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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatttgtgtttatatatgcagatgctacagtgtttctagatttgatctgtgtttgtactctaataattgctaactagttccctatgacttaaactgaaagGTGTACTTGATACTCGATGAGTTCATTCTTGCTGGGGAGCTCCAAGAAACAAGCAAAAGG

Basic information

species Arabidopsis thaliana
transcript AT1G47830.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G47830.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G052713_T01 (Zea mays), 3'ss of exon 4
tatttgtgtttatatatgcagatgctacagtgtttctagatttgatctgtgtttgtactctaataattgctaactagttccctatgacttaaactg------aaagGTGTACTTGATACTCGATGAGTTCATTCTTGCTGGGGAGCTCCAAGAAACAAGCAAAAGG
      || || |        ||  |      |   || |    |     || | ||  |||  | |||  || | | |   |     ||   ||         |||| ||||||||| | |||||||||||||||||||| ||||| ||||||||||||||||||
-----ctgcttttgctctttaatcttttgccttccttaaaccatactaaagtatctaa-ctatcatttgtgaatttgcttattgatcttttggctatctgctgtagGTTTACTTGATATTGGATGAGTTCATTCTTGCTGGAGAGCTTCAAGAAACAAGCAAAAGG

upper sequence: AT1G47830.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: AC195874.2_FGT002 (Zea mays), 3'ss of exon 4
tatttgtgtttatatatgcagatgctacagtgtttctagatttgatctgtgtttgtactctaataattgctaa-ctagt--tccctatgact----taaactgaaagGTGTACTTGATACTCGATGAGTTCATTCTTGCTGGGGAGCTCCAAGAAACAAGCAAAAGG
   |       | | | | || | |  |  | ||   |   |   ||| || |  ||    |||| |||  ||  ||||  ||| |||   |    | | ||  ||||| ||| ||||||| ||||| || ||||||||||||||||| |||||||||||||||| |
---taaaaaccaaacacgtagttacgcc--ttttatgaacctctgtctatgatgctatc--aatagttgtaaaattagtgatccttatttttctgtttaccttgaagGTTTACCTGATACTAGATGAATTTATTCTTGCTGGGGAGCTGCAAGAAACAAGCAAAAAG

upper sequence: AT1G47830.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv18s0001g14240.t01 (Vitis vinifera), 3'ss of exon 5
tatttgtgtttatatatgcagatgctacagt---gtttctagatttgatctgtgtt-tgtactctaataattgctaactagttccctatgacttaaactgaaagGTGTACTTGATACTCGATGAGTTCATTCTTGCTGGGGAGCTCCAAGAAACAAGCAAAAGG
| | |||||||     ||| || | |  |||   || | ||   ||| ||    || | | || |  |  ||||| | | |  |  | |   |   |   |||||| ||  | ||||| || || ||||||||||||||||||||||||||||||||||||| |
tgtatgtgtttgggcttgctgacg-tgtagtttggtgtatattattgctcatcattatattctttcctttttgctca-tggaactgtgtttgtctgat--aaagGTTTATCTTATACTTGACGAATTCATTCTTGCTGGGGAGCTCCAAGAAACAAGCAAAAAG

upper sequence: AT1G47830.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv04s0023g03340.t01 (Vitis vinifera), 3'ss of exon 4
--tatttgtgtttatatatgcagatgctacagtgtttctagatttgat-ctgtgtttgtactctaataattgctaactagttccctatgacttaaactgaaagGTGTACTTGATACTCGATGAGTTCATTCTTGCTGGGGAGCTCCAAGAAACAAGCAAAAGG
   |  |      || |||   |    ||  ||||   | | |||| | |   || | ||  | |  | ||||| |||  ||  || |   |    |  | |||| ||  | ||||| |||||||||||||||||||| |||||||| ||||||||||| | |
taaaaatagagccatgtataatgtctataacgtgtagattggtttgcttccaggtgtttagaccaccatttgctcactgcttttctttcgtt---gcatatagGTATATCTAATACTTGATGAGTTCATTCTTGCTGGAGAGCTCCAGGAAACAAGCAAGAAG

upper sequence: AT1G47830.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S220_70V6.1 (Physcomitrella patens), 3'ss of exon 4
----------------------------------------------------------------------tatttgtgtttatat--atgcagatgctacagtgtttc-tagatt---tga------tctgtgtttgtactctaataattgctaactagttccctatgacttaaactgaaagGTGTACTTGATACTCGATGAGTTCATTCTTGCTGGGGAGCTCCAAGAAACAAGCAAAAGG
                                                                       |  ||  | ||     ||| ||    || | | | || | ||||   |||      |  ||||||||  || | |   |   ||  |   |  | | |  |  ||||| ||||||| |||||| | |||||||||||||||||||| ||  | |||||||| ||||||| |
gtacacgcgcgtcgtttcttctggcatttgacgcatgtgcagtctatatattcgataacaatgcatcgtgcacctggatgtacccggatgtaggcaatagaatctatcgtggattatatgacgctttttagtgtttgttttcaagtgtgtaagaatgacaccattttcatct--actgacagGTGTATTTGATATTGGATGAGTTCATTCTTGCTGGTGAATTGCAAGAAACCAGCAAAAAG

upper sequence: AT1G47830.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ09792 (Selaginella moellendorffii), 3'ss of exon 4
tatttgtgtttatatatgcagatgctacagtgtttctagatttgatctgtgtttgtactctaataattgcta--actagttccctatgacttaaactgaaagGTGTACTTGATACTCGATGAGTTCATTCTTGCTGGGGAGCTCCAAGAAACAAGCAAAAGG
                       || |   | ||||     ||  | | |  |     |||  |  |||| |  |||     |||     ||    | | |||| |||||||| ||||| ||||||||||||||||| ||| | |||||||| ||||||| |
-----------------------gccagtttctttccttgcttt-tttattctcccggtctggtg-ttgcaagcactcagcgcctgctggtttcgtttacagGTTTACTTGATCCTCGACGAGTTCATTCTTGCTGGCGAGTTACAAGAAACCAGCAAAAAG

upper sequence: AT1G47830.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ11600 (Selaginella moellendorffii), 3'ss of exon 4
tatttgtgtttatatatgcagatgctacagtgtttctagatttgatctgtgtttgtactctaataattgcta--actagttccctatgacttaaactgaaagGTGTACTTGATACTCGATGAGTTCATTCTTGCTGGGGAGCTCCAAGAAACAAGCAAAAGG
                       || |   | ||||     ||  | | |  |     |||  |  |||| |  |||     |||     ||    | | |||| |||||||| ||||| ||||||||||||||||| ||| | |||||||| ||||||| |
-----------------------gccagtttctttccttgcttt-tttattctcccggtctggtg-ttgcaagcactcagcgcctgccggtttcgtttacagGTTTACTTGATCCTCGACGAGTTCATTCTTGCTGGCGAGTTACAAGAAACCAGCAAAAAG

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|19740606|gb|AU225959.1|AU225959
EST:     ATTTCTTCACCAATGTTTGTGAGCTAGATTTGGTGTTTAATTTCCACAAG                         GTGTACTTGATACTCGATGAGTTCATTCTTGCTGGGGAGCTCCAAGAAACA
genomic: ATTTCTTCAGCAATGTTTGTGAGCTAGATTTGGTGTTTAATTTCCACAAGgtacttaacc ... aaactgaaagGTGTACTTGATACTCGATGAGTTCATTCTTGCTGGGGAGCTCCAAGAAACA
EST: gi|116464176|gb|EG506768.1|EG506768
EST:     ATTTCTTCAGCAATGTTTGTGAGCTAGATTTGGTGTTTAATTTCCACAAG                         GTGTACTTGATACTCGATGAGTTCATTCTTGCTGGGGAGCTCCAAGAAACA
genomic: ATTTCTTCAGCAATGTTTGTGAGCTAGATTTGGTGTTTAATTTCCACAAGgtacttaacc ... aaactgaaagGTGTACTTGATACTCGATGAGTTCATTCTTGCTGGGGAGCTCCAAGAAACA
EST: gi|164152259|gb|ES092147.1|ES092147
EST:     TTTCTTCAGCAATGTTTTGTGAGCTAGATTTGGTGTTTAATTTCCACAAG                         GTGTACTTGATACTCGATGAGTTCATTCTTGCTGGGGAGCTCCAAGAAACA
genomic: TTTCTTCAGCAATG-TTTGTGAGCTAGATTTGGTGTTTAATTTCCACAAGgtacttaacc ... aaactgaaagGTGTACTTGATACTCGATGAGTTCATTCTTGCTGGGGAGCTCCAAGAAACA
EST: gi|116464171|gb|EG506763.1|EG506763
EST:     ATTTCTTCAGCAATGTTTGTGAGCTAGATTTGGTGTTTAATTTCCACAAG                         GTGTACTTGATACTCGATGAGTTCATTCTTGCTGGGGAGCTCCAAGAAACA
genomic: ATTTCTTCAGCAATGTTTGTGAGCTAGATTTGGTGTTTAATTTCCACAAGgtacttaacc ... aaactgaaagGTGTACTTGATACTCGATGAGTTCATTCTTGCTGGGGAGCTCCAAGAAACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgtgtttgtactctaataattgctaactagttccctatgacttaaactgaaagGTGTACTTGATACTCGATGAGTTCATTCTTGCTGGGGAGCTCCAAGAAACAAGCAAAAGG
                      tgctaac  putative branch site (score: 1)
             tctaataatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatttgtgtttatatatgcagatgctacagtgtttctagatttgatctgtgtttgtactctaataattgctaactagttccctatgacttaaactgaaagGTGTACTTGATACTCGATGAGTTCATTCTTGCTGGGGAGCTCCAAGAAACAAGCAAAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - gatttga
- - - - - - - - - - - - - - - - - - - - - - - - -tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - actctaa