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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgaatttttttcttgcattgatgcaaaaccaaatctgatttatcgtctcgaggttttgattttgatcctttgtttatagCCTGAGGACTGGGATGATGAAGAAGATGGTGAGTGGACTGCCCCTACCATTCCCAACCCCGAGTACAATGGTGAATGGAAGCCCAAG

Basic information

species Arabidopsis thaliana
transcript AT1G56340.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G56340.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os07g14270.2 (Oryza sativa), 3'ss of exon 6
gt-ttgaatttttttcttgcattgatgca-aaaccaaatctgatttatcgtc--tcgaggttttga-----ttttgatcctttgtttatagCCTGAGGACTGGGATGATGAAGAAGATGGTGAGTGGACTGCCCCTACCATTCCCAACCCCGAGTACAATGGTGAATGGAAGCCCAAG
||  | |||| || |      ||   |   |    | || ||||  | ||||  || ||||||| |      ||||||    | | | ||||||||||||||||||||||| |||||||||||||||||||| || |||||||| ||||| |||||||| ||   ||||||||  |||
gtacttaattgttataccattttatggtttatgttatatatgatg-agcgtcattctaggttttaaaatttctttgatgtgatttctgtagCCTGAGGACTGGGATGATGAGGAAGATGGTGAGTGGACTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAG

upper sequence: AT1G56340.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os03g61670.1 (Oryza sativa), 3'ss of exon 6
--------------------------------gtttgaatttttttcttgca---ttgatgcaa------aaccaa-atctgattt---atcgtctcg---aggttttgattttg----atcctttgtttatagCCTGAGGACTGGGATGATGAAGAAGATGGTGAGTGGACTGCCCCTACCATTCCCAACCCCGAGTACAATGGTGAATGGAAGCCCAAG
                                 |||  ||| || || | ||   | ||||  |      |||||  ||  |||||   ||| | | |   |   |   | ||      || |  | | || |||||||||||||||||||||| |||||||| || ||||| || || |||||||| ||||| |||||||| ||   |||||| |  |||
gtatgtgttgccatttttattttaaatggacattttccattcttctcatacaagttcgatgagatgcatcaaccagtatgcgatttcacatcattttgtccaacatgcaacttcacattatgcaatctgtacagCCTGAGGACTGGGATGATGAGGAAGATGGAGAATGGACAGCTCCAACCATTCCAAACCCTGAGTACAAGGGACCATGGAACCAAAAG

upper sequence: AT1G56340.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G074687_T01 (Zea mays), 3'ss of exon 6
----gtttgaatttttttcttgcattgatgcaaaaccaaatctgatttatcgtctcgaggttttgattttgatcctttgtttatagCCTGAGGACTGGGATGATGAAGAAGATGGTGAGTGGACTGCCCCTACCATTCCCAACCCCGAGTACAATGGTGAATGGAAGCCCAAG
     | ||   || ||| ||     | |      |  |   ||  | |  |  | |   | |  ||| | |    |   ||  ||||||||||||||||||| || ||||||||||| |||||||||||||||||||||||||| || ||||| ||   |||||| |  |||
gtacttatgtggttatttgttatgc-ggtctgtgtcgtaggatggataacagcatgggtttataaattctaaaatgtgcattgcagCCTGAGGACTGGGATGACGAGGAAGATGGTGAATGGACTGCCCCTACCATTCCCAACCCAGAATACAAAGGACCATGGAAACAAAAG

upper sequence: AT1G56340.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G358059_T01 (Zea mays), 3'ss of exon 6
----gtttgaatttttttcttgcattgatgcaaaaccaaatctgatttatcgtctcgaggttttgattttgatcctttgtttatagCCTGAGGACTGGGATGATGAAGAAGATGGTGAGTGGACTGCCCCTACCATTCCCAACCCCGAGTACAATGGTGAATGGAAGCCCAAG
     | ||   || ||| ||   | | | | |      || ||||| ||    | |   | |  ||| | |    |   ||  |||||||||||||||| ||||| ||||||||||| |||||||||||||||||||||||||| || ||||| ||   |||||| |  |||
gtacttatgtggttatttgttatgtagtttctatc----atatgattaataacatgggtatataaattctaaaatgtccattgcagCCTGAGGACTGGGACGATGAGGAAGATGGTGAATGGACTGCCCCTACCATTCCCAACCCAGAATACAAGGGACCATGGAAACAAAAG

upper sequence: AT1G56340.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA10G28890.1 (Glycine max), 3'ss of exon 6
----gtttgaatttttttcttgcat-tgatgcaaaaccaaatctgatttatcgtctcgaggttttgattttgatcctttgtttatagCCTGAGGACTGGGATGATGAAGAAGATGGTGAGTGGACTGCCCCTACCATTCCCAACCCCGAGTACAATGGTGAATGGAAGCCCAAG
     | | ||||||||  || | | || |||| || ||   ||  | |   ||    |  | ||   ||   | ||     | |||||||| || ||||||||||| |||||||||||||||||  ||||||||||| ||||||| |||||||| ||   ||||||| |  ||
gtatttctcaattttttgtttccttgtgctgcataaacatcactt-tatgctgtagttacttattagattaattgctgatgctgtagCCTGAAGATTGGGATGATGAGGAAGATGGTGAGTGGACACCCCCTACCATTGCCAACCCTGAGTACAAGGGCCCATGGAAGGCAGAG

upper sequence: AT1G56340.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA20G23080.2 (Glycine max), 3'ss of exon 6
----gtttgaatttttttcttgcat-tgatgcaaaaccaaatctgatttat--cgtctcgaggttttgattttgatcctttgtttatagCCTGAGGACTGGGATGATGAAGAAGATGGTGAGTGGACTGCCCCTACCATTCCCAACCCCGAGTACAATGGTGAATGGAAGCCCAAG
     | | ||||||||  || | | || |||| |   |       |||||   ||    | || ||   ||   |  |     | |||||||| || ||||||||||| |||||||||||||||||  ||||||||||| ||||||| || ||||| ||   ||||||| | |||
gtatttctcaattttttgtttccttgtgctgcatatgtatcatcactttatgctgtagttacgtattagattaattgttgatgctgtagCCTGAAGATTGGGATGATGAGGAAGATGGTGAGTGGACACCCCCTACCATTGCCAACCCTGATTACAAGGGCCCATGGAAGGCAAAG

upper sequence: AT1G56340.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv07s0005g01390.t01 (Vitis vinifera), 3'ss of exon 6
-------------------gtttgaatttttttcttgcattgatgcaaaacca-aatctgatttatcgtctcgaggttttgatt--ttgatcctttgtttatagCCTGAGGACTGGGATGATGAAGAAGATGGTGAGTGGACTGCCCCTACCATTCCCAACCCCGAGTACAATGGTGAATGGAAGCCCAAG
                     || | | |  |   | | || ||    ||||| ||| | ||     |   |  | |  ||| |  |      | ||    |||||||| || ||||||||||| ||||||||||| |||||  | || || ||  | ||||| |||||||| ||   |||||||||||||
gtaagtaattagaatttatagttcagtatggtaaattcttttataaggaaccataatttcatggggagaaacttgttactgaataatcagctttatgaccctagCCTGAAGATTGGGATGATGAGGAAGATGGTGAATGGACACCTCCAACAATAGCTAACCCTGAGTACAAGGGACCATGGAAGCCCAAG

upper sequence: AT1G56340.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv14s0060g01290.t01 (Vitis vinifera), 3'ss of exon 6
gtttgaatttttttcttgcattgatgcaaaa---ccaaatctgatttatcgtctcgaggttttgattttgatcctttgt--ttatagCCTGAGGACTGGGATGATGAAGAAGATGGTGAGTGGACTGCCCCTACCATTCCCAACCCCGAGTACAATGGTGAATGGAAGCCCAAG
   |  ||||  | |      |||| |||||        | | | || ||   |   |   |||| |   ||  ||||   ||||||||||| || ||||||||||| ||||||||||| ||||| || || |||||| |||||||||||||||| ||   ||||||||| |||
--gtatatttaatccaaattgtgattcaaaaggttttggttttagttttctgatttggtaattgactaaaattatttggaattatagCCTGAAGATTGGGATGATGAGGAAGATGGTGAATGGACAGCTCCAACCATTGCCAACCCCGAGTACAAGGGACCATGGAAGCCAAAG

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|124955594|gb|EL030595.1|EL030595
EST:     CGGGATATGATGACATCCCAAAGGAGATTCCAGACACTGACGCAAAGAAG                         CCTGAGGACTGGGA
genomic: CGGGATATGATGACATCCCAAAGGAGATTCCAGACACTGACGCAAAGAAGgtttgaattt ... ttgtttatagCCTGAGGACTGGGA
EST: gi|164216767|gb|ES108381.1|ES108381
EST:     CCAAAGGAGATTCCAGACACTGACGCAAAGAAG                         CCTGAGGACTGGGATGATGAAGAAGATGGTGAG
genomic: CCAAAGGAGATTCCAGACACTGACGCAAAGAAGgtttgaattt ... ttgtttatagCCTGAGGACTGGGATGATGAAGAAGATGGTGAG
EST: gi|164133920|gb|ES014992.1|ES014992
EST:     AGATTCCAGACACTGACGCAAAGAAG                         CCTTGAGGACTGGGATGATGAAGAAGATGGTGAGTGGACTGCCCCTACCAT
genomic: AGATTCCAGACACTGACGCAAAGAAGgtttgaattt ... ttgtttatagCC-TGAGGACTGGGATGATGAAGAAGATGGTGAGTGGACTGCCCCTACCAT
EST: gi|86070963|gb|DR366720.1|DR366720
EST:     NNGGATATGATGACATCCCAAAGGAGATTCCAGACACTGACGCAAAGAAG                         CCTGAGGACTGGGATGATGA
genomic: CGGGATATGATGACATCCCAAAGGAGATTCCAGACACTGACGCAAAGAAGgtttgaattt ... ttgtttatagCCTGAGGACTGGGATGATGA
EST: gi|116465699|gb|EG508291.1|EG508291
EST:     CGGGATATGATGACATCCCAAAGGAGATTCCAGACACTGACGCAAAGAAG                         CCTGAGGACTGGGATGATGAAGAAGATGGTGAGTGGACTGCCCCTACCATT
genomic: CGGGATATGATGACATCCCAAAGGAGATTCCAGACACTGACGCAAAGAAGgtttgaattt ... ttgtttatagCCTGAGGACTGGGATGATGAAGAAGATGGTGAGTGGACTGCCCCTACCATT
EST: gi|116471772|gb|EG514364.1|EG514364
EST:     CGGGATATGATGACATCCCAAAGGAGATTCCAGACACTGACGCAAAGAAG                         CCTGAGGACTGGGATGATGAAGAAGATGGTGAGTGGACTGCCCCTACCATT
genomic: CGGGATATGATGACATCCCAAAGGAGATTCCAGACACTGACGCAAAGAAGgtttgaattt ... ttgtttatagCCTGAGGACTGGGATGATGAAGAAGATGGTGAGTGGACTGCCCCTACCATT
EST: gi|116465718|gb|EG508310.1|EG508310
EST:     CGGGATATGATGACATCCCAAAGGAGATTCCAGACACTGACGCAAAGAAG                         CCTGAGGACTGGGATGATGAAGAAGATGGTGAGTGGACTGCCCCTACCATT
genomic: CGGGATATGATGACATCCCAAAGGAGATTCCAGACACTGACGCAAAGAAGgtttgaattt ... ttgtttatagCCTGAGGACTGGGATGATGAAGAAGATGGTGAGTGGACTGCCCCTACCATT
EST: gi|116465735|gb|EG508327.1|EG508327
EST:     CGGGATATGATGACATCCCAAAGGAGATTCCAGACACTGACGCAAAGAAG                         CCTGAGGACTGGGATGATGAAGAAGATGGTGAGTGGACTGCCCCTACCATT
genomic: CGGGATATGATGACATCCCAAAGGAGATTCCAGACACTGACGCAAAGAAGgtttgaattt ... ttgtttatagCCTGAGGACTGGGATGATGAAGAAGATGGTGAGTGGACTGCCCCTACCATT
EST: gi|116482410|gb|EG525002.1|EG525002
EST:     CGGGATATGATGACATCCCAAAGGAGATTCCAGACACTGACGCAAAGAAG                         CCTGAGGACTGGGATGATGAAGAAGATGGTGAGTGGACTGCCCCTACCATT
genomic: CGGGATATGATGACATCCCAAAGGAGATTCCAGACACTGACGCAAAGAAGgtttgaattt ... ttgtttatagCCTGAGGACTGGGATGATGAAGAAGATGGTGAGTGGACTGCCCCTACCATT
EST: gi|124785487|gb|EH875166.1|EH875166
EST:     CGGGATATGATGACATCCCAAAGGAGATTCCAGACACTGACGCAAAGAAG                         CCTGAGGACTGGGATGNTGAAGAAGATGGTGAGTGGACTG
genomic: CGGGATATGATGACATCCCAAAGGAGATTCCAGACACTGACGCAAAGAAGgtttgaattt ... ttgtttatagCCTGAGGACTGGGATGATGAAGAAGATGGTGAGTGGACTG
EST: gi|164224656|gb|EL998332.1|EL998332
EST:     GACATCCCAAAGGAGATTCCAGACACTGACGCAAAGAAG                         CCTGAGGACTGGGATGATGAAGAAGATGGTGAGTGGACTGCCCCTACCATT
genomic: GACATCCCAAAGGAGATTCCAGACACTGACGCAAAGAAGgtttgaattt ... ttgtttatagCCTGAGGACTGGGATGATGAAGAAGATGGTGAGTGGACTGCCCCTACCATT
EST: gi|124836770|gb|EH921209.1|EH921209
EST:     CGGGATATGATGACATCCCAAAGGAGATTCCAGACACTGACGCAAAGAAG                         CCTGAGGACTGGGATGATGAAGAAGATGGTGAGTGGACTG
genomic: CGGGATATGATGACATCCCAAAGGAGATTCCAGACACTGACGCAAAGAAGgtttgaattt ... ttgtttatagCCTGAGGACTGGGATGATGAAGAAGATGGTGAGTGGACTG
EST: gi|116465734|gb|EG508326.1|EG508326
EST:     CGGGATATGATGACATCCCAAAGGAGATTCCAGACACTGACGCAAAGAAG                         CCTGAGGACTGGGATGATGAAGAAGATGGTGAGTGGACTGCCCCTACCATT
genomic: CGGGATATGATGACATCCCAAAGGAGATTCCAGACACTGACGCAAAGAAGgtttgaattt ... ttgtttatagCCTGAGGACTGGGATGATGAAGAAGATGGTGAGTGGACTGCCCCTACCATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaccaaatctgatttatcgtctcgaggttttgattttgatcctttgtttatagCCTGAGGACTGGGATGATGAAGAAGATGGTGAGTGGACTGCCCCTACCATTCCCAACCCCGAGTACAATGGTGAATGGAAGCCCAAG
                                   ttttgat  putative branch site (score: 4)
                                         tcctttgttt  CT-rich tract
                             ttttgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgaatttttttcttgcattgatgcaaaaccaaatctgatttatcgtctcgaggttttgattttgatcctttgtttatagCCTGAGGACTGGGATGATGAAGAAGATGGTGAGTGGACTGCCCCTACCATTCCCAACCCCGAGTACAATGGTGAATGGAAGCCCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG