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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtcacactttctctaattcttgagcttcctttcatgttcagaaaactcattgttatagggacccactgactgaaactcagctctgatcaatcttgaagagtattgatcaataacatcaaatcattctgtaatttcagGACTTGGCAACAGCCTTTCTCAACGTGCTTGGTAACGAGAAAGCCAGCAGAGAGATATTCAACATCTCGGGGGAGAAATATGTTACCTTTGATGGGTTAG

Basic information

species Arabidopsis thaliana
transcript AT1G09340.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G09340.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA03G38930.1 (Glycine max), 3'ss of exon 7
gtcagtcacactttctctaattcttgagcttcctttcatgttcagaaaactcattgttatagggacccactgactgaaactcagctctgatcaatcttgaagagtattgatcaataacatcaaatcattctgtaatttcagGACTTGGCAACAGCCTTTCTCAACGTGCTTGGTAACGAGAAAGCCAGCAGAGAGATATTCAACATCTCGGGGGAGAAATATGTTACCTTTGATGGGTTAG
                                     ||    | |  | |   | | |  || |   |         |   |  | |  | ||| |||  || | |||   || |       ||  |||  |  |  ||||| ||||||| ||| ||| || | || |||||||| ||||| |||||||  ||  |||||||||||||||| || || ||||| || |||||||| ||||
----------------------------------aagattaataaatgatttcctataaatggaattgataagacagtaagtaaatttattgaattttgt-gatttttggctaaaat------attgttcaattgtgacagGATTTGGCAAAAGCTTTTATCCAGGTTCTTGGTAATGAGAAGGCCAGCAAGGAAGTATTCAACATCTCGGGAGATAAGTATGTCACATTTGATGGATTAG

upper sequence: AT1G09340.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA19G41540.2 (Glycine max), 3'ss of exon 7
gtcagtcacactttctctaattcttgagcttcctttcatgttcagaaaactcattgttatagggacccactgactgaaactcagctctgatcaatcttgaagagtattgatcaataacatcaaatcattctgtaatttcagGACTTGGCAACAGCCTTTCTCAACGTGCTTGGTAACGAGAAAGCCAGCAGAGAGATATTCAACATCTCGGGGGAGAAATATGTTACCTTTGATGGGTTAG
                                     |  ||  ||| | | ||   |   |    ||  ||| || |||     |  |  || |  |  ||  |  ||||       |  | ||  |||  | ||  ||||| ||||| ||||| ||| || | || |||||||| ||||| |||||||  ||  |||||||||||||||| ||||| ||||| || ||||| || ||||
-----------------------------------gaagcttttgaagattaataaat---gatttcctgtgaatggaac---agtaagtacatttattgagttttgtgattttggctaaaatattcttcaattatgacagGATTTGGCGACAGCTTTTATCCAAGTTCTTGGTAATGAGAAGGCCAGCAAGGAAGTATTCAACATCTCGGGAGAGAAGTATGTCACGTTTGACGGATTAG
















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|125043151|gb|EL115420.1|EL115420
EST:     TCCCGGTTCCAAACTCTGGGATACAGATCTCACAACTCGGTCACGTTAAG                         GACTTGGCAACA
genomic: TCCCGGTTCCAAACTCTGGGATACAGATCTCACAACTCGGTCACGTTAAGgtcagtcaca ... gtaatttcagGACTTGGCAACA
EST: gi|124983903|gb|EL056605.1|EL056605
EST:     TCCCGGTTCCAAACTCTGGGATACAGATCTCACAACTCGGTCACGTTAAG                         GACTTGGCAACAGCCTTTCTCAACGTGCTTGGTAACGAGAAAGCCAGCAGA
genomic: TCCCGGTTCCAAACTCTGGGATACAGATCTCACAACTCGGTCACGTTAAGgtcagtcaca ... gtaatttcagGACTTGGCAACAGCCTTTCTCAACGTGCTTGGTAACGAGAAAGCCAGCAGA
EST: gi|125046472|gb|EL118741.1|EL118741
EST:     GATCTCACAACTCGGTCACGTTAAG                         GACTTGGCAACAGCCTTTCTCAACGTGCTTGGTAACGAGAAAGCCAGCAGA
genomic: GATCTCACAACTCGGTCACGTTAAGgtcagtcaca ... gtaatttcagGACTTGGCAACAGCCTTTCTCAACGTGCTTGGTAACGAGAAAGCCAGCAGA
EST: gi|86080119|gb|DR375876.1|DR375876
EST:     TCCCGGTTCCAAACTCTGGGATACAGATCTCACAACTCGGTCACGTTAAG                         GACTTGGCAACAGCCTTTCTCAACGTGCTTGGTAACGAGAAAGCCAGCAGA
genomic: TCCCGGTTCCAAACTCTGGGATACAGATCTCACAACTCGGTCACGTTAAGgtcagtcaca ... gtaatttcagGACTTGGCAACAGCCTTTCTCAACGTGCTTGGTAACGAGAAAGCCAGCAGA
EST: gi|116482238|gb|EG524830.1|EG524830
EST:     TCCCGGTTCCAAATTTTGGGATACAGATCTCACAACTCGGTCACGTTAAG                         GACTTGGCAACAGCCTTTCTCAACGTGCTTGGTAACGAGAAAGCCAGCAGA
genomic: TCCCGGTTCCAAACTCTGGGATACAGATCTCACAACTCGGTCACGTTAAGgtcagtcaca ... gtaatttcagGACTTGGCAACAGCCTTTCTCAACGTGCTTGGTAACGAGAAAGCCAGCAGA
EST: gi|125315392|gb|EL329477.1|EL329477
EST:     TCCCGGTTCCAAACTCTGGGATACAGATCTCACAACTCGGTCACGTTAAG                         GACTTGGCAACAGCCTTTCTCAACGTGCTTGGTA
genomic: TCCCGGTTCCAAACTCTGGGATACAGATCTCACAACTCGGTCACGTTAAGgtcagtcaca ... gtaatttcagGACTTGGCAACAGCCTTTCTCAACGTGCTTGGTA
EST: gi|124818141|gb|EH903007.1|EH903007
EST:     CCCGGTTCCAAACTCTGGGATACAGATCTCTACAACTCGGTCACGTTAAG                         GACTTGGCAACAGCCTTTCTCAACGTGCTTGGTAACGAGAAAGCCAGCAGA
genomic: CCCGGTTCCAAACTCTGGGATACAGATCTC-ACAACTCGGTCACGTTAAGgtcagtcaca ... gtaatttcagGACTTGGCAACAGCCTTTCTCAACGTGCTTGGTAACGAGAAAGCCAGCAGA
EST: gi|125258838|gb|EL272923.1|EL272923
EST:     TCCCGGTTCCAAACTCTGGGATACAGATCTCACAACTCGGTCACGTTAAG                         GACTTGGCAACAGCCTTTCTCAACGTG
genomic: TCCCGGTTCCAAACTCTGGGATACAGATCTCACAACTCGGTCACGTTAAGgtcagtcaca ... gtaatttcagGACTTGGCAACAGCCTTTCTCAACGTG
EST: gi|124900632|gb|EH975250.1|EH975250
EST:     GGTCACGTTAAG                         GACTTGGCAACAGCCTTTCTCAACGTGCTTGGTAACGAGAAAGCCAGCAGA
genomic: GGTCACGTTAAGgtcagtcaca ... gtaatttcagGACTTGGCAACAGCCTTTCTCAACGTGCTTGGTAACGAGAAAGCCAGCAGA
EST: gi|124802210|gb|EH891215.1|EH891215
EST:     TCCCGGTTCCAAACTCTGGGATACAGATCTCACAACTCGGTCACGTTAAG                         GACTTGGCAACAGCCTTTCTCAACGTGCTTGGTAA
genomic: TCCCGGTTCCAAACTCTGGGATACAGATCTCACAACTCGGTCACGTTAAGgtcagtcaca ... gtaatttcagGACTTGGCAACAGCCTTTCTCAACGTGCTTGGTAA
EST: gi|124918260|gb|EH992116.1|EH992116
EST:     TCCCGGTTCCAAACTCTGGGATACAGATCTCACAACTCGGTCACGTTAAG                         GACTTGGCAACAGCCTTTCTCAACGTGCTTGGTAACGAGAAAGCCAGCAGA
genomic: TCCCGGTTCCAAACTCTGGGATACAGATCTCACAACTCGGTCACGTTAAGgtcagtcaca ... gtaatttcagGACTTGGCAACAGCCTTTCTCAACGTGCTTGGTAACGAGAAAGCCAGCAGA
EST: gi|124820891|gb|EH905757.1|EH905757
EST:     TCCCGGTTCCAAACTCTGGGATACAGATCTCACAACTCGGTCACGTTAAG                         GACTTGGCAACAGCCTTTCTCAA
genomic: TCCCGGTTCCAAACTCTGGGATACAGATCTCACAACTCGGTCACGTTAAGgtcagtcaca ... gtaatttcagGACTTGGCAACAGCCTTTCTCAA
EST: gi|125187634|gb|EL202588.1|EL202588
EST:     TCCCGGTTCCAAACTCTGGGATACAGATCTCACAACTCGGTCACGTTAAG                         GACTTGGCAACAGCCTTTCTCAACGTG
genomic: TCCCGGTTCCAAACTCTGGGATACAGATCTCACAACTCGGTCACGTTAAGgtcagtcaca ... gtaatttcagGACTTGGCAACAGCCTTTCTCAACGTG
EST: gi|86083439|gb|DR379198.1|DR379198
EST:     ACAACTCGGTCACGTTAAG                         GACTTGGCAACAGCCTTTCTCAACGTGCTTGGTAACGAGAAAGCCAGCAGA
genomic: ACAACTCGGTCACGTTAAGgtcagtcaca ... gtaatttcagGACTTGGCAACAGCCTTTCTCAACGTGCTTGGTAACGAGAAAGCCAGCAGA
EST: gi|124945686|gb|EL021672.1|EL021672
EST:     ACAGATCTCACAACTCGGTCACGTTAAG                         GACTTGGCAACAGCCTTTCTCAACGTGCTTGGTAACGAGAAAGCCAGCAGA
genomic: ACAGATCTCACAACTCGGTCACGTTAAGgtcagtcaca ... gtaatttcagGACTTGGCAACAGCCTTTCTCAACGTGCTTGGTAACGAGAAAGCCAGCAGA
EST: gi|124957523|gb|EL032350.1|EL032350
EST:     TCCCGGTTCCAAACTCTGGGATACAGATCTCACAACTCGGTCACGTTAAG                         GACTTGGCAACAGCCTTTCTCAACGTG
genomic: TCCCGGTTCCAAACTCTGGGATACAGATCTCACAACTCGGTCACGTTAAGgtcagtcaca ... gtaatttcagGACTTGGCAACAGCCTTTCTCAACGTG
EST: gi|124850207|gb|EH934644.1|EH934644
EST:     TCCCGGTTCCAAACTCTGGGATACAGATCTCACAACTCGGTCACGTTAAG                         GACTTGGCAACAGCCTTTCTCAA
genomic: TCCCGGTTCCAAACTCTGGGATACAGATCTCACAACTCGGTCACGTTAAGgtcagtcaca ... gtaatttcagGACTTGGCAACAGCCTTTCTCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgatcaatcttgaagagtattgatcaataacatcaaatcattctgtaatttcagGACTTGGCAACAGCCTTTCTCAACGTGCTTGGTAACGAGAAAGCCAGCAGAGAGATATTCAACATCTCGGGGGAGAAATATGTTACCTTTGATGGGTTAG
                         caataac  putative branch site (score: 2)
                       atcaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtcacactttctctaattcttgagcttcctttcatgttcagaaaactcattgttatagggacccactgactgaaactcagctctgatcaatcttgaagagtattgatcaataacatcaaatcattctgtaatttcagGACTTGGCAACAGCCTTTCTCAACGTGCTTGGTAACGAGAAAGCCAGCAGAGAGATATTCAACATCTCGGGGGAGAAATATGTTACCTTTGATGGGTTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA