RetrogeneDB ID:

retro_hsap_386

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:52627855..52628456(-)
Located in intron of:ENSG00000157077
Retrocopy
information
Ensembl ID:ENSG00000223429
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:TRA2A
Ensembl ID:ENSG00000164548
Aliases:TRA2A, AWMS1, HSU53209
Description:transformer 2 alpha homolog (Drosophila) [Source:HGNC Symbol;Acc:16645]


Retrocopy-Parental alignment summary:






>retro_hsap_386
AGGAGACGAAGTAGCTCATATACACCAGAATACTGGCAGTGAAGGAGCCGAAGTCATTCTCCAATGTCTAACCAGAGAAG
ACACACTGGCAGAAGGGCAAATCCAGATCCCAACACTTGCCTTAGAGTGTTTGGCCTTAGTTTGTACACAACAGACAGAG
ATCTTCGTGAAGTATGTTCTTGATATGGACCTTTGAATGGTGCCAATGTGGTTTACAACCAGCAAACTGGGCGATCTCAA
GGATTTGCTTTTGTGCATTTTTAGGGAATAGATGACTCAAAGGAGGCTATGGTAAGGGCAAACAGAAAGGAGCTGGATGA
TAGAAGAAATTCGGGTGGATTATTCTATTACCAAGACAATGCGCACACCTATACCAGGCATCTATATGGGCAGAACTCAT
AGTGGTGGTGGCGGAGGTGGTGGCAAAGGCGGCAGTGGAGGTGGTCACAGACGTCGAGATTCTTACTATGATAGAGGATA
TCATCGTGGATATGACAGATATGAAGACTATGATTACCGGTACAGAAGATGATCACCTTCTCCTTATTATAGTCGATACA
GATCACAATCAAGATCTCATTCCTGCAGCCCAAGACACTAT

ORF - retro_hsap_386 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.79 %
Parental protein coverage: 71.63 %
Number of stop codons detected: 4
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalRSRSRSYTPEYRRRRSRSHSPMSNRRRHTGSRANPDPNTCLGVFGLSLYTTERDLREVFSRYGPLSGVNV
R.RS.SYTPEY...RSRSHSPMSN.RRHTG.RANPDPNTCL.VFGLSLYTT.RDLREV.S.YGPL.G.NV
RetrocopyRRRSSSYTPEYWQ*RSRSHSPMSNQRRHTGRRANPDPNTCLRVFGLSLYTTDRDLREVCS*YGPLNGANV
ParentalVYDQRTGRSRGFAFVYFERIDDSKEAMERANGMELDGRR-IRVDYSITKRAHTPTPGIYMGRPTHSGGGG
VY.Q.TGRS.GFAFV.F..IDDSKEAM.RAN..ELD.RR.IRVDYSITK...TP.PGIYMGR.THS.GGG
RetrocopyVYNQQTGRSQGFAFVHF*GIDDSKEAMVRANRKELDDRR>IRVDYSITKTMRTPIPGIYMGR-THS-GGG
ParentalGGGGGGGGGGGGRRRDSYYDRGYDRGYDRYEDYDYRYRRRSPSPYYSRYRSRSRSRSYSPRRY
GGGG.GG.GGG.RRRDSYYDRGY.RGYDRYEDYDYRYRR.SPSPYYSRYRS.SRS.S.SPR.Y
RetrocopyGGGGKGGSGGGHRRRDSYYDRGYHRGYDRYEDYDYRYRR*SPSPYYSRYRSQSRSHSCSPRHY

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 38 .96 RPM
bodymap2_adrenal 0 .00 RPM 80 .61 RPM
bodymap2_brain 0 .00 RPM 45 .71 RPM
bodymap2_breast 0 .00 RPM 59 .75 RPM
bodymap2_colon 0 .00 RPM 49 .93 RPM
bodymap2_heart 0 .04 RPM 24 .79 RPM
bodymap2_kidney 0 .00 RPM 71 .86 RPM
bodymap2_liver 0 .00 RPM 14 .89 RPM
bodymap2_lung 0 .00 RPM 46 .52 RPM
bodymap2_lymph_node 0 .00 RPM 93 .23 RPM
bodymap2_ovary 0 .04 RPM 84 .05 RPM
bodymap2_prostate 0 .00 RPM 83 .19 RPM
bodymap2_skeletal_muscle 0 .00 RPM 16 .41 RPM
bodymap2_testis 0 .00 RPM 71 .38 RPM
bodymap2_thyroid 0 .00 RPM 57 .53 RPM
bodymap2_white_blood_cells 0 .00 RPM 54 .18 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_386 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_386 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_386 retrocopy 5' end.

Lab - click to see more details

retro_hsap_386 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_386 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_299
Parental genes homology:
Parental genes homology involve 13 parental genes, and 22 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000011301 retrocopy
retro_chof_974,
Callithrix jacchus ENSCJAG000000015091 retrocopy
retro_cjac_1759,
Echinops telfairi ENSETEG000000072502 retrocopies
retro_etel_323, retro_etel_692,
Homo sapiens ENSG000001023171 retrocopy
retro_hsap_265,
Homo sapiens ENSG000001472747 retrocopies
retro_hsap_23, retro_hsap_3074, retro_hsap_3587, retro_hsap_4144, retro_hsap_4846, retro_hsap_800, retro_hsap_91,
Homo sapiens ENSG00000164548 1 retrocopy
retro_hsap_386 ,
Gorilla gorilla ENSGGOG000000090531 retrocopy
retro_ggor_391,
Mustela putorius furoENSMPUG000000134801 retrocopy
retro_mputfur_1442,
Nomascus leucogenys ENSNLEG000000147941 retrocopy
retro_nleu_1481,
Otolemur garnettii ENSOGAG000000097333 retrocopies
retro_ogar_1966, retro_ogar_2558, retro_ogar_3027,
Pongo abelii ENSPPYG000000177281 retrocopy
retro_pabe_324,
Pan troglodytes ENSPTRG000000189881 retrocopy
retro_ptro_299,
Sorex araneus ENSSARG000000129001 retrocopy
retro_sara_467,

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 .03 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 .02 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .09 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 .00 RPM

Indel association:

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



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