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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagtatgttttcacattcgattattgtcttatatggtaaattcctgtttagctgattttatcaaatattatcctgagttcctacttcatgatcaatgcagATATCTGGTTCCTGCTGATCTGACTGTTGGGCAGTTTGTTTATGTGATCCGGAAGAGGATCAAGCTTAGTGCTGAGAAGGCTATTTTCATTTTTGTCAAG

Basic information

species Vitis vinifera
transcript Vv19s0090g00580.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0090g00580.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os04g53240.2 (Oryza sativa), 3'ss of exon 5
--tagtatgttttcacattcgattattgtcttatatggtaaattcctgtttagctgattttatcaaatattatcctgagttcctacttcatgatcaatgcagATATCTGGTTCCTGCTGATCTGACTGTTGGGCAGTTTGTTTATGTGATCCGGAAGAGGATCAAGCTTAGTGCTGAGAAGGCTATTTTCATTTTTGTCAAG
  | | |  ||||     ||    | | |  || ||| || ||      | |    || ||| |   ||| ||||| |||  ||  |   |    |||  || || ||||| ||||||||||| || |||||||||||||| |||||  | |||||| |||||||||| ||| ||||||| || || ||||| ||||| |||
gctcgaaacttttgttgctctgaaactttaatacatgttacatcaagtatcaatcaatattaccg--tatcatccttagtagcttatgattttctaatatagGTACCTGGTCCCTGCTGATCTTACCGTTGGGCAGTTTGTCTATGTTGTTCGGAAGCGGATCAAGCTCAGTCCTGAGAAAGCAATCTTCATCTTTGTGAAG

upper sequence: Vv19s0090g00580.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os08g09240.1 (Oryza sativa), 3'ss of exon 4
---tagta-tgttt-tcacattcgattattgtcttatatggtaaattcctgtttagctgattttatcaaatattatcctgagttcctacttcatgatcaatgcagATATCTGGTTCCTGCTGATCTGACTGTTGGGCAGTTTGTTTATGTGATCCGGAAGAGGATCAAGCTTAGTGCTGAGAAGGCTATTTTCATTTTTGTCAAG
   ||||  ||| | ||| | | ||| | | |   ||   |||| |  | |   | |   | ||  | ||    | | |  |||| |  ||    ||  |||||| || || ||||| ||||| || || ||||| |||||||| |||||  | |||||| |||||||||| |||||||||||||| || ||||| || ||||||
ttttagtcctgtctatcatacttgataactcttgcatcctgtaa-tggcagcaaaaccactgttgaccaac--caccatatgttcttttttatctat--atgcagGTACCTTGTTCCCGCTGACCTCACGGTTGGACAGTTTGTGTATGTTGTTCGGAAGCGGATCAAGCTCAGTGCTGAGAAGGCAATCTTCATCTTCGTCAAG

upper sequence: Vv19s0090g00580.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G419694_T05 (Zea mays), 3'ss of exon 4
------tagtatgttttcacattcgattattgtcttatatggtaaattcctgtttagctgattttatcaaatattatcctgagttcctact--tcatgatcaatgcagATATCTGGTTCCTGCTGATCTGACTGTTGGGCAGTTTGTTTATGTGATCCGGAAGAGGATCAAGCTTAGTGCTGAGAAGGCTATTTTCATTTTTGTCAAG
          ||| |    ||||  |  ||| |   | |    |||  |  |||  || |       |  | | | | |||| || ||  |   ||| | |  ||||| || || || ||||| ||||| || || ||||| || || |||||  |  ||||||| |||||||| ||||||||||||||||| ||||| ||||| || 
acaaaaagaaatgctactgcattaaagcattattgcacacatcaaaagcgagtt--gcag------ccgtaaactgttctgattttctgatggccatcaactttgcagGTACCTCGTCCCTGCAGATCTTACAGTCGGGCAATTCGTGTATGTTGTTAGGAAGAGAATCAAGCTCAGTGCTGAGAAGGCTATCTTCATATTTGTGAAA

upper sequence: Vv19s0090g00580.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G134613_T01 (Zea mays), 3'ss of exon 3
tagtatgttttcacattcgattattgtcttatatggtaaattcctgtttagctgattttatca--aatattatcctgagttcctacttcatgatcaat-gcagATATCTGGTTCCTGCTGATCTGACTGTTGGGCAGTTTGTTTATGTGATCCGGAAGAGGATCAAGCTTAGTGCTGAGAAGGCTATTTTCATTTTTGTCAAG
   |   ||    |||  || |   ||||| | |           |     |    |  | ||    | |   ||    |   |   |  ||||   | |||| || || |||||||| || || || || || |||||||| |||||| | |||||| |||||||||| || ||||||||||| || ||||| || || |||
---ttaattaattcatcagaatgaggtcttgtttatcggtacaaggcaagaccagctgcaacatttgtgtggcccctgatatgtgaattgtgattgcttgcagGTACCTTGTTCCTGCCGACCTCACAGTCGGACAGTTTGTGTATGTGGTACGGAAGCGGATCAAGCTCAGCGCTGAGAAGGCAATCTTCATCTTCGTAAAG

upper sequence: Vv19s0090g00580.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G076826_T02 (Zea mays), 3'ss of exon 5
-tagtatgttttcacattcgattattgtcttatatggtaaattcct----gtttagctgattttatcaaatattatcctgagttcctact-tcatgatcaatgcagATATCTGGTTCCTGCTGATCTGACTGTTGGGCAGTTTGTTTATGTGATCCGGAAGAGGATCAAGCTTAGTGCTGAGAAGGCTATTTTCATTTTTGTCAAG
  |  ||  ||   ||||  |  |   |   | |    ||| |  |    |||  |   |   ||  ||  | ||  |||  |||  | | |||| |    ||||| || || || ||||||||||| || ||||| || || || |||||  |  ||||||| |||||||| ||||||||||| ||||| ||||| ||||| |||
caaaaatactt---cattaaagcaccattgcacacatcaaagtgttatgtgttgtgtcaaccatagtaagcaataagctg--ttctgattgtcataactt-tgcagGTACCTCGTCCCTGCTGATCTTACGGTTGGACAATTCGTGTATGTTGTTAGGAAGAGAATCAAGCTCAGTGCTGAGAAAGCTATCTTCATCTTTGTGAAG

upper sequence: Vv19s0090g00580.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S249_51V6.1 (Physcomitrella patens), 3'ss of exon 2
---------------------------------------------------tagtat-gttttcacattcgattattgtcttatatggtaaattc---ctgtttagctga--------ttttatcaaatattatcctgagttcctacttcatg-atcaatgcagATATCTGGTTCCTGCTGATCTGACTGTTGGGCAGTTTGTTTATGTGATCCGGAAGAGGATCAAGCTTAGTGCTGAGAAGGCTATTTTCATTTTTGTCAAG
                                                    ||  | ||| |     || |||  |   |  | | |    | |   || ||||  |||          |   |      ||| ||||  |   |     |  ||   |||||||||||||| || |||||| |||| || ||||| ||||||||||| ||  ||||| | || ||  | ||| | ||||| || ||||| || ||||| || 
gcatgtttttacatctgttaacttgagaaagacggatctgttcttatgttccagggtcgttctttttctcaatttctaaatcgtgtcgaggttccgatctctttatgtgaaaagggaccctgcccttgctgtattctgaacttacagaatgtatatgtgtgcagATATCTGGTGCCAGCTGATTTGACAGTCGGGCAATTTGTTTATGTCATAAGGAAGCGTATTAAATTGAGTTCCGAGAAAGCCATTTTTATATTTGTGAAA

upper sequence: Vv19s0090g00580.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ09352 (Selaginella moellendorffii), 3'ss of exon 3
---------------------------------------tagtatgttttcacattcgattattgtcttatatggtaaattcc-tgtttagctgattttatcaaatattatcctga-gttcctacttcatgatcaa---tgcagATATCTGGTTCCTGCTGATCTGACTGTTGGGCAGTTTGTTTATGTGATCCGGAAGAGGATCAAGCTTAGTGCTGAGAAGGCTATTTTCATTTTTGTCAAG
                                          | | | |     |  || |   |  |||      |  || |    ||  ||   | |       ||||  || | | |    |   ||  ||      |||| || || || || |||||| | || ||||| ||||| || |||||||||||||||||||||||  | | | | |||||||| || ||| |||| ||||||
gtaagcgctctctctctctctctctctctctctctctctctctctctctctctctcggactccggaattactctaaagcttacgcaattctctctctcttctgggaattactctaaagctttcgcgcgatcttcttgctcgcagGTACCTCGTCCCGGCTGATTTAACCGTTGGCCAGTTCGTCTATGTGATCCGGAAGAGGATCAAAGTGACTCCGGAGAAGGCAATCTTCGTTTTCGTCAAG

upper sequence: Vv19s0090g00580.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ35003 (Selaginella moellendorffii), 3'ss of exon 3
tagtatgttttcacattcgattattgtcttatatggta-aattcctgtttagct-----gattttatc--------aaatattatcctga-gttcctacttcatgatcaa---tgcagATATCTGGTTCCTGCTGATCTGACTGTTGGGCAGTTTGTTTATGTGATCCGGAAGAGGATCAAGCTTAGTGCTGAGAAGGCTATTTTCATTTTTGTCAAG
  ||| | | || |  ||  |   | ||  | |      |||| || |  ||||      ||| | ||            ||||  || | | |    |   ||  ||      |||| || || || || |||||| | || ||||| ||||| || |||||||||||||||||||||||  | | | | |||||||| || ||| |||| ||||||
--gtaagctctctctctctctctctctcagagactccggaattactctaaagcttgcgcaattctctctctcttctgggaattactctaaagctttcgcgcgatcttcttgctcgcagGTACCTCGTCCCGGCTGATTTAACCGTTGGCCAGTTCGTCTATGTGATCCGGAAGAGGATCAAAGTGACTCCGGAGAAGGCAATCTTCGTTTTCGTCAAG

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|27584174|gb|CB006869.1|CB006869
EST:     GAAAGAAGTGACATACCTGACATTGACAAGAAGAA                         ATATCTGGTTCCTGCTGATCTGACTGTTGGGCAGTTTGTTTATGTGATCCG
genomic: GAAAGAAGTGACATACCTGACATTGACAAGAAGAAgttagtcaaa ... atcaatgcagATATCTGGTTCCTGCTGATCTGACTGTTGGGCAGTTTGTTTATGTGATCCG
EST: gi|110407776|gb|EC973391.1|EC973391
EST:     ATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAGAA                         ATATCTGGTTCCTGCTGATCTGACTGTTGGGCAGTTTGTTTATGTGATCCG
genomic: ATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAGAAgttagtcaaa ... atcaatgcagATATCTGGTTCCTGCTGATCTGACTGTTGGGCAGTTTGTTTATGTGATCCG
EST: gi|32459630|gb|CD800804.1|CD800804
EST:     ATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAGAA                         ATATCTGGTTCCTGCTGATCTGACTGTTGGGCAGTTTGTTTATGTGATCCG
genomic: ATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAGAAgttagtcaaa ... atcaatgcagATATCTGGTTCCTGCTGATCTGACTGTTGGGCAGTTTGTTTATGTGATCCG
EST: gi|110390932|gb|EC955876.1|EC955876
EST:     ATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAGAA                         ATATCTGGTTCCTGCTGATCTGACTGTTGGGCAGTTTGTTTATGTGATCCG
genomic: ATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAGAAgttagtcaaa ... atcaatgcagATATCTGGTTCCTGCTGATCTGACTGTTGGGCAGTTTGTTTATGTGATCCG
EST: gi|110694887|gb|EE072272.1|EE072272
EST:     ATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAGAA                         ATATCTGGTTCCTGCTGATCTGACTGTTGGGCAGTTTGTTTATGTGATCCG
genomic: ATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAGAAgttagtcaaa ... atcaatgcagATATCTGGTTCCTGCTGATCTGACTGTTGGGCAGTTTGTTTATGTGATCCG
EST: gi|46911389|gb|CN546764.1|CN546764
EST:     ATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAGAA                         ATATCTGGTTCCTGCTGATCTGACTGTTGGGCAGTTTGTTTATGTGATCCG
genomic: ATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAGAAgttagtcaaa ... atcaatgcagATATCTGGTTCCTGCTGATCTGACTGTTGGGCAGTTTGTTTATGTGATCCG
EST: gi|110421257|gb|EC987552.1|EC987552
EST:     ATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAGAA                         ATATCTGGTTCCTGCTGATCTGACTGTTGGGCAGTTTGTTTATGTGATCCG
genomic: ATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAGAAgttagtcaaa ... atcaatgcagATATCTGGTTCCTGCTGATCTGACTGTTGGGCAGTTTGTTTATGTGATCCG
EST: gi|110422502|gb|EC988827.1|EC988827
EST:     ATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAGAA                         ATATCTGGTTCCTGCTGATCTGACTGTTGGGCAGTTTGTTTATGTGATCCG
genomic: ATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAGAAgttagtcaaa ... atcaatgcagATATCTGGTTCCTGCTGATCTGACTGTTGGGCAGTTTGTTTATGTGATCCG
EST: gi|71888297|gb|DT037352.1|DT037352
EST:     ATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAGAA                         ATATCTGGTTCCTGCTGATCTGACTGTTGGGCAGTTTGTTTATGTGATCCG
genomic: ATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAGAAgttagtcaaa ... atcaatgcagATATCTGGTTCCTGCTGATCTGACTGTTGGGCAGTTTGTTTATGTGATCCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttagctgattttatcaaatattatcctgagttcctacttcatgatcaatgcagATATCTGGTTCCTGCTGATCTGACTGTTGGGCAGTTTGTTTATGTGATCCGGAAGAGGATCAAGCTTAGTGCTGAGAAGGCTATTTTCATTTTTGTCAAG
    agctgat  putative branch site (score: 4)
       tgattttatcaaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagtatgttttcacattcgattattgtcttatatggtaaattcctgtttagctgattttatcaaatattatcctgagttcctacttcatgatcaatgcagATATCTGGTTCCTGCTGATCTGACTGTTGGGCAGTTTGTTTATGTGATCCGGAAGAGGATCAAGCTTAGTGCTGAGAAGGCTATTTTCATTTTTGTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - -cacattc
- - - - - - - - - - - - - - - - - - - - ttcctgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atcaaat