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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatacatcttcttccattcacatgtctttactgccaacaacagtgtgatttctggctgcaacaatgctaatggcaacctgtgattaccatatcatattcagtttgtccttgatgtttcttcttttcttttcttcatgcagATTTTGAAGATATGAGTTGTGAAATGGTCTATGGGCAAGTCCCACCTCCATTTGAAGAGGATCCAGTGTCCAAACAGCCATGTTTTTCGGATATCT

Basic information

species Vitis vinifera
transcript Vv02s0025g02640.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g02640.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os08g02210.1 (Oryza sativa), 3'ss of exon 3
--------------------------------gtatacatcttc--ttccattcacatgtctttactgccaacaacagtgtgatttctggc-tgcaa-----caatgctaatggcaacctgtgattaccatatcatattcagtt-tgt-ccttgatgtttcttcttttcttttcttcatgcagATTTTGAAGATATGAGTTGTGAAATGGTCTATGGGCAAGTCCCACCTCCATTTGAAGAGGATCCAGTGTCCAAACAGCCATGTTTTTCGGATATCT
                                |   |  ||| |  || | |   | |||  ||  || |||  |||   |    | || | ||||      | || ||  |      |  |  ||||  | || ||     || ||| || ||| ||      |||     ||  |  |||||||||||||||||||| ||||||||| | || || ||||| || || || || ||||| || ||||  || |||||||| || | | |  || | |
gtaagacagacatcgttcttgtgctactcaatgccaaactctgcagtttcctcttcctgttctt-ttgacaatgacatactaccatttgacatgcatgttgtccatcctttttcttctcaatttttacactgtcctagctgattatgtaccctgaagtactgaatttatgaatcacc--gcagATTTTGAAGATATGAGCTGTGAAATGATTTACGGCCAAGTGCCCCCACCCTTGGAAGAAGACCCAGCATCAAAACAGCCCTGCTATGCCAATCTAT

upper sequence: Vv02s0025g02640.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA02G09680.2 (Glycine max), 3'ss of exon 5
gtatacatcttcttccattcacatgtc----tttactgccaacaacagtgt---gatttctggctgcaacaatgctaatggcaacctgtgattaccatatcat----------attcagtttgtccttgatgtttcttct----tttcttttcttcat-gcagATTTTGAAGATATGAGTTGTGAAATGGTCTATGGGCAAGTCCCACCTCCATTTGAAGAGGATCCAGTGTCCAAACAGCCATGTTTTTCGGATATCT
   ||  ||||||| |  | ||  | |    ||||  |   |||    ||     || | |  || |   ||   || |       | | ||||   | | ||          |||||| |  |  |  |  ||| |||     | |||   ||| ||   |||||||||||| ||||||||||| ||||| ||||| |||||||||||| |||||||||| || || || || |||||  | |||| | || |||| |
--gtatgtcttcttgctattactagccaaaatttaaggtttacattcttgattacatatataacttcccaaaaaatattattggattattattattttttaatttaaaaaataattcagatcattttaaacttttattcacgtgtatctgaacttaatcatagATTTTGAAGACATGAGTTGTGATATGGTGTATGGCCAAGTCCCACCTACATTTGAAGAAGACCCTGTTTCAAAACAAGCTTGTTATGCGAATATAT

upper sequence: Vv02s0025g02640.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA13G10340.1 (Glycine max), 3'ss of exon 5
gtatacatcttcttccattcac-------------atgtctttactgccaacaaca-gtgtgatttct-------ggctgcaacaatgctaatggcaacctgtgattaccatatcatattcagtttgtccttgatgtttcttcttttctttt----cttcatgc-agATTTTGAAGATATGAGTTGTGAAATGGTCTATGGGCAAGTCCCACCTCCATTTGAAGAGGATCCAGTGTCCAAACAGCCATGTTTTTCGGATATCT
   ||  ||||||| |  ||||             | ||||  | |    |  |||  | ||| ||         |  |  |  | |  || |   |   | | |||   | |  | ||| || |  |  |  |  ||| |||   | | |     ||| ||   |||||||||||||||||||||||| ||||| ||||| |||  ||||||| ||||||||||||| || || || ||||| || || | | ||||||| |
--gtatgtcttcttgctatcactagccaaaaattaaggtctacattcttgattacatatatgacttacccaaaaagattatagtattattattattattttttaatttgaaaaata-atttagatcattttaaacttttattcacctgtatctgaacttaatcttagATTTTGAAGATATGAGTTGTGATATGGTGTATGGCCAATCCCCACCTACATTTGAAGAGGACCCTGTTTCAAAACAACCTTGCTATGCGGATATAT

upper sequence: Vv02s0025g02640.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S6_190V6.1 (Physcomitrella patens), 3'ss of exon 5
gtatacatcttcttccattcacatgtctttactgccaacaacagtgtgatttctggctgcaacaatgctaatggcaacctg----tgatta--ccatatcata----ttcagtttgtcc-ttgatgtttcttcttttcttttcttcatgcagATTTTGAAGATATGAGTTGTGAAATGGTCTATGGGCAAGTCCCACCTCCATTTGAAGAGGATCCAGTGTCCAAACAGCCATGTTTTTCGGATATCT----
||       |   | ||    || | |||||   |         |  | ||| | |||||   | || || |       ||    ||| |   || | ||| |    | |  | ||| | |||| |    | |   |  |||  |  ||||||||||||||||||||| ||||||||| ||||||| ||    || |||||  | ||||| || || | |   || || || ||||||| | |||| |    
gtgagtgcttgacttcaca-gcaggactttaaaacgctgggtcattggttttttagctgccctattgttagttctgtgttgagtctgactgatccgtctcacaagaatgctatgtgtacgttgacgacaatcccaattctttact-gtgcagATTTTGAAGATATGAGCTGTGAAATGTTCTATGGACAGAGTCCGCCTCCCATAGAAGAAGACCCTGCGCTTAAGCAACCGTGTTTTTTGAATATGTGTAT

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|110384986|gb|EC949461.1|EC949461
EST:     TCAAGATTTCTTCACCAACGAATTCGGGCTTCCTTTAACTATGACCCCAA                         ATTTTGAAGATATGAGTTGTGAAATGGTCTATGGGCAAGTCCCACCTCCAT
genomic: TCAAGATTTCTTCACCAACGAATTCGGGCTTCCTTTAACTATGACCCCAAgtatacatct ... cttcatgcagATTTTGAAGATATGAGTTGTGAAATGGTCTATGGGCAAGTCCCACCTCCAT
EST: gi|110374326|gb|EC939496.1|EC939496
EST:     TCAAGATTTCTTCACCAACGAATTCGGGCTTCCTTTAACTATGACCCCAA                         ATTTTGAAGATATGAGTTGTGAAATGGTCTATGGGCAAGTCCCACCTCCAT
genomic: TCAAGATTTCTTCACCAACGAATTCGGGCTTCCTTTAACTATGACCCCAAgtatacatct ... cttcatgcagATTTTGAAGATATGAGTTGTGAAATGGTCTATGGGCAAGTCCCACCTCCAT
EST: gi|110379290|gb|EC944475.1|EC944475
EST:     TCAAGATTTCTTCACCAACGAATTCGGGCTTCCTTTAACTATGACCCCAA                         ATTTTGAAGATATGAGTTGTGAAATGGTCTATGGGCAAGTCCCACCTCCAT
genomic: TCAAGATTTCTTCACCAACGAATTCGGGCTTCCTTTAACTATGACCCCAAgtatacatct ... cttcatgcagATTTTGAAGATATGAGTTGTGAAATGGTCTATGGGCAAGTCCCACCTCCAT
EST: gi|110376860|gb|EC941936.1|EC941936
EST:     TCAAGATTTCTTCACCAACGAATTCGGGCTTCCTTTAACTATGACCCCAA                         ATTTTGAAGATATGAGTTGTGAAATGGTCTATGGGCAAGTCCCACCTCCAT
genomic: TCAAGATTTCTTCACCAACGAATTCGGGCTTCCTTTAACTATGACCCCAAgtatacatct ... cttcatgcagATTTTGAAGATATGAGTTGTGAAATGGTCTATGGGCAAGTCCCACCTCCAT
EST: gi|110422103|gb|EC988415.1|EC988415
EST:     TCAAGATTTCTTCACCAACGAATTCGGGCTTCCTTTAACTATGACCCCAA                         ATTTTGAAGATATGAGTTGTGAAATGGTCTATGGGCAAGTCCCACCTCCAT
genomic: TCAAGATTTCTTCACCAACGAATTCGGGCTTCCTTTAACTATGACCCCAAgtatacatct ... cttcatgcagATTTTGAAGATATGAGTTGTGAAATGGTCTATGGGCAAGTCCCACCTCCAT
EST: gi|110372636|gb|EC936820.1|EC936820
EST:     TCAAGATTTCTTCACCAACGAATTCGGGCTTCCTTTAACTATGACCCCAA                         ATTTTGAAGATATGAGTTGTGAAATGGTCTATGGGCAAGTCCCACCTCCAT
genomic: TCAAGATTTCTTCACCAACGAATTCGGGCTTCCTTTAACTATGACCCCAAgtatacatct ... cttcatgcagATTTTGAAGATATGAGTTGTGAAATGGTCTATGGGCAAGTCCCACCTCCAT
EST: gi|110429787|gb|EC996293.1|EC996293
EST:     CGAATTCGGGCTTCCTTTAACTATGACCCCAA                         ATTTTGAAGATATGAGTTGTGAAATGGTCTATGGGCAAGTCCCACCTCCAT
genomic: CGAATTCGGGCTTCCTTTAACTATGACCCCAAgtatacatct ... cttcatgcagATTTTGAAGATATGAGTTGTGAAATGGTCTATGGGCAAGTCCCACCTCCAT
EST: gi|27755371|gb|CB036126.1|CB036126
EST:     TCAAGATTTCTTCACCAACGAATTCGGGCTTCCTTTAACTATGACCCCAA                         ATTTTGAAGATATGAGTTGTGAAATGGTCTATGGGCAAGTCCCACCTCCAT
genomic: TCAAGATTTCTTCACCAACGAATTCGGGCTTCCTTTAACTATGACCCCAAgtatacatct ... cttcatgcagATTTTGAAGATATGAGTTGTGAAATGGTCTATGGGCAAGTCCCACCTCCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accatatcatattcagtttgtccttgatgtttcttcttttcttttcttcatgcagATTTTGAAGATATGAGTTGTGAAATGGTCTATGGGCAAGTCCCACCTCCATTTGAAGAGGATCCAGTGTCCAAACAGCCATGTTTTTCGGATATCT
                     ccttgat  putative branch site (score: 5)
                tttgtccttgatgttt  CT-rich tract
                                    ttttctttt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatacatcttcttccattcacatgtctttactgccaacaacagtgtgatttctggctgcaacaatgctaatggcaacctgtgattaccatatcatattcagtttgtccttgatgtttcttcttttcttttcttcatgcagATTTTGAAGATATGAGTTGTGAAATGGTCTATGGGCAAGTCCCACCTCCATTTGAAGAGGATCCAGTGTCCAAACAGCCATGTTTTTCGGATATCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT