RetrogeneDB ID:

retro_pabe_2298

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:3:32993607..32994130(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:VTI1B
Ensembl ID:ENSPPYG00000005927
Aliases:None
Description:vesicle transport through interaction with t-SNAREs 1B [Source:HGNC Symbol;Acc:17793]


Retrocopy-Parental alignment summary:






>retro_pabe_2298
ATGGCCACCTTCGCCGCCTCCTCAGAGCATTTCGAGAAGCTGTACGAGATCTTCCGCGGCCTCCATGAAGACCTACAAGG
GGTGCCCGAGCGGCTGCTGGGGGCGGCGGGGACCGAAGAGAAGAAGTTAATCAGGGATTTTGATGAAAAGCAACAGGAAG
CAAATGAAACGTTGGCAGAGATGGAGGCGGAGCTACGTTATGCACCCCTGTCTTTCTGTAACCCCATGATGTCTAAGCTT
CGAAACTATCAGAAGGACCTTGCCAAACTCCATTGGGAGGTGAGAAGCACACCTTTGACAGCCACACCTGGAGGCCGAGG
AGACATGAAATATGGCATATATGCTGTAGAGAATGAGCATATGAATCGGCTTACAGTCTCAAAGGGCAACGCTTCCGCAA
GGTACTGAAAGCCTGAAACAGGCCACCCAAAGTATTGAACGCTCTCATCAGATTGCCACGGAGACTGACCAGATTGGCTT
AGAAATCATAGAAGAGCTGGGAGAACAATGAGACCAGTTAGAG

ORF - retro_pabe_2298 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.34 %
Parental protein coverage: 75.43 %
Number of stop codons detected: 1
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalMAASAASSEHFEKLHEIFRGLHEDLQGVPERLLGTAGTEEKKKLIRDFDEKQQEANETLAEMEEELRYAP
MA..AASSEHFEKL.EIFRGLHEDLQGVPERLLG.AGTEEKK.LIRDFDEKQQEANETLAEME.ELRYAP
RetrocopyMATFAASSEHFEKLYEIFRGLHEDLQGVPERLLGAAGTEEKK-LIRDFDEKQQEANETLAEMEAELRYAP
ParentalLSFRNPMMSKLRNYRKDLAKLHREVRSTPLTATPGGRGDMKYGIYAVENEHMNRL-QSQRAMLLQGTESL
LSF.NPMMSKLRNY.KDLAKLH.EVRSTPLTATPGGRGDMKYGIYAVENEHMNRL.QSQRA.L.QGTESL
RetrocopyLSFCNPMMSKLRNYQKDLAKLHWEVRSTPLTATPGGRGDMKYGIYAVENEHMNRL>QSQRATLPQGTESL
ParentalNRATQSIERSHRIATETDQIGSEIIEELGEQRDQLE
..ATQSIERSH.IATETDQIG.EIIEELGEQ.DQLE
RetrocopyKQATQSIERSHQIATETDQIGLEIIEELGEQ*DQLE

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
SRP007412_brain_prefrontal_cortex 0 .11 RPM 80 .61 RPM
SRP007412_cerebellum 0 .00 RPM 47 .42 RPM
SRP007412_heart 0 .03 RPM 29 .11 RPM
SRP007412_kidney 0 .03 RPM 83 .36 RPM
SRP007412_liver 0 .00 RPM 40 .30 RPM

ChIP-Seq - click to see more details

Pongo abelii was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_pabe_2298 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_2298 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_2298 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_2682
Gorilla gorilla retro_ggor_1871
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 ENSG000001005683 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 ENSPPYG00000005927 5 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,


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