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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgagtttcactgtcctttgtgtatgtcccatgattcaaaatttgatttaagctttgaataaaattaacaaacgtgaactctagGTTTCTGCTGCTCGAGAAGAAGTTCCTGGAAGACGTGGATATCCGGGGTATATGTATACAGATCTTGCAACTATTTATGAACGCGCGGGACGTATTGAAG

Basic information

species Arabidopsis thaliana
transcript AT1G20260.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 3'ss of exon 9
-------gtaatgagtttcactgtcct---ttgtgtatgtcccatgattcaaaatttgatttaagctttgaataaaattaacaaacgtg---aactctagGTTTCTGCTGCTCGAGAAGAAGTTCCTGGAAGACGTGGATATCCGGGGTATATGTATACAGATCTTGCAACTATTTATGAACGCGCGGGACGTATTGAAG
        |  |  |||  ||||   |   |  |  ||  |  |   || |    |||   |  ||  | |   ||      ||  |||   |  | ||||| || || || ||||||||||| || || || ||||| ||||| || ||||||||||| ||||| ||||| || ||||| || || || ||||||||||
acatctccttttatgttcgactgcaataaatgataaattgctgaaattttatttattgtgattggcactaatacaacacggtaattgtgcttatatgtagGTATCAGCAGCCCGAGAAGAAGTGCCAGGTAGGCGTGGGTATCCTGGATATATGTATACTGATCTGGCAACCATATATGAGCGAGCTGGGCGTATTGAAG

upper sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G181151_T02 (Zea mays), 3'ss of exon 9
gtaatgagtttcactgtcctttgtgtatgtcccat-gattcaaaatttgatttaa--------gctttgaataaaatta-acaaacgt-gaactct----agGTTTCTGCTGCTCGAGAAGAAGTTCCTGGAAGACGTGGATATCCGGGGTATATGTATACAGATCTTGCAACTATTTATGAACGCGCGGGACGTATTGAAG
  | |   |   |    ||||||| | |     ||  | |   || ||||||| |        | ||  |||||   || |    | | |  || |    |||||||||| || |||||||| || || || || ||||| ||||| || ||||||||||| ||||| ||||| || ||||| || || || ||||||||||
--agtatttaagatcaacctttgtatttaggtaatcaaatggtaaattgatttcatgtttgatgtttctaataatgctacatgggcattgtgctttttgtagGTTTCTGCAGCCCGAGAAGAGGTGCCAGGTAGGCGTGGTTATCCTGGATATATGTATACTGATCTGGCAACAATATATGAGCGTGCTGGGCGTATTGAAG

upper sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G094497_T01 (Zea mays), 3'ss of exon 9
-gtaatgagtttca---ctgtcctttgtgtatgtcccatgattcaaaatttgatttaa--gctttgaataaaatta-acaaacgt-gaactct-----agGTTTCTGCTGCTCGAGAAGAAGTTCCTGGAAGACGTGGATATCCGGGGTATATGTATACAGATCTTGCAACTATTTATGAACGCGCGGGACGTATTGAAG
  | ||   ||| |       | ||| | |  |     | | | | || ||||| |    | ||  |||||   || |    | | |  || |     |||||||||| || |||||||| || || || || ||||| ||||| || ||||||||||| ||| | ||||| || ||||| || || || ||||||||||
ttttatatatttaagattaaccttttctattagctaattaaatgacaaattgatgtcgttgtttctaataatgctacatgggcattgtgcttttttgtagGTTTCTGCAGCCCGAGAAGAGGTGCCAGGTAGGCGTGGTTATCCTGGATATATGTATACTGATTTGGCAACAATATATGAGCGTGCTGGGCGTATTGAAG

upper sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv18s0001g01020.t01 (Vitis vinifera), 3'ss of exon 9
-gtaatgagtttcactgtcctttgtgta----------tgtcccatgattcaaa-atttgatttaagct--ttgaataaaattaacaaacgtgaactctagGTTTCTGCTGCTCGAGAAGAAGTTCCTGGAAGACGTGGATATCCGGGGTATATGTATACAGATCTTGCAACTATTTATGAACGCGCGGGACGTATTGAAG
  | ||  |||| |   || |  |  ||          | |  ||  ||||  | | ||  ||| | ||  |||| |  || |  |     ||| ||  |||| ||||| || || || ||||| |||||||| ||||| ||||| |||||||||||||| ||||||||||| |||||||| || || |||||||| ||||
cttcataggttttaaaatcatacggataatcgaatttctattgcaccattcccacacttactttcacctacttgactggaaatgtctgttttga-ctgcagGTATCTGCAGCCCGGGAGGAAGTACCTGGAAGGCGTGGGTATCCTGGGTATATGTATACTGATCTTGCAACAATTTATGAGCGTGCTGGACGTATAGAAG

upper sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 9
---gtaatgagtttcactgtcctttgtgtatgtc----ccatgat-tcaaaatttgatttaagctttgaataaaattaacaaacgtgaactct-----agGTTTCTGCTGCTCGAGAAGAAGTTCCTGGAAGACGTGGATATCCGGGGTATATGTATACAGATCTTGCAACTATTTATGAACGCGCGGGACGTATTGAAG
   | | |  ||| |   ||   |   |||| |     ||  ||| || |   |  || |||       |||   ||  |       |   ||     |||| ||||||||||| |||||||| || ||  | ||||| || || || |||||||| || |||||||| || ||||||||||| || ||||||||||| |
gctgcactcggttacttagttaatcaagtattttgaaacctcgatatcgagggtctatgtaatgacgatatatttttgtcgttttcaattacttaaacagGTGTCTGCTGCTCGTGAAGAAGTACCCGGTCGTCGTGGGTACCCTGGTTATATGTACACCGATCTTGCCACCATTTATGAACGTGCTGGACGTATTGAGG

upper sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S85_75V6.1 (Physcomitrella patens), 3'ss of exon 8
------------------------------------------------------------------------------------gtaatgagtttcactgtcctttgtgtatgtcccatgattcaaaatttgattta--agctttgaataaaattaacaaacgtgaactct------agGTTTCTGCTGCTCGAGAAGAAGTTCCTGGAAGACGTGGATATCCGGGGTATATGTATACAGATCTTGCAACTATTTATGAACGCGCGGGACGTATTGAAG
                                                                                     |||  | |  | || |  |||||    || | | |  |  |  |||  | |   ||  |   |||   |||   | | | |||| |      |||||||||| ||||| |||||||| |||||  | ||||||||||| || || ||||| || |||||||| |||||||| ||||| || || || ||||| |
gtaccagtctttaccttaaagatctgcttgcccttgtggtatggtacttctgactctgtttttggtttttgaaatgttagtgttctaaaaaatgcccctctattttgttg--gttctaagtctgcacctttagtatgccagaatgacatattctta-tgatccttaactatgcgaacagGTTTCTGCAGCTCGTGAAGAAGTACCTGGGCGTCGTGGATATCCTGGTTACATGTACACGGATCTTGCCACTATTTACGAACGTGCTGGGCGAATTGAGG

upper sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 8
----------------------------------------------------------------------------------------------gtaatgagtttcactgtcctttgtg-tatgtcccat-gattcaaaatttga--tttaagctttgaataaaattaacaaacg-tgaactct------agGTTTCTGCTGCTCGAGAAGAAGTTCCTGGAAGACGTGGATATCCGGGGTATATGTATACAGATCTTGCAACTATTTATGAACGCGCGGGACGTATTGAAG
                                                                                              | |||   ||| |      |||||  | | | |  | | ||   ||||      || ||  |   | ||| ||     ||  | || |||      |||||||||||||||| |||||||| |||||  | ||||||||||| || || |||||||| ||||| || || ||||||||||| || ||||| || ||||
gtacaagtgtttctcttaaagacttttcgcttggactcctttttcagaagttagctcctgtgaaattctacatgctactccgcagttggtatctgaaatagtttttaagcaaatttgtaatctattcagttggtttttaattaagaccttcagtgtgctacaaattttttccactctcaattcttcaaatagGTTTCTGCTGCTCGTGAAGAAGTGCCTGGGCGTCGTGGATATCCTGGTTACATGTATACTGATCTGGCCACCATTTATGAACGTGCTGGACGAATCGAAG

upper sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: EFJ11911 (Selaginella moellendorffii), 3'ss of exon 8
gtaatgagtttcactgtcctttgtgtatgtcccatgattcaaaatt-tgatttaagctttgaataaaattaacaaacgtgaactctagGTTTCTGCTGCTCGAGAAGAAGTTCCTGGAAGACGTGGATATCCGGGGTATATGTATACAGATCTTGCAACTATTTATGAACGCGCGGGACGTATTGAAG
                           | |   ||| |||||  || | ||   |||| |||       |||| |  |     | ||||| ||||| ||||| || || || |||||  | ||||||||||| || ||||||||||||||| | ||||| ||||| || || || ||||| |||||||
--------------------------gtatggtatgtttcaagtttgtcatgagagctatga-------taaccagggctttgtgtagGTGTCTGCCGCTCGTGAGGAGGTGCCTGGTCGTCGTGGATATCCTGGTTATATGTATACAGATTTGGCAACAATTTACGAGCGTGCTGGACGAATTGAAG

upper sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: EFJ13375 (Selaginella moellendorffii), 3'ss of exon 8
gtaatgagtttcactgtcctttgtgtatg-tcccatgattcaaaatttgatttaagctttgaataaaattaacaaacgtgaactctagGTTTCTGCTGCTCGAGAAGAAGTTCCTGGAAGACGTGGATATCCGGGGTATATGTATACAGATCTTGCAACTATTTATGAACGCGCGGGACGTATTGAAG
                        ||||| ||  ||| |||||  |||   | |      || | |   |||| |  |     | ||||| ||||| ||||| || || || |||||  | ||||||||||| || ||||||||||||||| | ||||| ||||| || || || ||||| |||||||
------------------------gtatgatcgtatgtttcaagtttttcatga------gagttatgataaccatggctttgtgtagGTGTCTGCCGCTCGTGAGGAGGTGCCTGGTCGTCGTGGATATCCTGGTTATATGTATACAGATTTGGCAACAATTTACGAGCGTGCTGGACGAATTGAAG

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|116471554|gb|EG514146.1|EG514146
EST:     TGCTTGTTATATTGACAGACATGAGTTCTTATGTAGATGCTCTTCGTGAG                         GTTTCTGCTGCTCGAGAAGAAGTTCCTGGAAGACGTGGATATCCGGGGTAT
genomic: TGCTTGTTATATTGACAGACATGAGTTCTTATGCAGATGCTCTTCGTGAGgtaatgagtt ... tgaactctagGTTTCTGCTGCTCGAGAAGAAGTTCCTGGAAGACGTGGATATCCGGGGTAT
EST: gi|124858641|gb|EH943078.1|EH943078
EST:     TGCTTGTTATATTGACAGACATGAGTTCTTATGCAGATGCTCTTCGTGAG                         GTTTCTGCTGCT
genomic: TGCTTGTTATATTGACAGACATGAGTTCTTATGCAGATGCTCTTCGTGAGgtaatgagtt ... tgaactctagGTTTCTGCTGCT
EST: gi|125031562|gb|EL103831.1|EL103831
EST:     AGATGCTCTTCGTGAG                         GTTTCTGCTTGCTCGAGAAGAAGTTCCTGGAAGACGTGGATATCCGGGGTA
genomic: AGATGCTCTTCGTGAGgtaatgagtt ... tgaactctagGTTTCTGC-TGCTCGAGAAGAAGTTCCTGGAAGACGTGGATATCCGGGGTA
EST: gi|125323115|gb|EL337197.1|EL337197
EST:     TGCTTGTTATATTGACAGACATGAGTTCTTATGCAGATGCTCTTCGTGAG                         GTTTCTGCTGCTCGAGAAGAAGTTCCTGGAAGACGTGGA
genomic: TGCTTGTTATATTGACAGACATGAGTTCTTATGCAGATGCTCTTCGTGAGgtaatgagtt ... tgaactctagGTTTCTGCTGCTCGAGAAGAAGTTCCTGGAAGACGTGGA
EST: gi|124885829|gb|EH964731.1|EH964731
EST:     AGATGCTCTTCGTGAG                         GTTTCTGCTGCTCGAGAAGAAGTTCCTGGAAGACGTGGATATCCGGGGTAT
genomic: AGATGCTCTTCGTGAGgtaatgagtt ... tgaactctagGTTTCTGCTGCTCGAGAAGAAGTTCCTGGAAGACGTGGATATCCGGGGTAT
EST: gi|124767281|gb|EH857411.1|EH857411
EST:     TGCTTGTTATATTGACAGACATGAGTTCTTATGCAGATGCTCTTCGTGAG                         GTTTCTGCTGCTCGAGAAGAAGTTCCTGGAAGACGTGG
genomic: TGCTTGTTATATTGACAGACATGAGTTCTTATGCAGATGCTCTTCGTGAGgtaatgagtt ... tgaactctagGTTTCTGCTGCTCGAGAAGAAGTTCCTGGAAGACGTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgattcaaaatttgatttaagctttgaataaaattaacaaacgtgaactctagGTTTCTGCTGCTCGAGAAGAAGTTCCTGGAAGACGTGGATATCCGGGGTATATGTATACAGATCTTGCAACTATTTATGAACGCGCGGGACGTATTGAAG
                                 aattaac  putative branch site (score: 2)
        aaaatttgatttaagc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgagtttcactgtcctttgtgtatgtcccatgattcaaaatttgatttaagctttgaataaaattaacaaacgtgaactctagGTTTCTGCTGCTCGAGAAGAAGTTCCTGGAAGACGTGGATATCCGGGGTATATGTATACAGATCTTGCAACTATTTATGAACGCGCGGGACGTATTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG