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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaacactttttgctatcaaaccttaccacatctgttgattcaagacaacacatggtgtgccctaaatctttgtttccatttttctccagGGTTCTGGGGAGGTCTGGTACCTGACAATGCACTCAACTCAAGTGCTCTTGAGTCTCTCTTAGATGCTGGAGTTCTTGGTCTCAAG

Basic information

species Arabidopsis thaliana
transcript AT4G04955.1
intron # 6
splice site 3'
intron type U2

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|116378121|gb|EG420713.1|EG420713
EST:     ATTGAAGCTGCGAAAAACAGAATACATGTTGATGTTG                         GGTTCTGGGGAGGTCTGGTACCTGACAATGCACTCAACTCAAGTGCTCTTG
genomic: ATTGAAGCTGCGAAAAACAGAATACATGTTGATGTTGgtaaacactt ... ttttctccagGGTTCTGGGGAGGTCTGGTACCTGACAATGCACTCAACTCAAGTGCTCTTG
EST: gi|116378124|gb|EG420716.1|EG420716
EST:     ATTGAAGCTGCGAAAAACAGAATACATGTTGATGTTG                         GGTTCTGGGGAGGTCTGGTACCTGACAATGCACTCAACTCAAGTGCTCTTG
genomic: ATTGAAGCTGCGAAAAACAGAATACATGTTGATGTTGgtaaacactt ... ttttctccagGGTTCTGGGGAGGTCTGGTACCTGACAATGCACTCAACTCAAGTGCTCTTG
EST: gi|116378122|gb|EG420714.1|EG420714
EST:     AAACTCAAGATTGAAGCTGCGAAAAACAGAATACATGTTGATGTTG                         GGTTCTGGGGAGGTCTGGTACCTGACAATGCACTCAACTCAAGTGCTCTTG
genomic: AAACTCAAGATTGAAGCTGCGAAAAACAGAATACATGTTGATGTTGgtaaacactt ... ttttctccagGGTTCTGGGGAGGTCTGGTACCTGACAATGCACTCAACTCAAGTGCTCTTG
EST: gi|125067582|gb|EL134037.1|EL134037
EST:     ATTGAAGCTGCGAAAAACAGAATACATGTTGATGTTG                         GGTTCTGGGGAGGTCTGGTACCTGACAATGCACTCAACTCAAGTGCT
genomic: ATTGAAGCTGCGAAAAACAGAATACATGTTGATGTTGgtaaacactt ... ttttctccagGGTTCTGGGGAGGTCTGGTACCTGACAATGCACTCAACTCAAGTGCT
EST: gi|124994657|gb|EL066926.1|EL066926
EST:     ATTGAAGCTTGCGAAAAACAGAATACATGTTGATGTTG                         GGTTCTGGGGAGGTCTGGTACCTGACAATGCACTCAACTCAAGTG
genomic: ATTGAAGC-TGCGAAAAACAGAATACATGTTGATGTTGgtaaacactt ... ttttctccagGGTTCTGGGGAGGTCTGGTACCTGACAATGCACTCAACTCAAGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgattcaagacaacacatggtgtgccctaaatctttgtttccatttttctccagGGTTCTGGGGAGGTCTGGTACCTGACAATGCACTCAACTCAAGTGCTCTTGAGTCTCTCTTAGATGCTGGAGTTCTTGGTCTCAAG
                         ccctaaa  putative branch site (score: 3)
                                tctttgtttccatttt  CT-rich tract
                            taaatcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaacactttttgctatcaaaccttaccacatctgttgattcaagacaacacatggtgtgccctaaatctttgtttccatttttctccagGGTTCTGGGGAGGTCTGGTACCTGACAATGCACTCAACTCAAGTGCTCTTGAGTCTCTCTTAGATGCTGGAGTTCTTGGTCTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA