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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttttttcctactctttgttctaaacagagtatgttgttattagattctctaatcattttatctttggatgattattagGTTGTTGAGATCACTAAAGGAAGCAAGGTCAAATACGAGCTTGACAAAAAGACAGGACTCATCAAG

Basic information

species Arabidopsis thaliana
transcript AT1G01050.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G01050.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os04g59040.3 (Oryza sativa), 3'ss of exon 3
---------------------gtaagttttttcctactctttgttctaaacagagtatgttgttattagattctctaatcattttatctttggatgattattagGTTGTTGAGATCACTAAAGGAAGCAAGGTCAAATACGAGCTTGACAAAAAGACAGGACTCATCAAG
                       ||| ||| || |||  |  ||||   |||| | |||       || ||  |  |    ||  || | |     |  |  |||||||||||||||| || |||||||| || ||||| ||||||||||| || || ||||| || |||
attgttctgtttaacgattctagaagctttatc-tacagtcggttcctgacagtgcatgcaacc--tacatggttaatggcttccatttatatcacaccac-agGTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAAACTGGACTGATTAAG

upper sequence: AT1G01050.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os10g26600.1 (Oryza sativa), 3'ss of exon 3
gtaagtttt---ttcctactct--ttgt--tctaaacagagta--tgttgttattagattctctaatcattttatctttggatgattatt-----agGTTGTTGAGATCACTAAAGGAAGCAAGGTCAAATACGAGCTTGACAAAAAGACAGGACTCATCAAG
|||||  |    ||| || | |  ||||  || ||    || |     ||  |||   |||   |  ||| |   | |   ||| || ||     |||||||||||||||| || || ||||| || || || ||||||||||| ||||| ||| | ||||||
gtaagcatcgtgttcataatatatttgtcatcaaattgaagcaaacactgcgatttatttcaggatgcatctggacctgacatgtttttttttgtagGTTGTTGAGATCACAAAGGGGAGCAAAGTGAAGTATGAGCTTGACAAGAAGACTGGAATGATCAAG

upper sequence: AT1G01050.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G104918_T03 (Zea mays), 3'ss of exon 3
-------------------gta-agttttttcctactctttgttctaaacagagtatgttgttattagattctctaatcattttatctttggatgattatt-agGTTGTTGAGATCACTAAAGGAAGCAAGGTCAAATACGAGCTTGACAAAAAGACAGGACTCATCAAG
                   | |  |||||||  || |     |  | |||| |    |||      | |  |  | | |   |||| |     |  ||||| |||||||||||||||| || |||||||| |||||||||||||||||||| || || ||||| || |||
ttgttgaggaaaaataagtgcatggtttttttttaattacgatatttaacaaatctagttagctccaaa--caatgaccgcgttatat--aattttttattcagGTTGTTGAGATCACAAAGGGAAGCAAAGTCAAATACGAGCTTGACAAGAAAACTGGACTGATTAAG

upper sequence: AT1G01050.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G061928_T04 (Zea mays), 3'ss of exon 3
-----------------gtaagttttttcctactctttgttctaaacagagtatgttgtt-attagattctctaatcattttatctttggatgattat-tagGTTGTTGAGATCACTAAAGGAAGCAAGGTCAAATACGAGCTTGACAAAAAGACAGGACTCATCAAG
                   ||||   ||  |  || |  |  | |||| |     | |||   |  || |  | |     ||||  ||  ||  ||||  |||||||||||||||| || |||||||| || ||||| ||||||||||| || || ||||| || |||
atttgcttgtcgagcaaaaaagtgcattttttatcataatgtttaacaaatctactagttcgcttcatacagtgactgcattat--ttacatctttatgcagGTTGTTGAGATCACAAAGGGAAGCAAAGTTAAATATGAGCTTGACAAGAAAACTGGACTGATTAAG

upper sequence: AT1G01050.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA03G42280.1 (Glycine max), 3'ss of exon 3
------gtaagttttttcctactctttgt-tctaaacagagtat---gttgttattagattctcta-----atcattttatctttggatgattatt--agGTTGTTGAGATCACTAAAGGAAGCAAGGTCAAATACGAGCTTGACAAAAAGACAGGACTCATCAAG
      | || |   |    || |      |||||    | | |   ||||  ||||  ||   |         | ||| |  |||    ||  ||  ||||||| ||||||||||||||||||||||||||||| || |||||||| ||||||||| | || |||
catacagcaattgcatgatcacaccacacctctaattccattcttgagttgcaattaattttcttgtaaaggggagtttctgcttgttcaatggttgtagGTTGTGGAGATCACTAAAGGAAGCAAGGTCAAATATGAACTTGACAAGAAGACAGGATTGATTAAG

upper sequence: AT1G01050.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA07G05390.2 (Glycine max), 3'ss of exon 3
---------gtaagttttttcctactctttgttctaaa---cagagtatgt-tgttatta--gattctctaatcattttatctttggatg--attattagGTTGTTGAGATCACTAAAGGAAGCAAGGTCAAATACGAGCTTGACAAAAAGACAGGACTCATCAAG
           || | |    | | ||||      |||   |  | ||||| |||||||   | || |  |||  ||   |  |  | ||  |||   ||||||| ||||||||||| |||||||||||||||||||| |||||||||||||| ||| | || |||
tattcatgcaaaactgtcactccattcttgaccagaaatttcctactatgtatgttatttatgcttgttcaatgcttacttgctcagttgctatttgcagGTTGTGGAGATCACTAAGGGAAGCAAGGTCAAATACGAACTTGACAAAAAGACTGGATTAATTAAG

upper sequence: AT1G01050.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA19G45050.1 (Glycine max), 3'ss of exon 2
---------------gtaagttttttcctact---ctttgttctaaacagagtatgttgttattagattctctaatcattttatct-ttggatgattattagGTTGTTGAGATCACTAAAGGAAGCAAGGTCAAATACGAGCTTGACAAAAAGACAGGACTCATCAAG
                | |       ||||      |   ||||  |    | || | ||| |    |       |  || |   | ||  |||  |   ||||||| |||||||||||||||||||||||||| || || |||||||| ||||| ||| | || |||
tatagcaattgcatgatgacaccacacctatataattccattcttgattt-gcatttagttttctagtaaaagggtgtttctgcttgttcaatggctgc-agGTTGTGGAGATCACTAAAGGAAGCAAGGTCAAGTATGAACTTGACAAGAAGACTGGATTGATTAAG

upper sequence: AT1G01050.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA18G18510.1 (Glycine max), 3'ss of exon 2
-------------------------gtaagttttttcctactctttgttctaaacagagtatgttgttattagattctctaatcattttatctttggatgattattagGTTGTTGAGATCACTAAAGGAAGCAAGGTCAAATACGAGCTTGACAAAAAGACAGGACTCATCAAG
                             || |  | | | ||||  ||   |||  ||| |  || ||  ||  | | |       |  |  ||  |||  ||| |||||||  |||||||||||||||||||||| || || || |||||||||||||| ||| | || |||
tacaacaattgcatgatgacaccacacttgtataattccattcttgatttgcaact-agttttctggtaaaagggtgttt------ctgcttgttcaatggctat-agGTTGTGCAGATCACTAAAGGAAGCAAGGTTAAGTATGAACTTGACAAAAAGACTGGATTGATTAAG

upper sequence: AT1G01050.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA11G18100.1 (Glycine max), 3'ss of exon 2
---------------gtaagttttttcctact---ctttgttctaaacagagtatgttgttattagattctctaatcattttatct-ttggatgattattagGTTGTTGAGATCACTAAAGGAAGCAAGGTCAAATACGAGCTTGACAAAAAGACAGGACTCATCAAG
                | |       |||       |   ||||  |      || | ||| |  | |       |  || ||  | ||  |||  |   ||||||| ||||||||||||||||||||||| |  || || |||||| ||||||  ||| | || |||
tacaacaattgcatgatgacaccacacctgtataattccattcttgatttgcaat-tagttttctggtaaaggggtatttctacttgttcaatggctgc-agGTTGTGGAGATCACTAAAGGAAGCAAGGTTATGTATGAACTTGACCAAAAGATTGGATTGATTAAG

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|152033655|gb|BP561551.2|BP561551
EST:     GACCTGGAGCTCCACAGATTTTCAATGTG                         GTTGTTGAGATCACTAAAGGAAGCAAGGTCAAATACGAGCTTGACAAAAAG
genomic: GACCTGGAGCTCCACAGATTTTCAATGTGgtaagttttt ... tgattattagGTTGTTGAGATCACTAAAGGAAGCAAGGTCAAATACGAGCTTGACAAAAAG
EST: gi|125045488|gb|EL117757.1|EL117757
EST:     ATTGGACCTGGAGCTCCACAGATTTTCAATGTG                         GTTGTTGAGATCACTAAAGGAAGCAAGGTCAAATACGAGCTTGAACAAAAA
genomic: ATTGGACCTGGAGCTCCACAGATTTTCAATGTGgtaagttttt ... tgattattagGTTGTTGAGATCACTAAAGGAAGCAAGGTCAAATACGAGCTTGA-CAAAAA
EST: gi|163968043|gb|ES068352.1|ES068352
EST:     GACCTGGAGCTCCACAGATTTTCAATGTG                         GTTGTTGAGATCACTAAAGGAAGCAAGGTCAAATACGAG
genomic: GACCTGGAGCTCCACAGATTTTCAATGTGgtaagttttt ... tgattattagGTTGTTGAGATCACTAAAGGAAGCAAGGTCAAATACGAG
EST: gi|47828474|gb|CK118158.1|CK118158
EST:     GACCTGGAGCTCCACAGATTTTCAATGTG                         GTTGTTGAGATCACTAAAGGAAGCAAGGTCAAATACGAGCTTGACAAAAAG
genomic: GACCTGGAGCTCCACAGATTTTCAATGTGgtaagttttt ... tgattattagGTTGTTGAGATCACTAAAGGAAGCAAGGTCAAATACGAGCTTGACAAAAAG
EST: gi|124751380|gb|EH841510.1|EH841510
EST:     CTCCACAGATTTTCAATGTG                         GTTGTTGAGATCACTAAAGGAAGCAAGGTCAAATACGAGCTTGACAAAAAG
genomic: CTCCACAGATTTTCAATGTGgtaagttttt ... tgattattagGTTGTTGAGATCACTAAAGGAAGCAAGGTCAAATACGAGCTTGACAAAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acagagtatgttgttattagattctctaatcattttatctttggatgattattagGTTGTTGAGATCACTAAAGGAAGCAAGGTCAAATACGAGCTTGACAAAAAGACAGGACTCATCAAG
                       ctctaat  putative branch site (score: 3)
                          taatcattttatcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttttttcctactctttgttctaaacagagtatgttgttattagattctctaatcattttatctttggatgattattagGTTGTTGAGATCACTAAAGGAAGCAAGGTCAAATACGAGCTTGACAAAAAGACAGGACTCATCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT