RetrogeneDB ID:

retro_hsap_559

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:10:37284142..37284515(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000225355
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:ARL6IP1
Ensembl ID:ENSG00000170540
Aliases:ARL6IP1, AIP1, ARL6IP, ARMER, SPG61
Description:ADP-ribosylation factor-like 6 interacting protein 1 [Source:HGNC Symbol;Acc:697]


Retrocopy-Parental alignment summary:






>retro_hsap_559
TTGGCTGACTACCTTGTTCCCATTCTGGTGTAGAATTTTTGGCTCCAATAAATGCACCACTGAACAACAGCAAAGATTCC
ATGAAATTTGCAGCAATCTAGTAAAAACTCGACGCAGAGCTGTGGGTTGATGGAAACGCCTCTTCACACTAAAGGAAGAA
AAACCTAAGATGTTCTTCATGACCATGATCGTTTCCCTTGCTGAGGTTGCTTAGGTGGGACAGCAGGTCCACAACCTGCT
TCTCACCTGCCTGATAGTGACTTCCTTACTATTGCTTCCTGGACTAAGCCAACATGGAATCATTTCAAAGTACATTGGAA
TGGCCAAAAGGGAGCTAACCAAACTTCTCAAACAAAAAGAATAGAAAAATGAA

ORF - retro_hsap_559 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.51 %
Parental protein coverage: 71.84 %
Number of stop codons detected: 3
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalLADY-LVPILAPRIFGSNKWTTEQQQRFHEICSNLVKTRRRAVGWWKRLFTLKEEKPKMYFMTMIVSLAA
LADY.L.P....RIFGSNK.TTEQQQRFHEICSNLVKTRRRAVG.WKRLFTLKEEKPKM.FMTMIVSLA.
RetrocopyLADY>LFPFWC-RIFGSNKCTTEQQQRFHEICSNLVKTRRRAVG*WKRLFTLKEEKPKMFFMTMIVSLAE
ParentalVAWVGQQVHNLLLTYLIVTSLLLLPGLNQHGIILKYIGMAKREINKLLKQKEKKNE
VA.VGQQVHNLLLT.LIVTSLLLLPGL.QHGII.KYIGMAKRE..KLLKQKE.KNE
RetrocopyVA*VGQQVHNLLLTCLIVTSLLLLPGLSQHGIISKYIGMAKRELTKLLKQKE*KNE

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 173 .93 RPM
bodymap2_adrenal 0 .00 RPM 111 .19 RPM
bodymap2_brain 0 .07 RPM 507 .76 RPM
bodymap2_breast 0 .00 RPM 192 .65 RPM
bodymap2_colon 0 .00 RPM 192 .72 RPM
bodymap2_heart 0 .00 RPM 43 .61 RPM
bodymap2_kidney 0 .00 RPM 179 .36 RPM
bodymap2_liver 0 .00 RPM 115 .93 RPM
bodymap2_lung 0 .00 RPM 155 .36 RPM
bodymap2_lymph_node 0 .00 RPM 148 .86 RPM
bodymap2_ovary 0 .00 RPM 175 .28 RPM
bodymap2_prostate 0 .00 RPM 149 .63 RPM
bodymap2_skeletal_muscle 0 .00 RPM 22 .64 RPM
bodymap2_testis 0 .02 RPM 211 .42 RPM
bodymap2_thyroid 0 .00 RPM 131 .72 RPM
bodymap2_white_blood_cells 0 .00 RPM 181 .50 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_559 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_559 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_559 retrocopy 5' end.

Lab - click to see more details

retro_hsap_559 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_559 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_418
Parental genes homology:
Parental genes homology involve 24 parental genes, and 71 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG0000001817420 retrocopies
retro_cfam_114, retro_cfam_1204, retro_cfam_1232, retro_cfam_1261, retro_cfam_127, retro_cfam_1301, retro_cfam_1348, retro_cfam_1364, retro_cfam_1525, retro_cfam_1582, retro_cfam_1605, retro_cfam_1642, retro_cfam_1745, retro_cfam_1966, retro_cfam_21, retro_cfam_427, retro_cfam_464, retro_cfam_699, retro_cfam_831, retro_cfam_888,
Choloepus hoffmanni ENSCHOG000000078005 retrocopies
retro_chof_1153, retro_chof_1320, retro_chof_2130, retro_chof_2284, retro_chof_270,
Callithrix jacchus ENSCJAG000000200682 retrocopies
retro_cjac_782, retro_cjac_857,
Cavia porcellus ENSCPOG000000126031 retrocopy
retro_cpor_291,
Erinaceus europaeus ENSEEUG000000054341 retrocopy
retro_eeur_186,
Echinops telfairi ENSETEG000000201522 retrocopies
retro_etel_2083, retro_etel_549,
Homo sapiens ENSG00000170540 3 retrocopies
retro_hsap_1393, retro_hsap_559 , retro_hsap_902,
Gorilla gorilla ENSGGOG000000029023 retrocopies
retro_ggor_1080, retro_ggor_505, retro_ggor_729,
Loxodonta africana ENSLAFG000000186322 retrocopies
retro_lafr_420, retro_lafr_741,
Macropus eugenii ENSMEUG000000078961 retrocopy
retro_meug_1842,
Microcebus murinus ENSMICG000000122465 retrocopies
retro_mmur_1383, retro_mmur_1561, retro_mmur_582, retro_mmur_939, retro_mmur_951,
Monodelphis domestica ENSMODG000000059441 retrocopy
retro_mdom_794,
Nomascus leucogenys ENSNLEG000000054992 retrocopies
retro_nleu_1079, retro_nleu_381,
Ornithorhynchus anatinus ENSOANG000000122282 retrocopies
retro_oana_100, retro_oana_77,
Oryctolagus cuniculus ENSOCUG000000057401 retrocopy
retro_ocun_1921,
Otolemur garnettii ENSOGAG000000132022 retrocopies
retro_ogar_3502, retro_ogar_3504,
Pongo abelii ENSPPYG000000071403 retrocopies
retro_pabe_1153, retro_pabe_2798, retro_pabe_777,
Pan troglodytes ENSPTRG000000078243 retrocopies
retro_ptro_418, retro_ptro_622, retro_ptro_957,
Pteropus vampyrus ENSPVAG000000029061 retrocopy
retro_pvam_1337,
Sarcophilus harrisii ENSSHAG000000173461 retrocopy
retro_shar_691,
Ictidomys tridecemlineatus ENSSTOG000000058161 retrocopy
retro_itri_1595,
Tupaia belangeri ENSTBEG000000139163 retrocopies
retro_tbel_1609, retro_tbel_3046, retro_tbel_3772,
Tarsius syrichta ENSTSYG000000110921 retrocopy
retro_tsyr_1528,
Tursiops truncatus ENSTTRG000000051715 retrocopies
retro_ttru_1610, retro_ttru_1701, retro_ttru_519, retro_ttru_71, retro_ttru_929,

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 = 0.06 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .03 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 .03 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 .02 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .02 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .03 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .03 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 .06 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .02 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 .03 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 .02 RPM

Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).





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