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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagattcttttttttttctttttttctctactctgcgtctcaaaatactgtatagatcaatttatcagtttccatgaaaaatatttttttgttgttgttgtggttgtttacatgaagGTTTATCTGGGAGCTGTGGAAGAAGGCAACATTGACGACAAAGGACAAGTTTGGAGATGTGCATACAAGATTGATGAAGAAGAATTATAAGGAAGTACCT

Basic information

species Arabidopsis thaliana
transcript AT4G26590.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G26590.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv19s0015g00890.t01 (Vitis vinifera), 3'ss of exon 3
gtaagattcttttttttttctttttttctctactctgcgtctcaaaatactgtatagatcaatttatcagtttccatgaaaaatatttttttgttgttgttgtggttgtttacatgaagGTTTATCTGGGAGCTGTGGAAGAAGGCAACATTGACGACAAAGGACAAGTTTGGAGATGTGCATACAAGATTGATGAAGAAGAATTATAAGGAAGTACCT
          |   | | |||    || |  ||  ||  || |||   | | | ||||   |||  |  |||  | | | |    | |  | ||| |              |  |  ||    || ||| |  ||||||  ||| |||      |   |   ||  ||||||||||| ||||||| ||| ||||||||||||| |||||   ||| |||
---------gtaggtctctctaacattgttaaccttgtctc-caatccattttctagac--attcctt-gttgacctcacattcttctcatggttttcccacccaaaaaaaatgtttagAACAATTTGGCAAATGTGGAGTAAGACAAGGGCAGCAGTAGGAGATCAGTTTGGAGATATGCATACGAGACTGATGAAGAAGAACTATAAAATAGTCCCT

upper sequence: AT4G26590.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv19s0015g00860.t01 (Vitis vinifera), 3'ss of exon 4
gtaagattctttt----ttttttctttttttctctactctgcgtctcaaaatactgtatagatcaatttatcagtttccatgaaaaatatttttttgttgttgttgtggttgtttacatgaagGTTTATCTGGGAGCTGTGGAAGAAGGCAACATTGACGACAAAGGACAAGTTTGGAGATGTGCATACAAGATTGATGAAGAAGAATTATAAGGAAGTACCT
|||||  |   ||    || ||   ||| |  || |  |    |||  | |  |  | | || |      ||  ||  ||||       ||||| |          |||||   |||         ||||||| |  ||||||  ||| | |      |  ||   || ||||||||||| |||||||| ||| ||||||||||||| |||||   ||| || 
gtaagtcttccttgaaattcttagctttgtcttcaatccattttcttgacaatccttgttgacctcacattc--ttctcatgg------tttttctaccaaaaaaatggtttagTAC---------TATCTGGCAAATGTGGAGTAAGACGAGGGCAGCAGCAGGAGAGAAGTTTGGAGACGTGCATACGAGACTGATGAAGAAGAACTATAAAATAGTCCCC

upper sequence: AT4G26590.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv19s0015g00850.t01 (Vitis vinifera), 3'ss of exon 4
gtaagattcttttttttttctttttttctctactctgcgtctcaaaatactgtatagatcaatttatcagtttccatgaaaaatatttttttgttgttgttgtggttgtttacatgaagGTTTATCTGGGAGCTGTGGAAGAAGGCAACATTGACGACAAAGGACAAGTTTGGAGATGTGCATACAAGATTGATGAAGAAGAATTATAAGGAAGTACCT
|||||  ||||     || |||   |  ||  || ||  ||    |||  | | | |||  |  || || ||| |       ||  ||||   |           |||||||   |||   ||||   | |  ||||||  ||  |||  |   ||  |   ||  |||||||||| ||||| |||||| ||||||||||||| ||| | | ||| || 
gtaagtatcttcaacatt-cttaagtagtcatctttgt-tcctttaattttttgt-gattgaactaacaattttctc-----atgattttccttctgaaaaaaaattgttta---gAACCATTAT---GCAAATGTGGAGAAAAACAAGGTCTGCGGTAGGAGATCAGTTTGGAGACGTGCACACAAGACTGATGAAGAAGAACTATGAAGCAGTCCCC

upper sequence: AT4G26590.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv19s0015g00870.t01 (Vitis vinifera), 3'ss of exon 3
gtaagattctttt----ttttttctttttttctctactctgcgtctcaaaatactgtatagatcaatttatcagtttccatgaaaaatatttttttgttgttgttgtggttgtttacatgaagGTTTATCTGGGAGCTGTGGAAGAAGGCAACATTGACGACAAAGGACAAGTTTGGAGATGTGCATACAAGATTGATGAAGAAGAATTATAAGGAAGTACCT
|||||  | | ||    || ||   ||| |  || |  |    |||  | |  |  | | || |      ||  ||  ||||       ||||| |             |||||||      |   ||||||| |  ||||||  ||| | |      |  ||   || ||||||||||| |||||||| ||| ||||||||||||| |||||   ||| || 
gtaagtctttcttaacattcttagctttgtcttcaatccattttcttgacaatccttgttgaccccacattc--ttctcatgg------tttttctacca--aaaaaaattgttta------gTACTATCTGGCAAATGTGGACTAAGACGAGGGCAGCAGCAGGAGAGAAGTTTGGAGACGTGCATACGAGACTGATGAAGAAGAACTATAAAATAGTCCCC

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|163984877|gb|ES106152.1|ES106152
EST:     TTCGGTACACTTACCGCAACCATTTCTCATGTCGCCCTCTTTGACGGAAA                         GTTTATCTGGGAGCTGTGGAAGAAG
genomic: TTCGGTACCCTTACCGCAACCATTTCTCATGTCGCCCTCTTTGACGGAAAgtaagattct ... ttacatgaagGTTTATCTGGGAGCTGTGGAAGAAG
EST: gi|164162512|gb|ES130276.1|ES130276
EST:     CTTACCGCAACCATTTCTCATGTCGCCCTCTTTGACGGAAA                         GTTTANCTGGGAGCTGTGGAAGAAGGCAACATTG
genomic: CTTACCGCAACCATTTCTCATGTCGCCCTCTTTGACGGAAAgtaagattct ... ttacatgaagGTTTATCTGGGAGCTGTGGAAGAAGGCAACATTG
EST: gi|164074895|gb|ES202057.1|ES202057
EST:     TTCGGTACACTTACCGCAACCATTTCTCATGTCGCCCTCTTTGACGGAAA                         GTTTATCTGGGAGCTGTGGAAGAAGGCAACATTGACGACAAAGGA
genomic: TTCGGTACCCTTACCGCAACCATTTCTCATGTCGCCCTCTTTGACGGAAAgtaagattct ... ttacatgaagGTTTATCTGGGAGCTGTGGAAGAAGGCAACATTGACGACAAAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatcagtttccatgaaaaatatttttttgttgttgttgtggttgtttacatgaagGTTTATCTGGGAGCTGTGGAAGAAGGCAACATTGACGACAAAGGACAAGTTTGGAGATGTGCATACAAGATTGATGAAGAAGAATTATAAGGAAGTACCT
           atgaaaaatatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagattcttttttttttctttttttctctactctgcgtctcaaaatactgtatagatcaatttatcagtttccatgaaaaatatttttttgttgttgttgtggttgtttacatgaagGTTTATCTGGGAGCTGTGGAAGAAGGCAACATTGACGACAAAGGACAAGTTTGGAGATGTGCATACAAGATTGATGAAGAAGAATTATAAGGAAGTACCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA