RetrogeneDB ID:

retro_hsap_2793

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:3:60715785..60716271(-)
Located in intron of:ENSG00000189283
Retrocopy
information
Ensembl ID:ENSG00000225673
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:TMED2
Ensembl ID:ENSG00000086598
Aliases:TMED2, P24A, RNP24, p24
Description:transmembrane emp24 domain trafficking protein 2 [Source:HGNC Symbol;Acc:16996]


Retrocopy-Parental alignment summary:






>retro_hsap_2793
GTCACCTCAGGCACCAAGATGGGCCTCATCTTCGAAGGTGGCTTCCTGGGCATCAACATGGAGATTACAGGACCTAAGAA
TAAAAGGATTTATAAAGGAGACAAAGAATCCAGTGGGAAATACACATTTTCTGCTCACATGGATGGAACAAATACATTTT
GTTTTAGTGACCGAGTGTCCACCATGACTCCAAAGATAGTGATATTCACCATTGATATTGGGGAGGCTACAAAAAGAGAA
GACATGGAAACAGAAGCTCACCAGAACAAACTAGAAGAAATGATCAGTGAGCTGGCTGTGGCCATGACAGCTGTACAGCA
CAAAGAGGAATACACGAAAATCTGGGAGAGGATACACAGAGCCATTAGTGACAACACAAACAGCCCAGTGGTCCTTCGGT
GCTTCTTTGAAGCTCTTGTTCTAATTGCCATGACATTGGGACACATCTACTACCTGAAGAGATTTTTTGAAGTCCAGAGG
GTTGTT

ORF - retro_hsap_2793 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80. %
Parental protein coverage: 82.09 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalVTSGTKMGLIFEVAEGGFLDIDVEITGPDNKGIYKGDRESSGKYTFAAHMDGTYKFCFSNRMSTMTPKIV
VTSGTKMGLIF...EGGFL.I..EITGP.NK.IYKGD.ESSGKYTF.AHMDGT..FCFS.R.STMTPKIV
RetrocopyVTSGTKMGLIF---EGGFLGINMEITGPKNKRIYKGDKESSGKYTFSAHMDGTNTFCFSDRVSTMTPKIV
ParentalMFTIDIGEAPKGQDMETEAHQNKLEEMINELAVAMTAVKHEQEYMEVRERIHRAINDNTNSRVVLWSFFE
.FTIDIGEA.K..DMETEAHQNKLEEMI.ELAVAMTAV.H..EY....ERIHRAI.DNTNS.VVL..FFE
RetrocopyIFTIDIGEATKREDMETEAHQNKLEEMISELAVAMTAVQHKEEYTKIWERIHRAISDNTNSPVVLRCFFE
ParentalALVLVAMTLGQIYYLKRFFEVRRVV
ALVL.AMTLG.IYYLKRFFEV.RVV
RetrocopyALVLIAMTLGHIYYLKRFFEVQRVV

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 256 .94 RPM
bodymap2_adrenal 0 .08 RPM 192 .74 RPM
bodymap2_brain 0 .00 RPM 149 .08 RPM
bodymap2_breast 0 .19 RPM 333 .91 RPM
bodymap2_colon 0 .00 RPM 286 .07 RPM
bodymap2_heart 0 .15 RPM 127 .58 RPM
bodymap2_kidney 0 .17 RPM 282 .14 RPM
bodymap2_liver 0 .04 RPM 388 .34 RPM
bodymap2_lung 0 .00 RPM 255 .08 RPM
bodymap2_lymph_node 0 .00 RPM 221 .15 RPM
bodymap2_ovary 0 .00 RPM 369 .27 RPM
bodymap2_prostate 0 .00 RPM 251 .73 RPM
bodymap2_skeletal_muscle 0 .00 RPM 186 .15 RPM
bodymap2_testis 0 .00 RPM 255 .69 RPM
bodymap2_thyroid 0 .00 RPM 351 .88 RPM
bodymap2_white_blood_cells 0 .00 RPM 209 .71 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2793 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2793 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2793 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2793 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2793 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_1943
Pongo abelii retro_pabe_2227
Macaca mulatta retro_mmul_1439
Callithrix jacchus retro_cjac_1392
Parental genes homology:
Parental genes homology involve 13 parental genes, and 26 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000152622 retrocopies
retro_amel_1923, retro_amel_337,
Bos taurus ENSBTAG000000396302 retrocopies
retro_btau_52, retro_btau_819,
Choloepus hoffmanni ENSCHOG000000127286 retrocopies
retro_chof_104, retro_chof_1277, retro_chof_2323, retro_chof_2601, retro_chof_2709, retro_chof_981,
Callithrix jacchus ENSCJAG000000204661 retrocopy
retro_cjac_1392,
Echinops telfairi ENSETEG000000005562 retrocopies
retro_etel_2109, retro_etel_2154,
Homo sapiens ENSG00000086598 1 retrocopy
retro_hsap_2793 ,
Gorilla gorilla ENSGGOG000000285361 retrocopy
retro_ggor_1943,
Macaca mulatta ENSMMUG000000314912 retrocopies
retro_mmul_1439, retro_mmul_613,
Mustela putorius furoENSMPUG000000015981 retrocopy
retro_mputfur_1241,
Mus musculus ENSMUSG000000293902 retrocopies
retro_mmus_1361, retro_mmus_3262,
Nomascus leucogenys ENSNLEG000000016522 retrocopies
retro_nleu_2454, retro_nleu_2794,
Otolemur garnettii ENSOGAG000000091921 retrocopy
retro_ogar_2548,
Pongo abelii ENSPPYG000000050903 retrocopies
retro_pabe_1919, retro_pabe_2227, retro_pabe_3597,

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 = 0.06 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 .04 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .03 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .03 RPM
FIN_HG00277 0 .04 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .03 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .06 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .05 RPM
GBR_HG00119 0 .02 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .03 RPM
GBR_HG00142 0 .03 RPM
GBR_HG00143 0 .03 RPM
TSI_NA20512 0 .03 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .03 RPM
TSI_NA20532 0 .03 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .02 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 .00 RPM
YRI_NA19093 0 .03 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .02 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .04 RPM

Indel association:

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



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