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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cacgtagctttatcataaaaatggttggttgggttttggcgttgcttgcttcagagtatgtgaccatcctactgaaattttcttcttctcttatggacagCAACGGTCAAAAACAAAGGTTACTTTCCCACTTGTGTGGACAAACACTTGTTGCAGCCATCCTCTTTACCGTGAATCCGAGCTTATTGAAGAGAATGTGC

Basic information

species Arabidopsis thaliana
transcript AT5G16440.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G16440.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os07g36190.1 (Oryza sativa), 3'ss of exon 3
--cacgtagctttatcataaaaatggttggttgggttttggcgttg---cttgcttcagagtatgtgaccatcctactgaaattttcttcttctcttatggacagCAACGGTCAAAAACAAAGGTTACTTTCCCACTTGTGTGGACAAACACTTGTTGCAGCCATCCTCTTTACCGTGAATCCGAGCTTATTGAAGAGAATGTGC
| | | | | | || | || | | | | || | || | | | | || |||| | | |||| || || |||||||| || |||||||||||| || || || || ||||| |||||||| |||||||||||||| |||||||| || |||||||| | || || |
tcttcaaatgctcaac-tggaagttatttttcatatctcatttctagcactgccatcttattcttcaaaacatctgctgattatctgttctacttttc----cagCAACGATCTGCAACAAAGGTTACATTTCCTCTAGTTTGGACCAACACTTGCTGCAGCCATCCTCTGTACCGTGAGTCTGAGCTTATACAGGAAAACTACC

upper sequence: AT5G16440.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os05g34180.1 (Oryza sativa), 3'ss of exon 3
-cacgtagctttatcataaaaatggttggttgggttt-tggcgttgcttgcttcagagtatgtgaccatcctactgaaattttcttcttctcttatggacagCAACGGTCAAAAACAAAGGTTACTTTCCCACTTGTGTGGACAAACACTTGTTGCAGCCATCCTCTTTACCGTGAATCCGAGCTTATTGAAGAGAATGTGC
|| || || || || | | | | | | | | | | ||| | | || | | ||| | |||| | |||||| |||| ||||| || || || |||||||| |||||||||||||| || ||||| ||||| ||||| || |||||||| |||||||| || |
tcatctattattttc-tacacttagcttatcaaataaatagaagtattaacttgttctgtcatagattttcttttaatattatagtcttgatcctttc-cagCAAAGGTCTGCTACAAAAGTGACATTTCCACTTGTCTGGACAAACACTTGCTGTAGCCACCCTCTATACCGCGAGTCCGAGCTCATTGAAGATAAAAGCC

upper sequence: AT5G16440.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA09G38550.1 (Glycine max), 3'ss of exon 3
------cacgtagctttatcataaaaatggttggttgggttttggcgttgcttgcttcagagtatgtgaccatcctactgaaattttcttcttctcttatggacagCAACGGTCAAAAACAAAGGTTACTTTCCCACTTGTGTGGACAAACACTTGTTGCAGCCATCCTCTTTACCGTGAATCCGAGCTTATTGAAGAGAATGTGC
| || ||| | | || | | || || | | | || || | | | | | ||||| ||| | | | | | || ||||||| || ||||||||| |||||||| ||||||||||||||||| ||||| ||||||||||| ||||||||||| ||||||||||| ||||||| |
ttggtgaaaaattctctatgttgcatgtgtattttcaagtctttgactcg--tgttttaatttg---gtctgtttgactgagattctttgttctttatgatga-agCAACGATCTGCAACAAAGGTAACTTTCCCTCTTGTGTGGACAAACACCTGTTGTAGCCATCCTCTGTACCGTGAATCTGAGCTTATTGATGAGAATGCCC

upper sequence: AT5G16440.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA18G47770.1 (Glycine max), 3'ss of exon 3
-----cacgtagctttatcataaaaatggttggttgggttttggcgttgcttgcttcagagtatgtgaccatcctactgaaattttcttcttctcttatggacagCAACGGTCAAAAACAAAGGTTACTTTCCCACTTGTGTGGACAAACACTTGTTGCAGCCATCCTCTTTACCGTGAATCCGAGCTTATTGAAGAGAATGTGC-
| | || ||| | || | | || |||| | | ||||| | || || | | | || ||| |||| | ||||||| || ||| ||||| || ||||| ||||||||||||||||| |||||||||||||| || ||||||||||| ||||||||||| ||||||| |
tggtggaaatttctctatgtatcatgtgtattttcatgtcttggactcg--tgcttta----atttggtctctttgactgagattccttgttctttatgatgaagcAACGATCTGCAACCAAGGTAACATTCCCTCTTGTGTGGACAAACACCTGTTGCAGCCATCCACTGTACCGTGAATCTGAGCTTATTGATGAGAATGCCCT

upper sequence: AT5G16440.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv11s0206g00020.t01 (Vitis vinifera), 3'ss of exon 1
cacgtagctttatcataaaaatggttggttgggttttggcgttgcttgcttcagagtatgtgaccatcctactgaaattttcttcttctcttatggacagCAACGGTCAAAAACAAAGGT-TACTTTCCCACT---TGTGTGGACAAACACTTGTTGCAGCCATCCTCTTTACCGTGAATCCGAGCTTATTGAAGAGAATGTGC--------------------------------------------------------
| | || || || | | | | |||| | | |||| | | | | | |||| | | | || |||||||| || |||||||||||||||||||||||||| || |||||| | ||||||||||
-----------------------------------------------------------tttcggaggctgacgagggcttactttgcagtcttgga-ggtttcactcaacagccgtgttattcttttatattgaatctggatacaaacacctgctgcagCCATCCTCTTTACCGTGAATCAGATCTTATTAATGAGAATGTGCTTGGAGTGCGGAATGCTGCACAAAGAAAGCTATTGGGTGAACTCGGCATTCCTGCT

upper sequence: AT5G16440.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv04s0023g00600.t01 (Vitis vinifera), 3'ss of exon 3
-cacgtagctttatcataaaaatggttggttgggttttggcgttgcttgcttcagagtatgtgaccatcctactgaaat-tttcttcttctcttatggacagCAACGGTCAAAAACAAAGGTTACTTTCCCACTTGTGTGGACAAACACTTGTTGCAGCCATCCTCTTTACCGTGAATCCGAGCTTATTGAAGAGAATGTGC
| | | | | | | |||| || |||| | || || | | ||| | ||||| | | | | || ||||||| |||| |||||||| || ||||| | |||||||||||||| || |||||||||||||||||||||||||| ||||||||||| ||||||| ||
ttgtttcaccctgattctatcaagatatagcattctttgtaaacatcagc--cagaatttgagaatcacatgctgtgttctttctgcatgtttcttgtacagCAAAGGTCTGCCACAAAGGTGACATTCCCTTTGGTGTGGACAAACACCTGCTGCAGCCATCCTCTTTACCGTGAATCAGAGCTTATTGATGAGAATGCGC

upper sequence: AT5G16440.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S28_399V6.1 (Physcomitrella patens), 3'ss of exon 3
----cacgtagctttatcataaaaatggttggttgggttttggcgttgcttgcttcagagtatgtgaccatcctactgaaattttcttcttctcttatggacagCAACGGTCAAAAACAAAGGTTACTTTCCCACTTGTGTGGACAAACACTTGTTGCAGCCATCCTCTTTACCGTGAATCCGAGCTTATTGAAGAGAATGTGC-
| ||| ||| || || || || | | || | ||| ||| || || | | | || | || | | ||| ||| |||| || || || || || || |||||||||||||| |||||||||||||||||||| || |||||||| || || |||||||| || || | |
ccaccgtgtatggttagagattggattagtgagtgacttgcagggatgtctcctttaga-cccatggacaaaatctt--atttatgttgatattatattt-cagAAACGTTCGGCTACGAAAGTGACCTTTCCACTTGTGTGGACCAACACTTGTTGCAGCCATCCACTGTACCGTGAGTCTGAACTTATTGAGGATAA-ATACC

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|86024853|gb|DR320606.1|DR320606
EST:     GAGCTTTCAGTGTGTTTTTATTCAACTCCAAGTATGAGTTGCTTCTCCAG                         CAACGGTCAAAAACAAAGGTTACTTTCCCACTTGTGTGGACAAACACTTGT
genomic: GAGCTTTCAGTGTGTTTTTATTCAACTCCAAGTATGAGTTGCTTCTCCAGgtattttctt ... ttatggacagCAACGGTCAAAAACAAAGGTTACTTTCCCACTTGTGTGGACAAACACTTGT
EST: gi|124834593|gb|EH919032.1|EH919032
EST:     TATGAGTTGCTTCTCCAG                         CAACGGTC-AAAACAAAGGTTACTTTCCCACTTGTGTGGACAAACACTTGT
genomic: TATGAGTTGCTTCTCCAGgtattttctt ... ttatggacagCAACGGTCAAAAACAAAGGTTACTTTCCCACTTGTGTGGACAAACACTTGT
EST: gi|124731097|gb|EH822499.1|EH822499
EST:     GAGCTTTCAGTGTGTTTTTATTCAACTCCAAGTATGAGTTGCTTCTCCAG                         CAACGGTCAAAAACAAAGGTTACTTTCCCACTTGTGTGGACAAACACTTGT
genomic: GAGCTTTCAGTGTGTTTTTATTCAACTCCAAGTATGAGTTGCTTCTCCAGgtattttctt ... ttatggacagCAACGGTCAAAAACAAAGGTTACTTTCCCACTTGTGTGGACAAACACTTGT
EST: gi|86024858|gb|DR320611.1|DR320611
EST:     GAGCTTTCAGTGTGTTTTTATTCAACTCCAAGTATGAGTTGCTTCTCCAG                         CAACGGTCAAAAACAAAGGTTACTTTCCCACTTGTGNGGACAAACACTTGT
genomic: GAGCTTTCAGTGTGTTTTTATTCAACTCCAAGTATGAGTTGCTTCTCCAGgtattttctt ... ttatggacagCAACGGTCAAAAACAAAGGTTACTTTCCCACTTGTGTGGACAAACACTTGT
EST: gi|86024851|gb|DR320604.1|DR320604
EST:     GAGCTTTCAGTGTGTTTTTATTCAACTCCAAGTATGAGTTGCTTCTCCAG                         CAACGGTCAAAAACAAAGGTTACTTTCCCACTTGTGTGGACAAACACTTGT
genomic: GAGCTTTCAGTGTGTTTTTATTCAACTCCAAGTATGAGTTGCTTCTCCAGgtattttctt ... ttatggacagCAACGGTCAAAAACAAAGGTTACTTTCCCACTTGTGTGGACAAACACTTGT
EST: gi|86024854|gb|DR320607.1|DR320607
EST:     GAGCTTTCAGTGTGTTTTTATTCAACTCCAAGTATGAGTTGCTTCTCCAG                         CAACGGTCAAAAACAAAGGTTACTTTCCCACTTGTGTGGACAAACACTTGT
genomic: GAGCTTTCAGTGTGTTTTTATTCAACTCCAAGTATGAGTTGCTTCTCCAGgtattttctt ... ttatggacagCAACGGTCAAAAACAAAGGTTACTTTCCCACTTGTGTGGACAAACACTTGT
EST: gi|86024862|gb|DR320615.1|DR320615
EST:     GAGCTTTCAGTGTGTTTTTATTCAACTCCAAGTATGAGTTGCTTCTCCAG                         CAACGGTCAAAAACAAAGGTTACTTTCCCACTTGTGTGGACAAACACTTGT
genomic: GAGCTTTCAGTGTGTTTTTATTCAACTCCAAGTATGAGTTGCTTCTCCAGgtattttctt ... ttatggacagCAACGGTCAAAAACAAAGGTTACTTTCCCACTTGTGTGGACAAACACTTGT
EST: gi|86024861|gb|DR320614.1|DR320614
EST:     GAGCTTTCAGTGTGTTTTTATTCAACTCCAAGTATGAGTTGCTTCTCCAG                         CAACGGTCAAAAACAAAGGTTACTTTCCCACTTGTGTGKACAAACACTTGT
genomic: GAGCTTTCAGTGTGTTTTTATTCAACTCCAAGTATGAGTTGCTTCTCCAGgtattttctt ... ttatggacagCAACGGTCAAAAACAAAGGTTACTTTCCCACTTGTGTGGACAAACACTTGT
EST: gi|86024856|gb|DR320609.1|DR320609
EST:     GAGCTTTCAGTGTGTTTTTATTCAACTCCAAGTATGAGTTGCTTCTCCAG                         CAACGGTCAAAAACAAAGGTTACTTTCCCACTTGTGTGAACAAACACTTGT
genomic: GAGCTTTCAGTGTGTTTTTATTCAACTCCAAGTATGAGTTGCTTCTCCAGgtattttctt ... ttatggacagCAACGGTCAAAAACAAAGGTTACTTTCCCACTTGTGTGGACAAACACTTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcttcagagtatgtgaccatcctactgaaattttcttcttctcttatggacagCAACGGTCAAAAACAAAGGTTACTTTCCCACTTGTGTGGACAAACACTTGTTGCAGCCATCCTCTTTACCGTGAATCCGAGCTTATTGAAGAGAATGTGC
                                ttttcttcttctctta  CT-rich tract
 aaattttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cacgtagctttatcataaaaatggttggttgggttttggcgttgcttgcttcagagtatgtgaccatcctactgaaattttcttcttctcttatggacagCAACGGTCAAAAACAAAGGTTACTTTCCCACTTGTGTGGACAAACACTTGTTGCAGCCATCCTCTTTACCGTGAATCCGAGCTTATTGAAGAGAATGTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - ataaaaa
- - - - - - - - - - - - - - - -ggttttg
- - - - - - - - - - - - - - - - - - - - - - -ttgcttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - accatcc