RetrogeneDB ID:

retro_hsap_2

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:14:50085501..50085822(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000165502
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL36A
Ensembl ID:ENSG00000241343
Aliases:RPL36A, L36A, L44L, MIG6, RPL44
Description:ribosomal protein L36a [Source:HGNC Symbol;Acc:10359]


Retrocopy-Parental alignment summary:






>retro_hsap_2
ATGGTCAACGTACCTAAAACCCGAAGAACCTTCTGTAAGAAGTGTGGCAAGCATCAGCCTCACAAAGTGACACAGTATAA
GAAGGGCAAGGATTCTTTGTATGCCCAGGGAAGGAGGCGCTATGATCGGAAGCAGAGTGGCTATGGTGGGCAGACAAAGC
CAATTTTCCGGAAGAAGGCTAAGACCACAAAGAAGATTGTGCTAAGGCTGGAATGTGTTGAGCCTAACTGCAGATCCAAG
AGGATGCTGGCCATTAAGAGATGCAAGCATTTTGAACTGGGAGGAGATAAGAAGAGAAAGGGCCAAGTGATCCAGTTCTA
A

ORF - retro_hsap_2 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 99.06 %
Parental protein coverage: 74.65 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMVNVPKTRRTFCKKCGKHQPHKVTQYKKGKDSLYAQGKRRYDRKQSGYGGQTKPIFRKKAKTTKKIVLRL
MVNVPKTRRTFCKKCGKHQPHKVTQYKKGKDSLYAQG.RRYDRKQSGYGGQTKPIFRKKAKTTKKIVLRL
RetrocopyMVNVPKTRRTFCKKCGKHQPHKVTQYKKGKDSLYAQGRRRYDRKQSGYGGQTKPIFRKKAKTTKKIVLRL
ParentalECVEPNCRSKRMLAIKRCKHFELGGDKKRKGQVIQF
ECVEPNCRSKRMLAIKRCKHFELGGDKKRKGQVIQF
RetrocopyECVEPNCRSKRMLAIKRCKHFELGGDKKRKGQVIQF

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 79 .57 RPM 3 .40 RPM
bodymap2_adrenal 99 .32 RPM 19 .04 RPM
bodymap2_brain 48 .69 RPM 4 .43 RPM
bodymap2_breast 57 .28 RPM 2 .22 RPM
bodymap2_colon 126 .53 RPM 1 .45 RPM
bodymap2_heart 48 .74 RPM 0 .78 RPM
bodymap2_kidney 76 .46 RPM 3 .81 RPM
bodymap2_liver 82 .80 RPM 1 .77 RPM
bodymap2_lung 115 .30 RPM 4 .13 RPM
bodymap2_lymph_node 105 .15 RPM 3 .09 RPM
bodymap2_ovary 136 .17 RPM 10 .31 RPM
bodymap2_prostate 153 .85 RPM 2 .42 RPM
bodymap2_skeletal_muscle 102 .40 RPM 1 .49 RPM
bodymap2_testis 67 .83 RPM 1 .55 RPM
bodymap2_thyroid 65 .82 RPM 4 .43 RPM
bodymap2_white_blood_cells 168 .96 RPM 1 .44 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_2 in 3 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF002CHO POLR2A 14:50086783..50088539
ENCFF002CZW POLR2A 14:50086820..50087936
ENCFF002DAY POLR2A 14:50086159..50086795

EST - click to see more details

No EST(s) were mapped for retro_hsap_2 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_38326591 libraries787 libraries437 libraries11 libraries3 libraries

The graphical summary, for retro_hsap_2 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_2 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2 has 6 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_208
Pongo abelii retro_pabe_55
Callithrix jacchus retro_cjac_55
Mus musculus retro_mmus_4
Bos taurus retro_btau_92
Equus caballus retro_ecab_204
Parental genes homology:
Parental genes homology involve 12 parental genes, and 92 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000085031 retrocopy
retro_acar_98,
Callithrix jacchus ENSCJAG000000048644 retrocopies
retro_cjac_304, retro_cjac_353, retro_cjac_55, retro_cjac_72,
Equus caballus ENSECAG000000154649 retrocopies
retro_ecab_129, retro_ecab_131, retro_ecab_204, retro_ecab_219, retro_ecab_265, retro_ecab_268, retro_ecab_294, retro_ecab_543, retro_ecab_646,
Homo sapiens ENSG00000241343 14 retrocopies
retro_hsap_1477, retro_hsap_1508, retro_hsap_1595, retro_hsap_1782, retro_hsap_2 , retro_hsap_2015, retro_hsap_2274, retro_hsap_2632, retro_hsap_3461, retro_hsap_3819, retro_hsap_3981, retro_hsap_4154, retro_hsap_4299, retro_hsap_647,
Homo sapiens ENSG000002575291 retrocopy
retro_hsap_1353,
Monodelphis domestica ENSMODG000000255782 retrocopies
retro_mdom_1878, retro_mdom_971,
Mus musculus ENSMUSG000000794351 retrocopy
retro_mmus_4,
Pongo abelii ENSPPYG0000002583737 retrocopies
retro_pabe_1141, retro_pabe_1174, retro_pabe_121, retro_pabe_1226, retro_pabe_1256, retro_pabe_1311, retro_pabe_141, retro_pabe_1463, retro_pabe_1539, retro_pabe_154, retro_pabe_1540, retro_pabe_1616, retro_pabe_1650, retro_pabe_1651, retro_pabe_1944, retro_pabe_195, retro_pabe_2011, retro_pabe_2331, retro_pabe_2443, retro_pabe_2622, retro_pabe_2857, retro_pabe_296, retro_pabe_3057, retro_pabe_3151, retro_pabe_3273, retro_pabe_3372, retro_pabe_3687, retro_pabe_3704, retro_pabe_441, retro_pabe_449, retro_pabe_55, retro_pabe_573, retro_pabe_574, retro_pabe_667, retro_pabe_73, retro_pabe_772, retro_pabe_931,
Pteropus vampyrus ENSPVAG000000015691 retrocopy
retro_pvam_17,
Rattus norvegicus ENSRNOG000000114941 retrocopy
retro_rnor_259,
Sarcophilus harrisii ENSSHAG000000134791 retrocopy
retro_shar_467,
Ictidomys tridecemlineatus ENSSTOG0000002725120 retrocopies
retro_itri_1171, retro_itri_1189, retro_itri_1364, retro_itri_1405, retro_itri_1471, retro_itri_161, retro_itri_1681, retro_itri_290, retro_itri_385, retro_itri_430, retro_itri_555, retro_itri_609, retro_itri_644, retro_itri_730, retro_itri_753, retro_itri_784, retro_itri_803, retro_itri_845, retro_itri_865, retro_itri_903,

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 = 322.14 RPM Legend:


Library Retrogene expression
CEU_NA11831 149 .69 RPM
CEU_NA11843 322 .14 RPM
CEU_NA11930 162 .19 RPM
CEU_NA12004 245 .15 RPM
CEU_NA12400 271 .27 RPM
CEU_NA12751 147 .18 RPM
CEU_NA12760 142 .69 RPM
CEU_NA12827 205 .56 RPM
CEU_NA12872 172 .92 RPM
CEU_NA12873 142 .01 RPM
FIN_HG00183 188 .62 RPM
FIN_HG00277 148 .71 RPM
FIN_HG00315 274 .18 RPM
FIN_HG00321 132 .45 RPM
FIN_HG00328 213 .28 RPM
FIN_HG00338 209 .04 RPM
FIN_HG00349 230 .90 RPM
FIN_HG00375 234 .89 RPM
FIN_HG00377 286 .15 RPM
FIN_HG00378 209 .37 RPM
GBR_HG00099 151 .44 RPM
GBR_HG00111 276 .02 RPM
GBR_HG00114 185 .32 RPM
GBR_HG00119 162 .55 RPM
GBR_HG00131 221 .10 RPM
GBR_HG00133 190 .61 RPM
GBR_HG00134 166 .15 RPM
GBR_HG00137 219 .59 RPM
GBR_HG00142 183 .07 RPM
GBR_HG00143 208 .58 RPM
TSI_NA20512 274 .03 RPM
TSI_NA20513 164 .29 RPM
TSI_NA20518 172 .25 RPM
TSI_NA20532 181 .62 RPM
TSI_NA20538 170 .08 RPM
TSI_NA20756 179 .07 RPM
TSI_NA20765 166 .65 RPM
TSI_NA20771 199 .71 RPM
TSI_NA20786 159 .31 RPM
TSI_NA20798 170 .70 RPM
YRI_NA18870 140 .30 RPM
YRI_NA18907 129 .64 RPM
YRI_NA18916 200 .45 RPM
YRI_NA19093 132 .99 RPM
YRI_NA19099 145 .26 RPM
YRI_NA19114 151 .05 RPM
YRI_NA19118 193 .54 RPM
YRI_NA19213 184 .71 RPM
YRI_NA19214 152 .32 RPM
YRI_NA19223 134 .44 RPM

Indel association:

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





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