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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagagacagttttgagacttaagattcttattgaaggctccaagtttcgaggttctgcttatgtgcgattacacctgagtttttattcggtgttttttgttgtgcttacagATGCGAACTTATGCAAGAACAGGGGAGAATCCTCCAGATGGATTTATGTGTCCGAGTGGATGGAATGTTCTTGTCAAATACTATGAGAGCTTGCAAGAGA

Basic information

species Arabidopsis thaliana
transcript AT1G19920.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G19920.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G158147_T01 (Zea mays), 3'ss of exon 4
gtaagagacagttttgagacttaagattcttattgaaggctccaagtttcgaggttctgcttatgtgcgattacacctgagtttttattcggtgttttttgttgtgcttacagATGCGAACTTATGCAAGAACAGGGGAGAATCCTCCAGATGGATTTATGTGTCCGAGTGGATGGAATGTTCTTGTCAAATACTATGAGAGCTTGCAAGAGA
                     || | |    |     | |    |||||     |  | |        |||||| ||||      ||  || ||   |    | | |   |||||||| |||||||| | ||| || |||||||||||||| || || ||||| ||| |||| ||||| ||||||||  | |||||  | ||| ||||||   
--------------------gtaggttcgccacaattgtcattcagttt-----tcgtaccagcagtggattactcctg-----ctaaccgttgacctcacatat-caaccagATGCGCACTTATGCCAAAACTGGAGAGAATCCTCCAGACGGTTTCATGTGCCCGGGTGGGTGGAAGGTTCTTGTTGACTACTACAACAGCCTGCAAGCTG

upper sequence: AT1G19920.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA19G05020.1 (Glycine max), 3'ss of exon 5
gtaagagacagttttgagacttaagattcttattgaaggc-tccaagtttcgaggttctgcttatgtgcgattacacctgagtttttattcggtgttttttgttgtgcttacagATGCGAACTTATGCAAGAACAGGGGAGAATCCTCCAGATGGATTTATGTGTCCGAGTGGATGGAATGTTCTTGTCAAATACTATGAGAGCTTGCAAGAGA
     | |     |  ||  | ||| |  ||  ||||  | | | |   |    |   || |  | | | | |     | |   ||| || | || ||| ||||     | ||||||||| ||| ||||| ||  ||||||||||| ||  | || |||||||| || || |||||||| ||||||||||| |||||||| || ||||| |   
-----acatcacatgtagcatcaagttggtttctgaaatccttcgacaattagagaagtgttc-tatacaaat---tttcatcgtttctttgatgatttatgtt-----tccagATGCGAGCTTTTGCAAAAAGTGGGGAGAATCCGCCCAAAGGTTTTATGTGCCCAAGCGGATGGAAGGTTCTTGTCAAGTACTATGAAAGTTTGCAGGCAG

upper sequence: AT1G19920.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA13G06940.1 (Glycine max), 3'ss of exon 4
gtaagagacagttttgagacttaagattcttattgaaggc-tccaagtttcgaggttctgcttatgtgcgattacacctgagtttttattcggtgttttttgttgtgcttacagATGCGAACTTATGCAAGAACAGGGGAGAATCCTCCAGATGGATTTATGTGTCCGAGTGGATGGAATGTTCTTGTCAAATACTATGAGAGCTTGCAAGAGA
     | |     |  ||    ||| |  ||  ||||  | |   |   | | |  |||| |  | | | | |   | ||    ||| ||   || ||| | ||     | ||||||||  ||| ||||| ||  ||||||||||| ||||| || || ||||| || ||||| ||||| |||||||||||||| ||||| || ||||| |   
-----acatcacatgtagcaacaagttggtttctgaaatcctttgacaattgggcatctgttctt-tacaaattttcgtgg---tttctttaatgatttatatt-----tccagATGCGGGCTTTTGCAAAAAGTGGGGAGAATCCGCCAGAAGGTTTCATGTGCCCAAGTGGGTGGAAGGTTCTTGTCAAATATTATGAAAGTTTGCAGGCAG

upper sequence: AT1G19920.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv18s0001g14010.t01 (Vitis vinifera), 3'ss of exon 4
gtaagagacagttttgagacttaagattcttattgaaggctccaagtttcgaggttctgcttatgtgcgattacacctgagtttttattcggtgttttttgt-tgtgcttacagATGCGAACTTATGCAAGAACAGGGGAGAATCCTCCAGATGGATTTATGTGTCCGAGTGGATGGAATGTTCTTGTCAAATACTATGAGAGCTTGCAAGAGA
         |  ||||   |  |  | | |||  ||||  | | || |   ||    |  |        |  ||   |   | || ||| ||||   ||  | |||  || |||||||| |||||||||||||  || ||||| ||||| ||||| |||||||| ||    ||||||| ||| ||||||| |||||||||||| |||||||   
---------acatttg---cccattaatgttaaagaagtttactagatattagaaaataatagaacttaa--actttttcttattaatttggtgaacttgttatgtcattgcagATGCGGACTTATGCAAGAAACGGTGAGAACCCTCCTGATGGTTTTATGTGCCCCCAGGGATGGAGTGTCCTTGTCAGATACTATGAGAGTTTGCAAGCAG

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|86077601|gb|DR373358.1|DR373358
EST:     TTTTCGATCCTTCTCGTGCAAAAGAGTTTCTTTTCATTTCTGGAACAAAG                         ATGCGAACTTATGCAAGAACAGGGGAGAATCCTCCAGATGGATTTATGTGT
genomic: TTTTCGATCCTTCTCGTGCAAAAGAGTTTCTTTTCATTTCTGGAACAAAGgtaagagaca ... gtgcttacagATGCGAACTTATGCAAGAACAGGGGAGAATCCTCCAGATGGATTTATGTGT
EST: gi|116412934|gb|EG455526.1|EG455526
EST:     TTTTCGATCCTTCTCGTGCAAAAGAGTTTCTTTTCATTTCTGGAACAAAG                         ATGCGAACTTATGCAAGAACAGGGGAGAATCCTCCAGATGGATTTATGTGT
genomic: TTTTCGATCCTTCTCGTGCAAAAGAGTTTCTTTTCATTTCTGGAACAAAGgtaagagaca ... gtgcttacagATGCGAACTTATGCAAGAACAGGGGAGAATCCTCCAGATGGATTTATGTGT
EST: gi|124808915|gb|EH894789.1|EH894789
EST:     GATCCTTCTCGTGCAAAAGAGTTTCTTTTCATTTCTGGAACAAAG                         ATGCGAACTTATGCAAGAACAGGGGAGAAT
genomic: GATCCTTCTCGTGCAAAAGAGTTTCTTTTCATTTCTGGAACAAAGgtaagagaca ... gtgcttacagATGCGAACTTATGCAAGAACAGGGGAGAAT
EST: gi|125308543|gb|EL322628.1|EL322628
EST:     TCTTTTCATTTCTGGAACAAAG                         ATGCGAACTTTATTGCAAGAACAGGGGAGAATCCTCCAGATGGATTTATGT
genomic: TCTTTTCATTTCTGGAACAAAGgtaagagaca ... gtgcttacagATGCGAAC-TTA-TGCAAGAACAGGGGAGAATCCTCCAGATGGATTTATGT
EST: gi|86034470|gb|DR330223.1|DR330223
EST:     TTTTCGATCCTTCTCGTGCAAAAGAGTTTCTTTTCATTTCTGGAACAAAG                         ATGCGAACTTATGCAAGAACAGGGGAGAATCCTCCAGATGGATTTATGTGT
genomic: TTTTCGATCCTTCTCGTGCAAAAGAGTTTCTTTTCATTTCTGGAACAAAGgtaagagaca ... gtgcttacagATGCGAACTTATGCAAGAACAGGGGAGAATCCTCCAGATGGATTTATGTGT
EST: gi|86034473|gb|DR330226.1|DR330226
EST:     TTTTCGATCCTTCTCGTGCAAAAGAGTTTCTTTTCATTTCTGGAACAAAG                         ATGCGAACTTATGCAAGAACAGGGGAGAATCCTCCAGATGGATTTATGTGT
genomic: TTTTCGATCCTTCTCGTGCAAAAGAGTTTCTTTTCATTTCTGGAACAAAGgtaagagaca ... gtgcttacagATGCGAACTTATGCAAGAACAGGGGAGAATCCTCCAGATGGATTTATGTGT
EST: gi|124858450|gb|EH942887.1|EH942887
EST:     CTGGAACAAAG                         ATGCGAACTTATGCAAGAACAGGGGAGAATCCTCCAGATGGATTTATGTGT
genomic: CTGGAACAAAGgtaagagaca ... gtgcttacagATGCGAACTTATGCAAGAACAGGGGAGAATCCTCCAGATGGATTTATGTGT
EST: gi|86034472|gb|DR330225.1|DR330225
EST:     TTTCGATCCTTCTCGTGCAAAAGAGTTTCTTTTCATTTTCTGGAACAAAG                         ATGCGAACTTTATGCAAGAACA
genomic: TTTCGATCCTTCTCGTGCAAAAGAGTTTCTTTTCATTT-CTGGAACAAAGgtaagagaca ... gtgcttacagATGCGAACTT-ATGCAAGAACA
EST: gi|116412935|gb|EG455527.1|EG455527
EST:     TTTTCGATCCTTTTCGTGCAAAAGAGTTTCTTTTCATTTTTGGAACAAAG                         ATGCGAACTTATGCAAGAACAGGGGAGAATCCTCCAGATGGATTTATGTGT
genomic: TTTTCGATCCTTCTCGTGCAAAAGAGTTTCTTTTCATTTCTGGAACAAAGgtaagagaca ... gtgcttacagATGCGAACTTATGCAAGAACAGGGGAGAATCCTCCAGATGGATTTATGTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttatgtgcgattacacctgagtttttattcggtgttttttgttgtgcttacagATGCGAACTTATGCAAGAACAGGGGAGAATCCTCCAGATGGATTTATGTGTCCGAGTGGATGGAATGTTCTTGTCAAATACTATGAGAGCTTGCAAGAGA
                     agtttttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagagacagttttgagacttaagattcttattgaaggctccaagtttcgaggttctgcttatgtgcgattacacctgagtttttattcggtgttttttgttgtgcttacagATGCGAACTTATGCAAGAACAGGGGAGAATCCTCCAGATGGATTTATGTGTCCGAGTGGATGGAATGTTCTTGTCAAATACTATGAGAGCTTGCAAGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA