RetrogeneDB ID:

retro_hsap_180

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:84710016..84710257(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000226970
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:NEDD8
Ensembl ID:ENSG00000129559
Aliases:NEDD8, NEDD-8
Description:neural precursor cell expressed, developmentally down-regulated 8 [Source:HGNC Symbol;Acc:7732]


Retrocopy-Parental alignment summary:






>retro_hsap_180
ATGCTAATTAAAGTGAAGACACTAACTGGAAAGGAGACTGAGATTGATATTGAACCTACAGACAAGGTGGAGTGAATCAA
GGAGCATGTGGAGGAGAAAGAGGGAATCCCTCCACAACAGCAGAGGCTCATCTACAGTGGCAAACATGAATGATGAGAAG
ACAGCAGCTGATTACAAGATTTTAGGTGGTTCAGTCCTTCACCTGGTGTTGGCTCTGAGAGGAGGAGGTGGTCTTAGGCA
G

ORF - retro_hsap_180 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.93 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQ-MNDEKTAADYKILGGSVLHL
MLIKVKTLTGKE.EIDIEPTDKVE.IKE.VEEKEGI.P.QQ.........MNDEKTAADYKILGGSVLHL
RetrocopyMLIKVKTLTGKETEIDIEPTDKVE*IKEHVEEKEGI-PPQQQRLIYSGK>MNDEKTAADYKILGGSVLHL
ParentalVLALRGGGGLRQ
VLALRGGGGLRQ
RetrocopyVLALRGGGGLRQ

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 .08 RPM 43 .93 RPM
bodymap2_adrenal 0 .04 RPM 58 .34 RPM
bodymap2_brain 0 .12 RPM 65 .30 RPM
bodymap2_breast 0 .02 RPM 50 .31 RPM
bodymap2_colon 0 .00 RPM 56 .34 RPM
bodymap2_heart 0 .00 RPM 33 .67 RPM
bodymap2_kidney 0 .00 RPM 55 .44 RPM
bodymap2_liver 0 .00 RPM 27 .48 RPM
bodymap2_lung 0 .00 RPM 35 .74 RPM
bodymap2_lymph_node 0 .09 RPM 46 .89 RPM
bodymap2_ovary 0 .02 RPM 46 .38 RPM
bodymap2_prostate 0 .00 RPM 49 .38 RPM
bodymap2_skeletal_muscle 0 .00 RPM 21 .30 RPM
bodymap2_testis 0 .02 RPM 54 .86 RPM
bodymap2_thyroid 0 .06 RPM 44 .72 RPM
bodymap2_white_blood_cells 0 .00 RPM 55 .40 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_180 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_180 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_180 retrocopy 5' end.

Lab - click to see more details

retro_hsap_180 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_180 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_261
Parental genes homology:
Parental genes homology involve 9 parental genes, and 18 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000388421 retrocopy
retro_btau_89,
Choloepus hoffmanni ENSCHOG000000012285 retrocopies
retro_chof_1012, retro_chof_1616, retro_chof_2696, retro_chof_613, retro_chof_788,
Callithrix jacchus ENSCJAG000000068761 retrocopy
retro_cjac_4064,
Erinaceus europaeus ENSEEUG000000116402 retrocopies
retro_eeur_165, retro_eeur_43,
Echinops telfairi ENSETEG000000183912 retrocopies
retro_etel_1118, retro_etel_1677,
Homo sapiens ENSG00000129559 1 retrocopy
retro_hsap_180 ,
Macaca mulatta ENSMMUG000000294091 retrocopy
retro_mmul_2236,
Monodelphis domestica ENSMODG000000032541 retrocopy
retro_mdom_1681,
Vicugna pacos ENSVPAG000000091044 retrocopies
retro_vpac_270, retro_vpac_316, retro_vpac_480, retro_vpac_558,

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 = 0.08 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 .08 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .03 RPM
FIN_HG00277 0 .04 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .03 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .02 RPM
FIN_HG00377 0 .03 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .03 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .03 RPM
GBR_HG00133 0 .05 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 .03 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .06 RPM
TSI_NA20771 0 .03 RPM
TSI_NA20786 0 .03 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 .05 RPM
YRI_NA19223 0 .06 RPM

Indel association:

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



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