLQEQKDRKQQEYE
ParentalEQFKFKNMVRGLDEDETNFLDEVSRQQELIEKQRREEELKELKEYRNNLKKVGISQENKKEVEKKLTVKP
EQFKFKNMVRGLDEDETNFLDEVSRQQELIEKQ.REEELKELKEYRNNLKKVGISQENKKEVEKKLTVKP
RetrocopyEQFKFKNMVRGLDEDETNFLDEVSRQQELIEKQQREEELKELKEYRNNLKKVGISQENKKEVEKKLTVKP
ParentalIETKNKFSQAKLLAGAVKHKSSESGNSVKRLKPDPEPDDKNQEPSSCKSLGNTSLSGPSIHCPSAAVCIG
.ETKNKFSQ.KLLAGAVK.KSSES.NSVKRLKPDPEPDDKNQEPSSCKSL.NTSLSG.SIHCPSAAVCI.
RetrocopyLETKNKFSQVKLLAGAVKRKSSESDNSVKRLKPDPEPDDKNQEPSSCKSLRNTSLSGSSIHCPSAAVCIS
ParentalILPGLGAYSGSSDSESSSDSEGTINATGKIVSSIFRTNTFLEAP
ILPGL..YSGSS.SESS.DSEGTINATGKIVS.IF.TNTFLEAP
RetrocopyILPGLCTYSGSSNSESSADSEGTINATGKIVSFIFQTNTFLEAP

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 .04 RPM 48 .90 RPM
bodymap2_adrenal 0 .04 RPM 73 .63 RPM
bodymap2_brain 0 .16 RPM 96 .71 RPM
bodymap2_breast 0 .00 RPM 43 .70 RPM
bodymap2_colon 0 .04 RPM 40 .91 RPM
bodymap2_heart 0 .00 RPM 33 .06 RPM
bodymap2_kidney 0 .02 RPM 56 .98 RPM
bodymap2_liver 0 .00 RPM 24 .31 RPM
bodymap2_lung 0 .02 RPM 34 .44 RPM
bodymap2_lymph_node 0 .02 RPM 59 .10 RPM
bodymap2_ovary 0 .17 RPM 54 .63 RPM
bodymap2_prostate 0 .14 RPM 55 .08 RPM
bodymap2_skeletal_muscle 0 .04 RPM 33 .36 RPM
bodymap2_testis 0 .04 RPM 81 .69 RPM
bodymap2_thyroid 0 .00 RPM 60 .02 RPM
bodymap2_white_blood_cells 0 .00 RPM 52 .65 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2994 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2994 retrocopy.

TSS - click to see more details



TSS No. TSS Name TSS expression level (Expr) in TPM range:
no expression 0 < Expr ≤ 1 1 < Expr ≤ 5 5 < Expr ≤ 10 Expr > 10
TSS #1 TSS_140644467 libraries708 libraries640 libraries10 libraries4 libraries

The graphical summary, for retro_hsap_2994 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Display detail expression values in each library
... or ...
Directly download all expression values

Lab - click to see more details

retro_hsap_2994 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2994 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2025
Gorilla gorilla retro_ggor_2074
Pongo abelii retro_pabe_2480
Parental genes homology:
Parental genes homology involve 15 parental genes, and 16 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000022421 retrocopy
retro_btau_1133,
Cavia porcellus ENSCPOG000000013921 retrocopy
retro_cpor_122,
Equus caballus ENSECAG000000093241 retrocopy
retro_ecab_710,
Echinops telfairi ENSETEG000000143791 retrocopy
retro_etel_930,
Homo sapiens ENSG00000172775 1 retrocopy
retro_hsap_2994 ,
Gorilla gorilla ENSGGOG000000039381 retrocopy
retro_ggor_2074,
Macaca mulatta ENSMMUG000000134921 retrocopy
retro_mmul_189,
Mus musculus ENSMUSG000000317741 retrocopy
retro_mmus_428,
Nomascus leucogenys ENSNLEG000000027161 retrocopy
retro_nleu_745,
Ochotona princeps ENSOPRG000000069092 retrocopies
retro_opri_175, retro_opri_579,
Pongo abelii ENSPPYG000000073821 retrocopy
retro_pabe_2480,
Pan troglodytes ENSPTRG000000081481 retrocopy
retro_ptro_2025,
Tarsius syrichta ENSTSYG000000133001 retrocopy
retro_tsyr_884,
Tursiops truncatus ENSTTRG000000127911 retrocopy
retro_ttru_1884,
Vicugna pacos ENSVPAG000000059731 retrocopy
retro_vpac_321,

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 = 0.33 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .09 RPM
CEU_NA11843 0 .20 RPM
CEU_NA11930 0 .26 RPM
CEU_NA12004 0 .15 RPM
CEU_NA12400 0 .07 RPM
CEU_NA12751 0 .07 RPM
CEU_NA12760 0 .31 RPM
CEU_NA12827 0 .14 RPM
CEU_NA12872 0 .11 RPM
CEU_NA12873 0 .16 RPM
FIN_HG00183 0 .27 RPM
FIN_HG00277 0 .26 RPM
FIN_HG00315 0 .19 RPM
FIN_HG00321 0 .12 RPM
FIN_HG00328 0 .02 RPM
FIN_HG00338 0 .09 RPM
FIN_HG00349 0 .23 RPM
FIN_HG00375 0 .22 RPM
FIN_HG00377 0 .20 RPM
FIN_HG00378 0 .08 RPM
GBR_HG00099 0 .29 RPM
GBR_HG00111 0 .17 RPM
GBR_HG00114 0 .16 RPM
GBR_HG00119 0 .24 RPM
GBR_HG00131 0 .03 RPM
GBR_HG00133 0 .17 RPM
GBR_HG00134 0 .17 RPM
GBR_HG00137 0 .19 RPM
GBR_HG00142 0 .33 RPM
GBR_HG00143 0 .13 RPM
TSI_NA20512 0 .17 RPM
TSI_NA20513 0 .24 RPM
TSI_NA20518 0 .33 RPM
TSI_NA20532 0 .20 RPM
TSI_NA20538 0 .14 RPM
TSI_NA20756 0 .26 RPM
TSI_NA20765 0 .21 RPM
TSI_NA20771 0 .26 RPM
TSI_NA20786 0 .16 RPM
TSI_NA20798 0 .16 RPM
YRI_NA18870 0 .03 RPM
YRI_NA18907 0 .10 RPM
YRI_NA18916 0 .15 RPM
YRI_NA19093 0 .03 RPM
YRI_NA19099 0 .21 RPM
YRI_NA19114 0 .05 RPM
YRI_NA19118 0 .10 RPM
YRI_NA19213 0 .07 RPM
YRI_NA19214 0 .12 RPM
YRI_NA19223 0 .22 RPM

Indel association:

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





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