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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaataagaatatcttatcactgaaacatttttgtctttcataatggtatatgtttgaaactaaacacatgattgttttggtagGTGAAATCTGGTTCCTTGTTCGACAATGTCTTGGTCAGCGATGACCCAGAGTACGCTAAGAAGTTGGCCGAGGAAACCTGGGGAAAGCACAAGGAT

Basic information

species Arabidopsis thaliana
transcript AT1G56340.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G56340.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA10G28890.2 (Glycine max), 3'ss of exon 9
gtaataagaatatcttatcactgaaacatttttgtctttcataatggtatatgtttgaaactaaacacatgattgttttggtagGTGAAATCTGGTTCCTTGTTCGACAATGTCTTGGTCAGCGATGACCCAGAGTACGCTAAGAAGTTGGCCGAGGAAACCTGGGGAAAGCACAAGGAT
|||| || || || | | | || |||| || || | | || || | | || | | |||||||||||||| | ||||| ||||||||||| | | ||||| || ||||| |||||| || ||| || ||||| ||||| ||||||||||||
gtaaacttttaatttttacatcgctatagttgatacttttgtatc--taaactctgacaagcaagc---tattttatcttacagGTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAGTATGCTAAGCAGCTGGTTGAAGAAACATGGGGCAAGCACAAGGAT

upper sequence: AT1G56340.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv07s0005g01390.t01 (Vitis vinifera), 3'ss of exon 9
---gtaataagaatatcttatcactgaaacatttttgtctttcataatggtatatgtttgaaactaaacacatgattgttttggtagGTGAAATCTGGTTCCTTGTTCGACAATGTCTTGGTCAGCGATGACCCAGAGTACGCTAAGAAGTTGGCCGAGGAAACCTGGGGAAAGCACAAGGAT
| || || ||| | ||| ||| || || | | | || | || | | ||| || | ||||||||||||| || ||||||||||| | ||||| ||||||| || || || || |||||| | || || ||||| |||||||||||||||| |
gtaatcatctctatggtttacc-ctgtgctattcttaaattata-attcacatcctaatcaagcaagctacaaaatgcatgcaccagGTGAAATCTGGGACCATGTTCGACAATATTTTGGTTTGCGATGATCCTGATTATGCAAAGAAGCTTGCTGAAGAAACTTGGGGAAAGCACAAGGGT
















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|164237441|gb|ES079564.1|ES079564
EST:     AACTCTATGTCTTCCCCAAATTGAAGTATGTTGGAGTTGAGTTGTGGCAG                         GTGAAATCTGGTTCCTTGTTCG
genomic: AACTCTATGTCTTCCCCAAATTGAAGTATGTTGGAGTTGAGTTGTGGCAGgtaataagaa ... gttttggtagGTGAAATCTGGTTCCTTGTTCG
EST: gi|86064682|gb|DR360439.1|DR360439
EST:     AACTCTATGTCTTCCCCAAATTGAAGTATGTTGGAGTTGAGTTGTGGCAG                         GTGAAATCTGGTTCCTTGTTCGACAATGTCTTGGTCAGCGATGACCCAGAG
genomic: AACTCTATGTCTTCCCCAAATTGAAGTATGTTGGAGTTGAGTTGTGGCAGgtaataagaa ... gttttggtagGTGAAATCTGGTTCCTTGTTCGACAATGTCTTGGTCAGCGATGACCCAGAG
EST: gi|116465699|gb|EG508291.1|EG508291
EST:     AACTCTATGTCTTCCCCAAATTGAAGTATGTTGGAGTTGAGTTGTGGCAG                         GTGAAATCTGGTTCCTTGTTCGACAATGTCTTGGTCAGCGATGACCCAGAG
genomic: AACTCTATGTCTTCCCCAAATTGAAGTATGTTGGAGTTGAGTTGTGGCAGgtaataagaa ... gttttggtagGTGAAATCTGGTTCCTTGTTCGACAATGTCTTGGTCAGCGATGACCCAGAG
EST: gi|163988219|gb|ES092534.1|ES092534
EST:     AACTCTATGTCTTCCCCAAATTGAAGTATGTTGGAGTTGAGTTGTGGCAG                         GTGAAATCTGGTTCCTTGTTCGACAATGTCTTGGTCA
genomic: AACTCTATGTCTTCCCCAAATTGAAGTATGTTGGAGTTGAGTTGTGGCAGgtaataagaa ... gttttggtagGTGAAATCTGGTTCCTTGTTCGACAATGTCTTGGTCA
EST: gi|116465718|gb|EG508310.1|EG508310
EST:     AACTCTATGTCTTCCCCAAATTGAAGTATGTTGGAGTTGAGTTGTGGCAG                         GTGAAATCTGGTTCCTTGTTCGACAATGTCTTGGTCAGCGATGACCCAGAG
genomic: AACTCTATGTCTTCCCCAAATTGAAGTATGTTGGAGTTGAGTTGTGGCAGgtaataagaa ... gttttggtagGTGAAATCTGGTTCCTTGTTCGACAATGTCTTGGTCAGCGATGACCCAGAG
EST: gi|116465735|gb|EG508327.1|EG508327
EST:     AACTCTATGTCTTCCCCAAATTGAAGTATGTTGGAGTTGAGTTGTGGCAG                         GTGAAATCTGGTTCCTTGTTCGACAATGTCTTGGTCAGCGATGACCCAGAG
genomic: AACTCTATGTCTTCCCCAAATTGAAGTATGTTGGAGTTGAGTTGTGGCAGgtaataagaa ... gttttggtagGTGAAATCTGGTTCCTTGTTCGACAATGTCTTGGTCAGCGATGACCCAGAG
EST: gi|125192254|gb|EL207208.1|EL207208
EST:     AACTCTATGTCTTCCCCAAATTGAAGTATGTTGGAGTTGAGTTGTGGCAG                         GTGAAATCTGGTTCCTTGTTCGACAATGTCTTGGTCAGCGATGACCCAG
genomic: AACTCTATGTCTTCCCCAAATTGAAGTATGTTGGAGTTGAGTTGTGGCAGgtaataagaa ... gttttggtagGTGAAATCTGGTTCCTTGTTCGACAATGTCTTGGTCAGCGATGACCCAG
EST: gi|116482410|gb|EG525002.1|EG525002
EST:     AACTCTATGTCTTCCCCAAATTGAAGTATGTTGGAGTTGAGTTGTGGCAG                         GTGAAATCTGGTTCCTTGTTCGACAATGTCTTGGTCAGCGATGACCCAGAG
genomic: AACTCTATGTCTTCCCCAAATTGAAGTATGTTGGAGTTGAGTTGTGGCAGgtaataagaa ... gttttggtagGTGAAATCTGGTTCCTTGTTCGACAATGTCTTGGTCAGCGATGACCCAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgtctttcataatggtatatgtttgaaactaaacacatgattgttttggtagGTGAAATCTGGTTCCTTGTTCGACAATGTCTTGGTCAGCGATGACCCAGAGTACGCTAAGAAGTTGGCCGAGGAAACCTGGGGAAAGCACAAGGAT
                             aactaaa  putative branch site (score: 2)
 ttgtttt  putative PPT
 tttcataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaataagaatatcttatcactgaaacatttttgtctttcataatggtatatgtttgaaactaaacacatgattgttttggtagGTGAAATCTGGTTCCTTGTTCGACAATGTCTTGGTCAGCGATGACCCAGAGTACGCTAAGAAGTTGGCCGAGGAAACCTGGGGAAAGCACAAGGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT