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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagggaacttgatctacttatatttgttactttccacaggagtttagtgtactcgtgacgatcagtatattttctaagtatctcacgatgaaatggcatgcagGTGAAGGGACTGGTTTGCTTCGTCTCCATAGTACGTACCGTCATGACCTTAAAATTTACAGCTCTGACGAGGGACGTGTTCAG

Basic information

species Arabidopsis thaliana
transcript AT3G01310.1
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GLYMA19G02260.1 (Glycine max), 3'ss of exon 15
gtaagggaacttgatctacttatatttgttactttccacaggagtttagtgtactcgtgacgatcagtatattttctaagtatctcacgatgaaatggcatgcagGTGAAGGGACTGGTTTGCTTCGTCTCCATAGTACGTACCGTCATGACCTTAAAATTTACAGCTCTGACGAGGGACGTGTTCAG
| | | | ||| || |||| | || | || | || | ||||| | || | | | |||| |||||| ||||| || || | ||||| ||||||||||| ||||||||||| || || |||||||||||||| ||||| ||||| |||
atgtttcatacaggatcatgtattcttattacatgtagcatcaacttgacagtggcttg-tactatgtataaaggcaaaattttgtgttttaaaat----tgcagGAGAAGGTACAGGGCTTCTTCGCCTCCATAGTACATACCGTCATGATCTCAAGATTTACAGCTCTGATGAGGGTCGTGTGCAG

upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GLYMA13G05060.1 (Glycine max), 3'ss of exon 19
gtaagggaacttgatctacttatatttgttactttccacaggagtttagtgtactcgtgacgatcagtatattttctaagtatctcacgatgaaatggcatgcagGTGAAGGGACTGGTTTGCTTCGTCTCCATAGTACGTACCGTCATGACCTTAAAATTTACAGCTCTGACGAGGGACGTGTTCAG
|| | | |||| | || || |||| | ||| | || || || | ||||| | || | | | | || |||||| ||||| || || | ||||| ||||||||||| ||||||||||| || || |||||||||||||| ||||| ||||| |||
gtttcata-caggatc-atgcattcttattacatgtaacatcaacttgacagtgtcttg-tagtatgtataaaggcaaatttttgtgtggtttaaaat--tgcagGAGAAGGTACAGGGCTTCTTCGCCTCCATAGTACATACCGTCATGATCTCAAGATTTACAGCTCTGATGAGGGTCGTGTGCAG

upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GLYMA09G37610.1 (Glycine max), 3'ss of exon 15
gtaagggaacttgatctacttatatttgttactttccacaggagtt-tagtgtactcgtgacgatcagt-atattttctaagtatctcacgatgaaatggca-----tgcagGTGAAGGGACTGGTTTGCTTCGTCTCCATAGTACGTACCGTCATGACCTTAAAATTTACAGCTCTGACGAGGGACGTGTTCAG
|||| || | | | | ||| || | || || | || | |||| || | || | | | || | || | | ||||| ||||| || || ||||||| |||||||| || ||||||||||| ||||| || ||||||||||| ||||| ||||| |||
-----------tgataggttt-caaatatgatttttcattgttcttgtaatatagacatgacaatggattgtaccatgcatgacatgcaaattaaattcttaaatgtcgcagGAGAAGGTACAGGGCTGCTTCGCCTCCATAGCACATACCGTCATGATCTTAAGATATACAGCTCTGATGAGGGTCGTGTGCAG

upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GLYMA18G49000.1 (Glycine max), 3'ss of exon 17
gtaagggaacttgatctacttatatttgttactttccacaggagtt-tagtgtactcgtgacgatcagtatattttctaagtatctcacga--tgaaatggca-----tgcagGTGAAGGGACTGGTTTGCTTCGTCTCCATAGTACGTACCGTCATGACCTTAAAATTTACAGCTCTGACGAGGGACGTGTTCAG
| | | || | || | | ||| || | || || | || | |||| | ||| | | | | | | | | || | | || ||| ||||| || || ||||||| |||||||| || ||||| ||||| ||||| || ||||||||||| ||||| ||||| |||
------------ggtatgttt-caattatgatttttcattgttcttgtaatatagacatgacaaacagattgtaccatgcatgacatgcaaattaaattcttaaatgttgaagGAGAAGGTACAGGGCTGCTTCGCCTCCATAGCACATACCGCCATGATCTTAAGATATACAGCTCTGATGAGGGTCGTGTGCAG

upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 17
gtaagggaacttgatctacttatatttgttactttccacaggagtttagtg-tactcgtgacgatcagtatattttctaagt-atctcacgatgaaatggcat-gcagGTGAAGGGACTGGTTTGCTTCGTCTCCATAGTACGTACCGTCATGACCTTAAAATTTACAGCTCTGACGAGGGACGTGTTCAG
| | | | | || ||| | | | | || | ||| || ||| | | |||| | | | | || ||| || ||||||||||| ||||| ||||||| || |||||||| || |||||||| || |||||||||||||| || ||||| ||||| |||
--------aatccttttgtgtggatgaattaatacctgtggtcttcctctgcttctcttggtgatttttttttttttttttttaaattgttattgtatgtaattgcagGTGAAGGCACTGGCCTGCTTCGCCTTCATAGTACTTATCGTCATGATCTAAAAATTTACAGCTCAGATGAGGGTCGTGTACAG

upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: PP1S112_67V6.1 (Physcomitrella patens), 3'ss of exon 17
--------------------------------------------------------gtaagggaacttgatctacttatatttgttactttccacaggagtttagtgtactcgtgacgatcagtatattttctaagtatctcacgatgaaatggcatgcagGTGAAGGGACTGGTTTGCTTCGTCTCCATAGTACGTACCGTCATGACCTTAAAATTTACAGCTCTGACGAGGGACGTGTTCAG
| || || | | || ||| | | | || || | || | || | | | | | | | ||| |||| |||||| || |||||||||||||| || ||||||||||| || || |||||| | ||||| ||||| || ||||| || | || |||
gtaaataccacggattagctgcatggaggaaactactacttctaagtgttgcacatgctagataagaaagtaaatttgacagagttgcacttaatgtagacatactgcattctggttcatttgaaaagcacatccatgtga-atcctgatatggattgcagGAGAGGGGACTGGTTTGCTGCGACTCCATAGTACTTATCGGCATGACTTGAAAATCTACAGTTCCGACGAAGGGAGGGTGCAG

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|124881521|gb|EH960423.1|EH960423
EST:     CAGGCAGAAGAACTTGGTAGATACTTTCGAAACAATATGTATCCAG                         GTGAAGGGACTGGTTTGCTTCGTCTCCA
genomic: CAGGCAGAAGAACTTGGTAGATACTTTCGAAACAATATGTATCCAGgtaagggaac ... tggcatgcagGTGAAGGGACTGGTTTGCTTCGTCTCCA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtactcgtgacgatcagtatattttctaagtatctcacgatgaaatggcatgcagGTGAAGGGACTGGTTTGCTTCGTCTCCATAGTACGTACCGTCATGACCTTAAAATTTACAGCTCTGACGAGGGACGTGTTCAG
                               atctcac  putative branch site (score: 3)
 tatattttctaagtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagggaacttgatctacttatatttgttactttccacaggagtttagtgtactcgtgacgatcagtatattttctaagtatctcacgatgaaatggcatgcagGTGAAGGGACTGGTTTGCTTCGTCTCCATAGTACGTACCGTCATGACCTTAAAATTTACAGCTCTGACGAGGGACGTGTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC