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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtctcccatctcagtttttcgattttgcatgttgttgttttcttttgacaaatcaattttgcatgttatgaatcttgatcattaaaagattttttttttgattcaatgatgatatgggtaattatggcttcagGCATGTTTGGATTGTGGATTTTTCTATGTGATCAATCATGGGATAAGCGAAGAGTTCATGGACGATGTTTTCGAGCAGAGCAAGAAGCTTTTTGCTCTTC

Basic information

species Arabidopsis thaliana
transcript AT1G35190.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G35190.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G147882_T01 (Zea mays), 3'ss of exon 1
gtttgtctcccatctcagtttttcgattttgcatgttgttgttttcttttgacaaatcaattttgcatgttatgaatcttgatcattaaaagattttttttttgattca--atgatgatatgggtaattatggctt-cagGCATGTTTGGATTGTGGATTTTTCTATGTGATCAATCATGGGATAAGCGAAGAGTTCATGGACGATGTTTTCGAGCAGAGCAAGAAGCTTTTTGCTCTTC
                                  |  ||| |     |||||||  |||| | |     || |      || || | ||||   | | | |   | ||    |  ||| |    |  || |   |   |||||||  ||||||  || || ||||||||  |  |||||||||||||| ||||||||||||| || ||||| |  |||||||||||| | ||||  ||||
----------------------------------gaagtt-tccatgtttgacagctcaaatct-----ttgttggctctgttcgtaaaaaagctctgtatcatactcttcttcctgaaaacaatgtttttatttggtagGCATGCCTGGATTCAGGCTTCTTCTATGTTGTGGATCATGGGATAAGCCAAGAGTTCATGGATGAAGTTTTTGCCCAGAGCAAGAAGTTCTTTGACCTTC

upper sequence: AT1G35190.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA01G01170.2 (Glycine max), 3'ss of exon 1
gtttgtctcccatctcagtttttcgattttgcatgttgttgt-tttcttttgaca-aatcaattttgcatgttatgaatcttgatcattaaaagattttttttttgattcaatgatgatatgggtaattatggcttcagGCATGTTTGGATTGTGGATTTTTCTATGTGATCAATCATGGGATAAGCGAAGAGTTCATGGACGATGTTTTCGAGCAGAGCAAGAAGCTTTTTGCTCTTC
                        | |||||| |  | || |   |  |||| || |||  | ||||    || |  | | ||||| ||       |||| | |    | |||| || | |   |     | | || |||||||||||||||  || |||||||| ||  |||||||||| |||||| | || ||||||||||| ||||| | ||||||||||||| | ||  ||||||
------------------------gtttttgcttcctcttttacatgatttgtcacaattcactttgt---ttttagaccatgatcttt-------ttttatgtcatcttaatgttgttgtttttttgctttgttttagGCATGTTTGGATTCCGGTTTTTTCTACGTTGTCAATCATGGAATAAGCCAGGAATTCATGGACGAGGTTTTTGCGCAGAGCAAGAAGTTCTTCTCTCTTC

upper sequence: AT1G35190.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA16G08470.1 (Glycine max), 3'ss of exon 1
gtttgtctcccatctcagtttttcgattttgcatgttgttgttttcttttgacaaatcaattttgcatgttatgaatcttgatcattaaaagattttttttttgattcaatgatgatatgggtaattatggcttcagGCATGTTTGGATTGTGGATTTTTCTATGTGATCAATCATGGGATAAGCGAAGAGTTCATGGACGATGTTTTCGAGCAGAGCAAGAAGCTTTTTGCTCTTC
                                        |||||   ||    |||  | ||||  | || |||| | ||||          ||||| |  ||    | | ||| | |  ||  || ||  || |||||||||||||||  || |||||||| ||  |||||||||| |||||| | || |||||||| || ||||| |  |||||||||||  | ||  ||||||
----------------------------------------gtttttgcttcctcaattcactttg--ttttttgaaccatgat----------tttttatcatgtcatattaatgttttttgt--ttttgtttttagGCATGTTTGGATTCCGGTTTTTTCTACGTTGTCAATCATGGAATAAGCCAGGAATTCATGGAAGAGGTTTTTGCACAGAGCAAGAAATTCTTCTCTCTTC

upper sequence: AT1G35190.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv11s0016g03200.t01 (Vitis vinifera), 3'ss of exon 1
gtttgtctcccatctcagtttttcgattttgcatgttgttgttttcttttgacaaatcaattttgcatgttatgaatcttgatcattaaaagattttttttttgattcaatgatgatatgggtaattatggcttcagGCATGTTTGGATTGTGGATTTTTCTATGTGATCAATCATGGGATAAGCGAAGAGTTCATGGACGATGTTTTCGAGCAGAGCAAGAAGCTTTTTGCTCTTC
||  || |   |||  || |  ||  ||| |    |||  |         || |    ||    | | |  | |      ||  |  | ||||    |||||      |||  |  | || |   || ||| |||||||||||||||||| |||||| ||||||||||||||||| || || ||| | || || |||||||| |||||||  || ||||| | | ||||  || | |
gtgcgttttgtatccaagctcctccgtttgg----ttgccga--------gaaaggagaaagaaggaagggaagg-----gagaaagagaagaaaacttttt------aatcttagtttgtgct-ttgtgg-ttcagGCATGTTTGGATTCTGGATTCTTCTATGTGATCAATCACGGAATCAGCCAGGAATTTATGGACGAGGTTTTCGCCCAAAGCAAAAGGTTTTTCACTTTGC

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|86031356|gb|DR327109.1|DR327109
EST:     TCGATCTAGCCAACGACGATCTTAATCATTCTGTTGTTTCCCTCAAACAG                         GCATGTTTGGATTGTGGATTTTTCTATGTGATCAATCATGGGATAAGCGAA
genomic: TCGATCTAGCCAACGACGATCTTAATCATTCTGTTGTTTCCCTCAAACAGgtttgtctcc ... atggcttcagGCATGTTTGGATTGTGGATTTTTCTATGTGATCAATCATGGGATAAGCGAA
EST: gi|86031354|gb|DR327107.1|DR327107
EST:     TCGATCTAGCCAACGACGATCTTAATCATTCTGTTGTTTCCCTCAAACAG                         GCATGTTTGGATTGTGGATTTTTCTATGTGATCAATCATGGGATAAGCGAA
genomic: TCGATCTAGCCAACGACGATCTTAATCATTCTGTTGTTTCCCTCAAACAGgtttgtctcc ... atggcttcagGCATGTTTGGATTGTGGATTTTTCTATGTGATCAATCATGGGATAAGCGAA
EST: gi|86031355|gb|DR327108.1|DR327108
EST:     TCGATCTAGCCAACGACGATCTTAATCATTCTGTTGTTTCCCTCAAACAG                         GCATGTTTGGATTGTGGATTTTTCTATGTGATCAATCATGGGATAAGCGAA
genomic: TCGATCTAGCCAACGACGATCTTAATCATTCTGTTGTTTCCCTCAAACAGgtttgtctcc ... atggcttcagGCATGTTTGGATTGTGGATTTTTCTATGTGATCAATCATGGGATAAGCGAA
EST: gi|86031347|gb|DR327100.1|DR327100
EST:     TCGATCTAGCCAACGACGATCTTAATCATTCTGTTGTTTCCCTCAAACAG                         GCATGTTTGGATTGTGGATTTTTCTATGTGATCAATCATGGGATAAGCGAA
genomic: TCGATCTAGCCAACGACGATCTTAATCATTCTGTTGTTTCCCTCAAACAGgtttgtctcc ... atggcttcagGCATGTTTGGATTGTGGATTTTTCTATGTGATCAATCATGGGATAAGCGAA
EST: gi|86031346|gb|DR327099.1|DR327099
EST:     TCGATCTAGCCAACGACGATCTTAATCATTCTGTTGTTTCCCTCAAACAG                         GCATGTTTGGATTGTGGATTTTTCTATGTGATCAATCATGGGATAAGCGAA
genomic: TCGATCTAGCCAACGACGATCTTAATCATTCTGTTGTTTCCCTCAAACAGgtttgtctcc ... atggcttcagGCATGTTTGGATTGTGGATTTTTCTATGTGATCAATCATGGGATAAGCGAA
EST: gi|86031353|gb|DR327106.1|DR327106
EST:     TCGATCTAGCCAACGACGATCTTAATCATTCTGTTGTTTCCCTCAAACAG                         GCATGTTTGGATTGTGGATTTTTCTATGTGATCAATCATGGGATAAGCGAA
genomic: TCGATCTAGCCAACGACGATCTTAATCATTCTGTTGTTTCCCTCAAACAGgtttgtctcc ... atggcttcagGCATGTTTGGATTGTGGATTTTTCTATGTGATCAATCATGGGATAAGCGAA
EST: gi|86031357|gb|DR327110.1|DR327110
EST:     TCGATCTAGCCAACGACGATCTTAATCATTCTGTTGTTTCCCTCAAACAG                         GCTTGTTTGGATTGTGGATTTTTCTATGTGWTCAATCATGGGATAWGCGAA
genomic: TCGATCTAGCCAACGACGATCTTAATCATTCTGTTGTTTCCCTCAAACAGgtttgtctcc ... atggcttcagGCATGTTTGGATTGTGGATTTTTCTATGTGATCAATCATGGGATAAGCGAA
EST: gi|86031340|gb|DR327093.1|DR327093
EST:     TCGATCTAGCCAACGACGATCTTAATCATTCTGTTGTTTCCCTCAAACAG                         GCATGTTTGGATTGTGGATTTTTCTATGTGATCAATCATGGGATAAGCGAA
genomic: TCGATCTAGCCAACGACGATCTTAATCATTCTGTTGTTTCCCTCAAACAGgtttgtctcc ... atggcttcagGCATGTTTGGATTGTGGATTTTTCTATGTGATCAATCATGGGATAAGCGAA
EST: gi|86031350|gb|DR327103.1|DR327103
EST:     TCGATCTAGCCAACGACGATCTTAATCATTCTGTTGTTTCCCTCAAACAG                         GCATGTTTGGATTGTGGATTTTTCTATGTGATCAATCATGGGATAAGCGAA
genomic: TCGATCTAGCCAACGACGATCTTAATCATTCTGTTGTTTCCCTCAAACAGgtttgtctcc ... atggcttcagGCATGTTTGGATTGTGGATTTTTCTATGTGATCAATCATGGGATAAGCGAA
EST: gi|86031335|gb|DR327088.1|DR327088
EST:     TCGATCTAGCCAACGACGATCTTAATCATTCTGTTGTTTCCCTCAAACAG                         GCATGTTTGGATTGTGGATTTTTCTATGTGATCAATCATGGGATAAGCGAA
genomic: TCGATCTAGCCAACGACGATCTTAATCATTCTGTTGTTTCCCTCAAACAGgtttgtctcc ... atggcttcagGCATGTTTGGATTGTGGATTTTTCTATGTGATCAATCATGGGATAAGCGAA
EST: gi|86031341|gb|DR327094.1|DR327094
EST:     TCGATCTAGCCAACGACGATCTTAATCATTCTGTTGTTTCCCTCAAACAG                         GCATGTTTGGATTGTGGATTTTTCTATGTGATCAATCATGGGATAAGCGAA
genomic: TCGATCTAGCCAACGACGATCTTAATCATTCTGTTGTTTCCCTCAAACAGgtttgtctcc ... atggcttcagGCATGTTTGGATTGTGGATTTTTCTATGTGATCAATCATGGGATAAGCGAA
EST: gi|86031349|gb|DR327102.1|DR327102
EST:     TCGATCTAGCCAACGACGATCTTAATCATTCTGTTGTTTCCCTCAAACAG                         GCATGTTTGGATTGTGGATTTTTCTATGTGATCAATCATGGGATAAGCGAA
genomic: TCGATCTAGCCAACGACGATCTTAATCATTCTGTTGTTTCCCTCAAACAGgtttgtctcc ... atggcttcagGCATGTTTGGATTGTGGATTTTTCTATGTGATCAATCATGGGATAAGCGAA
EST: gi|86031351|gb|DR327104.1|DR327104
EST:     TCGATCTAGCCAACGACGATCTTAATCATTCTGTTGTTTCCCTCAAACAG                         GCATGTTTGGATT-TGGATTTTTCTATGTGATCAATCATGGGATAAGCGAA
genomic: TCGATCTAGCCAACGACGATCTTAATCATTCTGTTGTTTCCCTCAAACAGgtttgtctcc ... atggcttcagGCATGTTTGGATTGTGGATTTTTCTATGTGATCAATCATGGGATAAGCGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcattaaaagattttttttttgattcaatgatgatatgggtaattatggcttcagGCATGTTTGGATTGTGGATTTTTCTATGTGATCAATCATGGGATAAGCGAAGAGTTCATGGACGATGTTTTCGAGCAGAGCAAGAAGCTTTTTGCTCTTC
                 ttttgat  putative branch site (score: 4)
     aaaagatttttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtctcccatctcagtttttcgattttgcatgttgttgttttcttttgacaaatcaattttgcatgttatgaatcttgatcattaaaagattttttttttgattcaatgatgatatgggtaattatggcttcagGCATGTTTGGATTGTGGATTTTTCTATGTGATCAATCATGGGATAAGCGAAGAGTTCATGGACGATGTTTTCGAGCAGAGCAAGAAGCTTTTTGCTCTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC