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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatatgccttttaaaagtctttacttacataaagatttgatctttcaaatgctgagacttttccatttgacagAATATATGCAAAGTGGTAGAGCAACTGAGAAAACCGATGTATACAGTTTTGGGGTTTTGGTTCTTGAAGTCTTGAGTGGGAAAAGACCAACCGATGCTTC

Basic information

species Arabidopsis thaliana
transcript AT1G31420.2
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G31420.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM5G886952_T01 (Zea mays), 3'ss of exon 12
--------------------------------------------------------------gtacatatgccttttaaaagt--ctttacttacataaagat-----ttgatctttcaa----atgctgagacttttccatttgacagAATATATGCAAAGTGGTAGAGCAACTGAGAAAACCGATGTATACAGTTTTGGGGTTTTGGTTCTTGAAGTCTTGAGTGGGAAAAGACCAACCGATGCTTC
                                                               |  |   |||  || | | |  || |  || |  ||| ||     || ||  |   |    |  |  |     | | | |  ||||| |||||||||  ||| ||||| || ||||| || ||||| |||||||||||||||||||| || ||| |  | ||||| ||  | || || ||||| ||
gtatgtggaagtccctctgttacatcctgaggggaaagagaagaaatgaacttctgtttactctttaatcgccgcttcagactttctctggttgctaaaatatcattgttaatgctctgagctaacaccaacgaaatccgaatccacagAGTATATGCAATTTGGCAGAGCCACCGAGAAGACTGATGTCTACAGTTTTGGGGTTTTGGTACTCGAAATACTCAGTGGAAAGCGGCCTACTGATGCATC

upper sequence: AT1G31420.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G479243_T01 (Zea mays), 3'ss of exon 12
--------------------------------------------------------------gtacatatgccttttaaaagtctttacttacataaagatt-----tgatcttt----caaatgctgagacttttccatttgacagAATATATGCAAAGTGGTAGAGCAACTGAGAAAACCGATGTATACAGTTTTGGGGTTTTGGTTCTTGAAGTCTTGAGTGGGAAAAGACCAACCGATGCTTC
                                                               ||  ||   | |   |   ||| |  || |  ||| ||      | ||  |     | ||     | |   | | | |  ||||| ||||||||   ||| ||||| || ||||| |||||||| ||||||||||||||| |||| |||||| |  | || || ||  | || || ||||| ||
gtatgtggaagtcgttctgctacatccagaggggaaaaaagaaatgaacttctgtttactctttaattaccgcatcggactttctctggttgctaaaatatcactgctaatgctctgagctaacatcaacaaaatccaactccacagAGTATATGCAGTTTGGCAGAGCCACCGAGAAGACCGATGTCTACAGTTTTGGGGTTCTGGTACTTGAAATACTCAGCGGAAAGCGGCCTACGGATGCATC

upper sequence: AT1G31420.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA01G35390.1 (Glycine max), 3'ss of exon 11
--------------------gtacatatgcct-tttaaaagtctttacttacataaagatttgatctttcaaatgctgagacttttccattt---gacagAATATATGCAAAGTGGTAGAGCAACTGAGAAAACCGATGTATACAGTTTTGGGGTTTTGGTTCTTGAAGTCTTGAGTGGGAAAAGACCAACCGATGCTTC
                      | || || || | |  ||   |    || |||    | |  ||  ||         ||  | |   | ||   |||||| |||||||||||||| ||||||||||||||  | ||||| || || ||||| || |||   ||||||||  ||||||| ||  | ||||| || ||  |
gggttatgtttggggtgtgctaaaatttggctatctttaaacttagttttgcattttaactccatggttgtctgagcaagcttctgttacttcatgacagAGTATATGCAAAGTGGCAGAGCAACTGAGAAGTCTGATGTGTATAGCTTTGGTGTGTTGACACTTGAAGTGCTGAGTGGAAAGCGGCCAACAGACGCAGC

upper sequence: AT1G31420.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA09G34940.2 (Glycine max), 3'ss of exon 12
----------------------gtacatatgccttttaaaagtctttacttacataaagatttgatctttcaaatgctgagacttttccattt---gacagAATATATGCAAAGTGGTAGAGCAACTGAGAAAACCGATGTATACAGTTTTGGGGTTTTGGTTCTTGAAGTCTTGAGTGGGAAAAGACCAACCGATGCTTC
                        |  |  |  | || | | |   |  || |||    | || ||  ||         ||  | |   | ||   |||||| |||||||||||||| ||||||||||||||  | ||||| || || ||||| || |||   || |||||  ||||||| ||  ||||||| || ||  |
gttatatgtttggggtgtgctaaaatttgggtatctttagacttagt-tttgcattttaacttcatggttgtctgagcaagcttctgttacttcatgacagAGTATATGCAAAGTGGCAGAGCAACTGAGAAGTCTGATGTGTATAGCTTTGGTGTGTTGACACTCGAAGTGCTGAGTGGAAAGCGACCAACAGACGCAGC

upper sequence: AT1G31420.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv02s0087g00170.t01 (Vitis vinifera), 3'ss of exon 12
----------------------------gtacatatgccttttaaaagtctttacttacataaagatttgatctttcaaatgctgagacttttccatttgacagAATATATGCAAAGTGGTAGAGCAACTGAGAAAACCGATGTATACAGTTTTGGGGTTTTGGTTCTTGAAGTCTTGAGTGGGAAAAGACCAACCGATGCTTC
                             || |  ||     || || | | |  | |  | ||  ||||||| |   | | |         ||||| || |||| ||||||||||| ||||||||||| |||||||||||  | || |||||||||||| || | |||||||| |||  ||||||  |||| || ||||||||
agaattggaccctattgtttttcttttgataaaactgtagcatagaaat-tgtgttgatttgaatctttgatcct--gagttcctctgtcactccatctg-cagAGTATATGCAAAGCGGTAGAGCAACAGAGAAAACCGACATTTATAGTTTTGGGGTTCTGATGCTTGAAGTATTGGCTGGGAAGCGACCCACTGATGCTTC

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|124980346|gb|EL053305.1|EL053305
EST:     CACATTTGGGTACCTAGCTCCAG                         AATATATGCAAAGTGGTAGAGCAACTGAGAAAACCGATGTATACAGTTTTG
genomic: CACATTTGGGTACCTAGCTCCAGgtacatatgc ... catttgacagAATATATGCAAAGTGGTAGAGCAACTGAGAAAACCGATGTATACAGTTTTG
EST: gi|124784908|gb|EH874589.1|EH874589
EST:     AGGCACATTTGGGTACCTAGCTCCAG                         AATATATGCAAAGTGGTAGAGCAACTGAGAAAACCGATGTATACAGTTTTG
genomic: AGGCACATTTGGGTACCTAGCTCCAGgtacatatgc ... catttgacagAATATATGCAAAGTGGTAGAGCAACTGAGAAAACCGATGTATACAGTTTTG
EST: gi|125086202|gb|EL145753.1|EL145753
EST:     TATCACAACCATTGTTGCAGGCACATTTGGGTACCTAGCTCCAG                         AATATATGCAAAGTGGTAGAGCAACTGAGAAAACCGA
genomic: TATCACAACCATTGTTGCAGGCACATTTGGGTACCTAGCTCCAGgtacatatgc ... catttgacagAATATATGCAAAGTGGTAGAGCAACTGAGAAAACCGA
EST: gi|125297381|gb|EL311466.1|EL311466
EST:     AACCATTGTTGCAGGCACATTTGGGTACCTAGCTCCAG                         AATATATGCAAAGTGGTAGAGCAACTGAGAAAACCGATGTATACAGTTTTG
genomic: AACCATTGTTGCAGGCACATTTGGGTACCTAGCTCCAGgtacatatgc ... catttgacagAATATATGCAAAGTGGTAGAGCAACTGAGAAAACCGATGTATACAGTTTTG
EST: gi|164128878|gb|EL978496.1|EL978496
EST:     ATCTCATATCACAACCATTGTTGCAGGCACATTTGGGTACCTAGCTCCAG                         AATATATGCAAAGTGGTAGAGCAAC
genomic: ATCTCATATCACAACCATTGTTGCAGGCACATTTGGGTACCTAGCTCCAGgtacatatgc ... catttgacagAATATATGCAAAGTGGTAGAGCAAC
EST: gi|124725812|gb|EH817214.1|EH817214
EST:     ATCACAACCATTGTTGCAGGCACATTTGGGTACCTAGCTCCAG                         AATATATGCAAAGTGGTAGAGCAACTGAGAAAACCGATGTATACAGTTTTG
genomic: ATCACAACCATTGTTGCAGGCACATTTGGGTACCTAGCTCCAGgtacatatgc ... catttgacagAATATATGCAAAGTGGTAGAGCAACTGAGAAAACCGATGTATACAGTTTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttacttacataaagatttgatctttcaaatgctgagacttttccatttgacagAATATATGCAAAGTGGTAGAGCAACTGAGAAAACCGATGTATACAGTTTTGGGGTTTTGGTTCTTGAAGTCTTGAGTGGGAAAAGACCAACCGATGCTTC
                                       cttttccattt  CT-rich tract
      ttacataaagattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacatatgccttttaaaagtctttacttacataaagatttgatctttcaaatgctgagacttttccatttgacagAATATATGCAAAGTGGTAGAGCAACTGAGAAAACCGATGTATACAGTTTTGGGGTTTTGGTTCTTGAAGTCTTGAGTGGGAAAAGACCAACCGATGCTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG