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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggaagtgttaaattcaaagcattgcaactttggtttgtatccttttcacacatttcactatttctcatttgtttttcctttggttctaaatgtgttgcagTCTCGGATCCCTAGTTCTAGCATTGAGTACACTGAAGAATTTGATTTTGAAGCAATGAATGAGAAGTTCAAGAAGAGTGAACTATGGGGTTATCTTGGAA

Basic information

species Arabidopsis thaliana
transcript AT5G45330.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G45330.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA01G35640.1 (Glycine max), 3'ss of exon 6
ggaagtgttaaattcaaagcattgcaactttggtttgtatccttttcacacatttcactatttctca-tttgtt--tttcctttggttctaaatgtgttgcagTCTCGGATCCCTAGTTCTAGCATTGAGTACACTGAAGAATTTGATTTTGAAGCAATGAATGAGAAGTTCAAGAAGAGTGAACTATGGGGTTATCTTGGAA------
|| |  |||| ||  | |    |  |  | |  | | |||   | | | | ||||   ||  | | | | || |  | |   |  ||| |  || | |||||| |||  || |  || || |      | |||||||| || ||||||||||| || |||||||| |||||||| ||   |||| ||||||||| ||||||||      
ggtatagttatatatatatatatatatatata-tatatatatatat-atatatttatatacatgtaaatatgatagtattggtgtgttgttgattt-ttgcagCCTCC-ATACACAGCTCCAC-----AATACACTGAGGAGTTTGATTTTGAGGCCATGAATGAAAAGTTCAAAAAAGATGAAGTATGGGGTTCTCTTGGAAAGACAA
















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|116433931|gb|EG476523.1|EG476523
EST:     CTCCCAGAAATCATGCACCATTGCTGCCTCTTCCAGTTTCAGCTCATCAG                         TCTCGGATCCCTAGTTCTAGCATTGAGTACACTGAAGAATTTGATTTTGAA
genomic: CTCCCAGAAATCATGCACCATTGCTGCCTCTTCCAGTTTCAGCTCATCAGgtatctacct ... tgtgttgcagTCTCGGATCCCTAGTTCTAGCATTGAGTACACTGAAGAATTTGATTTTGAA
EST: gi|116389885|gb|EG432477.1|EG432477
EST:     CTCCCAGAAATCATGCACCATTGCTGCCTCTTCCAGTTTCAGCTCATCAG                         TCTCGGATCCCTAGTTCTAGCATTGAGTACACTGAAGAATTTGATTTTGAA
genomic: CTCCCAGAAATCATGCACCATTGCTGCCTCTTCCAGTTTCAGCTCATCAGgtatctacct ... tgtgttgcagTCTCGGATCCCTAGTTCTAGCATTGAGTACACTGAAGAATTTGATTTTGAA
EST: gi|116389822|gb|EG432414.1|EG432414
EST:     CTCCCAGAAATCATGCACCATTGCTGCCTCTTCCAGTTTCAGCTCATCAG                         TCTCGGATCCCTAGTTCTAGCATTGAGTACACTGAAGAATTTGATTTTGAA
genomic: CTCCCAGAAATCATGCACCATTGCTGCCTCTTCCAGTTTCAGCTCATCAGgtatctacct ... tgtgttgcagTCTCGGATCCCTAGTTCTAGCATTGAGTACACTGAAGAATTTGATTTTGAA
EST: gi|116389763|gb|EG432355.1|EG432355
EST:     CTCCCAGAAATCATGCACCATTGCTGCCTCTTCCAGTTTCAGCTCATCAG                         TCTCGGATCCCTAGTCCTAGCATTGAGTACACTGAAGAATTTGATTTTGAA
genomic: CTCCCAGAAATCATGCACCATTGCTGCCTCTTCCAGTTTCAGCTCATCAGgtatctacct ... tgtgttgcagTCTCGGATCCCTAGTTCTAGCATTGAGTACACTGAAGAATTTGATTTTGAA
EST: gi|116389824|gb|EG432416.1|EG432416
EST:     CTCCCAGAAATCATGCACCATTGCTGCCTCTTCCAGTTTCAGCTCATCAG                         TCTCGGATCCCTAGTTCTAGCATTGAGTACACTGAAGAATTTGATTTTGAA
genomic: CTCCCAGAAATCATGCACCATTGCTGCCTCTTCCAGTTTCAGCTCATCAGgtatctacct ... tgtgttgcagTCTCGGATCCCTAGTTCTAGCATTGAGTACACTGAAGAATTTGATTTTGAA
EST: gi|116389847|gb|EG432439.1|EG432439
EST:     CTCCCAGAAATCATGCACCATTGCTGCCTCTTCCAGTTTCAGCTCATCAG                         TCTCGGATCCCTAGTTCTAGCATTGAGTACACTGAAGAATTTGATTTTGAA
genomic: CTCCCAGAAATCATGCACCATTGCTGCCTCTTCCAGTTTCAGCTCATCAGgtatctacct ... tgtgttgcagTCTCGGATCCCTAGTTCTAGCATTGAGTACACTGAAGAATTTGATTTTGAA
EST: gi|116389931|gb|EG432523.1|EG432523
EST:     CTCCCAGAAATCATGCACCATTGCTGCCTCTTCCAGTTTCAGCTCATCAG                         TCTCGGATCCCTAGTTCTAGCATTGAGTACACTGAAGAATTTGATTTTGAA
genomic: CTCCCAGAAATCATGCACCATTGCTGCCTCTTCCAGTTTCAGCTCATCAGgtatctacct ... tgtgttgcagTCTCGGATCCCTAGTTCTAGCATTGAGTACACTGAAGAATTTGATTTTGAA
EST: gi|86059877|gb|DR355634.1|DR355634
EST:     CTCCCAGAAATCATGCACCATTGCTGCCTCTTCCAGTTTCAGCTCATCAG                         TCTCGGATCCCTAGTTCTAGCATTGAGTACACTGAAGAATTTGATTTTGAA
genomic: CTCCCAGAAATCATGCACCATTGCTGCCTCTTCCAGTTTCAGCTCATCAGgtatctacct ... tgtgttgcagTCTCGGATCCCTAGTTCTAGCATTGAGTACACTGAAGAATTTGATTTTGAA
EST: gi|116389794|gb|EG432386.1|EG432386
EST:     CTCCCAGAAATCATGCACCATTGCTGCCTCTTCCAGTTTCAGCTCATCAG                         TCTCGGATCCCTAGTTCTAGCATTGAGTACACTGAAGAATTTGATTTTGAA
genomic: CTCCCAGAAATCATGCACCATTGCTGCCTCTTCCAGTTTCAGCTCATCAGgtatctacct ... tgtgttgcagTCTCGGATCCCTAGTTCTAGCATTGAGTACACTGAAGAATTTGATTTTGAA
EST: gi|116433932|gb|EG476524.1|EG476524
EST:     CTCCCAGAAATCATGCACCATTGCTGCCTCTTCCAGTTTCAGCTCATCAG                         TCTCGGATCCCTAGTTCTAGCATTGAGTACACTGAAGAATTTGATTTTGAA
genomic: CTCCCAGAAATCATGCACCATTGCTGCCTCTTCCAGTTTCAGCTCATCAGgtatctacct ... tgtgttgcagTCTCGGATCCCTAGTTCTAGCATTGAGTACACTGAAGAATTTGATTTTGAA
EST: gi|116389929|gb|EG432521.1|EG432521
EST:     CTCCCAGAAATCATGCACCATTGCTGCCTCTTCCAGTTTCAGCTCATCAG                         TCTCGGATCCCTAGTTCTAGCATTGAGTACACTGAAGAATTTGATTTTGAA
genomic: CTCCCAGAAATCATGCACCATTGCTGCCTCTTCCAGTTTCAGCTCATCAGgtatctacct ... tgtgttgcagTCTCGGATCCCTAGTTCTAGCATTGAGTACACTGAAGAATTTGATTTTGAA
EST: gi|116433930|gb|EG476522.1|EG476522
EST:     CTCCCAGAAATCATGCACCATTGCTGCCTCTTCCAGTTTCAGCTCATCAG                         TCTCGGATCCCTAGTTCTAGCATTGAGTACACTGAAGAATTTGATTTTGAA
genomic: CTCCCAGAAATCATGCACCATTGCTGCCTCTTCCAGTTTCAGCTCATCAGgtatctacct ... tgtgttgcagTCTCGGATCCCTAGTTCTAGCATTGAGTACACTGAAGAATTTGATTTTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcacacatttcactatttctcatttgtttttcctttggttctaaatgtgttgcagTCTCGGATCCCTAGTTCTAGCATTGAGTACACTGAAGAATTTGATTTTGAAGCAATGAATGAGAAGTTCAAGAAGAGTGAACTATGGGGTTATCTTGGAA
                                      ttctaaa  putative branch site (score: 2)
                     atttgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggaagtgttaaattcaaagcattgcaactttggtttgtatccttttcacacatttcactatttctcatttgtttttcctttggttctaaatgtgttgcagTCTCGGATCCCTAGTTCTAGCATTGAGTACACTGAAGAATTTGATTTTGAAGCAATGAATGAGAAGTTCAAGAAGAGTGAACTATGGGGTTATCTTGGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - caaagca
- - - - - - - - - - - - - - - -ggtttgt
- - - - - - - - - - - - - - - - - - - - - - -tcacaca