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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTGTCTCTGTTTCGGGAACTCTGTGGCATCTACTCGTTTTATGTTGCAAGATGAATTCAACATCCATACAACAAAATGCGACAATTGCATAATTgtactccctactttccctctttgttatcacttattcactttcgtcttatacatgtttgtgtgcgtcaacattttcccatcttctttcgttgttttgtag

Basic information

species Arabidopsis thaliana
transcript AT5G41390.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G41390.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os03g03180.1 (Oryza sativa), 5'ss of exon 5
GTGTGTCTCTGTTTCGGGAACTCTGTGGCATCTACTCGTTTTATGTTGCAAGATGAATTCAACATCCATACAACAAAATGCGACAATTGCATAATTgtactccctactttccctctttgttatcacttattcactttc--gtcttatac--atgtttgtgtgcgtcaacattttcccatctt------ctttcgttgttttgtag
|||| ||| || || || || || || || || || || ||  || | ||||||||||||||||| || ||||| |||||||| || ||||| ||||||||  |    | | ||  ||||| |   ||| | |||||   || | || |  |||||    | |    | | | |  ||                || |  |||||
GTGTTTCTGTGCTTTGGTAATTCAGTTGCTTCAACCCGCTTCTTGCTCCAAGATGAATTCAACATACAGACAACTAAATGCGATAACTGCATCATTgtactgtcactgtcctcttgttgtt-tgttttactaacttttaggtataattcctatgttccctttctatgagactataacactgcagaagatcactcttttcctgtag
















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|116448183|gb|EG490775.1|EG490775
EST:     TGCAAGATGAATTCAACATCCATACAACAAAATGCGACAATTGCATAATT                         GGATTTATGTTCTGCCTCAACCAAATCGCTTGCATTTTCTCTCTTGTCGCT
genomic: TGCAAGATGAATTCAACATCCATACAACAAAATGCGACAATTGCATAATTgtactcccta ... tgttttgtagGGATTTATGTTCTGCCTCAACCAAATCGCTTGCATTTTCTCTCTTGTCGCT
EST: gi|116448400|gb|EG490992.1|EG490992
EST:     TGCAAGATGAATTCAACATCCATACAACAAAATGCGACAATTGCATAATT                         GGATTTATGTTCTGCCTCAACCAAATCGCTTGCATTTTCTCTCTTGTCGCT
genomic: TGCAAGATGAATTCAACATCCATACAACAAAATGCGACAATTGCATAATTgtactcccta ... tgttttgtagGGATTTATGTTCTGCCTCAACCAAATCGCTTGCATTTTCTCTCTTGTCGCT
EST: gi|116448412|gb|EG491004.1|EG491004
EST:     TGCAAGATGAATTCAACATCCATACAACAAAATGCGACAATTGCATAATT                         AGATTTATGTTCTGCCTCAACCAAATCGCTTGCATTTTCTCTCTTGTCGCT
genomic: TGCAAGATGAATTCAACATCCATACAACAAAATGCGACAATTGCATAATTgtactcccta ... tgttttgtagGGATTTATGTTCTGCCTCAACCAAATCGCTTGCATTTTCTCTCTTGTCGCT
EST: gi|116448179|gb|EG490771.1|EG490771
EST:     TGCAAGATGAATTCAACATCCATACAACAAAATGCGACAATTGCATAATT                         GGATTTATGTTCTGCCTCAACCAAATCGCTTGCATTTTCTCTCTTGTCGCT
genomic: TGCAAGATGAATTCAACATCCATACAACAAAATGCGACAATTGCATAATTgtactcccta ... tgttttgtagGGATTTATGTTCTGCCTCAACCAAATCGCTTGCATTTTCTCTCTTGTCGCT
EST: gi|116448398|gb|EG490990.1|EG490990
EST:     CATACAACAAAATGCGACAATTGCATAATT                         GGATTTATGTTCTGCCTCAACCAAATCGCTTGCATTTTCTCTCTTGTCGCT
genomic: CATACAACAAAATGCGACAATTGCATAATTgtactcccta ... tgttttgtagGGATTTATGTTCTGCCTCAACCAAATCGCTTGCATTTTCTCTCTTGTCGCT
EST: gi|116448181|gb|EG490773.1|EG490773
EST:     TGCAAGATGAATTCAACATCCATACAACAAAATGCGACAATTGCATAATT                         GGATTTATGTTCTGCCTCAACCAAATCGCTTGCATTTTCTCTCTTGTCGCT
genomic: TGCAAGATGAATTCAACATCCATACAACAAAATGCGACAATTGCATAATTgtactcccta ... tgttttgtagGGATTTATGTTCTGCCTCAACCAAATCGCTTGCATTTTCTCTCTTGTCGCT
EST: gi|116448178|gb|EG490770.1|EG490770
EST:     TCAACATCCATACAACAAAATGCGACAATTGCATAATT                         GGATTTATGTTCTGCCTCAACCAAATCGCTTGCATTTTCTCTCTTGTCGCT
genomic: TCAACATCCATACAACAAAATGCGACAATTGCATAATTgtactcccta ... tgttttgtagGGATTTATGTTCTGCCTCAACCAAATCGCTTGCATTTTCTCTCTTGTCGCT
EST: gi|116448164|gb|EG490756.1|EG490756
EST:     TGCAAGATGAATTCAACATCCATACAACAAAATGCGACAATTGCATAATT                         GGATTTATGTTCTGCCTCAACCAAATCGCTTGCATTTTCTCTCTTGTCGCT
genomic: TGCAAGATGAATTCAACATCCATACAACAAAATGCGACAATTGCATAATTgtactcccta ... tgttttgtagGGATTTATGTTCTGCCTCAACCAAATCGCTTGCATTTTCTCTCTTGTCGCT
EST: gi|116448399|gb|EG490991.1|EG490991
EST:     CATACAACAAAATGCGACAATTGCATAATT                         GGATTTATGTTCTGCCTCAACCAAATCGCTTGCATTTTCTCTCTTGTCGCT
genomic: CATACAACAAAATGCGACAATTGCATAATTgtactcccta ... tgttttgtagGGATTTATGTTCTGCCTCAACCAAATCGCTTGCATTTTCTCTCTTGTCGCT
EST: gi|116448409|gb|EG491001.1|EG491001
EST:     TGCAAGATGAATTCAACATCCATACAACAAAATGCGACAATTGCATAATT                         AGATTTATGTTCTGCCTCAACCAAATCGCTTGCATTTTCTCTCTTGTCGCT
genomic: TGCAAGATGAATTCAACATCCATACAACAAAATGCGACAATTGCATAATTgtactcccta ... tgttttgtagGGATTTATGTTCTGCCTCAACCAAATCGCTTGCATTTTCTCTCTTGTCGCT
EST: gi|116448172|gb|EG490764.1|EG490764
EST:     TGCAAGATGAATTCAACATCCATACAACAAAATGCGACAATTGCATAATT                         GGATTTATGTTCTGCCTCAACCAAATCGCATGCATTTTCTCTCTTGTCGCT
genomic: TGCAAGATGAATTCAACATCCATACAACAAAATGCGACAATTGCATAATTgtactcccta ... tgttttgtagGGATTTATGTTCTGCCTCAACCAAATCGCTTGCATTTTCTCTCTTGTCGCT
EST: gi|116448401|gb|EG490993.1|EG490993
EST:     TGCAAGATGAATTCAACATCCATACAACAAAATGCGACAATTGCATAATT                         GGATTTATGTTCTGCCTCAACCAAATCGCTTGCATTTTCTCTCTTGTCGCT
genomic: TGCAAGATGAATTCAACATCCATACAACAAAATGCGACAATTGCATAATTgtactcccta ... tgttttgtagGGATTTATGTTCTGCCTCAACCAAATCGCTTGCATTTTCTCTCTTGTCGCT
EST: gi|116448177|gb|EG490769.1|EG490769
EST:     TGCAAGATGAATTCAACATCCATACAACAAAATGCGACAATTGCATAATT                         GGATTTATGTTCTGCCTCAACCAAATCGCTTGCATTTTCTCTCTTGTCGCT
genomic: TGCAAGATGAATTCAACATCCATACAACAAAATGCGACAATTGCATAATTgtactcccta ... tgttttgtagGGATTTATGTTCTGCCTCAACCAAATCGCTTGCATTTTCTCTCTTGTCGCT
EST: gi|116448166|gb|EG490758.1|EG490758
EST:     TGCAAGATGAATTCAACATCCATACAACAAAATGCGACAATTGCATAATT                         GGATTTATGTTCTGCCTCAACCAAATCGCTTGCATTTTCTCTCTTGTCGCT
genomic: TGCAAGATGAATTCAACATCCATACAACAAAATGCGACAATTGCATAATTgtactcccta ... tgttttgtagGGATTTATGTTCTGCCTCAACCAAATCGCTTGCATTTTCTCTCTTGTCGCT
EST: gi|116448168|gb|EG490760.1|EG490760
EST:     TGCAAGATGAATTCAACATCCATACAACAAAATGCGACAATTGCATAATT                         GGATTTATGTTCTGCCTCAACCAAATCGCTTGCATTTTCTCTCTTGTCGCT
genomic: TGCAAGATGAATTCAACATCCATACAACAAAATGCGACAATTGCATAATTgtactcccta ... tgttttgtagGGATTTATGTTCTGCCTCAACCAAATCGCTTGCATTTTCTCTCTTGTCGCT
EST: gi|116448176|gb|EG490768.1|EG490768
EST:     TGCAAGATGAATTCAACATCCATACAACAAAATGCGACAATTGCATAATT                         GGATTTATGTTCTGCCTCAACCAAATCGCTTGCATTTTCTCTCTTGTCGCT
genomic: TGCAAGATGAATTCAACATCCATACAACAAAATGCGACAATTGCATAATTgtactcccta ... tgttttgtagGGATTTATGTTCTGCCTCAACCAAATCGCTTGCATTTTCTCTCTTGTCGCT
EST: gi|116448174|gb|EG490766.1|EG490766
EST:     TGCAAGATGAATTCAACATCCATACAACAAAATGCGACAATTGCATAATT                         GGATTTATGTTCTGCCTCAACCAAATCGCTTGCATTTTCTCTCTTGTCGCT
genomic: TGCAAGATGAATTCAACATCCATACAACAAAATGCGACAATTGCATAATTgtactcccta ... tgttttgtagGGATTTATGTTCTGCCTCAACCAAATCGCTTGCATTTTCTCTCTTGTCGCT
EST: gi|116448169|gb|EG490761.1|EG490761
EST:     TGCAAGATGAATTCAACATCCATACAACAAAATGCGACAATTGCATAATT                         GGATTTATGTTCTGCCTCAACCAAATCACTTGCATTTTCTCTCTTGTCGCT
genomic: TGCAAGATGAATTCAACATCCATACAACAAAATGCGACAATTGCATAATTgtactcccta ... tgttttgtagGGATTTATGTTCTGCCTCAACCAAATCGCTTGCATTTTCTCTCTTGTCGCT
EST: gi|116448173|gb|EG490765.1|EG490765
EST:     TGCAAGATGAATTCAACATCCATACAACAAAATGCGACAATTGCATAATT                         GGATTTATGTTCTGCCTCAACCAAATCGCTTGCATTTTCTCTCTTGTCGCT
genomic: TGCAAGATGAATTCAACATCCATACAACAAAATGCGACAATTGCATAATTgtactcccta ... tgttttgtagGGATTTATGTTCTGCCTCAACCAAATCGCTTGCATTTTCTCTCTTGTCGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGTGTCTCTGTTTCGGGAACTCTGTGGCATCTACTCGTTTTATGTTGCAAGATGAATTCAACATCCATACAACAAAATGCGACAATTGCATAATTgtactccctactttccctctttgttatcacttattcactttcgtcttatacatgtttgtgtgcgtcaacattttcccatcttctttcgttgttttgtag

- - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - -  AAGATG