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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggttcttttatgaatcttcagctaatcaaattgatttgtttatactttgcaaatgttttggttttagtcttttaatggtttgtattgttttcagGTTTTCTTGTTTCTTAACTCAAAATGTAAGAGGTACTTCCATAACAAGTTGAAGCCATCCAAGCTTGCATGGACTGCCATGTACAGAAAGCAACACAAGA

Basic information

species Arabidopsis thaliana
transcript AT3G53020.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G53020.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os07g12250.1 (Oryza sativa), 3'ss of exon 3
gttggttcttttatgaat-cttcagctaatcaaattgatttgtttatactttgcaaatgttttggttttagtcttttaatggtttgtattgttttcagGTTTTCTTGTTTCTTAACTCAAAATGTAAGAGGTACTTCCATAACAAGTTGAAGCCATCCAAGCTTGCATGGACTGCCATGTACAGAAAGCAACACAAGA
             ||| | |||  || |     ||  |  ||| ||        |  |    |  || |  ||  ||  |    |  | | | | ||||| ||| |||||   ||||| || || ||| | |||||||| |||    |||||||| |||||||| ||||||| ||||||||||||||||| |||||||
------------gtgagtactttggcaagatggatacacatgtgtaggacaaa-agctaacctatttctgatcaatttctttggtaaactatat-cagGTGTTCCTGTTTTCAAACTCGAAGTGCAAGCGCTACTTCCACAACCGTCTGAAGCCAGCCAAGCTTACATGGACAGCCATGTACAGAAAGCAGCACAAGA

upper sequence: AT3G53020.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G07680.1 (Glycine max), 3'ss of exon 2
------------------------------------------------------gttggttcttttatgaatcttcagctaatcaa-attgattt-gtttatactttgcaaatgttttggttttagtcttttaatggtttgtattgttttcagGTTTTCTTGTTTCTTAACTCAAAATGTAAGAGGTACTTCCATAACAAGTTGAAGCCATCCAAGCTTGCATGGACTGCCATGTACAGAAAGCAACACAAGA
                                                        ||| | || | || |  || |   |||||  ||  |||| | |  |  ||| | | |  ||    |    |     | | ||||||    | | ||||||||| |||||  |||||| |||||||||||||| ||||| |||| |||||||||||| |||||  | |||||||| ||||||||||||||||||||||
gtgacataatatgtttctcattgaattttgggttgatgtattgtgttattttgatatggatgttctgtgtactttgacaaaatcatcatcaattttgatcgttttttactagttattatactgatataggggatttgtttgttgaatatacagGTTTTCCTGTTTGCTAACTCGAAATGTAAGAGGTATTTCCACAACAGGTTGAAGCCATCAAAGCTCACCTGGACTGCAATGTACAGAAAGCAACACAAGA

upper sequence: AT3G53020.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA13G21520.1 (Glycine max), 3'ss of exon 2
----------------------------------------------------gttggttcttttatgaatcttcagctaatcaaatt--------------gatttgtttatactttgcaaatgttttggttttagtcttttaatggtttgtattgttttcagGTTTTCTTGTTTCTTAACTCAAAATGTAAGAGGTACTTCCATAACAAGTTGAAGCCATCCAAGCTTGCATGGACTGCCATGTACAGAAAGCAACACAAGA
                                                      ||| | || | |  |   | |   ||||| |||              | ||||||| |  ||||  |   |  || | | ||   |||  |   ||| |    || ||||||||| |||||  ||||||||||||||||||||| ||||| |||| ||||||||| || |||||  | |||||||| |||||| ||||||| || ||||
gtgacaatatgtttctcgttgagttttgggttgatgtatcgtttcatttgaaactggatgttctgtttactatgatgcaatcatattataagttatgaggggttttgtttgttatttgttatgatactgatatgaggggttttgtttgttgaa--acttacagGTTTTCCTGTTTGCTAACTCAAAATGTAAGAGGTATTTCCACAACAGGTTGAAGCCGTCAAAGCTCACGTGGACTGCAATGTACCGAAAGCAGCATAAGA

upper sequence: AT3G53020.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA19G37370.2 (Glycine max), 3'ss of exon 2
--------------------------------------------------------gttggttcttttatga--atcttcagctaatcaaattgatttgtttatactttgcaaatgttttggttttagtcttttaatg---gtttgtattgttttcagGTTTTCTTGTTTCTTAACTCAAAATGTAAGAGGTACTTCCATAACAAGTTGAAGCCATCCAAGCTTGCATGGACTGCCATGTACAGAAAGCAACACAAGA
                                                        ||| |   |  | |||  || ||    | || |   |  ||||||| |   | |  |   | ||| |  |  | |    ||    ||||||    | | ||||||||| |||||   |||||||||||||||||||| ||||| ||     ||||||| || |||||  | |||||||| |||||||||||||||||||| |
gtaacataaaatatgttttgggttgatgtgtcgcattatttcagtctggttgttctgtttgcaatgatgtgatcattttttagttatgagggttttttgtttgttgctagttatgatattgatactgatatgaggatttttgtttgttgaatctacagGTTTTCCTGTTTGCAAACTCAAAATGTAAGAGGTATTTCCACAATCGCCTGAAGCCTTCAAAGCTCACCTGGACTGCAATGTACAGAAAGCAACACAAAA

upper sequence: AT3G53020.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA03G34700.1 (Glycine max), 3'ss of exon 2
------------------------------------------------------gttggttcttttatgaatcttcagctaatcaaattgattt-----gtttatactttgcaaat-gttttggttttagtcttttaat---ggtttgtattgttttcagGTTTTCTTGTTTCTTAACTCAAAATGTAAGAGGTACTTCCATAACAAGTTGAAGCCATCCAAGCTTGCATGGACTGCCATGTACAGAAAGCAACACAAGA
                                                        ||| | ||  ||      | |  | ||||  || | ||     |||| | |||||  | | ||| || |  |  | |     |    ||||||    | |  |||||||| |||||   ||||||||||||||| |||| ||||| |||    ||||||| || |||||  | |||||||| |||||||||||||||||||| |
gtgacataaaatatgtctcattgaattttgggtggatgtatctcatcatttcagtctggatgttcaatttgctatgatttgatcatttttaattatggggttttttctttgttactagttatgatactgatatgagggtttttgtttgttgaatctatagGTTTTCCTGTTTGCCAACTCAAAATGTAAGCGGTATTTCCACAACCGCCTGAAGCCCTCAAAGCTCACCTGGACTGCTATGTACAGAAAGCAACACAAAA

upper sequence: AT3G53020.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv08s0007g04210.t01 (Vitis vinifera), 3'ss of exon 2
--------------------------------------------------gttggttcttttatgaatcttcagctaatcaa---attgatttgtttatactttgcaaatg--ttttggttttagtct--------tttaatggtttgtattgttttcagGTTTTCTTGTTTCTTAACTCAAAATGTAAGAGGTACTTCCATAACAAGTTGAAGCCATCCAAGCTTGCATGGACTGCCATGTACAGAAAGCAACACAAGA
                                                    |   | | |  ||||| || | ||  |      ||||  ||| ||   ||  |    ||   | | ||  | || |        || |||   |   | | | || |||| ||  | |||   || |||||||| |||||||||||||| |||  | |||||||||| |||||| | ||||| ||||||||||| |||||||| || |
gtaattttatagctcattaaaatttatgttctgtatcagattattagccaactaaatttctactgaatgttaatcttctttcttcattgtcttggttgggctcaggggttgacctcttgtacttgtttaattgacattaaattactctcaatatatttagGTGTTTCTATTTGCCAATTCAAAATGCAAGAGGTACTTCCACAACCGGCTGAAGCCATCAAAGCTTACCTGGACAGCCATGTACAGGAAGCAACATAAAA

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|164144130|gb|ES075785.1|ES075785
EST:     CCGATCTGATTCTCAG                         GTTTTCTTGTTTCTTAACTCAAAATGTAAGAGGTACTTCCATAACAAGTTG
genomic: CCGATCTGATTCTCAGgttggttctt ... ttgttttcagGTTTTCTTGTTTCTTAACTCAAAATGTAAGAGGTACTTCCATAACAAGTTG
EST: gi|116421955|gb|EG464547.1|EG464547
EST:     AGAAGATTTACCCAGGAAGAGGAATTAGGTTTATCCGATCTGATTCTCAG                         GTTTTCTTGTTTCTTAACTCAAAATGTAAGAGGTACTTCCATAACAAGTTG
genomic: AGAAGATTTACCCAGGAAGAGGAATTAGGTTTATCCGATCTGATTCTCAGgttggttctt ... ttgttttcagGTTTTCTTGTTTCTTAACTCAAAATGTAAGAGGTACTTCCATAACAAGTTG
EST: gi|124719374|gb|EH810776.1|EH810776
EST:     TATCCGATCTGATTCTCAG                         GTTTTCTTGTTTCTTAACTCAAAATGTAAGAGGTACTTCCATAACAAGTTG
genomic: TATCCGATCTGATTCTCAGgttggttctt ... ttgttttcagGTTTTCTTGTTTCTTAACTCAAAATGTAAGAGGTACTTCCATAACAAGTTG
EST: gi|164070921|gb|ES138895.1|ES138895
EST:     ATCCGATCTGATTCTCAG                         GTTTTCTTGTTTCTTAACTCAAAATGTAAGAGGTACTTCCATAACAAGTTG
genomic: ATCCGATCTGATTCTCAGgttggttctt ... ttgttttcagGTTTTCTTGTTTCTTAACTCAAAATGTAAGAGGTACTTCCATAACAAGTTG
EST: gi|164121032|gb|ES167395.1|ES167395
EST:     ACCCAGGAAGAGGAATTAGGTTTATCCGATCTGATTCTCTAG                         GTTTTCTTGTTTCTTAACTCAAAATGTAAGAGGTACTTCCATAACAAGTT
genomic: ACCCAGGAAGAGGAATTAGGTTTATCCGATCTGATTCTC-AGgttggttctt ... ttgttttcagGTTTTCTTGTTTCTTAACTCAAAATGTAAGAGGTACTTCCATAACAAGTT
EST: gi|152038275|gb|BP812779.2|BP812779
EST:     AGAAGATTTACCCAGGAAGAGGAATTAGGTTTATCCGATCTGATTCTCAG                         GTTTTCTTGTTTCTTAACTCAAAATGTAAGAGGTACTTCCATAACAAGTTG
genomic: AGAAGATTTACCCAGGAAGAGGAATTAGGTTTATCCGATCTGATTCTCAGgttggttctt ... ttgttttcagGTTTTCTTGTTTCTTAACTCAAAATGTAAGAGGTACTTCCATAACAAGTTG
EST: gi|116410667|gb|EG453259.1|EG453259
EST:     AGAAGATTTACCCAGGAAGAGGAATTAGGTTTATCCGATCTGATTCTCAG                         GTTTTCTTGTTTCTTAACTCAAAATGTAAGAGGTACTTCCATAACAAGTTG
genomic: AGAAGATTTACCCAGGAAGAGGAATTAGGTTTATCCGATCTGATTCTCAGgttggttctt ... ttgttttcagGTTTTCTTGTTTCTTAACTCAAAATGTAAGAGGTACTTCCATAACAAGTTG
EST: gi|116452319|gb|EG494911.1|EG494911
EST:     AGAAGATTTACCCAGGAAGAGGAATTAGGTTTATCCGATCTGATTCTCAG                         GTTTTCTTGTTTCTTAACTCAAAATGTAAGAGGTACTTCCATAACAAGTTG
genomic: AGAAGATTTACCCAGGAAGAGGAATTAGGTTTATCCGATCTGATTCTCAGgttggttctt ... ttgttttcagGTTTTCTTGTTTCTTAACTCAAAATGTAAGAGGTACTTCCATAACAAGTTG
EST: gi|164032895|gb|EL994482.1|EL994482
EST:     CCGATCTGATTCTCAG                         GTTTTCTTGTTTCTTAACTCAAAATGTAAGAGGTACT-CCATAACAAGTTG
genomic: CCGATCTGATTCTCAGgttggttctt ... ttgttttcagGTTTTCTTGTTTCTTAACTCAAAATGTAAGAGGTACTTCCATAACAAGTTG
EST: gi|86082625|gb|DR378384.1|DR378384
EST:     AGAAGATTTACCCAGGAAGAGGAATTAGGTTTATCCGATCTGATTCTCAG                         GTTTTCTTGTTTCTTAACTCAAAATGTAAGAGGTACTTCCATAACAAGTTG
genomic: AGAAGATTTACCCAGGAAGAGGAATTAGGTTTATCCGATCTGATTCTCAGgttggttctt ... ttgttttcagGTTTTCTTGTTTCTTAACTCAAAATGTAAGAGGTACTTCCATAACAAGTTG
EST: gi|152035093|gb|BP844349.2|BP844349
EST:     AGAAGATTTACCCAGGAAGAGGAATTAGGTTTATCCGATCTGATTCTCAG                         GTTTTCTTGTTTCTTAACTCAAAATGTAAGAGGTACTTCCATAACAAGTTG
genomic: AGAAGATTTACCCAGGAAGAGGAATTAGGTTTATCCGATCTGATTCTCAGgttggttctt ... ttgttttcagGTTTTCTTGTTTCTTAACTCAAAATGTAAGAGGTACTTCCATAACAAGTTG
EST: gi|116483020|gb|EG525612.1|EG525612
EST:     AGAAGATTTACCCAGGAAGAGGAATTAGGTTTATCCGATCTGATTCTCAG                         GTTTTCTTGTTTCTTAACTCAAAATGTAAGAGGTACTTCCATAACAAGTTG
genomic: AGAAGATTTACCCAGGAAGAGGAATTAGGTTTATCCGATCTGATTCTCAGgttggttctt ... ttgttttcagGTTTTCTTGTTTCTTAACTCAAAATGTAAGAGGTACTTCCATAACAAGTTG
EST: gi|116472837|gb|EG515429.1|EG515429
EST:     AGAAGATTTACCCAGGAAGAGGAATTAGGTTTATCCGATCTGATTCTCAG                         GTTTTCTTGTTTCTTAACTCAAAATGTAAGAGGTACTTCCATAACAAGTTG
genomic: AGAAGATTTACCCAGGAAGAGGAATTAGGTTTATCCGATCTGATTCTCAGgttggttctt ... ttgttttcagGTTTTCTTGTTTCTTAACTCAAAATGTAAGAGGTACTTCCATAACAAGTTG
EST: gi|116483018|gb|EG525610.1|EG525610
EST:     AGAAGATTTACCCAGGAAGAGGAATTAGGTTTATCCGATCTGATTCTCAG                         GTTTTCTTGTTTCTTAACTCAAAATGTAAGAGGTACTTCCATAACAAGTTG
genomic: AGAAGATTTACCCAGGAAGAGGAATTAGGTTTATCCGATCTGATTCTCAGgttggttctt ... ttgttttcagGTTTTCTTGTTTCTTAACTCAAAATGTAAGAGGTACTTCCATAACAAGTTG
EST: gi|152038145|gb|BP809467.2|BP809467
EST:     AGAAGATTTACCCAGGAAGAGGAATTAGGTTTATCCGATCTGATTCTCAG                         GTTTTCTTGTTTCTTAACTCAAAATGTAAGAGGTACTTCCATAACAAGTTG
genomic: AGAAGATTTACCCAGGAAGAGGAATTAGGTTTATCCGATCTGATTCTCAGgttggttctt ... ttgttttcagGTTTTCTTGTTTCTTAACTCAAAATGTAAGAGGTACTTCCATAACAAGTTG
EST: gi|86081830|gb|DR377589.1|DR377589
EST:     GGAATTAGGTTTATCCGATCTGATTCTCAG                         GTTTTCTTGTTTCTTAACTCWAAATGTWAGAGGTACTTCCATAACAAGTTG
genomic: GGAATTAGGTTTATCCGATCTGATTCTCAGgttggttctt ... ttgttttcagGTTTTCTTGTTTCTTAACTCAAAATGTAAGAGGTACTTCCATAACAAGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatactttgcaaatgttttggttttagtcttttaatggtttgtattgttttcagGTTTTCTTGTTTCTTAACTCAAAATGTAAGAGGTACTTCCATAACAAGTTGAAGCCATCCAAGCTTGCATGGACTGCCATGTACAGAAAGCAACACAAGA
                              ttttaat  putative branch site (score: 3)
                                             ttgttttc  putative PPT
                      ttttagtcttttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggttcttttatgaatcttcagctaatcaaattgatttgtttatactttgcaaatgttttggttttagtcttttaatggtttgtattgttttcagGTTTTCTTGTTTCTTAACTCAAAATGTAAGAGGTACTTCCATAACAAGTTGAAGCCATCCAAGCTTGCATGGACTGCCATGTACAGAAAGCAACACAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA