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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATTCACCACATTCCTGGCCCGGAAGGTGTTCGTGGTCGTAACTCAGACAACAATCTGATCAAAGAAAAGCTTGGTTGGGCTCCTAATATGAGATTGAAGgtaccaacattatttacttaagtagctcaaagacaagataataatctaattcttttattactgatattgttttgaccataatcgttaaacag

Basic information

species Arabidopsis thaliana
transcript AT5G28840.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G28840.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G124434_T01 (Zea mays), 5'ss of exon 6
AATTCACCACATTCCTGGCCCGGAAGGTGTTCGTGGTCGTAACTCAGACAACAATCTGATCAAAGAAAAGCTTGGTTGGGCTCCTAATATGAGATTGAAGgtaccaacattatttacttaagta-gctcaaagacaagataataatctaattcttttattactgatat-tgttttgaccataatcgttaaacag
 || |||||||| |||||||||||||| || || || || ||||| |||||||  || ||||| || |||||||| ||||| || |  ||||   | |||||||   || ||| |   ||  ||    |     |   ||  |      ||  |   |  ||  | |  |||    |  |||  | ||   |||
CATCCACCACATCCCTGGCCCGGAAGGGGTCCGCGGGCGCAACTCTGACAACACCCTTATCAAGGAGAAGCTTGGCTGGGCCCCGACGATGAAGCTCAAGgtactgtcactatcttgctagatatagcctccatcgccatgctgga--gatgttgggaggacaaacagatgtaaacaaaataccctttgtgcag

upper sequence: AT5G28840.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA10G30400.1 (Glycine max), 5'ss of exon 5
AATTCACCACATTCCTGGCCCGGAAGGTGTTCGTGGTCGTAACTCAGACAACAATCTGATCAAAGAAAAGCTTGGTTGGGCTCCTAATATGAGATTGAAGgtaccaacattatttacttaagtagctcaaagacaagataataatctaattcttttattactgatattgttttgaccataa---tcgttaaacag--------
 |||||||||||||||||||| || |||||||| |||||||| |||||||| |  ||||| |||||||| |||||||||||||| | |||||| |||||||||  || |||| |  | | | | |  | || |  |  | ||  |   | ||| | || | | ||    | || |   |||     ||  |||||        
TATTCACCACATTCCTGGCCCTGAGGGTGTTCGAGGTCGTAATTCAGACAATACACTGATAAAAGAAAAACTTGGTTGGGCTCCAACTATGAGGTTGAAGgtaataatattactatcatgaattgggcgaaaattatcttat--ttccactctat-ataatttattccatgttcatattaagttctgtggaacagtcatagct

upper sequence: AT5G28840.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA20G36740.3 (Glycine max), 5'ss of exon 5
AATTCACCACATTCCTGGCCCGGAAGGTGTTCGTGGTCGTAACTCAGACAACAATCTGATCAAAGAAAAGCTTGGTTGGGCTCCTAATATGAGATTGAAGgtaccaacattatttacttaagtagctcaaagacaagataata--atctaattcttttattactgatatt--gttttg----accataatcgttaaacag
 |||||||||||||||||||| || ||||| || |||||||| |||||||| |  || || |||||||| |||||||||||||| | |||||| |||||||||  || || ||  | |     | |   |    |     |    || |||||  ||   | || |||||  ||| ||    ||  | || | | |   |
TATTCACCACATTCCTGGCCCCGAGGGTGTCCGAGGTCGTAATTCAGACAATACACTTATAAAAGAAAAACTTGGTTGGGCTCCAACTATGAGGTTGAAGgtaataatatcatgaattgggcgaacattatcttatttccactctatataatttgttccatgctcatattaagttctgtggaacagtcatagcttatagg

upper sequence: AT5G28840.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA03G40720.1 (Glycine max), 5'ss of exon 6
AATTCACCACATTCCTGGCCCGGAAGGTGTTCGTGGTCGTAACTCAGACAACAATCTGATCAAAGAAAAGCTTGGTTGGGCTCCTAATATGAGATTGAAGgtaccaacattatttacttaagtagctcaaagacaa---gataataatctaattcttttattactgatat-tgttttgaccataa--tcgttaaacag-----
|||  |||| ||||||||||| ||||||||||| |||||||| |||||||| |   | |||||||| || ||||| |||||||| | |||||  |||||||||  |   ||||||   |||   | | |||  ||    | |     | ||     |||||  ||  |   |  ||       ||  |  || |||||     
AATATACCATATTCCTGGCCCTGAAGGTGTTCGGGGTCGTAATTCAGACAATACATTAATCAAAGAGAAACTTGGCTGGGCTCCAACTATGAAGTTGAAGgtattattgttattt---taatggggttaaaatcaccttgttttctctttatacaatttatccctatttcctacttcagatgaaaggttttttaacagtcatt

upper sequence: AT5G28840.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA19G43400.1 (Glycine max), 5'ss of exon 6
AATTCACCACATTCCTGGCCCGGAAGGTGTTCGTGGTCGTAACTCAGACAACAATCTGATCAAAGAAAAGCTTGGTTGGGCTCCTAATATGAGATTGAAGgtaccaacattatttacttaagtagctcaaagacaa---gataataatctaattcttttattactgatattg--ttttgaccataatcgttaaacag------
|||  |||| ||||||||||| ||||||||||| || ||||| |||||||| |   | |||||||| || ||||| |||||||| | |||||  |||||||||  |   ||||||   |||   | | |||  ||    | |   | | ||     |||||| ||  |  |   || |||  |   |  || |||||      
AATATACCATATTCCTGGCCCAGAAGGTGTTCGGGGCCGTAATTCAGACAATACATTAATCAAAGAGAAACTTGGCTGGGCTCCAACTATGAAGTTGAAGgtattattgttattt---taatggggttaaaatcaccttgttttcactttatacaatttattcctatttcttacttctgatgaaggttttttaacagtcatta

upper sequence: AT5G28840.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA19G43410.1 (Glycine max), 5'ss of exon 6
AATTCACCACATTCCTGGCCCGGAAGGTGTTCGTGGTCGTAACTCAGACAACAATCTGATCAAAGAAAAGCTTGGTTGGGCTCCTAATATGAGATTGAAGgtaccaacattatttacttaagtagctcaaag-acaagataataatctaattct-tttattactgata-ttgttttgaccataa--tcgttaaacag-----
|||  |||| ||||||||||| ||||||||||| || ||||| |||||||| |   | |||||||| || ||||| |||||||| | |||||  |||||||||  |   ||||||  | | |  | | |||  ||    |  | | |  || |  |||||  ||  |  ||  ||       ||  |  || ||| |     
AATATACCATATTCCTGGCCCAGAAGGTGTTCGGGGCCGTAATTCAGACAATACATTAATCAAAGAGAAACTTGGCTGGGCTCCAACTATGAAGTTGAAGgtattattgttattt--taatggggttaaaatcaccttgttttcaccgtatacaatttatccctatttcttacttcagatgaaaggttttttaaccgtcatt

upper sequence: AT5G28840.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: EFJ09286 (Selaginella moellendorffii), 5'ss of exon 5
AATTCACCACATTCCTGGCCCGGAAGGTGTTCGTGGTCGTAACTCAGACAACAATCTGATCAAAGAAAAGCTTGGTTGGGCTCCTAATATGAGATTGAAGgtaccaacattatttacttaagtagctcaaagacaagataataatctaattcttttattactgatattgttttgaccataatcgttaaacag
||| ||||| || ||||| || ||||||||||||||| | || || |||||| ||||||| || || ||||| |||||||| || |  ||| || | |||||   || |  | ||  ||   |          |    |   |    ||      ||    ||| ||||| | |    ||            
AATCCACCATATCCCTGGGCCAGAAGGTGTTCGTGGTAGAAATTCGGACAACGATCTGATAAAGGAGAAGCTCGGTTGGGCCCCAACAATGCGACTCAAGgtgaaaaaacgagttttttttttcctctctctcctgttttgcag---aagcaaactaacg-tgagattgtgtggtgtgtag-----------

upper sequence: AT5G28840.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: EFJ12864 (Selaginella moellendorffii), 5'ss of exon 5
AATTCACCACATTCCTGGCCCGGAAGGTGTTCGTGGTCGTAACTCAGACAACAATCTGATCAAAGAAAAGCTTGGTTGGGCTCCTAATATGAGATTGAAGgtaccaacattatttacttaagtagctcaaagacaagataataatcta-attcttttattac--tgatattgttttgaccataatcgttaaacag
||| ||||| || ||||| || ||||||||||||||| | || || |||||||||||||| || || ||||| |||||||| || |  ||| || | |||||   || |  | ||  |||  ||  ||     |    |  |  | |  |       | ||   ||| ||||| | |    ||            
AATCCACCATATCCCTGGGCCAGAAGGTGTTCGTGGTAGAAATTCGGACAACAATCTGATAAAGGAGAAGCTCGGTTGGGCCCCAACAATGCGACTCAAGgtgaaaaaacgagtt-tttatttatttcttcctctctctcctgttttgcagaagcaaactaacgtgagattgtgtggtgtgtag-----------

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|164192044|gb|ES075988.1|ES075988
EST:     TATGAGATTGAAG                         GAGGGGCTTAGAATAACCTACTTCTGGATAAAGGAACAGATCGAGAAAGAG
genomic: TATGAGATTGAAGgtaccaacat ... cgttaaacagGAGGGGCTTAGAATAACCTACTTCTGGATAAAGGAACAGATCGAGAAAGAG
EST: gi|124912032|gb|EH986112.1|EH986112
EST:     ACAATCTGATCAAAGAAAAGCTTGGTTGGGCTCCTAATATGAGATTGAAG                         GAGGGGCTTAGAATAACCTACTTCTGG
genomic: ACAATCTGATCAAAGAAAAGCTTGGTTGGGCTCCTAATATGAGATTGAAGgtaccaacat ... cgttaaacagGAGGGGCTTAGAATAACCTACTTCTGG
EST: gi|86080157|gb|DR375914.1|DR375914
EST:     ACAATCTGATCAAAGAAAAGCTTGGTTGGGCTCCTAATATGAGATTGAAG                         GAGGGGCTTAGAATAACCTACTTCTGGATAAAGGAACAGATCGAGAAAGAG
genomic: ACAATCTGATCAAAGAAAAGCTTGGTTGGGCTCCTAATATGAGATTGAAGgtaccaacat ... cgttaaacagGAGGGGCTTAGAATAACCTACTTCTGGATAAAGGAACAGATCGAGAAAGAG
EST: gi|124710159|gb|EH801561.1|EH801561
EST:     ACAATCTGATCAAAGAAAAGCTTGGTTGGGCTCCTAATATGAGATTGAAG                         GAGGGGCTTAGAATAACCTACTTCTGGATAAAGGAACAGATCGAGAAAGAG
genomic: ACAATCTGATCAAAGAAAAGCTTGGTTGGGCTCCTAATATGAGATTGAAGgtaccaacat ... cgttaaacagGAGGGGCTTAGAATAACCTACTTCTGGATAAAGGAACAGATCGAGAAAGAG
EST: gi|116412576|gb|EG455168.1|EG455168
EST:     ACAATCTGATCAAAGAAAAGCTTGGTTGGGCTCCTAATATGAGATTGAAG                         GAGGGGCTTAGAATAACCTACTTCTGGATAAAGGAACAGATCGAGAAAGAG
genomic: ACAATCTGATCAAAGAAAAGCTTGGTTGGGCTCCTAATATGAGATTGAAGgtaccaacat ... cgttaaacagGAGGGGCTTAGAATAACCTACTTCTGGATAAAGGAACAGATCGAGAAAGAG
EST: gi|47830746|gb|CK120430.1|CK120430
EST:     ACAATCTGATCAAAGAAAAGCTTGGTTGGGCTCCTAATATGAGATTGAAG                         GAGGGGCTTAGAATAACCTACTTCTGGATAAAGGAACAGATCGAGAAAGAG
genomic: ACAATCTGATCAAAGAAAAGCTTGGTTGGGCTCCTAATATGAGATTGAAGgtaccaacat ... cgttaaacagGAGGGGCTTAGAATAACCTACTTCTGGATAAAGGAACAGATCGAGAAAGAG
EST: gi|125290057|gb|EL304142.1|EL304142
EST:     ACAATCTGATCAAAGAAAAGCTTGGTTGGGCTCCTAATATGAGATTGAAG                         GAGGGGCTTAG
genomic: ACAATCTGATCAAAGAAAAGCTTGGTTGGGCTCCTAATATGAGATTGAAGgtaccaacat ... cgttaaacagGAGGGGCTTAG
EST: gi|124978617|gb|EL051769.1|EL051769
EST:     ACAATCT-ATCAAAGAAAAGCTTGGTTGGGCTCCTAATATGAGATTGAAG                         GAGGGGCTTAGAA
genomic: ACAATCTGATCAAAGAAAAGCTTGGTTGGGCTCCTAATATGAGATTGAAGgtaccaacat ... cgttaaacagGAGGGGCTTAGAA
EST: gi|164108205|gb|ES153385.1|ES153385
EST:     ATCTGATCAAAGAAAAGCTTGGTTGGGCTCCTAATATGAGATTGAAG                         GAGGGGCTTAGAATAACCTACTTCTGGAATAAAGGAACAGATCGAGAAAGA
genomic: ATCTGATCAAAGAAAAGCTTGGTTGGGCTCCTAATATGAGATTGAAGgtaccaacat ... cgttaaacagGAGGGGCTTAGAATAACCTACTTCTGGA-TAAAGGAACAGATCGAGAAAGA
EST: gi|124881866|gb|EH960768.1|EH960768
EST:     ACAATCTGATCAAAGAAAAGCTTGGTTGGGCTCCTAATATGAGATTGAAG                         GAGGGGCTTAGAATAACCTACTTCTGGATAAA
genomic: ACAATCTGATCAAAGAAAAGCTTGGTTGGGCTCCTAATATGAGATTGAAGgtaccaacat ... cgttaaacagGAGGGGCTTAGAATAACCTACTTCTGGATAAA
EST: gi|124967938|gb|EL041929.1|EL041929
EST:     CAATCTGATCAAAGAAAAGCTTGGTTGGGCTACCTAATATGAGATTGAAG                         GAGGGGCTTAG
genomic: CAATCTGATCAAAGAAAAGCTTGGTTGGGCT-CCTAATATGAGATTGAAGgtaccaacat ... cgttaaacagGAGGGGCTTAG
EST: gi|125225384|gb|EL239469.1|EL239469
EST:     AAAAGCTTGGTTGGGCTCCTAATATGAGATTGAAG                         GAGGGGCTTAGAATAACCTACTTCTGGATAAAGGAACAGATCG
genomic: AAAAGCTTGGTTGGGCTCCTAATATGAGATTGAAGgtaccaacat ... cgttaaacagGAGGGGCTTAGAATAACCTACTTCTGGATAAAGGAACAGATCG
EST: gi|125094615|gb|EL152047.1|EL152047
EST:     ACAATCTGATCAAAGAAAAGCTTGGTTGGGCTCCTAATATGAGATTGAAG                         GAGGGGCTTAGAA
genomic: ACAATCTGATCAAAGAAAAGCTTGGTTGGGCTCCTAATATGAGATTGAAGgtaccaacat ... cgttaaacagGAGGGGCTTAGAA
EST: gi|86079152|gb|DR374909.1|DR374909
EST:     ACAATCTGATCAAAGAAAAGCTTGGTTGGGCTCCTAATATGAGATTGAAG                         GAGGGGCTTAGAATAACCTACTTCTGGATAAAGGAACAGATCGAGAAAGAG
genomic: ACAATCTGATCAAAGAAAAGCTTGGTTGGGCTCCTAATATGAGATTGAAGgtaccaacat ... cgttaaacagGAGGGGCTTAGAATAACCTACTTCTGGATAAAGGAACAGATCGAGAAAGAG
EST: gi|86084740|gb|DR380499.1|DR380499
EST:     ACAATCTGATCAAAGAAAAGCTTGGTTGGGCTCCTAATATGAGATTGAAG                         GAGGGGCTTAGAATAACCTACTTCTGGATAAAGGAACAGATCGAGAAAGAG
genomic: ACAATCTGATCAAAGAAAAGCTTGGTTGGGCTCCTAATATGAGATTGAAGgtaccaacat ... cgttaaacagGAGGGGCTTAGAATAACCTACTTCTGGATAAAGGAACAGATCGAGAAAGAG
EST: gi|116412564|gb|EG455156.1|EG455156
EST:     ACAATCTGATCAAAGAAAAGCTTGGTTGGGCTCCTAATATGAGATTGAAG                         GAGGGGCTTAGAATAACCTACTTCTGGATAAAGGAACAGATCGAGAAAGAG
genomic: ACAATCTGATCAAAGAAAAGCTTGGTTGGGCTCCTAATATGAGATTGAAGgtaccaacat ... cgttaaacagGAGGGGCTTAGAATAACCTACTTCTGGATAAAGGAACAGATCGAGAAAGAG
EST: gi|125212746|gb|EL227700.1|EL227700
EST:     ACAATCTGATCAAAGAAAAGCTTGGTTGGGCTCCTAATATGAGATTGAAG                         GAGGGGCTTAGAATAACCTACTT
genomic: ACAATCTGATCAAAGAAAAGCTTGGTTGGGCTCCTAATATGAGATTGAAGgtaccaacat ... cgttaaacagGAGGGGCTTAGAATAACCTACTT
EST: gi|124776143|gb|EH866270.1|EH866270
EST:     TCAAAGAAAAGCTTGGTTGGGCTCCTAATATGAGATTGAAG                         GAGGGGCTTAGAATAACCTACTTCTGGATAAAGGAACAGATCGAGAAAGAG
genomic: TCAAAGAAAAGCTTGGTTGGGCTCCTAATATGAGATTGAAGgtaccaacat ... cgttaaacagGAGGGGCTTAGAATAACCTACTTCTGGATAAAGGAACAGATCGAGAAAGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATTCACCACATTCCTGGCCCGGAAGGTGTTCGTGGTCGTAACTCAGACAACAATCTGATCAAAGAAAAGCTTGGTTGGGCTCCTAATATGAGATTGAAGgtaccaacattatttacttaagtagctcaaagacaagataataatctaattcttttattactgatattgttttgaccataatcgttaaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG