RetrogeneDB ID:

retro_hsap_80

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:20:23334678..23335101(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000132661
Aliases:NXT1, MTR2, P15
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:NXT2
Ensembl ID:ENSG00000101888
Aliases:NXT2, P15-2
Description:nuclear transport factor 2-like export factor 2 [Source:HGNC Symbol;Acc:18151]


Retrocopy-Parental alignment summary:






>retro_hsap_80
ATGGCATCTGTGGATTTCAAGACCTATGTGGATCAGGCCTGCAGAGCTGCTGAGGAGTTTGTCAATGTCTACTACACCAC
CATGGATAAGCGGCGGCGTTTGCTGTCCCGCCTGTACATGGGCACAGCCACCCTGGTCTGGAATGGCAATGCTGTTTCAG
GACAAGAATCCTTGAGTGAGTTTTTTGAAATGTTGCCTTCCAGCGAGTTCCAAATCAGCGTGGTAGACTGCCAGCCTGTT
CATGATGAAGCCACACCAAGCCAGACCACGGTCCTTGTTGTCATCTGTGGATCAGTGAAGTTTGAGGGGAACAAACAACG
GGACTTCAACCAGAACTTCATCCTGACCGCCCAGGCCTCACCCAGCAACACAGTGTGGAAGATCGCAAGTGACTGCTTCC
GCTTCCAGGACTGGGCCAGCTAG

ORF - retro_hsap_80 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 75.36 %
Parental protein coverage: 70.05 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalSLDFKTYVDQACRAAEEFVNIYYETMDKRRRALTRLYLDKATLIWNGNAVSGLDALNNFFDTLPSSEFQV
S.DFKTYVDQACRAAEEFVN.YY.TMDKRRR.L.RLY...ATL.WNGNAVSG...L..FF..LPSSEFQ.
RetrocopySVDFKTYVDQACRAAEEFVNVYYTTMDKRRRLLSRLYMGTATLVWNGNAVSGQESLSEFFEMLPSSEFQI
ParentalNMLDCQPVHEQATQSQTTVLVVTSGTVKFDGNKQHFFNQNFLLTAQSTPNNTVWKIASDCFRFQDWSS
...DCQPVH..AT.SQTTVLVV..G.VKF.GNKQ..FNQNF.LTAQ..P.NTVWKIASDCFRFQDW.S
RetrocopySVVDCQPVHDEATPSQTTVLVVICGSVKFEGNKQRDFNQNFILTAQASPSNTVWKIASDCFRFQDWAS

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 4 .59 RPM 9 .36 RPM
bodymap2_adrenal 15 .37 RPM 13 .39 RPM
bodymap2_brain 2 .79 RPM 9 .94 RPM
bodymap2_breast 4 .67 RPM 20 .23 RPM
bodymap2_colon 5 .70 RPM 10 .09 RPM
bodymap2_heart 2 .34 RPM 3 .45 RPM
bodymap2_kidney 4 .57 RPM 13 .79 RPM
bodymap2_liver 2 .64 RPM 6 .55 RPM
bodymap2_lung 13 .94 RPM 11 .16 RPM
bodymap2_lymph_node 11 .86 RPM 14 .60 RPM
bodymap2_ovary 11 .86 RPM 11 .74 RPM
bodymap2_prostate 10 .83 RPM 14 .62 RPM
bodymap2_skeletal_muscle 3 .18 RPM 1 .96 RPM
bodymap2_testis 9 .94 RPM 51 .49 RPM
bodymap2_thyroid 5 .01 RPM 17 .49 RPM
bodymap2_white_blood_cells 5 .97 RPM 34 .45 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity near the 5' end of retro_hsap_80 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_80 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_80 retrocopy 5' end.

Lab - click to see more details

retro_hsap_80 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_80 has 10 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_67
Pongo abelii retro_pabe_101
Macaca mulatta retro_mmul_140
Callithrix jacchus retro_cjac_98
Mus musculus retro_mmus_12
Rattus norvegicus retro_rnor_254
Oryctolagus cuniculus retro_ocun_210
Bos taurus retro_btau_118
Sus scrofa retro_sscr_8
Canis familiaris retro_cfam_1137
Parental genes homology:
Parental genes homology involve 28 parental genes, and 36 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000179991 retrocopy
retro_amel_59,
Bos taurus ENSBTAG000000207391 retrocopy
retro_btau_118,
Canis familiaris ENSCAFG000000285741 retrocopy
retro_cfam_1137,
Callithrix jacchus ENSCJAG000000073691 retrocopy
retro_cjac_98,
Cavia porcellus ENSCPOG000000033101 retrocopy
retro_cpor_29,
Dipodomys ordii ENSDORG000000107141 retrocopy
retro_dord_2,
Echinops telfairi ENSETEG000000080022 retrocopies
retro_etel_1926, retro_etel_1979,
Felis catus ENSFCAG000000022401 retrocopy
retro_fcat_20,
Homo sapiens ENSG00000101888 1 retrocopy
retro_hsap_80 ,
Gorilla gorilla ENSGGOG000000135931 retrocopy
retro_ggor_67,
Loxodonta africana ENSLAFG000000071161 retrocopy
retro_lafr_124,
Microcebus murinus ENSMICG000000145113 retrocopies
retro_mmur_149, retro_mmur_1531, retro_mmur_25,
Myotis lucifugus ENSMLUG000000006313 retrocopies
retro_mluc_1513, retro_mluc_160, retro_mluc_473,
Macaca mulatta ENSMMUG000000132041 retrocopy
retro_mmul_140,
Monodelphis domestica ENSMODG000000213431 retrocopy
retro_mdom_1611,
Mustela putorius furoENSMPUG000000039731 retrocopy
retro_mputfur_74,
Mus musculus ENSMUSG000000422711 retrocopy
retro_mmus_12,
Oryctolagus cuniculus ENSOCUG000000082611 retrocopy
retro_ocun_210,
Procavia capensis ENSPCAG000000080061 retrocopy
retro_pcap_9,
Pongo abelii ENSPPYG000000206251 retrocopy
retro_pabe_101,
Pteropus vampyrus ENSPVAG000000061491 retrocopy
retro_pvam_14,
Rattus norvegicus ENSRNOG000000191682 retrocopies
retro_rnor_2365, retro_rnor_254,
Sorex araneus ENSSARG000000093071 retrocopy
retro_sara_4,
Sus scrofa ENSSSCG000000125811 retrocopy
retro_sscr_8,
Ictidomys tridecemlineatus ENSSTOG000000052433 retrocopies
retro_itri_1138, retro_itri_141, retro_itri_793,
Tarsius syrichta ENSTSYG000000019241 retrocopy
retro_tsyr_42,
Tursiops truncatus ENSTTRG000000051151 retrocopy
retro_ttru_19,
Vicugna pacos ENSVPAG000000073141 retrocopy
retro_vpac_624,

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 = 20.97 RPM Legend:


Library Retrogene expression
CEU_NA11831 14 .27 RPM
CEU_NA11843 15 .78 RPM
CEU_NA11930 12 .39 RPM
CEU_NA12004 20 .97 RPM
CEU_NA12400 15 .43 RPM
CEU_NA12751 8 .91 RPM
CEU_NA12760 12 .58 RPM
CEU_NA12827 14 .48 RPM
CEU_NA12872 11 .62 RPM
CEU_NA12873 10 .98 RPM
FIN_HG00183 9 .31 RPM
FIN_HG00277 11 .46 RPM
FIN_HG00315 14 .96 RPM
FIN_HG00321 10 .85 RPM
FIN_HG00328 15 .22 RPM
FIN_HG00338 15 .73 RPM
FIN_HG00349 16 .53 RPM
FIN_HG00375 11 .81 RPM
FIN_HG00377 17 .12 RPM
FIN_HG00378 14 .96 RPM
GBR_HG00099 15 .58 RPM
GBR_HG00111 18 .64 RPM
GBR_HG00114 15 .02 RPM
GBR_HG00119 9 .08 RPM
GBR_HG00131 11 .44 RPM
GBR_HG00133 13 .70 RPM
GBR_HG00134 14 .11 RPM
GBR_HG00137 15 .39 RPM
GBR_HG00142 9 .81 RPM
GBR_HG00143 16 .37 RPM
TSI_NA20512 20 .40 RPM
TSI_NA20513 13 .78 RPM
TSI_NA20518 15 .04 RPM
TSI_NA20532 12 .01 RPM
TSI_NA20538 12 .07 RPM
TSI_NA20756 15 .16 RPM
TSI_NA20765 11 .50 RPM
TSI_NA20771 13 .87 RPM
TSI_NA20786 18 .73 RPM
TSI_NA20798 16 .37 RPM
YRI_NA18870 15 .43 RPM
YRI_NA18907 14 .73 RPM
YRI_NA18916 13 .35 RPM
YRI_NA19093 16 .87 RPM
YRI_NA19099 14 .70 RPM
YRI_NA19114 16 .02 RPM
YRI_NA19118 14 .90 RPM
YRI_NA19213 13 .66 RPM
YRI_NA19214 14 .91 RPM
YRI_NA19223 15 .30 RPM

Indel association:

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



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