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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacattcctcctgtggccataaatccgtaatattgtttctcgcattcatctctagcataggttattgatatcttcctttttgacatttgtgactctaaagGTCTGGAACACGGTTGAGAAGCACAAGAAGGGGGAATACACATCAGTAATCCATGGTAAATATAATCATGAAGAGACGATTGCAACTGCGTCTTTTGCAG

Basic information

species Arabidopsis thaliana
transcript AT4G34350.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G34350.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv03s0063g02030.t01 (Vitis vinifera), 3'ss of exon 3
-----------gtacatt--cctcctgtggccataaatccgtaatattgtttctcgcattcatctctagcataggttattgat---atcttcctttttg-acatttgtgactcta----aagGTCTGGAACACGGTTGAGAAGCACAAGAAGGGGGAATACACATCAGTAATCCATGGTAAATATAATCATGAAGAGACGATTGCAACTGCGTCTTTTGCAG
             |  ||  ||| |  |    || |   | |     ||||  ||   |  || ||| ||||   ||  || |   | ||||   |||      |||||||| |     ||||| ||||| |  |||||||||||||||||||| || ||||| ||| | || ||||||||||||  |||||| ||||| ||||||||||| ||||||||||
gtatccttttcagaggttgacctgccattttgatgatatctttgc-ctgttcttcaattatatgtcttgcatctttttctgtttagaacttcggatttatgtccttgtgactttgtttgaagGTTTGGAATATTGTTGAGAAGCACAAGAAGGGAGAGTACACTTCAATCATTCATGGTAAATATTCTCATGAGGAGACTATTGCAACTGCATCTTTTGCAG
















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|116447470|gb|EG490062.1|EG490062
EST:     ATGATAAAAAGGTGCAAATTGTTGACACGACTTGTCCTTGGGTGACAAAG                         GTCTGGAACACGGTTGAGAAGCACAAGAAGGGGGAATACACATCAGTAATC
genomic: ATGATAAAAAGGTGCAAATTGTTGACACGACTTGTCCTTGGGTGACAAAGgtacattcct ... gactctaaagGTCTGGAACACGGTTGAGAAGCACAAGAAGGGGGAATACACATCAGTAATC
EST: gi|125241118|gb|EL255203.1|EL255203
EST:     CCTTGGGTGACAAAG                         GTCTGGAACACGGTTGAGAAGCACAAGAAGGGGGAATACACATCAGTAATC
genomic: CCTTGGGTGACAAAGgtacattcct ... gactctaaagGTCTGGAACACGGTTGAGAAGCACAAGAAGGGGGAATACACATCAGTAATC
EST: gi|124792354|gb|EH882033.1|EH882033
EST:     ATGATAAAAAGGTGCAAATTGTTGACACGACTTGTCCTTGGGTGACAAAG                         GTCTGGAACACGGTTGAGAAGCACAAG
genomic: ATGATAAAAAGGTGCAAATTGTTGACACGACTTGTCCTTGGGTGACAAAGgtacattcct ... gactctaaagGTCTGGAACACGGTTGAGAAGCACAAG
EST: gi|124940492|gb|EL016938.1|EL016938
EST:     CAAATTGTTGACACGACTTGTCCTTGGGTGACAAAG                         GTCTGGAACACGGTTGAGAAGCACAAGAAGGGGGAATACACATCAGTAATC
genomic: CAAATTGTTGACACGACTTGTCCTTGGGTGACAAAGgtacattcct ... gactctaaagGTCTGGAACACGGTTGAGAAGCACAAGAAGGGGGAATACACATCAGTAATC
EST: gi|116447469|gb|EG490061.1|EG490061
EST:     ATGATAAAAAGGTGCAAATTGTTGACACGACTTGTCCTTGGGTGACAAAG                         GTCTGGAACACGGTTGAGAAGCACAAG
genomic: ATGATAAAAAGGTGCAAATTGTTGACACGACTTGTCCTTGGGTGACAAAGgtacattcct ... gactctaaagGTCTGGAACACGGTTGAGAAGCACAAG
EST: gi|125202523|gb|EL217477.1|EL217477
EST:     ATGATAAAAAGGTGCAAATTGTTGACACGACTTGTCCTTGGGTGACAAAG                         GTCTGGAACACGGTTGAGAAGCACAAGAAGGGGGAATA
genomic: ATGATAAAAAGGTGCAAATTGTTGACACGACTTGTCCTTGGGTGACAAAGgtacattcct ... gactctaaagGTCTGGAACACGGTTGAGAAGCACAAGAAGGGGGAATA
EST: gi|124847540|gb|EH931977.1|EH931977
EST:     ATGATAAAAAGGTGCAAATTGTTGACACGACTTGTCCTTGGGTGACAAAG                         GTCTGGAACACGGTT
genomic: ATGATAAAAAGGTGCAAATTGTTGACACGACTTGTCCTTGGGTGACAAAGgtacattcct ... gactctaaagGTCTGGAACACGGTT
EST: gi|125280892|gb|EL294977.1|EL294977
EST:     TGATAAAAAGGTGCAAATTGTTCGACACGACTTGTCCTTGGGTGACAAAG                         GTCTGGAACACGG
genomic: TGATAAAAAGGTGCAAATTGTT-GACACGACTTGTCCTTGGGTGACAAAGgtacattcct ... gactctaaagGTCTGGAACACGG
EST: gi|86036634|gb|DR332387.1|DR332387
EST:     ATGATAAAAAGGTGCAAATTGTTGACACGACTTGTCCTTGGGTGACAAAG                         GTCTGGAACACGGTTGAGAAGCACAAGAAGGGGGAATACACATCAGTAATC
genomic: ATGATAAAAAGGTGCAAATTGTTGACACGACTTGTCCTTGGGTGACAAAGgtacattcct ... gactctaaagGTCTGGAACACGGTTGAGAAGCACAAGAAGGGGGAATACACATCAGTAATC
EST: gi|124998533|gb|EL070802.1|EL070802
EST:     ATAAAAAGGTGCAAATTGTTGACACGACTTGTCCTTGGGTGACAAAG                         GTCTGGAACACGGTTGAGAAGCACAAGAAGGGGGAATACACATCAGTAATC
genomic: ATAAAAAGGTGCAAATTGTTGACACGACTTGTCCTTGGGTGACAAAGgtacattcct ... gactctaaagGTCTGGAACACGGTTGAGAAGCACAAGAAGGGGGAATACACATCAGTAATC
EST: gi|124967607|gb|EL041632.1|EL041632
EST:     AAAAAGGTGCAAATTGTTGACACGACTTGTCCTTGGGTGACAAAG                         GTCTGGAACACGGTTGAGAAGCACAAGAAGGGGGAATACACATCAGTAATC
genomic: AAAAAGGTGCAAATTGTTGACACGACTTGTCCTTGGGTGACAAAGgtacattcct ... gactctaaagGTCTGGAACACGGTTGAGAAGCACAAGAAGGGGGAATACACATCAGTAATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatctctagcataggttattgatatcttcctttttgacatttgtgactctaaagGTCTGGAACACGGTTGAGAAGCACAAGAAGGGGGAATACACATCAGTAATCCATGGTAAATATAATCATGAAGAGACGATTGCAACTGCGTCTTTTGCAG
                                ttttgac  putative branch site (score: 3)
                ttattgatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacattcctcctgtggccataaatccgtaatattgtttctcgcattcatctctagcataggttattgatatcttcctttttgacatttgtgactctaaagGTCTGGAACACGGTTGAGAAGCACAAGAAGGGGGAATACACATCAGTAATCCATGGTAAATATAATCATGAAGAGACGATTGCAACTGCGTCTTTTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA