RetrogeneDB ID:

retro_hsap_1074

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:12:4744510..4745001(-)
Located in intron of:ENSG00000139180
Retrocopy
information
Ensembl ID:ENSG00000256799
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RAB5A
Ensembl ID:ENSG00000144566
Aliases:RAB5A, RAB5
Description:RAB5A, member RAS oncogene family [Source:HGNC Symbol;Acc:9783]


Retrocopy-Parental alignment summary:






>retro_hsap_1074
ACAGATTCAGCTGATTTTCTAACCCAAAATGTGTGTCTTGATGACACTACAGTATAGTTTGAAATACAGGATACAGCTGG
TCAAGAATGATACCGTAGCCTAGCACCAATGTACTACAGAGGAGCACAAGCAGCCATAGCTGTATATGATACCACAAATG
AGGAGTCCTTTGCAAGAGCAAAAAATTGGGTTAAAGAACTTCAGAGGCAAGCATGTCCTGATATTGTAATAGCTTTATCA
GGAAACAAGGCTGACCTAGCAAATAAAAGAGCAGTAGATTTCCAGGAAGCACAGTCCTATGCAGATGACAATAGTTTATT
ATTCATGAAGACATCAGCTAAACATCAGTGAATGTAAATGAAATGTTCGTGGCAATAGCTAAAAAATTGCCAAAGAATGA
ACCACAAAATCCAGAAGCAAATTCTGCCAGAAAAAGAGGAGTAGCCCTTACTGAACCCACACAACCAAACAGGAGTCAGT
GTTGTAGTAAC

ORF - retro_hsap_1074 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.67 %
Parental protein coverage: 76.28 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalTIGAAFLTQTVCLDDTTVKFEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNEESFARAKNWVKELQRQ
T..A.FLTQ.VCLDDTTV.FEI.DTAGQE.Y.SLAPMYYRGAQAAI.VYD.TNEESFARAKNWVKELQRQ
RetrocopyTDSADFLTQNVCLDDTTV*FEIQDTAGQE*YRSLAPMYYRGAQAAIAVYDTTNEESFARAKNWVKELQRQ
ParentalASPNIVIALSGNKADLANKRAVDFQEAQSYADDNSLLFMETSAK-TSMNVNEIFMAIAKKLPKNEPQNPG
A.P.IVIALSGNKADLANKRAVDFQEAQSYADDNSLLFM.TSAK.TS.NVNE.F.AIAKKLPKNEPQNP.
RetrocopyACPDIVIALSGNKADLANKRAVDFQEAQSYADDNSLLFMKTSAK<TSVNVNEMFVAIAKKLPKNEPQNPE
ParentalANSARGRGVDLTEPTQPTRNQCCSN
ANSAR.RGV.LTEPTQP.R.QCCSN
RetrocopyANSARKRGVALTEPTQPNRSQCCSN

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 83 .19 RPM
bodymap2_adrenal 0 .00 RPM 73 .22 RPM
bodymap2_brain 0 .00 RPM 129 .93 RPM
bodymap2_breast 0 .06 RPM 85 .58 RPM
bodymap2_colon 0 .00 RPM 78 .12 RPM
bodymap2_heart 0 .00 RPM 56 .80 RPM
bodymap2_kidney 0 .00 RPM 76 .02 RPM
bodymap2_liver 0 .00 RPM 39 .10 RPM
bodymap2_lung 0 .05 RPM 111 .16 RPM
bodymap2_lymph_node 0 .22 RPM 58 .62 RPM
bodymap2_ovary 0 .08 RPM 64 .37 RPM
bodymap2_prostate 0 .00 RPM 86 .34 RPM
bodymap2_skeletal_muscle 0 .00 RPM 39 .38 RPM
bodymap2_testis 0 .00 RPM 68 .40 RPM
bodymap2_thyroid 0 .00 RPM 101 .35 RPM
bodymap2_white_blood_cells 0 .00 RPM 71 .86 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1074 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1074 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1074 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1074 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1074 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_848
Pongo abelii retro_pabe_894
Macaca mulatta retro_mmul_839
Callithrix jacchus retro_cjac_3268
Parental genes homology:
Parental genes homology involve 19 parental genes, and 26 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000009541 retrocopy
retro_amel_958,
Bos taurus ENSBTAG000000463851 retrocopy
retro_btau_300,
Callithrix jacchus ENSCJAG000000037311 retrocopy
retro_cjac_3268,
Cavia porcellus ENSCPOG000000053222 retrocopies
retro_cpor_1213, retro_cpor_219,
Dipodomys ordii ENSDORG000000124291 retrocopy
retro_dord_288,
Felis catus ENSFCAG000000044552 retrocopies
retro_fcat_1349, retro_fcat_984,
Homo sapiens ENSG00000144566 1 retrocopy
retro_hsap_1074 ,
Gorilla gorilla ENSGGOG000000159811 retrocopy
retro_ggor_848,
Loxodonta africana ENSLAFG000000083211 retrocopy
retro_lafr_267,
Macaca mulatta ENSMMUG000000069922 retrocopies
retro_mmul_227, retro_mmul_839,
Monodelphis domestica ENSMODG000000147932 retrocopies
retro_mdom_1219, retro_mdom_1993,
Mus musculus ENSMUSG000000178311 retrocopy
retro_mmus_1645,
Nomascus leucogenys ENSNLEG000000034341 retrocopy
retro_nleu_2466,
Oryctolagus cuniculus ENSOCUG000000122001 retrocopy
retro_ocun_1034,
Pongo abelii ENSPPYG000000140742 retrocopies
retro_pabe_3094, retro_pabe_894,
Pan troglodytes ENSPTRG000000146821 retrocopy
retro_ptro_731,
Ictidomys tridecemlineatus ENSSTOG000000262291 retrocopy
retro_itri_398,
Tarsius syrichta ENSTSYG000000076423 retrocopies
retro_tsyr_1544, retro_tsyr_315, retro_tsyr_946,
Tursiops truncatus ENSTTRG000000013741 retrocopy
retro_ttru_949,

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 = 0.1 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 .03 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 .10 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 .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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