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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttgtattagacgcattacaactaatatttgaatatcttctttttcacgttttgatcagtcaatcaagcagcagttggatgctcaatcaatttattgcggtactcatgcatgtataataatttccttgcataacagATGATGGAAAATTAGATACAGAATCAGATTCTGGCGAGTTCTGGGTCCTCTTTGGGGGGTTTGCTCCAATAGCAAGGAAAGTTGCGAGTGAGGATGAAAT

Basic information

species Arabidopsis thaliana
transcript AT3G57410.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G57410.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os03g24220.1 (Oryza sativa), 3'ss of exon 6
gtaagttgtattagacgcattacaactaatatttgaatatcttctttttcacgttttgatcagtcaatcaagcagcagttggatgctcaatcaatttattgcggtactcatgcatgtata-ataatttccttgcataacagATGATGGAAAATTAGATACAGAATCAGATTCTGGCGAGTTCTGGGTCCTCTTTGGGGGGTTTGCTCCAATAGCAAGGAAAGTTGCGAGTGAGGATGAAAT
                                                      | || ||   ||| |||    || ||  |||    | |  | |    |   |   |  ||| |  | | ||  |  |||  | | |||||||||||||||  |  |||||||||||||||| || |||||||| || ||||| || ||||| |||||||  | ||||| |    |||| |||||  |
-----------------------------------------------------gtatgctcga-caaccaaatctcaattc-atgt---aactttctggcacaa-atctacacattttcatacaaaatttttg--tgatagATGATGGAAAATTGCAAGCAGAATCAGATTCTGGTGAATTCTGGGTTCTTTTTGGAGGTTTTGCACCAATAGGGAAGAAAGCTATATGTGACGATGATGT

upper sequence: AT3G57410.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G081322_T01 (Zea mays), 3'ss of exon 6
gtaagttgtattagacgcattacaactaatatttgaatatcttctttttcacgttttgatcagtcaatcaagcagcagttggatgctcaatcaatttattgcggtactcatgcatgtataataatttccttgcataacagATGATGGAAAATTAGATACAGAATCAGATTCTGGCGAGTTCTGGGTCCTCTTTGGGGGGTTTGCTCCAATAGCAAGGAAAGTTGCGAGTGAGGATGAAAT
                                                | |  |    || || | |        ||  || |   |||   | || |       ||| || ||| | |  |  || ||||| |||| ||||||||| ||| |  |  ||||||||||||| || || ||||||||||| ||||| || ||||| |||||||  |  ||||     ||||| |||||  |
-----------------------------------------------gtgagatgagaatgagacgaatctcatacatgtgaaacgtcagcaagttcacac--acacttatacattttt--ttgttgccttg-ataatagATGATGGGAAACTGCAAGCAGAATCAGATTCAGGAGAATTCTGGGTCCTTTTTGGAGGTTTTGCGCCAATAGGGAAAAAAGCAATAAGTGATGATGATGT

upper sequence: AT3G57410.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G180988_T01 (Zea mays), 3'ss of exon 6
gtaagttgtattagacgcattacaactaatatttgaatatcttctttttcacgttttgatcagtcaatcaagcagcagttggatgctcaatcaatttattgcggtactcatgcatgtataataatttccttgcataacagATGATGGAAAATTAGATACAGAATCAGATTCTGGCGAGTTCTGGGTCCTCTTTGGGGGGTTTGCTCCAATAGCAAGGAAAGTTGCGAGTGAGGATGAAAT
                                                | | |  |  || | |   |  |   ||| ||   || ||       || || |  ||    |     |||     |||      ||  |||||||||| |||||| |  |||| ||||| ||||| || ||||||||||| ||||| || ||||| ||||| |  |  |||   | |||||| |||||  |
-----------------------------------------------gtgagggatatat-aatatttggattggcaatt---tggtcgtctggcttttttctctatctctattcttatggggttttt-----atgccagATGATGGGAAATTACAGGCAGAGTCAGACTCTGGTGAATTCTGGGTCCTTTTTGGAGGTTTTGCACCAATTGGGAAAAAAACCGTGAGTGATGATGATGT

upper sequence: AT3G57410.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA02G32100.1 (Glycine max), 3'ss of exon 4
gtaagttgtattagacgcattacaactaatatttgaatatcttctttttcacgttttgatcagtcaatcaagcagcagttggatgctcaatcaatttattgcggtactcatgcatgtataataatttccttgcataacagATGATGGAAAATTAGATACAGAATCAGATTCTGGCGAGTTCTGGGTCCTCTTTGGGGGGTTTGCTCCAATAGCAAGGAAAGTTGCGAGTGAGGATGAAAT
                                              |    |  |||    | |   |    ||| | ||   | ||  |||  |  | |    |  |  |   |  |||| |  |  |   |||  ||||||||||||||||||| || || ||||| || || ||||| |||||||||||||| || |||||||| || |  | ||| ||    ||||||||||| ||
---------------------------------------------gtaaggcaatttttctattatgtattccagtatttctgttcttcatc--tgcaattttttgtttttaacttcataaaatctatcccacattccagATGATGGAAAATTAGACACTGAGTCAGACTCAGGTGAGTTTTGGGTCCTCTTTGGTGGTTTTGCTCCCATTGGGAAGAAGGTAATTAGTGAGGATGATAT

upper sequence: AT3G57410.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA10G21350.2 (Glycine max), 3'ss of exon 5
gtaagttgtattagacgcattacaactaatatttgaatatcttctttttcacgttttgatcagtcaatcaagcagcagttggatgctcaatcaatttattgcggtactcatgcatgtataataatttccttgcataacagATGATGGAAAATTAGATACAGAATCAGATTCTGGCGAGTTCTGGGTCCTCTTTGGGGGGTTTGCTCCAATAGCAAGGAAAGTTGCGAGTGAGGATGAAAT
                                |     |  ||   | | | || ||  |||||   ||         |   |||| || ||| ||  ||    ||||         |||| |  |  |   |||  |||| |||||||||||||| || || ||||| || || || || |||||||||||||| || |||||||| || |  | ||| ||    ||||||||||| ||
-------------------------------gtaaggcaattttcctattatgtatt--tcagtatttc---tgttcttccaatgcacattcatttgttttt--tactt-------cataaaatctatcccacattgcagACGATGGAAAATTAGACACTGAGTCAGACTCAGGTGAATTTTGGGTCCTCTTTGGTGGTTTTGCTCCCATTGGGAAGAAGGTAATCAGTGAGGATGATAT

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|116482622|gb|EG525214.1|EG525214
EST:     ATATTTGAAAGACAAGTTTCATGAAGGAACTTCTGACGTTGCTATTGTTG                         ATGATGGAAAATTAGATACAGAATCAG
genomic: ATATTTGAAAGACAAGTTTCATGAAGGAACTTCTGACGTTGCTATTGTTGgtaagttgta ... tgcataacagATGATGGAAAATTAGATACAGAATCAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcaatcaatttattgcggtactcatgcatgtataataatttccttgcataacagATGATGGAAAATTAGATACAGAATCAGATTCTGGCGAGTTCTGGGTCCTCTTTGGGGGGTTTGCTCCAATAGCAAGGAAAGTTGCGAGTGAGGATGAAAT
                                       tttccttgc  CT-rich tract
                            atgtataataattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttgtattagacgcattacaactaatatttgaatatcttctttttcacgttttgatcagtcaatcaagcagcagttggatgctcaatcaatttattgcggtactcatgcatgtataataatttccttgcataacagATGATGGAAAATTAGATACAGAATCAGATTCTGGCGAGTTCTGGGTCCTCTTTGGGGGGTTTGCTCCAATAGCAAGGAAAGTTGCGAGTGAGGATGAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG