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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgtattaattttcgtcacccatgcatgtctccttaaataagcttaattatcttgtaaatttgtttgttctttttaagactttaaatagacctttgtataacattttgcttttctactattttttgctctagTGATCATGAAGGTGGAAATGTTAGTGCTCACACTGGTCACCTG

Basic information

species Arabidopsis thaliana
transcript AT2G44350.2
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G44350.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 12
gtctgtattaattttcgtcacccatgcatgtctccttaaataagcttaattatcttgtaaatttgtttgttc--tttttaagactttaaatagacctttgtataacattttgcttttctactattttttgctctagTGATCATGAAGGTGGAAATGTTAGTGCTCACACTGGTCACCTG
                                      |||    |  ||  |  | |  | || | | ||   || ||||    ||   | ||  ||| | |  | |  | | ||        || ||   | ||||||||||||||||||||||| |||||||| ||||| || |||
------------------------------------gtaatgtattccatccttgttttgacttatatatttgtttcttaaagacttggtttga--tttattttccctcataccttcacctgggttctt---ccagTGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTG

upper sequence: AT2G44350.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 12
gtctgtattaattttcgtcacccatgcatgtctccttaaataagcttaattatcttgtaaatttgtttgttctttttaagactttaaatagacctttgtataacattttgcttttctactattttttgctctagTGATCATGAAGGTGGAAATGTTAGTGCTCACACTGGTCACCTG
                                              |||||   ||  |   ||||||    || |    | ||  || |||| || || | |  | ||  |  | |    | | ||  || |||||||||||||||||||| || |||||||| ||||| || |||
---------------------------------------------gtaatt-cattccatccttgttttagtttctatttatttctaaaagac-ttggtttgatttctttttcctttcacctgtgttcttccagTGATCATGAAGGTGGAAACGTCAGTGCTCATACTGGACATCTG

upper sequence: AT2G44350.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 13
gtctgtattaattttcgtcacccatgcatgtctccttaaataagcttaattatcttgtaaatttgtttgttctttttaagactttaaatagacctttgtataacattttgcttttctactattttttgctctagTGATCATGAAGGTGGAAATGTTAGTGCTCACACTGGTCACCTG
                                        |||  ||    |||   |   | | | | || || ||| | ||   ||       |||| |  |   |     |   ||| | | ||  ||||||||||||||||| || ||||| |||||||| |||||||| |||
---------------------------------------gtaattttg--catcc-atccctgtttctatttttgttatgtctcggaagtacttgttgttttcc-cctcatactgtgact-tgtgttcttctagTGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTG

upper sequence: AT2G44350.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G063851_T04 (Zea mays), 3'ss of exon 12
gtctgtattaattttcgtcacccatgcatgtctccttaaataagcttaattatcttgtaaatttgtttgttctttttaagactttaaatagacctttgtataacattttgcttttctactattttttgctctagTGATCATGAAGGTGGAAATGTTAGTGCTCACACTGGTCACCTG
                                    ||| |  || |   |  |||||   |   ||| || | ||| |||  |   |      ||  | | | | | ||   |   ||  | | ||  ||||||||||||||||| || ||||| |||||||| |||||||| |||
-----------------------------------gtaattttgcatccat-ccttgtttgtacttttattatgtttcagaagt---actcgttttcctctcatactgtgacctgtcacc-tgtgttcttctagTGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTG

upper sequence: AT2G44350.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv13s0156g00180.t01 (Vitis vinifera), 3'ss of exon 12
gtctgtattaattttcgtcacccatgcatgtctccttaaataagcttaattatcttgtaaatttgtttgttctttttaagactttaaatagacctttgtataacattttgcttttctactattttttgctctagTGATCATGAAGGTGGAAATGTTAGTGCTCACACTGGTCACCTG
                        ||  ||| |  ||   | | |||| |     ||  ||| |||  | | || |||     | | ||| ||  |  |||     ||   ||||  | |      || || |||||||||||||| || ||||| ||||||||||||||||| || 
-----------------------gtgggtgtatatttc--tcatctta-tggcaatgataatatgtaggattttcttattggatcatata-acaatcatatgcttattaatttttaaaatg-----tgttccagTGATCATGAAGGCGGGAATGTCAGTGCTCACACTGGTCATCTA

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|116471055|gb|EG513647.1|EG513647
EST:     GATGATGAAAAGGTGAAAGAGCTCATGAGGCTTTACATCACCATCCACAG                         TGATCATGAAGGTGGAAATGTTAGTGCTCACACTGGTCACCTG
genomic: GATGATGAAAAGGTGAAAGAGCTCATGAGGCTTTACATCACCATCCACAGgtctgtatta ... tttgctctagTGATCATGAAGGTGGAAATGTTAGTGCTCACACTGGTCACCTG
EST: gi|124972090|gb|EL045807.1|EL045807
EST:     GATGATGAAAAGGTGAAAGAGCTCATGAGGCTTTACATCACCATCCACAG                         TGATCATGAAGGTGGAAATGTTAGTGCTCACACTGGT
genomic: GATGATGAAAAGGTGAAAGAGCTCATGAGGCTTTACATCACCATCCACAGgtctgtatta ... tttgctctagTGATCATGAAGGTGGAAATGTTAGTGCTCACACTGGT
EST: gi|47832067|gb|CK121751.1|CK121751
EST:     GATGATGAAAAGGTGAAAGAGCTCATGAGGCTTTACATCACCATCCACAG                         TGATCATGAAGGTGGAAATGTTAGTGCTCACACTGGTCACCTG
genomic: GATGATGAAAAGGTGAAAGAGCTCATGAGGCTTTACATCACCATCCACAGgtctgtatta ... tttgctctagTGATCATGAAGGTGGAAATGTTAGTGCTCACACTGGTCACCTG
EST: gi|116453292|gb|EG495884.1|EG495884
EST:     GATGATGAAAAGGTGAAAGAGCTCATGAGGCTTTACATCACCATCCACAG                         TGATCATGAAGGTGGAAATGTTAGTGCTCACACTGGTCACCTG
genomic: GATGATGAAAAGGTGAAAGAGCTCATGAGGCTTTACATCACCATCCACAGgtctgtatta ... tttgctctagTGATCATGAAGGTGGAAATGTTAGTGCTCACACTGGTCACCTG
EST: gi|301502837|gb|HO208377.1|HO208377
EST:     GATGATGAAAAGGTGAAAGAGCTCATGAGGCTTTACATCACCATCCACAG                         TGATCATGAAGGTGGAAATGTTAGTGCTCACACTGGTCACCTG
genomic: GATGATGAAAAGGTGAAAGAGCTCATGAGGCTTTACATCACCATCCACAGgtctgtatta ... tttgctctagTGATCATGAAGGTGGAAATGTTAGTGCTCACACTGGTCACCTG
EST: gi|125041130|gb|EL113399.1|EL113399
EST:     AAAGAGCTCATGAGGCTTTACATCACCATCCACAG                         TGATCATGAAGGTGGAAATGTTAGTGCTCACACTGGTCACCTGGTTG
genomic: AAAGAGCTCATGAGGCTTTACATCACCATCCACAGgtctgtatta ... tttgctctagTGATCATGAAGGTGGAAATGTTAGTGCTCACACTGGTCACCTGGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gactttaaatagacctttgtataacattttgcttttctactattttttgctctagTGATCATGAAGGTGGAAATGTTAGTGCTCACACTGGTCACCTG
                  gtataac  putative branch site (score: 3)
                          ttttgcttttctacta  CT-rich tract
                                ttttctactatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgtattaattttcgtcacccatgcatgtctccttaaataagcttaattatcttgtaaatttgtttgttctttttaagactttaaatagacctttgtataacattttgcttttctactattttttgctctagTGATCATGAAGGTGGAAATGTTAGTGCTCACACTGGTCACCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA