RetrogeneDB ID:

retro_hsap_2130

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:2:101125738..101126074(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000204637
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:ARPP19
Ensembl ID:ENSG00000128989
Aliases:ARPP19, ARPP-16, ARPP-19, ARPP16, ENSAL
Description:cAMP-regulated phosphoprotein, 19kDa [Source:HGNC Symbol;Acc:16967]


Retrocopy-Parental alignment summary:






>retro_hsap_2130
ATGTCTGTGGAAGTCTCCGAGGCAGCCTCTGTGGAGGAGCAGAAGGAAATGGAAGATACAGTGACTAGTCCAGAGAAAGT
TGAAGCAGCAAAATTAAAAGCAAGATATCCTCATCTGGGACAAATGCCTGGAGGTTCAGATTTCTTAAGGAAACGATTGC
AGAAAGGGCAAAAATATTTTGATTCTGGGGATTACAACATGGCTAAAGCAAAAATGAAGAACGAGCAACTTCCTACTGCA
GCTCTGGATAAGATGGAGGTCACGGGTGACCACATTCCCACTCCAGAGGACCTTCCTCAACAGAAACCATCCATTGTTGC
TAGCAAGCTGGCTGGT

ORF - retro_hsap_2130 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.39 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMSAEVPEAASAEEQKEMEDKVTSPEKAEEAKLKARYPHLGQKPGGSDFLRKRLQKGQKYFDSGDYNMAKA
MS.EV.EAAS.EEQKEMED.VTSPEK.E.AKLKARYPHLGQ.PGGSDFLRKRLQKGQKYFDSGDYNMAKA
RetrocopyMSVEVSEAASVEEQKEMEDTVTSPEKVEAAKLKARYPHLGQMPGGSDFLRKRLQKGQKYFDSGDYNMAKA
ParentalKMKNKQLPTAAPDKTEVTGDHIPTPQDLPQRKPSLVASKLAG
KMKN.QLPTAA.DK.EVTGDHIPTP.DLPQ.KPS.VASKLAG
RetrocopyKMKNEQLPTAALDKMEVTGDHIPTPEDLPQQKPSIVASKLAG

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 274 .53 RPM
bodymap2_adrenal 0 .00 RPM 139 .15 RPM
bodymap2_brain 0 .00 RPM 404 .39 RPM
bodymap2_breast 0 .00 RPM 348 .12 RPM
bodymap2_colon 0 .00 RPM 209 .12 RPM
bodymap2_heart 0 .00 RPM 166 .17 RPM
bodymap2_kidney 0 .00 RPM 202 .01 RPM
bodymap2_liver 0 .00 RPM 72 .07 RPM
bodymap2_lung 0 .00 RPM 236 .18 RPM
bodymap2_lymph_node 0 .00 RPM 171 .52 RPM
bodymap2_ovary 0 .00 RPM 167 .67 RPM
bodymap2_prostate 0 .00 RPM 241 .03 RPM
bodymap2_skeletal_muscle 0 .00 RPM 147 .99 RPM
bodymap2_testis 0 .00 RPM 215 .75 RPM
bodymap2_thyroid 0 .00 RPM 229 .74 RPM
bodymap2_white_blood_cells 0 .00 RPM 224 .97 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2130 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2130 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2130 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2130 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2130 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1559
Parental genes homology:
Parental genes homology involve 14 parental genes, and 38 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000110225 retrocopies
retro_btau_1259, retro_btau_1821, retro_btau_1845, retro_btau_952, retro_btau_981,
Canis familiaris ENSCAFG000000325152 retrocopies
retro_cfam_1375, retro_cfam_1402,
Dasypus novemcinctus ENSDNOG000000044749 retrocopies
retro_dnov_1086, retro_dnov_1576, retro_dnov_1960, retro_dnov_2150, retro_dnov_2427, retro_dnov_557, retro_dnov_616, retro_dnov_644, retro_dnov_662,
Dipodomys ordii ENSDORG000000113212 retrocopies
retro_dord_194, retro_dord_33,
Echinops telfairi ENSETEG000000155501 retrocopy
retro_etel_585,
Homo sapiens ENSG00000128989 2 retrocopies
retro_hsap_2130 , retro_hsap_3280,
Homo sapiens ENSG000001434203 retrocopies
retro_hsap_1449, retro_hsap_2208, retro_hsap_2452,
Gorilla gorilla ENSGGOG000000252501 retrocopy
retro_ggor_198,
Otolemur garnettii ENSOGAG000000138651 retrocopy
retro_ogar_591,
Pongo abelii ENSPPYG000000064872 retrocopies
retro_pabe_120, retro_pabe_1923,
Pan troglodytes ENSPTRG000000421831 retrocopy
retro_ptro_1559,
Sus scrofa ENSSSCG000000046181 retrocopy
retro_sscr_603,
Ictidomys tridecemlineatus ENSSTOG000000036777 retrocopies
retro_itri_1075, retro_itri_1290, retro_itri_1339, retro_itri_1643, retro_itri_1657, retro_itri_1865, retro_itri_594,
Tursiops truncatus ENSTTRG000000048041 retrocopy
retro_ttru_172,

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 = 0.03 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 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 .00 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 .03 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 .00 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .03 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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