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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attttcctcagattagggattattcattatgcttcatggttggtttcttatgtttttgacaaagccatctaacttcacatctgttttctttgtttttaagATTGTATTGGTTCGGCTTTCAATGCAAAGGGAGTGATGCAATGCCCCAACTGTCGGAAAGTAGAAAAAGGCCAGTGGCTTTATGCAAACGGTTGTCGTTC

Basic information

species Arabidopsis thaliana
transcript AT3G05545.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G05545.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os01g24880.1 (Oryza sativa), 3'ss of exon 1
attttcctcagattagggattattcattatgcttcatg-gttggtttcttatgtttttgacaaagccatctaacttcacatctgttttctttgtttttaagATTGTATTGGTTCGGCTTTCAATGCAAAGGGAGTGATGCAATGCCCCAACTGTCGGAAAGTAGAAAAAGGCCAGTGGCTTTATGCAAACGGTTGTCGTTC
 || |  |    | |  | | |    |  || |   |    |    |  |   ||| |            | | || |   |||  |      ||  | |||||| |||||||| || || ||||| || ||||| ||||||||||||||||||||  || | || |  ||  | ||||| |||||||| ||||  ||| |
-ttgttatattgtcacagttgagctttcttgttctgtacaataaaattatgcatttgtattgctctttattgattttaatgctgcctatacatttcatcagATTGCATTGGTTCAGCATTTAATGCCAAAGGAGTTATGCAATGCCCCAACTGTCGCCAAATTGAGAGGGGGAATTGGCTCTATGCAAATGGTTCGCGTCC

upper sequence: AT3G05545.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G011473_T01 (Zea mays), 3'ss of exon 1
--attttcctcagattaggga--ttattcattatgcttcatggttggtttcttatg-tttttgacaaagccatctaacttcacatctgttttctttgtttttaagATTGTATTGGTTCGGCTTTCAATGCAAAGGGAGTGATGCAATGCCCCAACTGTCGGAAAGTAGAAAAAGGCCAGTGGCTTTATGCAAACGGTTGTCGTTC
    |  |||||   | | |   |||| |  ||   | ||||     |   ||||| |   | ||  ||    || |  | |     | |||  |||      |||||||||||| || || ||||||||||| |||| |||||||||||| |||||||||||  | || ||||| |  ||||||||||||| |||   |||  |
tctgtcccctcacccttgtgtgtttatgcgataatgtgcatgaaaaatacattatgataccttacgcagattgctgaactaat-caagattttgttgcc----agATTGTATTGGGTCTGCATTCAATGCAAAAGGAGCGATGCAATGCCCTAACTGTCGGAAGATTGAGAAAGGTCGCTGGCTTTATGCAAGCGGACATCGCGC

upper sequence: AT3G05545.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G053027_T01 (Zea mays), 3'ss of exon 1
attttcctcagattagggattattcatt---atgctt-catggttggtttcttatgt--ttttgacaaagccatctaacttcacatctgttttctttgtttttaagATTGTATTGGTTCGGCTTTCAATGCAAAGGGAGTGATGCAATGCCCCAACTGTCGGAAAGTAGAAAAAGGCCAGTGGCTTTATGCAAACGGTTGTCGTTC
  | ||| |  |     |    || ||    ||| || ||||     |   |||||   | || |  |        ||||   ||     |||  |||      |||||||||||| || || ||||||||||| |||| |||||||||||| |||||||||||  | || ||||| |  |||||||||||||  ||  |||   |
tctgtcccctcacccatgtgcgtttatgtgaatgtttgcatgaaaaatacattatgatatcttaagcagattgctgaactaagcaa--aattttcttgcc----agATTGTATTGGGTCTGCATTCAATGCAAAAGGAGCGATGCAATGCCCTAACTGTCGGAAGATTGAGAAAGGTCGCTGGCTTTATGCAAGTGGACGTCACCC

upper sequence: AT3G05545.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA19G42100.1 (Glycine max), 3'ss of exon 1
--attttcctcagattagggattattcattatgcttcatggttggtttcttatgtttttg-acaaagccatctaacttcacatc-tgttttctttgtttttaagATTGTATTGGTTCGGCTTTCAATGCAAAGGGAGTGATGCAATGCCCCAACTGTCGGAAAGTAGAAAAAGGCCAGTGGCTTTATGCAAACGGTTGTCGTTC
   |||| ||   || |   ||| |  | || |||  || | ||  |    |||   |      |          ||||  ||  |  | | | | || || |||||| ||||| || || ||||||  |||||| |  ||||| |||||||| ||||| || || |||||||| |||||||||||||| || |||||||| ||
atgttttacttgaatca---attttataataagctg-atagctgcatctgcatggcatcatgtcatattgctatgcttcttattatagtctttatattgttcagATTGCATTGGCTCAGCCTTCAATATAAAGGGGGCAATGCAGTGCCCCAATTGTCGTAAGGTTGAAAAAGGTCAGTGGCTTTATGCTAATGGTTGTCGATC

upper sequence: AT3G05545.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv14s0060g02280.t01 (Vitis vinifera), 3'ss of exon 1
---attttcctcagattagggattattcattatgcttcatggttggtttcttatgtttttgacaaagccatctaacttcacatctgttttctt--tgtttttaagATTGTATTGGTTCGGCTTTCAATGCAAAGGGAGTGATGCAATGCCCCAACTGTCGGAAAGTAGAAAAAGGCCAGTGGCTTTATGCAAACGGTTGTCGTTC
   ||| |  | | | | |  |||| | ||     |  |    | |  | || |  ||| | || | |    ||   |      | || || |  || | |  |||||| |||||||| || ||||||   || || |  |||||||| || || ||||||||| | |||||||| || |||||||||||||| ||||||||| |
atcattctattaatacttg--attagtgatacgtatctagcacttgcatattgtcctttggccataac---ttattcttgtgattattgtcataatgctctccagATTGCATTGGTTCAGCATTCAATATCAAAGGGGCAATGCAATGTCCTAATTGTCGGAAAATTGAAAAAGGTCAATGGCTTTATGCAAATGGTTGTCGTAC

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|125015195|gb|EL087464.1|EL087464
EST:     GCGATCGAGCATGGGCTAATCTTCAATGTGACCATCAGTTCCATCTAG                         ATTGTATTGGTTCGGCTTTCAATGCAAAGGGAGTGATGCAA
genomic: GCGATCGAGCATGGGCTAATCTTCAATGTGACCATCAGTTCCATCTAGgtgagtttgt ... tgtttttaagATTGTATTGGTTCGGCTTTCAATGCAAAGGGAGTGATGCAA
EST: gi|116447321|gb|EG489913.1|EG489913
EST:     CGGCGATCGAGCATGGGCTAATCTTCAATGTGACCATCAGTTCCATCTAG                         ATTGTATTGGTTCGGCTTTCAATGCAAAGGGAGTGATGCAATGCCCCAACT
genomic: CGGCGATCGAGCATGGGCTAATCTTCAATGTGACCATCAGTTCCATCTAGgtgagtttgt ... tgtttttaagATTGTATTGGTTCGGCTTTCAATGCAAAGGGAGTGATGCAATGCCCCAACT
EST: gi|116463813|gb|EG506405.1|EG506405
EST:     CGGCGATCGAGCATGGGCTAATCTTCAATGTGACCATCAGTTCCATCTAG                         ATTGTATCGGTTCGGCTTTCAATGCAAAGGGAGTGATGCAATGCCCCAACT
genomic: CGGCGATCGAGCATGGGCTAATCTTCAATGTGACCATCAGTTCCATCTAGgtgagtttgt ... tgtttttaagATTGTATTGGTTCGGCTTTCAATGCAAAGGGAGTGATGCAATGCCCCAACT
EST: gi|301502796|gb|HO208336.1|HO208336
EST:     CGGCGATCGAGCATGGGCTAATCTTCAATGTGACCATCAGTTCCATCTAG                         ATTGTATTGGTTCGGCTTTCAATGCAAAGGGAGTGATGCAATGCCCCAACT
genomic: CGGCGATCGAGCATGGGCTAATCTTCAATGTGACCATCAGTTCCATCTAGgtgagtttgt ... tgtttttaagATTGTATTGGTTCGGCTTTCAATGCAAAGGGAGTGATGCAATGCCCCAACT
EST: gi|116485580|gb|EG528172.1|EG528172
EST:     CGGCGATCGAGCATGGGCTAATCTTCAATGTGACCATCAGTTCCATCTAG                         ATTGTATTGGTTCGGCTTTCAATGCAAAGGGAGTGATGCAATGCCCCAACT
genomic: CGGCGATCGAGCATGGGCTAATCTTCAATGTGACCATCAGTTCCATCTAGgtgagtttgt ... tgtttttaagATTGTATTGGTTCGGCTTTCAATGCAAAGGGAGTGATGCAATGCCCCAACT
EST: gi|116463809|gb|EG506401.1|EG506401
EST:     CGGCGATCGAGCATGGGCTAATCTTCAATGTGACCATCAGTTCCATCTAG                         ATTGTATCGGTTCGGCTTTCAATGCAAAGGGAGTGATGCAATGCCCCAACT
genomic: CGGCGATCGAGCATGGGCTAATCTTCAATGTGACCATCAGTTCCATCTAGgtgagtttgt ... tgtttttaagATTGTATTGGTTCGGCTTTCAATGCAAAGGGAGTGATGCAATGCCCCAACT
EST: gi|116421007|gb|EG463599.1|EG463599
EST:     CGGCGATCGAGCATGGGCTAATCTTCAATGTGACCATCAGTTCCATCTAG                         ATTGTATTGGTTCGGCTTTCAATGCAAAGGGAGTGATGCAATGCCCCAACT
genomic: CGGCGATCGAGCATGGGCTAATCTTCAATGTGACCATCAGTTCCATCTAGgtgagtttgt ... tgtttttaagATTGTATTGGTTCGGCTTTCAATGCAAAGGGAGTGATGCAATGCCCCAACT
EST: gi|125247807|gb|EL261892.1|EL261892
EST:     CGGCGATCGAGCATGGGCTAATCTTCAATGTGACCATCAGTTCCATCTAG                         ATTGTATTGGTTCGGCTTTCAATG
genomic: CGGCGATCGAGCATGGGCTAATCTTCAATGTGACCATCAGTTCCATCTAGgtgagtttgt ... tgtttttaagATTGTATTGGTTCGGCTTTCAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttatgtttttgacaaagccatctaacttcacatctgttttctttgtttttaagATTGTATTGGTTCGGCTTTCAATGCAAAGGGAGTGATGCAATGCCCCAACTGTCGGAAAGTAGAAAAAGGCCAGTGGCTTTATGCAAACGGTTGTCGTTC
                     atctaac  putative branch site (score: 2)
                                  tctgttttctttgttt  putative PPT
                                      ttttctttgtttttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attttcctcagattagggattattcattatgcttcatggttggtttcttatgtttttgacaaagccatctaacttcacatctgttttctttgtttttaagATTGTATTGGTTCGGCTTTCAATGCAAAGGGAGTGATGCAATGCCCCAACTGTCGGAAAGTAGAAAAAGGCCAGTGGCTTTATGCAAACGGTTGTCGTTC

- - - - - - - - - - - - - - atgcttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaagcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcacatc