RetrogeneDB ID:

retro_hsap_4768

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:X:145619052..145619426(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000234748
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:ARL5A
Ensembl ID:ENSG00000162980
Aliases:None
Description:ADP-ribosylation factor-like 5A [Source:HGNC Symbol;Acc:696]


Retrocopy-Parental alignment summary:






>retro_hsap_4768
AGAATATGGAGACTGTTCAGTTACTCTCAACACAAAGTTATCATTTTTGGGCTGGATAATTCAAGATAATCTACCAGTCT
TTACCAGCTTTTTATGAATGAAGATTCACATCCATTTCCCACAATAGGAAGTAATGTTGAAGAGACAGTGGTTTAGTAAT
ACATATTTCCTAATGTGAGATACTGGTGTCCAAGAACATCTTCATTTTTCCTGGACACTTACTATGCTAACTGGATTTGT
AATAGTTGTCATGGACGGTACAGACCGAGAGAGAAAGGATTTCTGTAACTAGAGAAGAACTTTATAAAAAGTTAGCACTT
GTGCACCCAAGGAAAGTTGGAATGCTGATTTTTGCTAATAAACAAGGTGCTAAA

ORF - retro_hsap_4768 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 57.94 %
Parental protein coverage: 69.27 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalRIWRLFNHQEHKVIIVGLDNAGKTTILYQFSMNEVVHTSPTIGSNVEEIVI-NNTRFLMWDIGGQESLRS
RIWRLF....HKVII.GLDN....T.LYQ..MNE..H..PTIGSNVEE.V...NT.FLM.D.G.QE.L..
RetrocopyRIWRLFSYSQHKVIIFGLDNSR*STSLYQLFMNEDSHPFPTIGSNVEETVV>SNTYFLM*DTGVQEHLHF
ParentalSWNTYYTNTEFVIVVVDS-TDRERISVTREELYKMLAHEDLRKAGLLIFANKQDVK
SW...........V.....T.RERISVTREELYK.LA....RK.G.LIFANKQ..K
RetrocopySWTLTMLTGFVIVVMDGT>TERERISVTREELYKKLALVHPRKVGMLIFANKQGAK

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 86 .51 RPM
bodymap2_adrenal 0 .00 RPM 72 .97 RPM
bodymap2_brain 0 .00 RPM 83 .05 RPM
bodymap2_breast 0 .00 RPM 76 .73 RPM
bodymap2_colon 0 .00 RPM 85 .04 RPM
bodymap2_heart 0 .00 RPM 108 .14 RPM
bodymap2_kidney 0 .00 RPM 74 .86 RPM
bodymap2_liver 0 .00 RPM 40 .73 RPM
bodymap2_lung 0 .00 RPM 80 .52 RPM
bodymap2_lymph_node 0 .00 RPM 71 .40 RPM
bodymap2_ovary 0 .00 RPM 75 .37 RPM
bodymap2_prostate 0 .00 RPM 90 .67 RPM
bodymap2_skeletal_muscle 0 .00 RPM 91 .96 RPM
bodymap2_testis 0 .06 RPM 62 .16 RPM
bodymap2_thyroid 0 .00 RPM 116 .17 RPM
bodymap2_white_blood_cells 0 .00 RPM 111 .26 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4768 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4768 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4768 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4768 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4768 has 5 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_3175
Gorilla gorilla retro_ggor_2971
Pongo abelii retro_pabe_3711
Macaca mulatta retro_mmul_2543
Callithrix jacchus retro_cjac_4131
Parental genes homology:
Parental genes homology involve 17 parental genes, and 102 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG0000000506225 retrocopies
retro_chof_1109, retro_chof_1132, retro_chof_1205, retro_chof_1218, retro_chof_1407, retro_chof_1414, retro_chof_1443, retro_chof_1573, retro_chof_1712, retro_chof_1953, retro_chof_206, retro_chof_2081, retro_chof_2131, retro_chof_2142, retro_chof_2433, retro_chof_2464, retro_chof_2470, retro_chof_2713, retro_chof_373, retro_chof_547, retro_chof_836, retro_chof_857, retro_chof_865, retro_chof_972, retro_chof_98,
Callithrix jacchus ENSCJAG000000033119 retrocopies
retro_cjac_1054, retro_cjac_1111, retro_cjac_1255, retro_cjac_1921, retro_cjac_2949, retro_cjac_3920, retro_cjac_4131, retro_cjac_4175, retro_cjac_4211,
Cavia porcellus ENSCPOG000000052091 retrocopy
retro_cpor_913,
Dasypus novemcinctus ENSDNOG0000001333116 retrocopies
retro_dnov_105, retro_dnov_1165, retro_dnov_1244, retro_dnov_1953, retro_dnov_2159, retro_dnov_226, retro_dnov_2265, retro_dnov_2268, retro_dnov_2344, retro_dnov_2394, retro_dnov_563, retro_dnov_671, retro_dnov_713, retro_dnov_811, retro_dnov_818, retro_dnov_881,
Felis catus ENSFCAG000000147422 retrocopies
retro_fcat_569, retro_fcat_65,
Homo sapiens ENSG00000162980 5 retrocopies
retro_hsap_2549, retro_hsap_4715, retro_hsap_4768 , retro_hsap_4894, retro_hsap_721,
Loxodonta africana ENSLAFG000000321044 retrocopies
retro_lafr_1178, retro_lafr_1228, retro_lafr_1244, retro_lafr_599,
Microcebus murinus ENSMICG000000157887 retrocopies
retro_mmur_1271, retro_mmur_1487, retro_mmur_1586, retro_mmur_1618, retro_mmur_468, retro_mmur_652, retro_mmur_923,
Macaca mulatta ENSMMUG000000105215 retrocopies
retro_mmul_2519, retro_mmul_2543, retro_mmul_2630, retro_mmul_616, retro_mmul_641,
Monodelphis domestica ENSMODG000000039781 retrocopy
retro_mdom_75,
Mus musculus ENSMUSG000000360931 retrocopy
retro_mmus_2232,
Nomascus leucogenys ENSNLEG000000111912 retrocopies
retro_nleu_1259, retro_nleu_2280,
Otolemur garnettii ENSOGAG000000114246 retrocopies
retro_ogar_1879, retro_ogar_2112, retro_ogar_2675, retro_ogar_3146, retro_ogar_3465, retro_ogar_728,
Pongo abelii ENSPPYG000000128484 retrocopies
retro_pabe_3711, retro_pabe_3806, retro_pabe_3832, retro_pabe_621,
Pan troglodytes ENSPTRG000000125385 retrocopies
retro_ptro_1486, retro_ptro_3134, retro_ptro_3175, retro_ptro_3262, retro_ptro_514,
Ictidomys tridecemlineatus ENSSTOG000000163261 retrocopy
retro_itri_62,
Tupaia belangeri ENSTBEG000000115118 retrocopies
retro_tbel_1173, retro_tbel_1540, retro_tbel_3202, retro_tbel_3464, retro_tbel_3681, retro_tbel_3835, retro_tbel_4207, retro_tbel_4665,

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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