RetrogeneDB ID:

retro_hsap_2427

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:20:39959762..39960297(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000235102
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:ADI1
Ensembl ID:ENSG00000182551
Aliases:ADI1, APL1, ARD, Fe-ARD, MTCBP1, Ni-ARD, SIPL, mtnD
Description:acireductone dioxygenase 1 [Source:HGNC Symbol;Acc:30576]


Retrocopy-Parental alignment summary:






>retro_hsap_2427
ATGGTGCAGGCCTAGTACATGGATGAGTTCCCAGACTGCTGGAGGCAGCCCCACCACCCCGAGCCCCTGGCCACCCAGTG
GGCCAGAAACAGCCATGCTGGCTCAGGGTGCACTACTAAAGCTGGACACTGACAAATGAGAGAATGATCCAGAATTAGAA
AAGACTCAAAGAGAGAGAAGCTACTCCTGGATAGACATAATAACCATATGTAAAGATAAATTACCAAATTATGAAGAAAA
GATTAAGGTGTTTTATGGGGAGCATTTACACTTGGATGATCGGATCTGTTACATCCCGGGTGGCAGTGGATACTTTTGAT
ATGACAGATAAAGAAGACAAGTGAATCTACATCTTCATGGAGAAAGGAGACATAACTCTCCCCACAGGAATTCGTCACCA
CCTCACTCTGGATGAAAAGAAGTACGTGAAGGCCATATGGCCATTCAGGGAGACCCAGTGTGGACAGCATACAATGGGCC
AGCTGACCATTTCAATGTCCAGGGACAATACATGAAATTTCTGGCACAGACAGCA

ORF - retro_hsap_2427 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 67.93 %
Parental protein coverage: 100. %
Number of stop codons detected: 3
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalMVQAWYMDDAPGDPRQ-PHRPDP-GRPVGLEQLRRLGVLY-WKLDADKYENDPELEKIRRERNYSWMDII
MVQA.YMD..P...RQ.P..P.P.G.PVG..Q...L.V.Y..KLD.DK.ENDPELEK..RER.YSW.DII
RetrocopyMVQA*YMDEFPDCWRQ>PTTPSP>GHPVGQKQPCWLRVHY<LKLDTDK*ENDPELEKTQRERSYSWIDII
ParentalTICKDKLPNYEEKIKMFYEEHLHLDDEIRYILDGSGY-FDVRDKEDQWIRIFMEKGDMVTLPAGIYHRFT
TICKDKLPNYEEKIK.FY.EHLHLDD.I.YI..GSGY.FD..DKED..I.IFMEKGD..TLP.GI.H..T
RetrocopyTICKDKLPNYEEKIKVFYGEHLHLDDRICYIPGGSGY>FDMTDKEDK*IYIFMEKGD-ITLPTGIRHHLT
ParentalVDEKNYTKAMRLF-VGEPVWTAYNRPADHFEARGQYVKFLAQTA
.DEK.Y.KA...F..G.PVWTAYN.PADHF...GQY.KFLAQTA
RetrocopyLDEKKYVKAIWPF<QGDPVWTAYNGPADHFNVQGQYMKFLAQTA

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 45 .10 RPM
bodymap2_adrenal 0 .00 RPM 66 .22 RPM
bodymap2_brain 0 .00 RPM 44 .68 RPM
bodymap2_breast 0 .00 RPM 96 .81 RPM
bodymap2_colon 0 .00 RPM 69 .51 RPM
bodymap2_heart 0 .00 RPM 113 .37 RPM
bodymap2_kidney 0 .00 RPM 160 .01 RPM
bodymap2_liver 0 .00 RPM 299 .89 RPM
bodymap2_lung 0 .00 RPM 49 .86 RPM
bodymap2_lymph_node 0 .00 RPM 68 .75 RPM
bodymap2_ovary 0 .00 RPM 53 .09 RPM
bodymap2_prostate 0 .00 RPM 111 .52 RPM
bodymap2_skeletal_muscle 0 .00 RPM 48 .36 RPM
bodymap2_testis 0 .00 RPM 68 .38 RPM
bodymap2_thyroid 0 .00 RPM 66 .08 RPM
bodymap2_white_blood_cells 0 .00 RPM 66 .07 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2427 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2427 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2427 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2427 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2427 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1400
Gorilla gorilla retro_ggor_1510
Pongo abelii retro_pabe_1789
Macaca mulatta retro_mmul_622
Parental genes homology:
Parental genes homology involve 21 parental genes, and 42 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000184322 retrocopies
retro_amel_1306, retro_amel_1350,
Canis familiaris ENSCAFG000000032573 retrocopies
retro_cfam_1764, retro_cfam_554, retro_cfam_603,
Choloepus hoffmanni ENSCHOG000000104968 retrocopies
retro_chof_1146, retro_chof_1212, retro_chof_1800, retro_chof_2067, retro_chof_2163, retro_chof_401, retro_chof_742, retro_chof_748,
Dasypus novemcinctus ENSDNOG000000075233 retrocopies
retro_dnov_181, retro_dnov_1891, retro_dnov_2106,
Equus caballus ENSECAG000000057651 retrocopy
retro_ecab_870,
Echinops telfairi ENSETEG000000158601 retrocopy
retro_etel_1732,
Felis catus ENSFCAG000000257632 retrocopies
retro_fcat_1465, retro_fcat_882,
Homo sapiens ENSG00000182551 2 retrocopies
retro_hsap_165, retro_hsap_2427 ,
Gorilla gorilla ENSGGOG000000348552 retrocopies
retro_ggor_1510, retro_ggor_250,
Loxodonta africana ENSLAFG000000049021 retrocopy
retro_lafr_173,
Macaca mulatta ENSMMUG000000194711 retrocopy
retro_mmul_622,
Monodelphis domestica ENSMODG000000144842 retrocopies
retro_mdom_1128, retro_mdom_723,
Nomascus leucogenys ENSNLEG000000075182 retrocopies
retro_nleu_1559, retro_nleu_237,
Oryctolagus cuniculus ENSOCUG000000005301 retrocopy
retro_ocun_1236,
Otolemur garnettii ENSOGAG000000076682 retrocopies
retro_ogar_2871, retro_ogar_535,
Pongo abelii ENSPPYG000000126832 retrocopies
retro_pabe_1789, retro_pabe_463,
Pan troglodytes ENSPTRG000000116242 retrocopies
retro_ptro_1400, retro_ptro_157,
Pteropus vampyrus ENSPVAG000000036601 retrocopy
retro_pvam_689,
Rattus norvegicus ENSRNOG000000089501 retrocopy
retro_rnor_1316,
Tarsius syrichta ENSTSYG000000041381 retrocopy
retro_tsyr_1271,
Tursiops truncatus ENSTTRG000000059422 retrocopies
retro_ttru_1485, retro_ttru_1562,

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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