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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAACGCCGAATCTCTATGGGAATTTAGTTGCAAACACTGCTGCTGGTATTGCTGGAGGCACAGGAGTCATGCCTGGAGgtaaaaaaacatcctgtattgatattctctcgagctatacattagtggataaagaatagttctaaaatttatacatctgcgacattaaatacaaaaacag

Basic information

species Arabidopsis thaliana
transcript AT4G35260.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G35260.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os04g40310.2 (Oryza sativa), 5'ss of exon 3
GTAACGCCGAATCTCTATGGGAATTTAGTTGCAAACACTGCTGCTGGTATTGCTGGAGGCACAGGAGTCATGCCTGGAGgtaaaaaaacatcctgtattgatattctctcgagctata----cattagtgga-taaagaatagttctaaaatttatacatctgcgacattaaatacaaaaacag
|| || || || || ||||| ||||| ||||| ||||| ||||| |||||||||||||| ||||| || |||||||||||||  |    | | | ||    | |||  |  |    ||    ||  ||   | |||| ||| |      |    |||  | |  | ||   |  | |       
GTTACACCAAACCTTTATGGCAATTTGGTTGCTAACACGGCTGCAGGTATTGCTGGAGGGACAGGTGTTATGCCTGGAGgtaggatcttaacttttacct-tgttcctttaattcgtataagcaacagcacactaaacaatcggctgggagacaatatttttctgtcaccgacaatattt----

upper sequence: AT4G35260.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os02g38200.1 (Oryza sativa), 5'ss of exon 3
GTAACGCCGAATCTCTATGGGAATTTAGTTGCAAACACTGCTGCTGGTATTGCTGGAGGCACAGGAGTCATGCCTGGAGgtaaaaaaacatcctgtattgatattctctcgagctatacattagtggataaagaata---gttctaaaatttatacatctgcgacattaaatacaaaaacag
|| ||||| ||||| ||||| ||| | || || ||||| ||||| ||||||||||||||||| || ||||||||||||||||||     | |      |  || | |||  |  | ||| |      |||   ||||    |   |  |  |  | | |  |    ||   |    |     
GTCACGCCAAATCTTTATGGCAATCTGGTGGCTAACACGGCTGCAGGTATTGCTGGAGGCACTGGTGTCATGCCTGGAGgtaaattttgaactatcgcttgtaat-tctgtacttttacctgcacaaatagtcaatacggctatcaggagctggaaaccgacaggcttgcttttgcagtt--

upper sequence: AT4G35260.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G006672_T01 (Zea mays), 5'ss of exon 2
GTAACGCCGAATCTCTATGGGAATTTAGTTGCAAACACTGCTGCTGGTATTGCTGGAGGCACAGGAGTCATGCCTGGAGgtaaaaaaacatcctgtattgatattctctcgagctatacattagtggataaagaatagttctaaaatttatacatctgcgacattaaatacaaaaacag-
|| || || ||||| ||||| ||| | || || ||    ||||| ||||||||||||||||| || ||||||||||||||||      || |    ||| ||     ||  |  |  | || |    |    |  |  |   ||  | |||   |    | |  |||   | | |     
GTCACCCCAAATCTTTATGGCAATCTGGTGGCTAATGTAGCTGCAGGTATTGCTGGAGGCACTGGTGTCATGCCTGGAGgtagggtttcaactatgatttatgaatcctacatatgcaaat-aacatacttggttttatgtaaagttgtatttgttaaggcccataaggcccatattgcc

upper sequence: AT4G35260.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G025366_T02 (Zea mays), 5'ss of exon 3
GTAACGCCGAATCTCTATGGGAATTTAGTTGCAAACACTGCTGCTGGTATTGCTGGAGGCACAGGAGTCATGCCTGGAGgtaaaaaaacatcctgtattgatattctctcgagctatacattagtggataaagaatagttctaaaatttatacatctgcgacattaaatacaaaaacag----
|| ||||| ||||| ||||| ||||| || || ||||| ||||| ||||||| |||||| || ||  |||||||||||||||   |      ||   |   |||| | |   | | | |  |  ||   ||| ||  |||||   |    | ||| |  |  ||| | ||||||||       
GTTACGCCTAATCTTTATGGCAATTTGGTGGCTAACACGGCTGCAGGTATTGTTGGAGGGACGGGCATCATGCCTGGAGgtagggattgcagctaattctttattatttgttgttttcccctc-tg---aaaaaaatgttctggcagcgtttcatttctgtaatttattacaaaaaataatgt

upper sequence: AT4G35260.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: PP1S152_81V6.1 (Physcomitrella patens), 5'ss of exon 3
GTAACGCCGAATCTCTATGGGAATTTAGTTGCAAACACTGCTGCTGGTATTGCTGGAGGCACAGGAGTCATGCCTGGAGgtaaaaaaacatcctgtattgatattctctcgagctatacattagtggataaagaatagttctaa--aatttatacatctgcgacattaaatacaaaaacag
||||| || ||| | ||||| |   | || || || ||||| ||||||||||| || || || |||||||||||||||||||    |      |  ||| ||| | ||||      |    |     ||||  ||    | ||   | ||  ||||| |      || | |   |  ||  
GTAACACCAAATTTGTATGGAACACTGGTGGCCAATACTGCAGCTGGTATTGCAGGCGGAACTGGAGTCATGCCTGGAGgtaccctactccatttcatt-ataatatctcataacttttgcttcaaaataatcaaagactgtagtgacttagtacatatttctttttcacttggagcacc-

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|125072192|gb|EL136970.1|EL136970
EST:     CAAACACTGCTGCTGGTATTGCTGGAGGCACAGGGGTCATGCCTGGAG                         GAAATGTTGGGGCTGACCATGCGGTATTCGAGCAAGGTGCATC
genomic: CAAACACTGCTGCTGGTATTGCTGGAGGCACAGGAGTCATGCCTGGAGgtaaaaaaac ... acaaaaacagGAAATGTTGGGGCTGACCATGCGGTATTCGAGCAAGGTGCATC
EST: gi|163991855|gb|ES088470.1|ES088470
EST:     TGCAAACACTGCTGCTGGTATTGCTGGAGGCACAGGAGTCATGCCTGGAG                         GAAATGTTGGGGCTGACCATGCGGTATTCGAGCAA
genomic: TGCAAACACTGCTGCTGGTATTGCTGGAGGCACAGGAGTCATGCCTGGAGgtaaaaaaac ... acaaaaacagGAAATGTTGGGGCTGACCATGCGGTATTCGAGCAA
EST: gi|125265566|gb|EL279651.1|EL279651
EST:     CAGGAGTCATGCCTGGAG                         GAAATGTTGGGGCTGACCATGCGGTATTCGAGCAAGGT
genomic: CAGGAGTCATGCCTGGAGgtaaaaaaac ... acaaaaacagGAAATGTTGGGGCTGACCATGCGGTATTCGAGCAAGGT
EST: gi|125207271|gb|EL222225.1|EL222225
EST:     CTGGTATTGCTGGAGGCACAGGAGTCATGCCTGGAG                         GAAATGTTGGGGCTGACCATGCGGTATTCGAGCAAGGTGCATCAGCAGGAA
genomic: CTGGTATTGCTGGAGGCACAGGAGTCATGCCTGGAGgtaaaaaaac ... acaaaaacagGAAATGTTGGGGCTGACCATGCGGTATTCGAGCAAGGTGCATCAGCAGGAA
EST: gi|124915223|gb|EH989097.1|EH989097
EST:     TGCAAACACTGCTGCTGGTATTGCTGGAGGCACAGGAGTCATGCCTGGAG                         GAAATGTTGGGGCTGACCATGTGGTATTCGAGCAAGG
genomic: TGCAAACACTGCTGCTGGTATTGCTGGAGGCACAGGAGTCATGCCTGGAGgtaaaaaaac ... acaaaaacagGAAATGTTGGGGCTGACCATGCGGTATTCGAGCAAGG
EST: gi|124730596|gb|EH821998.1|EH821998
EST:     TATTGCTGGAGGCACAGGAGTCATGCCTGGAG                         GAAATGTTGGGGCTGACCATGCGGTATTCGTGCAAGGTGCATCAGCAGGAA
genomic: TATTGCTGGAGGCACAGGAGTCATGCCTGGAGgtaaaaaaac ... acaaaaacagGAAATGTTGGGGCTGACCATGCGGTATTCGAGCAAGGTGCATCAGCAGGAA
EST: gi|164143596|gb|ES121245.1|ES121245
EST:     GCAAACACTGCTGCTGGTATTGCTGGAGGCACAGGAGTCATGCCTGGAAG                         GAAATGTTGGGGCTGACCATGCGGTATTCGA
genomic: GCAAACACTGCTGCTGGTATTGCTGGAGGCACAGGAGTCATGCCTGGA-Ggtaaaaaaac ... acaaaaacagGAAATGTTGGGGCTGACCATGCGGTATTCGA
EST: gi|125017873|gb|EL090142.1|EL090142
EST:     TGCAAACACTGCTGCTGGTATTGCTGGAGGCACAGGAGTCATGCCTGGAG                         GAAATGTTGGGGCTGACCATGCGGTATTCGAGCAAGG
genomic: TGCAAACACTGCTGCTGGTATTGCTGGAGGCACAGGAGTCATGCCTGGAGgtaaaaaaac ... acaaaaacagGAAATGTTGGGGCTGACCATGCGGTATTCGAGCAAGG
EST: gi|125072197|gb|EL136974.1|EL136974
EST:     TGCAAACACTGCTGCTGGTATTGCTGGAGGCACAGGAGTCATGCCTGGAG                         GAAATGTTGGGGCTGACCATGCGGTATTCGAGCAA
genomic: TGCAAACACTGCTGCTGGTATTGCTGGAGGCACAGGAGTCATGCCTGGAGgtaaaaaaac ... acaaaaacagGAAATGTTGGGGCTGACCATGCGGTATTCGAGCAA
EST: gi|124900278|gb|EH974896.1|EH974896
EST:     TGCAAACACTGCTGCTGGTATTGCTGGAGGCACAGGAGTCATGCCTGGAG                         GAAATGTTGGGGCTGACCATGCGGTATTCGAG
genomic: TGCAAACACTGCTGCTGGTATTGCTGGAGGCACAGGAGTCATGCCTGGAGgtaaaaaaac ... acaaaaacagGAAATGTTGGGGCTGACCATGCGGTATTCGAG
EST: gi|125055519|gb|EL125709.1|EL125709
EST:     AGGAGTCATGCCTGGAG                         GAAATGTTGGGGCTGACCATGCGGTATTCGAGCAAGGTGCATCAGCAGGAA
genomic: AGGAGTCATGCCTGGAGgtaaaaaaac ... acaaaaacagGAAATGTTGGGGCTGACCATGCGGTATTCGAGCAAGGTGCATCAGCAGGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTAACGCCGAATCTCTATGGGAATTTAGTTGCAAACACTGCTGCTGGTATTGCTGGAGGCACAGGAGTCATGCCTGGAGgtaaaaaaacatcctgtattgatattctctcgagctatacattagtggataaagaatagttctaaaatttatacatctgcgacattaaatacaaaaacag

- - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG