RetrogeneDB ID:

retro_hsap_2611

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:3:18580164..18581388(+)
Located in intron of:ENSG00000228956
Retrocopy
information
Ensembl ID:ENSG00000236570
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RAD23B
Ensembl ID:ENSG00000119318
Aliases:RAD23B, HHR23B, HR23B, P58
Description:RAD23 homolog B (S. cerevisiae) [Source:HGNC Symbol;Acc:9813]


Retrocopy-Parental alignment summary:






>retro_hsap_2611
ATGCAGGTCACCCTGAAGACCCTCCAGCCGCAGACCTTGACCTGCAAGATAGACATTGACCCCGAGGAGACAGTGAAAGC
ACTGAAAGAGAAGACGGAATCTGAAAAGGGGAAAGTTGCCTCTCTGGTAGCAGGTCAAACATTAATTTATGCAGGCAAAA
TCCTCAATGATGATACTGCTCTCAAAGAATATAAAATTGATGAGAAAAACTTTGTGGTGGTTATGGTGACCGAACCCAAA
GCAGTGTCCACACCAGCACTAGCTACAACTCAGCAGTCAGCTCCTGCCAGCACTACAGCAGTTACTTCCTCCACAACAAC
AACTGTGGCTCAGGCTCCAACCCCTGTCCCTGCTTTGGCTCCCCCTTTCACACCTGCATTCATCACTCCAGTATCAGTGA
CAGTGTCCTCTGAACCTGCAACTGCTAGTGCAACTAAACAAGAGAAACCTGCAGAAAAGCCAGCAGAGACACCAGTGGCT
ACTAGCCTGACATCAACTCATAGTACATCAGGAGATTCTTCTTGGTCAAACCTTTTTGAAGATGCAACGAGTGCACTTGT
GATGGGTCAGTCTTACGATAATATGGTAACTGAGATCATGTCAATGGGCTATGAACGAGAGCAAGTAATTGCAGCCCCAA
GAGCCAGTTCCAACAACCCTGACAGGGCAGTGGAGTACCTTTTAATGGGAATCCCTGGAGATAAAGTCAGGTTGTGGTTG
ACCCCCACCAAGCAGCTAGTACTGGGGCTCCTCAGTCTTCAACAGTGGCTGCAGCTGCAGCAACTACGACAGCAACAACT
ACAGCAAGTTCTGGAACATCCCCTTGAATTTTTATGGAATCAGCCTCAGTTTCAACAGATGAGACAAATTATTCAACAGA
GTCCTTCCCTTCTTCCAGTGTTACTACAGTAGATAGATTGAGAGAATCCTCAATTACTTCAGCAAATTAGCCAACACCAG
GAGCATTTTATTCAGATGTTAAATGAAACAGTTTGAGAAGCTGGTGGTCAAAGAGGAAGAGGTGGAGGTGTCAGTGGAGG
AATTGCAGAAGCTGGAAATGGTCTTATGAACTACATTCAAGTAATGCCTCAGGAAAAAGAAGCTACAGAAAGGTTAAAGG
CATTAGGATTTCCTGAAGGACTTGTGATACAAGCATATTTTGCTTGTGAGAAGAATAAGAATTTGGGTGCCGATTTTCTT
CTACAGCAGAACTTTGATGAAGAT

ORF - retro_hsap_2611 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.51 %
Parental protein coverage: 100. %
Number of stop codons detected: 4
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMQVTLKTLQQQTF--KIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALKEYKIDEKN
MQVTLKTLQ.QT...KIDIDPEETVKALKEK.ESEKGK.A..VAGQ.LIYAGKILNDDTALKEYKIDEKN
RetrocopyMQVTLKTLQPQTLTCKIDIDPEETVKALKEKTESEKGKVASLVAGQTLIYAGKILNDDTALKEYKIDEKN
ParentalFVVVMVTKPKAVSTPAPATTQQSAPASTTAVTSSTTTTVAQAPTPVPALAPTSTPASITPASATASSEPA
FVVVMVT.PKAVSTPA.ATTQQSAPASTTAVTSSTTTTVAQAPTPVPALAP..TPA.ITP.S.T.SSEPA
RetrocopyFVVVMVTEPKAVSTPALATTQQSAPASTTAVTSSTTTTVAQAPTPVPALAPPFTPAFITPVSVTVSSEPA
ParentalPASAAKQEKPAEKPAETPVATSPTATDSTSGDSSRSNLFEDATSALVTGQSYENMVTEIMSMGYEREQVI
.ASA.KQEKPAEKPAETPVATS.T.T.STSGDSS.SNLFEDATSALV.GQSY.NMVTEIMSMGYEREQVI
RetrocopyTASATKQEKPAEKPAETPVATSLTSTHSTSGDSSWSNLFEDATSALVMGQSYDNMVTEIMSMGYEREQVI
ParentalAALRASFNNPDRAVEYLLM-GIPGDRESQAVVDPPQAASTGAPQSSAVAAAAATTTATTTTTSSGGHP-L
AA.RAS.NNPDRAVEYLLM.G.P..R.SQ.VVDP.QAASTGAPQSS.VAAAAATTTATTT..SSG..P.L
RetrocopyAAPRASSNNPDRAVEYLLM<GNPW-R*SQVVVDPHQAASTGAPQSSTVAAAAATTTATTT-ASSGTSP<L
ParentalEF-LRNQPQFQQMRQIIQQNPSLLPALLQQIGRENPQLLQQISQHQEHFIQMLNEPVQEAGGQGGGGGGG
.F.L.NQPQFQQMRQIIQQ.PSLLP.LLQ.I..ENPQLLQQISQHQEHFIQMLNE.V.EAGGQ.G.GGG.
RetrocopyNF<LWNQPQFQQMRQIIQQSPSLLPVLLQ*ID*ENPQLLQQISQHQEHFIQMLNETV*EAGGQRGRGGGV
ParentalSGGIAEAGSGHMNYIQVTPQEKEAIERLKALGFPEGLVIQAYFACEKNENLAANFLLQQNFDED
SGGIAEAG.G.MNYIQV.PQEKEA.ERLKALGFPEGLVIQAYFACEKN.NL.A.FLLQQNFDED
RetrocopySGGIAEAGNGLMNYIQVMPQEKEATERLKALGFPEGLVIQAYFACEKNKNLGADFLLQQNFDED

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 232 .53 RPM
bodymap2_adrenal 0 .14 RPM 141 .61 RPM
bodymap2_brain 0 .07 RPM 185 .60 RPM
bodymap2_breast 0 .00 RPM 366 .37 RPM
bodymap2_colon 0 .14 RPM 249 .14 RPM
bodymap2_heart 0 .02 RPM 136 .45 RPM
bodymap2_kidney 0 .02 RPM 157 .87 RPM
bodymap2_liver 0 .00 RPM 201 .33 RPM
bodymap2_lung 0 .00 RPM 188 .40 RPM
bodymap2_lymph_node 0 .00 RPM 141 .95 RPM
bodymap2_ovary 0 .00 RPM 221 .53 RPM
bodymap2_prostate 0 .00 RPM 211 .79 RPM
bodymap2_skeletal_muscle 0 .02 RPM 310 .28 RPM
bodymap2_testis 0 .00 RPM 277 .89 RPM
bodymap2_thyroid 0 .00 RPM 240 .53 RPM
bodymap2_white_blood_cells 0 .20 RPM 178 .02 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2611 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2611 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_132593755 libraries832 libraries235 libraries7 libraries0 libraries

The graphical summary, for retro_hsap_2611 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_2611 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2611 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pongo abelii retro_pabe_2344
Parental genes homology:
Parental genes homology involve 14 parental genes, and 18 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000019261 retrocopy
retro_btau_877,
Callithrix jacchus ENSCJAG000000169082 retrocopies
retro_cjac_3865, retro_cjac_4184,
Equus caballus ENSECAG000000219281 retrocopy
retro_ecab_361,
Homo sapiens ENSG00000119318 2 retrocopies
retro_hsap_2611 , retro_hsap_3754,
Gorilla gorilla ENSGGOG000000025111 retrocopy
retro_ggor_1829,
Macaca mulatta ENSMMUG000000149442 retrocopies
retro_mmul_1476, retro_mmul_1725,
Nomascus leucogenys ENSNLEG000000173191 retrocopy
retro_nleu_1590,
Oryctolagus cuniculus ENSOCUG000000073161 retrocopy
retro_ocun_1429,
Otolemur garnettii ENSOGAG000000142161 retrocopy
retro_ogar_3040,
Pongo abelii ENSPPYG000000194772 retrocopies
retro_pabe_2344, retro_pabe_3162,
Pan troglodytes ENSPTRG000000212291 retrocopy
retro_ptro_1760,
Sarcophilus harrisii ENSSHAG000000119251 retrocopy
retro_shar_248,
Sus scrofa ENSSSCG000000054361 retrocopy
retro_sscr_770,
Tursiops truncatus ENSTTRG000000075971 retrocopy
retro_ttru_1401,

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 = 0.08 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .07 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 .03 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 .03 RPM
FIN_HG00375 0 .02 RPM
FIN_HG00377 0 .03 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .03 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .03 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .08 RPM
GBR_HG00143 0 .03 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .05 RPM
TSI_NA20518 0 .06 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .03 RPM
TSI_NA20765 0 .00 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 .06 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .05 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .02 RPM
YRI_NA19214 0 .02 RPM
YRI_NA19223 0 .00 RPM

Indel association:

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





Copyright © RetrogeneDB 2014-2017