RetrogeneDB ID:

retro_hsap_1707

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:16:76912428..76912824(-)
Located in intron of:ENSG00000259995
Retrocopy
information
Ensembl ID:ENSG00000260797
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:MAD2L1
Ensembl ID:ENSG00000164109
Aliases:None
Description:MAD2 mitotic arrest deficient-like 1 (yeast) [Source:HGNC Symbol;Acc:6763]


Retrocopy-Parental alignment summary:






>retro_hsap_1707
GCACTAAAGCTTTCCTGGGAGAAGGATATCACCTTGTGCAGGAGTGCCAAAATCGTGGTCAAGTTCTTCTCATTTGGCAT
CAACAGCATTTTATTTCAGCATGGCATATATCCATCTGGAACATTTACTCCAGTGTGGAAATATGGGCTCACCTTGCTTG
TAACCACTAATCTTGAGCTCATGAAACACCTAAATAACACGGTGGAACAACTAAAGCATTGGCTATACAAACGTTCAGGT
CAGAAACTGATTGGAGTCATCTCAACAACTGAAAGTGATGAGGTCCTTCAAAGATGGCAGTTTGACCCTAAGTGTGATAA
GACTGCAAAAGATCATCTTGGGCCCAGAGAATAGTCGCAGAAAACTATCCAGGATGAAATCTGTTTAGTAATCAGA

ORF - retro_hsap_1707 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.73 %
Parental protein coverage: 64.39 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalALQLSREQGITLRGSAEIVAEFFSFGINSILYQRGIYPSETFTRVQKYGLTLLVTTDLELIKYLNNVVEQ
AL.LS.E..ITL..SA.IV..FFSFGINSIL.Q.GIYPS.TFT.V.KYGLTLLVTT.LEL.K.LNN.VEQ
RetrocopyALKLSWEKDITLCRSAKIVVKFFSFGINSILFQHGIYPSGTFTPVWKYGLTLLVTTNLELMKHLNNTVEQ
ParentalLKDWLYKCSVQKLVVVISNIESGEVLERWQFDIECDKTAKDDSAPREKSQKAIQDEIRSVIR
LK.WLYK.S.QKL..VIS..ES.EVL.RWQFD..CDKTAKD...PRE.SQK.IQDEI..VIR
RetrocopyLKHWLYKRSGQKLIGVISTTESDEVLQRWQFDPKCDKTAKDHLGPRE*SQKTIQDEICLVIR

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 1 .79 RPM
bodymap2_adrenal 0 .00 RPM 5 .92 RPM
bodymap2_brain 0 .00 RPM 8 .32 RPM
bodymap2_breast 0 .00 RPM 3 .68 RPM
bodymap2_colon 0 .00 RPM 3 .98 RPM
bodymap2_heart 0 .00 RPM 2 .05 RPM
bodymap2_kidney 0 .00 RPM 1 .78 RPM
bodymap2_liver 0 .00 RPM 0 .46 RPM
bodymap2_lung 0 .00 RPM 4 .11 RPM
bodymap2_lymph_node 0 .00 RPM 6 .07 RPM
bodymap2_ovary 0 .00 RPM 3 .35 RPM
bodymap2_prostate 0 .00 RPM 3 .79 RPM
bodymap2_skeletal_muscle 0 .00 RPM 1 .04 RPM
bodymap2_testis 0 .00 RPM 26 .07 RPM
bodymap2_thyroid 0 .00 RPM 2 .99 RPM
bodymap2_white_blood_cells 0 .00 RPM 5 .18 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1707 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1707 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1707 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1707 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1707 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1156
Gorilla gorilla retro_ggor_1281
Pongo abelii retro_pabe_1403
Parental genes homology:
Parental genes homology involve 17 parental genes, and 33 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000128132 retrocopies
retro_chof_1340, retro_chof_2524,
Dasypus novemcinctus ENSDNOG000000134561 retrocopy
retro_dnov_1348,
Erinaceus europaeus ENSEEUG000000096291 retrocopy
retro_eeur_446,
Echinops telfairi ENSETEG000000157561 retrocopy
retro_etel_724,
Homo sapiens ENSG00000164109 2 retrocopies
retro_hsap_1350, retro_hsap_1707 ,
Gorilla gorilla ENSGGOG000000025161 retrocopy
retro_ggor_1281,
Loxodonta africana ENSLAFG000000296191 retrocopy
retro_lafr_1138,
Myotis lucifugus ENSMLUG000000110928 retrocopies
retro_mluc_1242, retro_mluc_165, retro_mluc_1802, retro_mluc_1904, retro_mluc_1986, retro_mluc_2434, retro_mluc_609, retro_mluc_696,
Macaca mulatta ENSMMUG000000048752 retrocopies
retro_mmul_1292, retro_mmul_1701,
Mus musculus ENSMUSG000000299102 retrocopies
retro_mmus_1684, retro_mmus_2573,
Nomascus leucogenys ENSNLEG000000090921 retrocopy
retro_nleu_1832,
Otolemur garnettii ENSOGAG000000040541 retrocopy
retro_ogar_199,
Pongo abelii ENSPPYG000000150292 retrocopies
retro_pabe_1121, retro_pabe_1403,
Pan troglodytes ENSPTRG000000164012 retrocopies
retro_ptro_1156, retro_ptro_925,
Ictidomys tridecemlineatus ENSSTOG000000254102 retrocopies
retro_itri_1592, retro_itri_327,
Tupaia belangeri ENSTBEG000000110653 retrocopies
retro_tbel_4460, retro_tbel_4666, retro_tbel_664,
Tursiops truncatus ENSTTRG000000110171 retrocopy
retro_ttru_1754,

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 = 0.02 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 .02 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:

The presence of retro_hsap_1707 across human populations is associated with 1 indel. The percentage values indicate the frequencies of retro_hsap_1707 presence in various populations. Based on Kabza et al. 2015 (PubMed).


# Indel coordinates AFR, African AMR, Ad Mixed American EUR, European EAS, East Asian
ASW YRI LWK MXL PUR CLM CEU IBS GBR FIN TSI JPT CHB CHS
1. 16:76887741..76945300 100 100 100 100 100 100 100 100 100 100 99.49 100 100 100

Indel #1, located at the genomic coordinates 16:76887741..76945300.

image/svg+xml Mexican Ancestryfrom Los Angeles USA MXL 100 % Puerto Ricansfrom Puerto Rico PUR 100 % Colombians fromMedellin, Colombia CLM 100 % Americans of AfricanAncestry in SW USA ASW 100 % Yoruba in Ibadan,Nigeria YRI 100 % Luhya in Webuye,Kenya LWK 100 % Utah Residents (CEPH)with Northern andWestern European Ancestry CEU 100 % Iberian Populationin Spain IBS 100 % British in Englandand Scotland GBR 100 % Finnish in Finland FIN 100 % Toscani in Italia TSI 99.49 % Han Chinese in Bejing,China CHB 100 % Japanese in Tokyo,Japan 100 % Southern Han Chinese CHS 100 % JPT EUROPE AMERICAS AFRICA EAST ASIA




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