RetrogeneDB ID:

retro_cjac_1439

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:15:96608367..96608910(-)
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:ENSCJAG00000015263
Aliases:None
Description:vesicle transport through interaction with t-SNAREs 1B [Source:HGNC Symbol;Acc:17793]


Retrocopy-Parental alignment summary:






>retro_cjac_1439
AGGAAGCAAATGAAACAAATGCCGGCAGAGATGGAGGATGAGCTACGTTATGCACCCCTCTTTCAATAACCACATGATAT
GTCAAAGCTTTGAAACCACCAGAAGCATTTGCCAAACTCCACCTGGAGGTGAGAAGTACACATTTGACAGCCACACCTGG
AGGCTGAGGAGACATGAAATACGGCACAGATGTCGTAGAGAACGAGCATATGAATCAGCTACAGTCTCAAAGGGCAATGC
TTCCACAAGGCACTGAAAGCCTGAACTTGGCCACCCAAAGTATTGAACGTTCTCATTGGATTGCCATGGAGACTGACCAG
ATTGGCTCTATGATTTATAGAAGAGGTGGGGGAACAACGAGACCAGTTAGAATGCACCAAGAGTAGACTGGTAAACACAA
GCGAAAACTTGAGCAAAAGTCAAAAGATTCTGTGCTCAATGTCCAGAAAAGTGACAACCAACAAGCTGCTGCTTTCCATC
ATTATCCTACTGGAGCTCGCCATTGTGAGAGGCTGGGTTTACTACAAATTCTTTGGCAACCAT

ORF - retro_cjac_1439 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 74.86 %
Parental protein coverage: 78.02 %
Number of stop codons detected: 3
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalQQEANETLAEMEEELRYAPLSFRNPMMSKLRNYRKDL-AKIHREVRSTPLTATPGGRGDMKYGIYAVENE
........AEME.ELRYAPL......MSKL.N..K.L.AK.H.EVRST.LTATPGG.GDMKYG...VENE
RetrocopyRKQMKQMPAEMEDELRYAPLFQ*PHDMSKL*NHQKHL<AKLHLEVRSTHLTATPGG*GDMKYGTDVVENE
ParentalHMNRLQSQRSLLLQGTESLNRATQSIERSHRIATETDQIGSEI-IEELGEQRDQLERTKNRLVNTSENLS
HMN.LQSQR..L.QGTESLN.ATQSIERSH.IA.ETDQIGS.I.IEE.GEQRDQLE.TK.RLVNTSENLS
RetrocopyHMNQLQSQRAMLPQGTESLNLATQSIERSHWIAMETDQIGSMI>IEEVGEQRDQLECTKSRLVNTSENLS
ParentalKSRKILRSMSRKVTTNKLLLSIIILLELAILGGLVYYKFFRSH
KS.KIL.SMSRKVTTNKLLLSIIILLELAI..G.VYYKFF..H
RetrocopyKSQKILCSMSRKVTTNKLLLSIIILLELAIVRGWVYYKFFGNH

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
SRP051959_colon 0 .04 RPM 8 .59 RPM
SRP051959_heart 0 .11 RPM 13 .52 RPM
SRP051959_kidney 0 .07 RPM 17 .48 RPM
SRP051959_liver 0 .15 RPM 12 .26 RPM
SRP051959_lung 0 .08 RPM 12 .64 RPM
SRP051959_lymph_node 0 .07 RPM 12 .85 RPM
SRP051959_skeletal_muscle 0 .02 RPM 17 .23 RPM
SRP051959_spleen 0 .06 RPM 14 .71 RPM

ChIP-Seq - click to see more details

Callithrix jacchus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_cjac_1439 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_1439 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_1439 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 18 parental genes, and 38 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG00000015263 1 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 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,


Copyright © RetrogeneDB 2014-2017