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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcaaagtagtcaatttcttaccagtgttacttgtcctggattctatcaaatctatatcagcttggagctatttgggaatttatctttgttaatcatatgcctgtatccaatgcattgaccaagcaatcccctgtctttggttcagAAACTTTCCTCAGGGGACAATTAGTGATATGGTAAGTGATGCAGCTCAAGGAATCTCATTTGTCTGCAATAACATCTCTGCATTTGGAGGTGATCCTAAC

Basic information

species Arabidopsis thaliana
transcript AT3G02410.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G02410.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os06g49440.1 (Oryza sativa), 3'ss of exon 5
gtaagcaaagtagtcaatttcttaccagtgttacttgtcctggattctatcaaatctatatcagcttggagctatttgggaatttatctttgttaatcatatgcctgtatccaatgcattgaccaagcaatcccctgtctttggttcagAAACTTTCCTCAGGGGACAATTAGTGATATGGTAAGTGATGCAGCTCAAGGAATCTCATTTGTCTGCAATAACATCTCTGCATTTGGAGGTGATCCTAAC
                                                                ||   |   | ||   ||| |   | |   ||  ||  |  |  || | ||   || |   ||||  ||  |   ||   | ||||||||||||||| ||||| ||| |||| ||||||   |||||| ||||||| ||  | |||||||||||||| ||  ||   | ||||||||||||| | 
-------------------------------------------------------------gtactcaaaataaattccaaatatgcatatag-aagaatgagggttcataccatt--ttcatggagcataccaattatttgtttgcagAAACTTTCCTCAAGGGACTATTGGTGACATGGTAGAAGATGCATCTCAAGGGATTGCCTTTGTCTGCAATAATATAGCTAGTTATGGAGGTGATCCTGAA

upper sequence: AT3G02410.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G439203_T01 (Zea mays), 3'ss of exon 5
gtaagcaaagtagtcaatttcttaccagtgttacttgtcctggattctatcaaatctatatcagcttggagctatttgggaatttatctttgttaatcatatgcctgtatccaatgcattg--accaagcaatcccctgtctttggttcagAAACTTTCCTCAGGGGACAATTAGTGATATGGTAAGTGATGCAGCTCAAGGAATCTCATTTGTCTGCAATAACATCTCTGCATTTGGAGGTGATCCTAAC
                                                              |   || |  |||||        |  | ||  || ||         || ||   |||||  ||  || |      ||  ||   ||||||||||||||||| ||||| ||| |||| ||||||   |||||  ||||||||||  | ||||||||||| || ||  |    | |||||||||||||| |
------------------------------------------------------------gtactctgaatgtattt------ccaattatgcaaagca-gcataatcattcaggccattgtcactgaggatgtaaatgctttgttttcagAAACTTTCCTCAAGGGACTATTGGTGACATGGTAGAAGATGCTTCTCAAGGAATAGCTTTTGTCTGCAAGAATATAACAAGTTATGGAGGTGATCCTAGC
















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|116389289|gb|EG431881.1|EG431881
EST:     GGACTACAGCTAGCAGAAAGGGACATAATTGTGGCATGTCTAGATTACAG                         AAACTTTCCTCAGGGGACAATTAGTGATATGGTAAGTGATGCAGCTCAAGG
genomic: GGACTACAGCTAGCAGAAAGGGACATAATTGTGGCATGTCTAGATTACAGgtaagcaaag ... tttggttcagAAACTTTCCTCAGGGGACAATTAGTGATATGGTAAGTGATGCAGCTCAAGG
EST: gi|116389287|gb|EG431879.1|EG431879
EST:     GGACTACAGCTAGCAGAAAGGGACATAATTGTGGCATGTCTAGATTACAG                         AAACTTTCCTCAGGGGACAATTAGTGATATGGTAAGTGATGCAGCTCAAGG
genomic: GGACTACAGCTAGCAGAAAGGGACATAATTGTGGCATGTCTAGATTACAGgtaagcaaag ... tttggttcagAAACTTTCCTCAGGGGACAATTAGTGATATGGTAAGTGATGCAGCTCAAGG
EST: gi|116389292|gb|EG431884.1|EG431884
EST:     GGACTACAGCTAGCAGAAAGGGACATAATTGTGGCATGTCTAGATTACAG                         AAACTTTCCTCAGGGGACAATTAGTGATATGGTAAGTGATGCGGCTCAAGG
genomic: GGACTACAGCTAGCAGAAAGGGACATAATTGTGGCATGTCTAGATTACAGgtaagcaaag ... tttggttcagAAACTTTCCTCAGGGGACAATTAGTGATATGGTAAGTGATGCAGCTCAAGG
EST: gi|116389288|gb|EG431880.1|EG431880
EST:     GGACTACAGCTAGCAGAAAGGGACATAATTGTGGCATGTCTAGATTACAG                         AAACTTTCCTCAGGGGACAATTAGTGATATGGTAAGTGATGCAGCTCAAGG
genomic: GGACTACAGCTAGCAGAAAGGGACATAATTGTGGCATGTCTAGATTACAGgtaagcaaag ... tttggttcagAAACTTTCCTCAGGGGACAATTAGTGATATGGTAAGTGATGCAGCTCAAGG
EST: gi|116389291|gb|EG431883.1|EG431883
EST:     GGACTACAGCTAGCAGAAAGGGACATAATTGTGGCATGTCTAGATTACAG                         AAACTTTCCTCAGGGGACAATTAGTGATATGGTAAGTGATGCGGCTCAAGG
genomic: GGACTACAGCTAGCAGAAAGGGACATAATTGTGGCATGTCTAGATTACAGgtaagcaaag ... tttggttcagAAACTTTCCTCAGGGGACAATTAGTGATATGGTAAGTGATGCAGCTCAAGG
EST: gi|116389290|gb|EG431882.1|EG431882
EST:     GGACTACAGCTAGCAGAAAGGGACATAATTGTGGCATGTCTAGATTACAG                         AAACTTTCCTCAGGGGACAATTAGTGATATGGTAAGTGATGCAGCTCAAGG
genomic: GGACTACAGCTAGCAGAAAGGGACATAATTGTGGCATGTCTAGATTACAGgtaagcaaag ... tttggttcagAAACTTTCCTCAGGGGACAATTAGTGATATGGTAAGTGATGCAGCTCAAGG
EST: gi|116389281|gb|EG431873.1|EG431873
EST:     GGACTACAGCTAGCAGAAAGGGACATAATTGTGGCATGTCTAGATTACAG                         AAACTTTCCTCAGGGGACAATTAGTGATATGGTAAGTGATGCAGCTCAAGG
genomic: GGACTACAGCTAGCAGAAAGGGACATAATTGTGGCATGTCTAGATTACAGgtaagcaaag ... tttggttcagAAACTTTCCTCAGGGGACAATTAGTGATATGGTAAGTGATGCAGCTCAAGG
EST: gi|116389278|gb|EG431870.1|EG431870
EST:     GGACTACAGCTAGCAGAAAGGGACATAATTGTGGCATGTCTAGATTACAG                         AAACTTTCCTCAGGGGACAATTAGTGATATGGTAAGTGATGCAGCTCAAGG
genomic: GGACTACAGCTAGCAGAAAGGGACATAATTGTGGCATGTCTAGATTACAGgtaagcaaag ... tttggttcagAAACTTTCCTCAGGGGACAATTAGTGATATGGTAAGTGATGCAGCTCAAGG
EST: gi|116389280|gb|EG431872.1|EG431872
EST:     GGACTACAGCTAGCAGAAAGGGACATAATTGTGGCATGTCTAGATTACAG                         AAACTTTCCTCAGGGGACAATTAGTGATATGGTAAGTGATGCAGCTCAAGG
genomic: GGACTACAGCTAGCAGAAAGGGACATAATTGTGGCATGTCTAGATTACAGgtaagcaaag ... tttggttcagAAACTTTCCTCAGGGGACAATTAGTGATATGGTAAGTGATGCAGCTCAAGG
EST: gi|116389279|gb|EG431871.1|EG431871
EST:     GGACTACAGCTAGCAGAAAGGGACATAATTGTGGCATGTCTAGATTACAG                         AAACTTTCCTCAGGGGACAATTAGTGATATGGTAAGTGATGCAGCTCAAGG
genomic: GGACTACAGCTAGCAGAAAGGGACATAATTGTGGCATGTCTAGATTACAGgtaagcaaag ... tttggttcagAAACTTTCCTCAGGGGACAATTAGTGATATGGTAAGTGATGCAGCTCAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatcatatgcctgtatccaatgcattgaccaagcaatcccctgtctttggttcagAAACTTTCCTCAGGGGACAATTAGTGATATGGTAAGTGATGCAGCTCAAGGAATCTCATTTGTCTGCAATAACATCTCTGCATTTGGAGGTGATCCTAAC
                      cattgac  putative branch site (score: 3)
                                    tcccctgtcttt  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcaaagtagtcaatttcttaccagtgttacttgtcctggattctatcaaatctatatcagcttggagctatttgggaatttatctttgttaatcatatgcctgtatccaatgcattgaccaagcaatcccctgtctttggttcagAAACTTTCCTCAGGGGACAATTAGTGATATGGTAAGTGATGCAGCTCAAGGAATCTCATTTGTCTGCAATAACATCTCTGCATTTGGAGGTGATCCTAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG