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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtctactctactaacatacatttcaaacttctccttcttctaatctctaacttttccgacgatatttcaaaaatctcagGTTGACTTATCCGGTGGTTACTACGACGCCGGAGACAACATCAAGTTCGGTTTTCCGATGGCGTTCACAACAACGATGCTTTCATGGAGTATAATCGATT

Basic information

species Arabidopsis thaliana
transcript AT1G70710.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G70710.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os06g14540.1 (Oryza sativa), 3'ss of exon 1
------------------------gtaagtctactcta---ctaacatacatttcaaacttctccttcttctaa-----tctctaacttttcc-------gacgatatttca-aaaatctcagGTTGACTTATCCGGTGGTTACTACGACGCCGGAGACAACATCAAGTTCGGTTTTCCGATGGCGTTCACAACAACGATGCTTTCATGGAGTATAATCGATT
                         |   |||  ||||    |||      || |||  |  |  |  |  | |     || || ||  || |       |  |   |  |      |  ||||| ||| |  | || || |||||||||||||| |||||| | |||||||| || ||||||||||||||  | ||| |  | || ||| |  | ||||| |
gtacggaccaccaccgctctctctctctctctgttctagcattaatgcggtttgcaatgtagtagtaatgatgacgatgtcgctgacggtttcttggaatggtggcgtggcgtggcgtggcagGTGGACCTGACGGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGGTTCCCGATGGCGTTCACGGCGACGCTCATGTCGTGGGGGCTGATCGACT

upper sequence: AT1G70710.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os02g50040.1 (Oryza sativa), 3'ss of exon 1
gtaagtctactctactaaca--tacatttcaaacttctccttcttctaat----ctctaacttttccgacgatatttcaaaaatctc----agGTTGACTTATCCGGTGGTTACTACGACGCCGGAGACAACATCAAGTTCGGTTTTCCGATGGCGTTCACAACAACGATGCTTTCATGGAGTATAATCGATT
||| || | |||  |  | |  |     | ||   | | || ||  | |     |  |    |||  ||  |   | |      | |    |||| |||||  |||| || |||||||||||||| |||||| | |||||||| || ||||||||||||||  | ||| || | || ||| |  | ||||| |
gtacgtattctcgtcctataacttggcgttaagaatgtactactggtgaagcagcattgtgatttgtgagtaacctgctgtggccgcgtgtagGTGGACTTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGGTTCCCGATGGCGTTCACGGCGACGCTGATGTCGTGGGGGCTGATCGACT

upper sequence: AT1G70710.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G076049_T01 (Zea mays), 3'ss of exon 1
--------------------------gtaagtctactctactaacatacatttcaaact------tctccttcttctaa----tctctaacttttccgacgatatttcaaaa----atctcagGTTGACTTATCCGGTGGTTACTACGACGCCGGAGACAACATCAAGTTCGGTTTTCCGATGGCGTTCACAACAACGATGCTTTCATGGAGTATAATCGATT
                           ||| || |||||    |  | | |||    ||      |  | ||     ||    | | | |   || |  ||  ||||          |  ||||| ||  |  |||| || |||||||||||||| |||||| | |||||||| || ||||||||||||||  | ||| |  | || ||| |  | ||||| |
gtacgtgcaccgacccagtccgactaataaatc-actctctatagttgccttttggcctatagagtaccgttgaagcaagacatgtgtgagcattaccgcgccatttggtcgtcgcgtaacagGTGGATCTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGGTTCCCGATGGCGTTCACGGCGACGCTCATGTCGTGGGGCCTGATCGACT

upper sequence: AT1G70710.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA08G04840.1 (Glycine max), 3'ss of exon 1
gtaagtctactctactaacat-acatttcaaacttctc---cttcttctaatctctaacttttccgacgatatttcaaaaat--ctcagGTTGACTTATCCGGTGGTTACTACGACGCCGGAGACAACATCAAGTTCGGTTTTCCGATGGCGTTCACAACAACGATGCTTTCATGGAGTATAATCGATT
|||||| |  | | ||   || | | |  | | |  |      | |  | ||   |||       | | | |||       |  ||||||| |||||    || || |||||||||||||| || ||||| |||||||| ||||||||||||||||| || |||||||| || |||||  | |||||||
gtaagtttcttgttctgttatgaaaatgtagattgatagagaatatgatgatgattaatgaggtaggc-acattgtgttgtttactcagGTGGACTTGAGTGGAGGGTACTACGACGCCGGGGATAACATAAAGTTCGGGTTTCCGATGGCGTTCACGACGACGATGCTGTCGTGGAGCGTGATCGATT

upper sequence: AT1G70710.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA05G34850.1 (Glycine max), 3'ss of exon 1
gtaagtcta-ctctactaacatacatttcaaacttctccttcttctaatctctaacttttccgacg-atatttcaaaaatctcagGTTGACTTATCCGGTGGTTACTACGACGCCGGAGACAACATCAAGTTCGGTTTTCCGATGGCGTTCACAACAACGATGCTTTCATGGAGTATAATCGATT
|||||| |  || |  |    |  |     ||    |        | ||   |||       |    ||  |       |||||||| |||||   ||| || |||||||||||||| |||||||| |||||||| ||||||||||||||| | || || ||||| || |||||  | |||||||
gtaagtttttctgttttgttctgaaagggtaataggtagagaaaatgatgattaatgaggttggtacattgtgtttttttctcagGTGGACTTGAGCGGAGGGTACTACGACGCCGGGGACAACATAAAGTTCGGGTTTCCGATGGCGTTCTCGACGACAATGCTGTCGTGGAGCGTGATCGATT

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|164190916|gb|ES069065.1|ES069065
EST:     CGCGACGGTTCCTCCGCCGGC                         GTTGACTTATCCGGTGGTTACTACGACGCCGGAGACAACATCAAGTTCGGT
genomic: CGCGACGGTTCCTCCGCCGGCgtaagtctac ... aaaatctcagGTTGACTTATCCGGTGGTTACTACGACGCCGGAGACAACATCAAGTTCGGT
EST: gi|164036584|gb|EL972018.1|EL972018
EST:     GCTTAAAATGGCGCCGTGACTCAGCATTACGCGACGGTTCCTCCGCCGGC                         GTTGACTTATCCGGTGGTTACTACGACGCCGGAGACAACATCAAGTTCGGT
genomic: GCTTAAAATGGCGCCGTGACTCAGCATTACGCGACGGTTCCTCCGCCGGCgtaagtctac ... aaaatctcagGTTGACTTATCCGGTGGTTACTACGACGCCGGAGACAACATCAAGTTCGGT
EST: gi|125200707|gb|EL215661.1|EL215661
EST:     GCTTAAAATGGCGCCGTGACTCAGCATTACGCGACGGTTCCTCCGCCGGC                         GTTGACTTATCCGGTGG
genomic: GCTTAAAATGGCGCCGTGACTCAGCATTACGCGACGGTTCCTCCGCCGGCgtaagtctac ... aaaatctcagGTTGACTTATCCGGTGG
EST: gi|86069496|gb|DR365253.1|DR365253
EST:     GCTTAAAATGGCGCCGTGACTCAGCATTACGCGACGGTTCCTCCGCCGGC                         GTTGACTTATCCGGTGGTTACTACGACGCCGGAGACAACATCAAGTTCGGT
genomic: GCTTAAAATGGCGCCGTGACTCAGCATTACGCGACGGTTCCTCCGCCGGCgtaagtctac ... aaaatctcagGTTGACTTATCCGGTGGTTACTACGACGCCGGAGACAACATCAAGTTCGGT
EST: gi|86069495|gb|DR365252.1|DR365252
EST:     GCTTAAAATGGCGCCGTGACTCAGCATTACGCGACGGTTCCTCCGCCGGC                         GTTGACTTATCCGGTGGTTACTACGACGCCGGAGACAACATCAAGTTCGGT
genomic: GCTTAAAATGGCGCCGTGACTCAGCATTACGCGACGGTTCCTCCGCCGGCgtaagtctac ... aaaatctcagGTTGACTTATCCGGTGGTTACTACGACGCCGGAGACAACATCAAGTTCGGT
EST: gi|164153874|gb|ES071274.1|ES071274
EST:     GCTTAAAATGGCGCCGTGACTCAGCATTACGCGACGGTTCCTCCGCCGGC                         GTTGACTTATCCGGTGGTTACTACGACGCCGGAGACAACA
genomic: GCTTAAAATGGCGCCGTGACTCAGCATTACGCGACGGTTCCTCCGCCGGCgtaagtctac ... aaaatctcagGTTGACTTATCCGGTGGTTACTACGACGCCGGAGACAACA
EST: gi|124831553|gb|EH915992.1|EH915992
EST:     CCTCCGCCGGC                         GTTGACTTATCCGGTGGTTACTACGACGCCGGAGACAACATCAAGTTCGGT
genomic: CCTCCGCCGGCgtaagtctac ... aaaatctcagGTTGACTTATCCGGTGGTTACTACGACGCCGGAGACAACATCAAGTTCGGT
EST: gi|86069497|gb|DR365254.1|DR365254
EST:     GCTTAAAATGGCGCCGTGACTCAGCATTACGCGACGGTTCCTCCGCCGGC                         GTTGACTTATCCGGTGGTTACTACGACGCCGGAGACAACATCAAGTTCGGT
genomic: GCTTAAAATGGCGCCGTGACTCAGCATTACGCGACGGTTCCTCCGCCGGCgtaagtctac ... aaaatctcagGTTGACTTATCCGGTGGTTACTACGACGCCGGAGACAACATCAAGTTCGGT
EST: gi|164066652|gb|ES203501.1|ES203501
EST:     CCTCCGCCGGC                         GTTGACTTATCCGGTGGTTACTACGACGCCGGAGACAACATCAAGTTCGGT
genomic: CCTCCGCCGGCgtaagtctac ... aaaatctcagGTTGACTTATCCGGTGGTTACTACGACGCCGGAGACAACATCAAGTTCGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaacttctccttcttctaatctctaacttttccgacgatatttcaaaaatctcagGTTGACTTATCCGGTGGTTACTACGACGCCGGAGACAACATCAAGTTCGGTTTTCCGATGGCGTTCACAACAACGATGCTTTCATGGAGTATAATCGATT
                    ctctaac  putative branch site (score: 2)
                                     atatttcaaaaatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtctactctactaacatacatttcaaacttctccttcttctaatctctaacttttccgacgatatttcaaaaatctcagGTTGACTTATCCGGTGGTTACTACGACGCCGGAGACAACATCAAGTTCGGTTTTCCGATGGCGTTCACAACAACGATGCTTTCATGGAGTATAATCGATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA