RetrogeneDB ID:

retro_hsap_4234

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:9:18717973..18718525(-)
Located in intron of:ENSG00000178031
Retrocopy
information
Ensembl ID:ENSG00000236857
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RAP1B
Ensembl ID:ENSG00000127314
Aliases:RAP1B, K-REV, RAL1B
Description:RAP1B, member of RAS oncogene family [Source:HGNC Symbol;Acc:9857]


Retrocopy-Parental alignment summary:






>retro_hsap_4234
ATGCATGAGTATAAGCTAGTCATTCTTGGCCCAGGAGGCGTTGGAAAGTCTGCTTTGAATGTACAATTTGTTCAAGGAAT
TTTTGTTGAAAAATATGTCCTATGATAGAAGATTCTTATAGAAAGCAAGTTGAAGTAGATGCACAGCAGTGTATGCTTGC
AATCTTGGATACTGCAGGAACGGAACAATGTATAGCAAGGAGGGATTTGTACATGAGAAATGGACAAGGCTTTGCATTAG
TTTATTCCATCAAAGCACAGTCCACATTTAATGATTTGCAAGACTTGAGAGAACAGATTCTTTGAGTTAAAGACACTGAT
GATGTTCCAATGATTCTTGTTGGTAATAAGTATGACTTGGAAGATGAAAGAGCTGTAGGGAAGGAAGAAGGTCAAAAATC
TAGCAAGACAATGGAACAACTGTGCATTCTTAGATTCTTCTACAAAATTCAAAATAAATGTTAATGAGATCTTTTATGAC
CTAGTGCGGCAGATTAACAGAAAAACTCCAGTGCCTGGGAAGGCTCGCAAAAAGTCATCATGTCAGCTGCTT

ORF - retro_hsap_4234 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.71 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMREYKLVVLGSGGVGKSALTVQFVQGIFVEKYD-PTIEDSYRKQVEVDAQQCMLEILDTAGTEQFTAMRD
M.EYKLV.LG.GGVGKSAL.VQFVQGIFVEKY..P.IEDSYRKQVEVDAQQCML.ILDTAGTEQ..A.RD
RetrocopyMHEYKLVILGPGGVGKSALNVQFVQGIFVEKYV<PMIEDSYRKQVEVDAQQCMLAILDTAGTEQCIARRD
ParentalLYMKNGQGFALVYSITAQSTFNDLQDLREQILRVKDTDDVPMILVGNKCDLEDERVVGKEQGQ-NLARQW
LYM.NGQGFALVYSI.AQSTFNDLQDLREQIL.VKDTDDVPMILVGNK.DLEDER.VGKE.GQ.NLARQW
RetrocopyLYMRNGQGFALVYSIKAQSTFNDLQDLREQIL*VKDTDDVPMILVGNKYDLEDERAVGKEEGQ>NLARQW
ParentalNNCAFLESSAKSKINVNEIFYDLVRQINRKTPVPGKARKKSSCQLL
NNCAFL.SS.K.KINVNEIFYDLVRQINRKTPVPGKARKKSSCQLL
RetrocopyNNCAFLDSSTKFKINVNEIFYDLVRQINRKTPVPGKARKKSSCQLL

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 102 .25 RPM
bodymap2_adrenal 0 .16 RPM 94 .14 RPM
bodymap2_brain 0 .05 RPM 32 .39 RPM
bodymap2_breast 0 .08 RPM 111 .32 RPM
bodymap2_colon 0 .00 RPM 78 .62 RPM
bodymap2_heart 0 .00 RPM 23 .45 RPM
bodymap2_kidney 0 .00 RPM 59 .41 RPM
bodymap2_liver 0 .00 RPM 32 .61 RPM
bodymap2_lung 0 .00 RPM 180 .94 RPM
bodymap2_lymph_node 0 .00 RPM 116 .59 RPM
bodymap2_ovary 0 .08 RPM 55 .19 RPM
bodymap2_prostate 0 .02 RPM 100 .02 RPM
bodymap2_skeletal_muscle 0 .00 RPM 25 .19 RPM
bodymap2_testis 0 .00 RPM 73 .24 RPM
bodymap2_thyroid 0 .00 RPM 49 .81 RPM
bodymap2_white_blood_cells 0 .00 RPM 247 .30 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4234 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4234 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4234 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4234 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4234 has 5 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2877
Gorilla gorilla retro_ggor_2836
Pongo abelii retro_pabe_3403
Macaca mulatta retro_mmul_1151
Callithrix jacchus retro_cjac_607
Parental genes homology:
Parental genes homology involve 18 parental genes, and 32 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000086371 retrocopy
retro_amel_103,
Cavia porcellus ENSCPOG000000082724 retrocopies
retro_cpor_1194, retro_cpor_632, retro_cpor_739, retro_cpor_85,
Dipodomys ordii ENSDORG000000010861 retrocopy
retro_dord_521,
Echinops telfairi ENSETEG000000002421 retrocopy
retro_etel_11,
Homo sapiens ENSG000000064512 retrocopies
retro_hsap_1136, retro_hsap_3707,
Homo sapiens ENSG000001164731 retrocopy
retro_hsap_1364,
Homo sapiens ENSG00000127314 2 retrocopies
retro_hsap_3338, retro_hsap_4234 ,
Homo sapiens ENSG000001337031 retrocopy
retro_hsap_3474,
Loxodonta africana ENSLAFG000000164601 retrocopy
retro_lafr_482,
Myotis lucifugus ENSMLUG000000166062 retrocopies
retro_mluc_1126, retro_mluc_2211,
Monodelphis domestica ENSMODG000000073235 retrocopies
retro_mdom_11, retro_mdom_1570, retro_mdom_1756, retro_mdom_1897, retro_mdom_429,
Otolemur garnettii ENSOGAG000000057462 retrocopies
retro_ogar_2260, retro_ogar_272,
Procavia capensis ENSPCAG000000109771 retrocopy
retro_pcap_8,
Pongo abelii ENSPPYG000000047511 retrocopy
retro_pabe_3403,
Sus scrofa ENSSSCG000000211481 retrocopy
retro_sscr_1125,
Sus scrofa ENSSSCG000000300142 retrocopies
retro_sscr_435, retro_sscr_909,
Tursiops truncatus ENSTTRG000000157122 retrocopies
retro_ttru_1105, retro_ttru_134,
Vicugna pacos ENSVPAG000000009312 retrocopies
retro_vpac_283, retro_vpac_408,

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 ) 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 .00 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 .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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