RetrogeneDB ID:

retro_hsap_999

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:12:53157189..53157674(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000258071
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:ARL2BP
Ensembl ID:ENSG00000102931
Aliases:ARL2BP, BART, BART1, RP66
Description:ADP-ribosylation factor-like 2 binding protein [Source:HGNC Symbol;Acc:17146]


Retrocopy-Parental alignment summary:






>retro_hsap_999
GAAGCCCCAGAGGAAGAGAGCTTTGCACTACCCATCTCTTCCACCTCTGAAGCCAAATTCAATACTGTGGTTGGTTCTAT
TGAGGCCATCATCATGGATCCCGAGTTCCAGTACCACAGAGAAATTTCATGGACAAATACTACCAGGAATTTGAAGACAC
AGAAGAGAATAAACTCACCTACACACCAATCTTTAACGAATACCTTTCTTTGGTAGAAAAATATATTGAAGAACAGCTGC
TGGAGCGGATTCCAGAATTCAACATGGCGACCTTCACAGCAACATTAAAGCACCATAAAAATGAAGTGGCTGATGACATA
TTCAACATGCTAGTCACATTTACAGACTTTCTGGCATTTAAAGAGATGTTTCTGGACTACAGAGCAGAAAAAGAAGGCCA
GGGACTGGATTTAAGTGGCGATTTAGTGGTGACTTCGTTGTGCAAAACACCTTCCACGCCAGCTATCCAAAACAATCTGT
GGCAC

ORF - retro_hsap_999 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.91 %
Parental protein coverage: 99.39 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalDALEGESFALSFSSASDAEFDAVVGYLEDIIMDDEFQ-LLQRNFMDKYYLEFEDTEENKLIYTPIFNEYI
.A.E.ESFAL..SS.S.A.F..VVG..E.IIMD.EFQ...QRNFMDKYY.EFEDTEENKL.YTPIFNEY.
RetrocopyEAPEEESFALPISSTSEAKFNTVVGSIEAIIMDPEFQ<VPQRNFMDKYYQEFEDTEENKLTYTPIFNEYL
ParentalSLVEKYIEEQLLQRIPEFNMAAFTTTLQHHKDEVAGDIFDMLLTFTDFLAFKEMFLDYRAEKEGRGLDLS
SLVEKYIEEQLL.RIPEFNMA.FT.TL.HHK.EVA.DIF.ML.TFTDFLAFKEMFLDYRAEKEG.GLDLS
RetrocopySLVEKYIEEQLLERIPEFNMATFTATLKHHKNEVADDIFNMLVTFTDFLAFKEMFLDYRAEKEGQGLDLS
ParentalSGLVVTSLCKSSSLPASQNNLRH
..LVVTSLCK..S.PA.QNNL.H
RetrocopyGDLVVTSLCKTPSTPAIQNNLWH

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 60 .53 RPM
bodymap2_adrenal 0 .00 RPM 65 .42 RPM
bodymap2_brain 0 .00 RPM 55 .20 RPM
bodymap2_breast 0 .00 RPM 76 .46 RPM
bodymap2_colon 0 .00 RPM 55 .94 RPM
bodymap2_heart 0 .00 RPM 49 .62 RPM
bodymap2_kidney 0 .00 RPM 64 .87 RPM
bodymap2_liver 0 .00 RPM 17 .39 RPM
bodymap2_lung 0 .00 RPM 35 .13 RPM
bodymap2_lymph_node 0 .00 RPM 52 .12 RPM
bodymap2_ovary 0 .00 RPM 101 .65 RPM
bodymap2_prostate 0 .00 RPM 67 .01 RPM
bodymap2_skeletal_muscle 0 .00 RPM 26 .72 RPM
bodymap2_testis 0 .06 RPM 94 .36 RPM
bodymap2_thyroid 0 .00 RPM 41 .69 RPM
bodymap2_white_blood_cells 0 .00 RPM 75 .17 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_999 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_999 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_999 retrocopy 5' end.

Lab - click to see more details

retro_hsap_999 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_999 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_752
Pongo abelii retro_pabe_843
Parental genes homology:
Parental genes homology involve 21 parental genes, and 91 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000121169 retrocopies
retro_cjac_1766, retro_cjac_1920, retro_cjac_1928, retro_cjac_2548, retro_cjac_2580, retro_cjac_2698, retro_cjac_4074, retro_cjac_625, retro_cjac_689,
Cavia porcellus ENSCPOG000000114065 retrocopies
retro_cpor_1501, retro_cpor_203, retro_cpor_249, retro_cpor_299, retro_cpor_571,
Equus caballus ENSECAG000000166213 retrocopies
retro_ecab_307, retro_ecab_344, retro_ecab_754,
Felis catus ENSFCAG000000029373 retrocopies
retro_fcat_400, retro_fcat_69, retro_fcat_974,
Homo sapiens ENSG00000102931 7 retrocopies
retro_hsap_1189, retro_hsap_1846, retro_hsap_3237, retro_hsap_3263, retro_hsap_3270, retro_hsap_4293, retro_hsap_999 ,
Gorilla gorilla ENSGGOG000000054715 retrocopies
retro_ggor_2159, retro_ggor_2202, retro_ggor_2222, retro_ggor_2868, retro_ggor_927,
Loxodonta africana ENSLAFG000000086333 retrocopies
retro_lafr_103, retro_lafr_228, retro_lafr_418,
Microcebus murinus ENSMICG000000124676 retrocopies
retro_mmur_1066, retro_mmur_1385, retro_mmur_1444, retro_mmur_1515, retro_mmur_247, retro_mmur_499,
Myotis lucifugus ENSMLUG000000126803 retrocopies
retro_mluc_1338, retro_mluc_1843, retro_mluc_746,
Macaca mulatta ENSMMUG000000203527 retrocopies
retro_mmul_1260, retro_mmul_2037, retro_mmul_2055, retro_mmul_2059, retro_mmul_223, retro_mmul_2232, retro_mmul_2458,
Monodelphis domestica ENSMODG000000135111 retrocopy
retro_mdom_1182,
Nomascus leucogenys ENSNLEG000000028037 retrocopies
retro_nleu_1050, retro_nleu_1939, retro_nleu_1946, retro_nleu_2114, retro_nleu_2332, retro_nleu_2428, retro_nleu_955,
Oryctolagus cuniculus ENSOCUG000000005821 retrocopy
retro_ocun_431,
Ochotona princeps ENSOPRG000000069312 retrocopies
retro_opri_675, retro_opri_98,
Pongo abelii ENSPPYG000000073848 retrocopies
retro_pabe_1318, retro_pabe_1348, retro_pabe_1453, retro_pabe_2684, retro_pabe_2704, retro_pabe_3498, retro_pabe_843, retro_pabe_990,
Pan troglodytes ENSPTRG000000081507 retrocopies
retro_ptro_1231, retro_ptro_2189, retro_ptro_2207, retro_ptro_2910, retro_ptro_2948, retro_ptro_752, retro_ptro_816,
Rattus norvegicus ENSRNOG000000169911 retrocopy
retro_rnor_780,
Sorex araneus ENSSARG000000054421 retrocopy
retro_sara_190,
Ictidomys tridecemlineatus ENSSTOG000000102541 retrocopy
retro_itri_638,
Tupaia belangeri ENSTBEG000000144411 retrocopy
retro_tbel_2991,
Tarsius syrichta ENSTSYG0000000492310 retrocopies
retro_tsyr_1003, retro_tsyr_1066, retro_tsyr_1205, retro_tsyr_1728, retro_tsyr_1755, retro_tsyr_1958, retro_tsyr_2144, retro_tsyr_28, retro_tsyr_298, retro_tsyr_351,

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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