RetrogeneDB ID:

retro_hsap_2678

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:3:96496099..96496531(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000176243
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:CDV3
Ensembl ID:ENSG00000091527
Aliases:CDV3, H41
Description:CDV3 homolog (mouse) [Source:HGNC Symbol;Acc:26928]


Retrocopy-Parental alignment summary:






>retro_hsap_2678
AAGAGACAAGATCCAGGTGATAACTGGGAAGAAGGCGGAGGTGGTGGTGATACAGAAAAATCTTCAGGTCCCTGGAATAA
AACAGCTCTGGTACAAGCACCTCTTGCTCCAGTAATTGTTACAGAAACCCCAGAACTGGCAATGACTAGTGGTGTGTGTG
TGTGTAGGCCTCCTGGGGCCAGGTTAACCACAACAAGGAAAACACCACAAGGACCACCAGAAATCTACAGCAATACACAG
TTCCCATCCCTGCAGTCAACTGCCAAGCACATAGAAAGCTGGAAGGATAAAGAAATGGAGAAGAGCTTTCAAGTAATAAG
ACACAAAAATAGAGGTAGGGATGAAGTTTCAAAAAACCAGGCCCTTAAACTTCAGCTAGACAACCAGTATGCTGTGCTTG
AAAATCAGAAAAGGAGTCACTCACAATACAAT

ORF - retro_hsap_2678 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.28 %
Parental protein coverage: 91.67 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalKRQDPGDNWEEGGGGGGGMEKSSGPWNKTAPVQAPPAPVIVTETPEPAMTS--GVYRPPGARLTTTRKTP
KRQDPGDNWEEGGGGG...EKSSGPWNKTA.VQAP.APVIVTETPE.AMTS.....RPPGARLTTTRKTP
RetrocopyKRQDPGDNWEEGGGGGD-TEKSSGPWNKTALVQAPLAPVIVTETPELAMTSXXXXXRPPGARLTTTRKTP
ParentalQGPPEIYSDTQFPSLQSTAKHVESRKDKEMEKSFEVVRHKNRGRDEVSKNQALKLQLDNQYAVLENQKSS
QGPPEIYS.TQFPSLQSTAKH.ES.KDKEMEKSF.V.RHKNRGRDEVSKNQALKLQLDNQYAVLENQK.S
RetrocopyQGPPEIYSNTQFPSLQSTAKHIESWKDKEMEKSFQVIRHKNRGRDEVSKNQALKLQLDNQYAVLENQKRS
ParentalHSQYN
HSQYN
RetrocopyHSQYN

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 356 .99 RPM
bodymap2_adrenal 0 .00 RPM 296 .97 RPM
bodymap2_brain 0 .00 RPM 135 .23 RPM
bodymap2_breast 0 .00 RPM 358 .91 RPM
bodymap2_colon 0 .00 RPM 213 .97 RPM
bodymap2_heart 0 .00 RPM 183 .87 RPM
bodymap2_kidney 0 .00 RPM 175 .72 RPM
bodymap2_liver 0 .00 RPM 119 .64 RPM
bodymap2_lung 0 .00 RPM 249 .05 RPM
bodymap2_lymph_node 0 .00 RPM 295 .19 RPM
bodymap2_ovary 0 .00 RPM 263 .73 RPM
bodymap2_prostate 0 .00 RPM 186 .52 RPM
bodymap2_skeletal_muscle 0 .00 RPM 700 .01 RPM
bodymap2_testis 0 .08 RPM 205 .61 RPM
bodymap2_thyroid 0 .00 RPM 384 .57 RPM
bodymap2_white_blood_cells 0 .00 RPM 395 .35 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2678 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2678 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2678 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2678 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2678 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1805
Gorilla gorilla retro_ggor_1869
Parental genes homology:
Parental genes homology involve 14 parental genes, and 38 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000355561 retrocopy
retro_btau_253,
Choloepus hoffmanni ENSCHOG000000089635 retrocopies
retro_chof_1355, retro_chof_1701, retro_chof_1763, retro_chof_2308, retro_chof_818,
Callithrix jacchus ENSCJAG000000029981 retrocopy
retro_cjac_2928,
Dasypus novemcinctus ENSDNOG000000102085 retrocopies
retro_dnov_2359, retro_dnov_2616, retro_dnov_460, retro_dnov_496, retro_dnov_656,
Equus caballus ENSECAG000000156892 retrocopies
retro_ecab_444, retro_ecab_636,
Homo sapiens ENSG00000091527 1 retrocopy
retro_hsap_2678 ,
Gorilla gorilla ENSGGOG000000278211 retrocopy
retro_ggor_1869,
Myotis lucifugus ENSMLUG000000098641 retrocopy
retro_mluc_1296,
Mus musculus ENSMUSG0000003280310 retrocopies
retro_mmus_1266, retro_mmus_2405, retro_mmus_2408, retro_mmus_2411, retro_mmus_2412, retro_mmus_2416, retro_mmus_2418, retro_mmus_2422, retro_mmus_2423, retro_mmus_2534,
Ochotona princeps ENSOPRG000000036003 retrocopies
retro_opri_1017, retro_opri_739, retro_opri_740,
Pongo abelii ENSPPYG000000258981 retrocopy
retro_pabe_2301,
Pan troglodytes ENSPTRG000000154091 retrocopy
retro_ptro_1805,
Sus scrofa ENSSSCG000000116371 retrocopy
retro_sscr_701,
Tupaia belangeri ENSTBEG000000149105 retrocopies
retro_tbel_2284, retro_tbel_2443, retro_tbel_4022, retro_tbel_4157, retro_tbel_4378,

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 .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 .03 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 .02 RPM
GBR_HG00131 0 .06 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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