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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgtattgtaaagacctcttaaaaattggtttctttagagtattgcaactaatcttactcttttctctgttccagGATCGTCAGGGCCTTCTTGGTTGAAGAACAGAAGATTGTGAAGAAGGTTTTGAAGCTTCAGAAGGCGAAAGAGAAGACTGCACCAAAGAGTTAGAAGAAA

Basic information

species Arabidopsis thaliana
transcript AT3G28900.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G28900.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os09g24690.1 (Oryza sativa), 3'ss of exon 3
gtaagtgta--ttgtaaagacctcttaaaaattggtttc----tttagagtattgcaactaatcttactcttttctctgttccagGATCGTCAGGGCCTTCTTGGTTGAAGAACAGAAGATTGTGAAGAAGGTTTTGAAGCTTCAGAAGGCGAAAGAGAAGACTGCACCAAAGAGTTAGAAGAAA---
|| ||  ||   ||     || | |  | | ||| ||      | ||   | |  || || |  | | || | |  |  |  ||||||| |  | || |||||||||||||| ||||||||||||||||| || |||||  | |||||  | || || ||| | ||  |||||   ||||  |     
gtcagcataacatgctccaacatatccacatttgattataacatgtatcttctgtcacctcacatgattcatattgcc-tcgcagGATCATTCGTGCTTTCTTGGTTGAAGAGCAGAAGATTGTGAAGAAAGTCTTGAAAATACAGAAAACCAAGGACAAGTCAGCCTCAAAG---TAGACAACTCTT

upper sequence: AT3G28900.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os08g06040.1 (Oryza sativa), 3'ss of exon 3
gtaagtgtattgtaaagacctcttaaaaattggtttctttagagtattgcaactaatcttactcttttctctgttccagGATCGTCAGGGCCTTCTTGGTTGAAGAACAGAAGATTGTGAAGAAGGTTTTGAAGCTTCAGAAGGCGAAAGAGAAGACTGCACCAAAGAGTTAGAAGAAA--
    ||  |   |  | ||   ||| |   |  ||||||  ||  |  |    | | |  |    | |     |  ||||||| || |||| || ||||| || || |||||||||||||||||||| |||||| | |||||| | || || ||| | ||   |||   ||  |||| |  
----gtaaaccatccaaacacattacatgctcctttcttgcgatca--gttggtgaaccaatctatctgcacctcgcagGATCATCCGGGCTTTTTTGGTCGAGGAGCAGAAGATTGTGAAGAAGGTGTTGAAGATCCAGAAGACCAAGGACAAGTCAGC--TAAATGATTGCAAGATAGA

upper sequence: AT3G28900.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G152573_T04 (Zea mays), 3'ss of exon 3
gtaagtgtattgtaaagacctcttaaaaattggtttctttagagtattgcaactaatcttactcttttctc-tgttccagGATCGTCAGGGCCTTCTTGGTTGAAGAACAGAAGATTGTGAAGAAGGTTTTGAAGCTTCAGAAGGCGAAAGAGAAGACTGCACCAAAGAGTTAGAAGAAA---
|| |   |  | |     ||  |       | |  | |||| |  ||||      |   || |||   | |  |   ||||||| || | ||||| ||||| || ||||||||||| ||||||||||| |||||| | || ||| | || || ||| |     | ||||| |||| || |   
gtgatcattctttcgcatcccat-----gcttgcctgtttaaatgattgtttgagaaactaatctgcccgcacgcctcagGATCATCCGTGCCTTTTTGGTCGAGGAACAGAAGATAGTGAAGAAGGTGTTGAAGATCCAAAAGACCAAGGATAAGGCC---TCCAAGAGCTAGACGATATAG

upper sequence: AT3G28900.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G166963_T01 (Zea mays), 3'ss of exon 3
gtaagtgtattgtaaagacctcttaaaaattggtttctttagagtattgcaact-------aatcttactctttt-----ctctgttccagGATCGTCAGGGCCTTCTTGGTTGAAGAACAGAAGATTGTGAAGAAGGTTTTGAAGCTTCAGAAGGCGAAAGAGAAGACTGCACCAAAGAGTTAGAAGAAA
|| ||   || ||    |  | ||   | ||| |  |  || |||     | ||       |  |  ||   |||     || | || ||||||| || | || ||| |||||||||| ||||||||||| |||||||| |||||  | |||||| | ||||| |||||| |  |||| |  ||      |
gttagcaaatagtttccatatattttgatttgataaccctaaagttgcaaacctctatgtaacccccacatgttttcacactgtcttgcagGATCATCCGTGCTTTCCTGGTTGAAGAGCAGAAGATTGTCAAGAAGGTGTTGAAATTACAGAAGACCAAAGACAAGACTTCCTCAAAAAAGTAACTCTGA

upper sequence: AT3G28900.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G032564_T01 (Zea mays), 3'ss of exon 3
gtaagtgtattgtaaagacctcttaaaaattggtttctttagagtattgcaactaat-cttactcttttctctgttccagGATCGTCAGGGCCTTCTTGGTTGAAGAACAGAAGATTGTGAAGAAGGTTTTGAAGCTTCAGAAGGCGAAAGAGAAGACTGCACCAAAGAGTTAGAAGAAA---
|| |   |  | |    ||   |         ||   || | |  |||     | || || | ||   |   |||  ||||||| || | ||||| ||||| || || |||||||| |||||||||||||||||| | || ||  | || || ||| |     | ||||  |||  || |   
gtgaccattctttcgcaactcat-----gcccgtccattgaaatgattaatggtgatactaagtcacctgcatgtctcagGATCATCCGTGCCTTTTTGGTCGAGGAGCAGAAGATCGTGAAGAAGGTTTTGAAGATCCAAAAAACCAAGGATAAGGCC---TCCAAGAACTAGGCGATATAG

upper sequence: AT3G28900.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S200_25V6.1 (Physcomitrella patens), 3'ss of exon 3
--------------gtaagtgtattgtaaagacct---cttaaaaattggtttctttaga-gtattgc-aactaatcttactc--ttttctctgttccagGATCGTCAGGGCCTTCTTGGTTGAAGAACAGAAGATTGTGAAGAAGGTTTTGAAGCTTCAGAAGGCGAAAGAGAAGACTGCACCAAAGAGTTAGAAGAAA
               ||  |||        | |||     |   | ||||  || | |   ||||| | ||  |||| |  ||  |||| || | | ||| ||  || | || ||  | ||||| ||||||||||| |||||||||||||||||| | |||||| | || |||||    ||  | ||||   |     ||
ttacatgtattgttatagttgtgcatgtttgccctagctgtgtgacttggaatcatcatctgtatttctaataaatcgtgatcaattttgtccgatgcagCATTATCCGAGCTTTTCTAGTTGAGGAACAGAAGATCGTGAAGAAGGTTTTGAAGATCCAGAAGTCAAAGGAGAAATTGGCTGCTAAGACCCAATCCTAA

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|164062320|gb|ES182298.1|ES182298
EST:     CTGTTAGGGAGAG                         GATCGTCAGGGCCTTCTTGGTTGAAGAACAGAAGATTGTGAAGAAGGTTTT
genomic: CTGTTAGGGAGAGgtaagtgtat ... tctgttccagGATCGTCAGGGCCTTCTTGGTTGAAGAACAGAAGATTGTGAAGAAGGTTTT
EST: gi|86081909|gb|DR377668.1|DR377668
EST:     GTGAATCGTGCATATGGTGGTGTTCTATCTGGAGTTGCTGTTAGGGAGAG                         GATCGTCAGGGCCTTCTTGGTTGAAGAACAGAAGATTGTGAAGAAGGTTTT
genomic: GTGAATCGTGCATATGGTGGTGTTCTATCTGGAGTTGCTGTTAGGGAGAGgtaagtgtat ... tctgttccagGATCGTCAGGGCCTTCTTGGTTGAAGAACAGAAGATTGTGAAGAAGGTTTT
EST: gi|124848384|gb|EH932821.1|EH932821
EST:     TTGCTGTTAGGGAGAG                         GATCGTCAGGGCCTTCTTGGTTGAAGAACAGAAGATTGTGAAGAAGGTTTT
genomic: TTGCTGTTAGGGAGAGgtaagtgtat ... tctgttccagGATCGTCAGGGCCTTCTTGGTTGAAGAACAGAAGATTGTGAAGAAGGTTTT
EST: gi|152038453|gb|AV823465.2|AV823465
EST:     GTGAATCGTGCATATGGTGGTGTTCTATCTGGAGTTGCTGTTAGGGAGAG                         GATCGTCAGGGCCTTCTTGGTTGAAGAACAGAAGATTGTGAAGAAGGTTTT
genomic: GTGAATCGTGCATATGGTGGTGTTCTATCTGGAGTTGCTGTTAGGGAGAGgtaagtgtat ... tctgttccagGATCGTCAGGGCCTTCTTGGTTGAAGAACAGAAGATTGTGAAGAAGGTTTT
EST: gi|164209704|gb|ES016635.1|ES016635
EST:     TCTGGAGTCGCTGTTAGGGAGAG                         GATCGTCAGGGCCTTCTTGGTTGAAGAACAGAAGATTGTGAAGAAGGTTTT
genomic: TCTGGAGTTGCTGTTAGGGAGAGgtaagtgtat ... tctgttccagGATCGTCAGGGCCTTCTTGGTTGAAGAACAGAAGATTGTGAAGAAGGTTTT
EST: gi|164154898|gb|ES075394.1|ES075394
EST:     TCTATCTGGAGTCGCTGTTAGGGAGAG                         GATCGTCAGGGCCTTCTTGGTTGAAGAACAGAAGATTGTGAAGAAGGTTTT
genomic: TCTATCTGGAGTTGCTGTTAGGGAGAGgtaagtgtat ... tctgttccagGATCGTCAGGGCCTTCTTGGTTGAAGAACAGAAGATTGTGAAGAAGGTTTT
EST: gi|86027917|gb|DR323670.1|DR323670
EST:     GTGAATCGTGCATATGGTGGTGTTCTATCTGGAGTTGCTGTTAGGGAGAG                         GATCGTCAGGGCCTTCTTGGTTGAAGAACAGAAGATTGTGAAGAAGGTTTT
genomic: GTGAATCGTGCATATGGTGGTGTTCTATCTGGAGTTGCTGTTAGGGAGAGgtaagtgtat ... tctgttccagGATCGTCAGGGCCTTCTTGGTTGAAGAACAGAAGATTGTGAAGAAGGTTTT
EST: gi|86027914|gb|DR323667.1|DR323667
EST:     GTGAATCGTGCATATGGTGGTGTTCTATCTGGAGTTGCTGTTAGGGAGAG                         GATCGTCAGGGCC
genomic: GTGAATCGTGCATATGGTGGTGTTCTATCTGGAGTTGCTGTTAGGGAGAGgtaagtgtat ... tctgttccagGATCGTCAGGGCC
EST: gi|164141359|gb|ES079868.1|ES079868
EST:     TGGAGTCGCTGTTAGGGAGAG                         GATCGTCAGGGCCTTCTTGGTTGAAGAACAGAAGATTGTGAAGAAGGTTTT
genomic: TGGAGTTGCTGTTAGGGAGAGgtaagtgtat ... tctgttccagGATCGTCAGGGCCTTCTTGGTTGAAGAACAGAAGATTGTGAAGAAGGTTTT
EST: gi|163977464|gb|ES020492.1|ES020492
EST:     TCTATCTGGAGTCGCTGTTAGGGAGAG                         GATCGTCAGGGCCTTCTTGGTTGAAGAACAGAAGATTGTAGAAGAAGGTTT
genomic: TCTATCTGGAGTTGCTGTTAGGGAGAGgtaagtgtat ... tctgttccagGATCGTCAGGGCCTTCTTGGTTGAAGAACAGAAGATTGT-GAAGAAGGTTT
EST: gi|86027921|gb|DR323674.1|DR323674
EST:     GTGAATCGTGCATATGGTGGTGTTCTATCTGGAGTTGCTGTTAGGGAGAG                         GATCGTCAGGGCCTTCTTGGTTGAAGAACAGAAGATTGTGAAGAAGGTTTT
genomic: GTGAATCGTGCATATGGTGGTGTTCTATCTGGAGTTGCTGTTAGGGAGAGgtaagtgtat ... tctgttccagGATCGTCAGGGCCTTCTTGGTTGAAGAACAGAAGATTGTGAAGAAGGTTTT
EST: gi|86027920|gb|DR323673.1|DR323673
EST:     GTGAATCGTGCATATGGTGGTGTTCTATCTGGAGTTGCTGTTAGGGAGAG                         GATCGTCAGGGCCTTCTTGGTTGAAGAACAGAAGATTGTGAAGAAGGTTTT
genomic: GTGAATCGTGCATATGGTGGTGTTCTATCTGGAGTTGCTGTTAGGGAGAGgtaagtgtat ... tctgttccagGATCGTCAGGGCCTTCTTGGTTGAAGAACAGAAGATTGTGAAGAAGGTTTT
EST: gi|86027912|gb|DR323665.1|DR323665
EST:     GTGAATCGTGCATATGGTGGTGTTCTATCTGGAGTTGCTGTTAGGGAGAG                         GATCGTCAGGGCCTTCTTGGTTGAAGAACAGAAGATTGTGAAGAAGGTTTT
genomic: GTGAATCGTGCATATGGTGGTGTTCTATCTGGAGTTGCTGTTAGGGAGAGgtaagtgtat ... tctgttccagGATCGTCAGGGCCTTCTTGGTTGAAGAACAGAAGATTGTGAAGAAGGTTTT
EST: gi|86027922|gb|DR323675.1|DR323675
EST:     GTGAATCGTGCATATGGTGGTGTTCTATCTGGAGTTGCTGTTAGGGAGAG                         GATCGTCAGGGCSTTCTTGGTTGAAGAACAGAAGATTGTGAAGAAGGTTTT
genomic: GTGAATCGTGCATATGGTGGTGTTCTATCTGGAGTTGCTGTTAGGGAGAGgtaagtgtat ... tctgttccagGATCGTCAGGGCCTTCTTGGTTGAAGAACAGAAGATTGTGAAGAAGGTTTT
EST: gi|86027915|gb|DR323668.1|DR323668
EST:     GTGAATCGTGCATATGGTGGTGTTCTATCTGGAGTTGCTGTTAGGGAGAG                         GATCGTCAGGGCCTTCTTGGTTGAAGAACAGAAGATTGTGAAGAAGGTTTT
genomic: GTGAATCGTGCATATGGTGGTGTTCTATCTGGAGTTGCTGTTAGGGAGAGgtaagtgtat ... tctgttccagGATCGTCAGGGCCTTCTTGGTTGAAGAACAGAAGATTGTGAAGAAGGTTTT
EST: gi|86027924|gb|DR323677.1|DR323677
EST:     GTGAATCGTGCATATGGTGGTGTTCTATCTGRAGTTGCTGTTAGGGAGAG                         GATCGTCAGGGCCTTCTTGGTTGAAGAACAGAAGATTGTGAAGAAGGTTTT
genomic: GTGAATCGTGCATATGGTGGTGTTCTATCTGGAGTTGCTGTTAGGGAGAGgtaagtgtat ... tctgttccagGATCGTCAGGGCCTTCTTGGTTGAAGAACAGAAGATTGTGAAGAAGGTTTT
EST: gi|164198833|gb|ES080731.1|ES080731
EST:     GGAGTCGCTGTTAGGGAGAG                         GATCGTCAGGGCCTTCTTGGTTGAAGAACAGAAGATTGTGAAGAAGGTTTT
genomic: GGAGTTGCTGTTAGGGAGAGgtaagtgtat ... tctgttccagGATCGTCAGGGCCTTCTTGGTTGAAGAACAGAAGATTGTGAAGAAGGTTTT
EST: gi|86027918|gb|DR323671.1|DR323671
EST:     GTGAATCGTGCATATGGTGGTGTTCTATCTGGAGTTGCTGTTAGGGAGAG                         GATCGTCAGGGCCTTCTTGGTTGAAGAACAGAAGATTGTGAAGAAGGTTTT
genomic: GTGAATCGTGCATATGGTGGTGTTCTATCTGGAGTTGCTGTTAGGGAGAGgtaagtgtat ... tctgttccagGATCGTCAGGGCCTTCTTGGTTGAAGAACAGAAGATTGTGAAGAAGGTTTT
EST: gi|86027919|gb|DR323672.1|DR323672
EST:     GTGAATCGTGCATATGGTGGTGTTCTATCTGGAGTTGCTGTTAGGGAGAG                         GATCGTCAGGGCCTTCTTGGTTGAAGAACAGAAGATTGTGAAGAAGGTTTT
genomic: GTGAATCGTGCATATGGTGGTGTTCTATCTGGAGTTGCTGTTAGGGAGAGgtaagtgtat ... tctgttccagGATCGTCAGGGCCTTCTTGGTTGAAGAACAGAAGATTGTGAAGAAGGTTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaattggtttctttagagtattgcaactaatcttactcttttctctgttccagGATCGTCAGGGCCTTCTTGGTTGAAGAACAGAAGATTGTGAAGAAGGTTTTGAAGCTTCAGAAGGCGAAAGAGAAGACTGCACCAAAGAGTTAGAAGAAA
                                tcttactcttttctct  CT-rich tract
         tttcttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgtattgtaaagacctcttaaaaattggtttctttagagtattgcaactaatcttactcttttctctgttccagGATCGTCAGGGCCTTCTTGGTTGAAGAACAGAAGATTGTGAAGAAGGTTTTGAAGCTTCAGAAGGCGAAAGAGAAGACTGCACCAAAGAGTTAGAAGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA