RetrogeneDB ID:

retro_hsap_2682

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:3:99944217..99944914(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000243974
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:VTI1B
Ensembl ID:ENSG00000100568
Aliases:VTI1B, VTI1, VTI1-LIKE, VTI1L, VTI2, v-SNARE, vti1-rp1
Description:vesicle transport through interaction with t-SNAREs 1B [Source:HGNC Symbol;Acc:17793]


Retrocopy-Parental alignment summary:






>retro_hsap_2682
ATGGCCACCTTCACCGCCTCCTCAGAGCATTTCGAGAAGCTGTACGAGATCTTCCGCGGCCTCCATGAAGACCTACAAGG
GGTGCCCGAGCGGCTGCTGGGGGCGGCGGGGACCGAAGAGAAGAAGAAGTTAATCAGGGATTTTGATGAAAAGCAACAGG
AAGCAAATGAAACGTTGGCAGAGATGGAGGAGGAGCTACGTTATGCACCCCTGTCTTTCTGTAACCCCATGATGTCTAAG
CTTCGAAACTACCAAAAGGACCTTGCCAAACTCCATCGGGAGGTGAGAAGCACACCTTTGACAGCCACACCTGGAGGCCG
AGGAGACATGAAATATGGCATATATGCTGTAGAGACTGAGCATATGAATCAGCTTACAGTCTCAAAGGGCAACGCTTCCG
CAAGGCACTGAAAGCCTAAAACAGGCCACCCAAAGTATTGAACATTCTCATCAGATTGCCACGGAGACTGACCAGATTGG
CTCAGAAATCATAGAAGAGCTGGGAGAACAACGAGACCAGTTAGAACGCACCAAGAGTAGACTGGTAAACACAAGTGAAA
ACTTGGGCAACAGTCGAAAGATTCTCCGTTCAATGTCCAGAAAAGTGACAACCAACAAGCTGCTGCTTTCCATCATCATC
TTACTGGAGCTTGCCATCCTGGGAGGCCTGGTTTACTACAAATTCTTTCGCAACCAT

ORF - retro_hsap_2682 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.85 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMASSAASSEHFEKLHEIFRGLHEDLQGVPERLLGTAGTEEKKKLIRDFDEKQQEANETLAEMEEELRYAP
MA...ASSEHFEKL.EIFRGLHEDLQGVPERLLG.AGTEEKKKLIRDFDEKQQEANETLAEMEEELRYAP
RetrocopyMATFTASSEHFEKLYEIFRGLHEDLQGVPERLLGAAGTEEKKKLIRDFDEKQQEANETLAEMEEELRYAP
ParentalLSFRNPMMSKLRNYRKDLAKLHREVRSTPLTATPGGRGDMKYGIYAVENEHMNR-LQSQRAMLLQGTESL
LSF.NPMMSKLRNY.KDLAKLHREVRSTPLTATPGGRGDMKYGIYAVE.EHMN..LQSQRA.L.QGTESL
RetrocopyLSFCNPMMSKLRNYQKDLAKLHREVRSTPLTATPGGRGDMKYGIYAVETEHMNQ>LQSQRATLPQGTESL
ParentalNRATQSIERSHRIATETDQIGSEIIEELGEQRDQLERTKSRLVNTSENLSKSRKILRSMSRKVTTNKLLL
..ATQSIE.SH.IATETDQIGSEIIEELGEQRDQLERTKSRLVNTSENL..SRKILRSMSRKVTTNKLLL
RetrocopyKQATQSIEHSHQIATETDQIGSEIIEELGEQRDQLERTKSRLVNTSENLGNSRKILRSMSRKVTTNKLLL
ParentalSIIILLELAILGGLVYYKFFRSH
SIIILLELAILGGLVYYKFFR.H
RetrocopySIIILLELAILGGLVYYKFFRNH

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 .04 RPM 102 .13 RPM
bodymap2_adrenal 0 .00 RPM 62 .92 RPM
bodymap2_brain 0 .00 RPM 85 .16 RPM
bodymap2_breast 0 .02 RPM 172 .34 RPM
bodymap2_colon 0 .00 RPM 88 .62 RPM
bodymap2_heart 0 .00 RPM 58 .15 RPM
bodymap2_kidney 0 .00 RPM 96 .06 RPM
bodymap2_liver 0 .00 RPM 35 .85 RPM
bodymap2_lung 0 .00 RPM 44 .69 RPM
bodymap2_lymph_node 0 .00 RPM 63 .63 RPM
bodymap2_ovary 0 .00 RPM 74 .41 RPM
bodymap2_prostate 0 .02 RPM 67 .62 RPM
bodymap2_skeletal_muscle 0 .00 RPM 46 .72 RPM
bodymap2_testis 0 .00 RPM 73 .23 RPM
bodymap2_thyroid 0 .02 RPM 102 .08 RPM
bodymap2_white_blood_cells 0 .00 RPM 76 .27 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2682 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2682 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2682 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2682 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2682 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_1871
Pongo abelii retro_pabe_2298
Macaca mulatta retro_mmul_1420
Parental genes homology:
Parental genes homology involve 18 parental genes, and 38 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000152631 retrocopy
retro_cjac_1439,
Dasypus novemcinctus ENSDNOG000000036432 retrocopies
retro_dnov_1503, retro_dnov_2031,
Dipodomys ordii ENSDORG000000159392 retrocopies
retro_dord_52, retro_dord_716,
Echinops telfairi ENSETEG000000061011 retrocopy
retro_etel_783,
Felis catus ENSFCAG000000140901 retrocopy
retro_fcat_1855,
Homo sapiens ENSG00000100568 3 retrocopies
retro_hsap_1002, retro_hsap_2682 , retro_hsap_3013,
Gorilla gorilla ENSGGOG000000056202 retrocopies
retro_ggor_1871, retro_ggor_797,
Macropus eugenii ENSMEUG000000049102 retrocopies
retro_meug_499, retro_meug_697,
Microcebus murinus ENSMICG000000108431 retrocopy
retro_mmur_849,
Myotis lucifugus ENSMLUG000000111843 retrocopies
retro_mluc_1299, retro_mluc_2393, retro_mluc_781,
Macaca mulatta ENSMMUG000000158661 retrocopy
retro_mmul_1420,
Mustela putorius furoENSMPUG000000071301 retrocopy
retro_mputfur_1516,
Nomascus leucogenys ENSNLEG000000007804 retrocopies
retro_nleu_1184, retro_nleu_2241, retro_nleu_231, retro_nleu_83,
Pongo abelii ENSPPYG000000059275 retrocopies
retro_pabe_2298, retro_pabe_2498, retro_pabe_2602, retro_pabe_845, retro_pabe_974,
Pan troglodytes ENSPTRG000000064683 retrocopies
retro_ptro_1808, retro_ptro_2037, retro_ptro_751,
Pteropus vampyrus ENSPVAG000000116713 retrocopies
retro_pvam_132, retro_pvam_592, retro_pvam_797,
Tupaia belangeri ENSTBEG000000030491 retrocopy
retro_tbel_3432,
Tarsius syrichta ENSTSYG000000076882 retrocopies
retro_tsyr_1662, retro_tsyr_94,

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 .00 RPM
CEU_NA12004 0 .08 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .02 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 .03 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 .05 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 .03 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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