RetrogeneDB ID:

retro_hsap_3626

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:6:86880161..86880519(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000217272
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RAB1A
Ensembl ID:ENSG00000138069
Aliases:RAB1A, RAB1, YPT1
Description:RAB1A, member RAS oncogene family [Source:HGNC Symbol;Acc:9758]


Retrocopy-Parental alignment summary:






>retro_hsap_3626
CACAGGAGCCTAAGGCTGTATGATATGACAGATCAGGAGTCCTTCGATAATGTCAAATAGTGGTTGCAGGAAATTGATCA
CTAGGCCAGTGAAAATGTCAACAAATTGTTGGTAGGAAACAAATGTGATTGCCCACAAAGAAAGTAGACTACACAACAAC
AAAGGAATTTGCTGATTCCCTTGGAATTCCATTTTTGGAAACTGGTGCTAAGAACACAGCAAATGTAGAACAGACTTTCA
TGAAAATGGCATCTGAGATTAAAAAGCAAATGGGACTAGAGCAACAGCTGGTGATGCAGAGAAGTCTAATTTTAAAATTT
AGACCACTTTGGTCAAGCAGTCAGGTGAAGGTTGATGC

ORF - retro_hsap_3626 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 74.8 %
Parental protein coverage: 69.94 %
Number of stop codons detected: 4
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalHGIIVVYDVTDQESFNNVKQWLQEIDRYASENVNKLLVGNKCD-LTTKKVVDYTTAKEFADSLGIPFLET
H.....YD.TDQESF.NVK.WLQEID..ASENVNKLLVGNKCD.L.TKKV.DYTT.KEFADSLGIPFLET
RetrocopyHRSLRLYDMTDQESFDNVK*WLQEIDH*ASENVNKLLVGNKCD<LPTKKV-DYTTTKEFADSLGIPFLET
ParentalSAKNATNVEQSFMTMAAEIKKRM-GPGATAGGAEKSNVKIQSTPVKQSGGGCC
.AKN..NVEQ.FM.MA.EIKK.M.G..ATAG.AEKSN.KI..T.VKQSG.G.C
RetrocopyGAKNTANVEQTFMKMASEIKKQM<GTRATAGDAEKSNFKI*TTLVKQSGEG*C

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 155 .62 RPM
bodymap2_adrenal 0 .00 RPM 128 .40 RPM
bodymap2_brain 0 .00 RPM 148 .66 RPM
bodymap2_breast 0 .00 RPM 170 .24 RPM
bodymap2_colon 0 .00 RPM 165 .26 RPM
bodymap2_heart 0 .00 RPM 104 .88 RPM
bodymap2_kidney 0 .00 RPM 245 .15 RPM
bodymap2_liver 0 .00 RPM 140 .41 RPM
bodymap2_lung 0 .00 RPM 207 .52 RPM
bodymap2_lymph_node 0 .00 RPM 132 .43 RPM
bodymap2_ovary 0 .04 RPM 169 .58 RPM
bodymap2_prostate 0 .00 RPM 156 .00 RPM
bodymap2_skeletal_muscle 0 .00 RPM 50 .18 RPM
bodymap2_testis 0 .00 RPM 163 .53 RPM
bodymap2_thyroid 0 .00 RPM 197 .88 RPM
bodymap2_white_blood_cells 0 .00 RPM 112 .56 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3626 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3626 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3626 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3626 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3626 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 11 parental genes, and 13 retrocopies.

Species Parental gene accession Retrocopies number
Echinops telfairi ENSETEG000000022052 retrocopies
retro_etel_1687, retro_etel_413,
Homo sapiens ENSG00000138069 2 retrocopies
retro_hsap_2362, retro_hsap_3626 ,
Homo sapiens ENSG000001435451 retrocopy
retro_hsap_1122,
Homo sapiens ENSG000001749031 retrocopy
retro_hsap_4252,
Macaca mulatta ENSMMUG000000217211 retrocopy
retro_mmul_951,
Oryctolagus cuniculus ENSOCUG000000170031 retrocopy
retro_ocun_800,
Pongo abelii ENSPPYG000000123601 retrocopy
retro_pabe_2135,
Pan troglodytes ENSPTRG000000119891 retrocopy
retro_ptro_1727,
Rattus norvegicus ENSRNOG000000049921 retrocopy
retro_rnor_110,
Ictidomys tridecemlineatus ENSSTOG000000206931 retrocopy
retro_itri_1541,
Drosophila melanogaster FBgn00167001 retrocopy
retro_dmel_36,

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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