RetrogeneDB ID:

retro_hsap_948

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:12:5692962..5693250(+)
Located in intron of:ENSG00000047617
Retrocopy
information
Ensembl ID:ENSG00000255973
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:DYNLRB1
Ensembl ID:ENSG00000125971
Aliases:DYNLRB1, BITH, BLP, DNCL2A, DNLC2A, ROBLD1
Description:dynein, light chain, roadblock-type 1 [Source:HGNC Symbol;Acc:15468]


Retrocopy-Parental alignment summary:






>retro_hsap_948
ATATCAGAGGTGGAGGAGACACTGAAGTGACTTCAGAGCCAGAGGGGAGTGCAGAATATCATCATGGTGAACAAAGATGG
CATTCCCATCAAGAGCACCATGGTCAACCTCACCACCACAGAGTGTGCCAGCTTCCTGCACAGCTTCATCCTGAAGGCAC
GGAGCACCATGCATGAAAGTGACCCCCAGAATGATCTCACCTTCCTTCGAATTTGCTCCAAGTAAAATGGAATTATGGTT
GCACCAGATAAAGACTATTTCCCGATTGTGATTCAGAATCCAAACAAA

ORF - retro_hsap_948 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 75. %
Parental protein coverage: 100. %
Number of stop codons detected: 2
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMAEVEETLKRLQSQKGVQGIIVVNTEGIPIKSTMDNPTTTQYASLMHSFILKARSTVRDIDPQNDLTFLR
..EVEETLK.LQSQ.GVQ.II.VN..GIPIKSTM.N.TTT..AS..HSFILKARST....DPQNDLTFLR
RetrocopyISEVEETLK*LQSQRGVQNIIMVNKDGIPIKSTMVNLTTTECASFLHSFILKARSTMHESDPQNDLTFLR
ParentalIRSKKNEIMVAPDKDYFLIVIQNPTE
I.SK.N.IMVAPDKDYF.IVIQNP..
RetrocopyICSK*NGIMVAPDKDYFPIVIQNPNK

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 66 .55 RPM
bodymap2_adrenal 0 .00 RPM 78 .36 RPM
bodymap2_brain 0 .00 RPM 117 .43 RPM
bodymap2_breast 0 .12 RPM 66 .01 RPM
bodymap2_colon 0 .00 RPM 81 .77 RPM
bodymap2_heart 0 .00 RPM 48 .70 RPM
bodymap2_kidney 0 .00 RPM 75 .46 RPM
bodymap2_liver 0 .00 RPM 20 .91 RPM
bodymap2_lung 0 .00 RPM 67 .60 RPM
bodymap2_lymph_node 0 .00 RPM 57 .91 RPM
bodymap2_ovary 0 .00 RPM 71 .29 RPM
bodymap2_prostate 0 .00 RPM 81 .73 RPM
bodymap2_skeletal_muscle 0 .00 RPM 49 .34 RPM
bodymap2_testis 0 .08 RPM 57 .97 RPM
bodymap2_thyroid 0 .00 RPM 66 .91 RPM
bodymap2_white_blood_cells 0 .00 RPM 42 .96 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_948 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_948 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_948 retrocopy 5' end.

Lab - click to see more details

retro_hsap_948 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_948 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_764
Pongo abelii retro_pabe_810
Macaca mulatta retro_mmul_779
Parental genes homology:
Parental genes homology involve 20 parental genes, and 43 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000091791 retrocopy
retro_amel_1111,
Canis familiaris ENSCAFG000000075476 retrocopies
retro_cfam_1161, retro_cfam_1294, retro_cfam_1577, retro_cfam_1601, retro_cfam_1782, retro_cfam_930,
Callithrix jacchus ENSCJAG0000001819910 retrocopies
retro_cjac_1010, retro_cjac_1172, retro_cjac_1274, retro_cjac_1539, retro_cjac_2071, retro_cjac_2902, retro_cjac_3185, retro_cjac_3215, retro_cjac_3260, retro_cjac_882,
Equus caballus ENSECAG000000084042 retrocopies
retro_ecab_102, retro_ecab_553,
Echinops telfairi ENSETEG000000186372 retrocopies
retro_etel_218, retro_etel_699,
Felis catus ENSFCAG000000023041 retrocopy
retro_fcat_1228,
Homo sapiens ENSG00000125971 2 retrocopies
retro_hsap_1946, retro_hsap_948 ,
Gorilla gorilla ENSGGOG000000239001 retrocopy
retro_ggor_764,
Loxodonta africana ENSLAFG000000298202 retrocopies
retro_lafr_722, retro_lafr_852,
Microcebus murinus ENSMICG000000032531 retrocopy
retro_mmur_263,
Myotis lucifugus ENSMLUG000000048203 retrocopies
retro_mluc_1200, retro_mluc_1763, retro_mluc_443,
Macaca mulatta ENSMMUG000000312531 retrocopy
retro_mmul_779,
Nomascus leucogenys ENSNLEG000000100822 retrocopies
retro_nleu_1478, retro_nleu_2456,
Oryctolagus cuniculus ENSOCUG000000210272 retrocopies
retro_ocun_351, retro_ocun_745,
Otolemur garnettii ENSOGAG000000168022 retrocopies
retro_ogar_7, retro_ogar_983,
Ochotona princeps ENSOPRG000000047141 retrocopy
retro_opri_888,
Pongo abelii ENSPPYG000000109371 retrocopy
retro_pabe_810,
Pan troglodytes ENSPTRG000000134161 retrocopy
retro_ptro_655,
Rattus norvegicus ENSRNOG000000257151 retrocopy
retro_rnor_1883,
Ictidomys tridecemlineatus ENSSTOG000000148201 retrocopy
retro_itri_1244,

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 = 0.02 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 .02 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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