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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcctctacttctgtacctctccgtttcagacaaacttgattatgtattcctttgttgcctcagatgtgaaggtgtttattggaattttcaaacacaattaatgcagATATTTGTAATGTGGTTGGACTTCGTCACTTACTTGCACCACCATGGACATGAAGACAAGCTCCCTTGGTATCGTGGAAAG

Basic information

species Arabidopsis thaliana
transcript AT5G05580.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G05580.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os03g18070.1 (Oryza sativa), 3'ss of exon 5
gtatcctctacttctgtacctctccgtttcagacaaacttgattatgtattcctttgttgcctcagatgtgaaggtgtttattggaattttcaaacacaattaatgcagATATTTGTAATGTGGTTGGACTTCGTCACTTACTTGCACCACCATGGACATGAAGACAAGCTCCCTTGGTATCGTGGAAAG
|||    |   |  | |   | |  ||||| |  |||    | | || |||  |  |        |   || | ||||| |    | |||  |||| |   | |||||||||||||| |||||| | || || ||||| || |||||||| ||||| ||||| |||||||| |||||||| |||||||||
gtaagagca--tgatatttttattagtttctgcaaaatgataatttggattgatgggagtgtctggtgatgtatgtgttcac---attttgtaaaccc---ttatgcagATATTTGTTATGTGGCTTGATTTTGTCACATATTTGCACCATCATGGCCATGAGGACAAGCTTCCTTGGTACCGTGGAAAG

upper sequence: AT5G05580.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os07g49310.1 (Oryza sativa), 3'ss of exon 4
---------------------------------------------------------------gtatcctctacttctgtacctctccgtttcagacaaacttgattatgtattcctttgttgcctcagatgtgaaggtgtttattggaattttcaaacacaattaatgcagATATTTGTAATGTGGTTGGACTTCGTCACTTACTTGCACCACCATGGACATGAAGACAAGCTCCCTTGGTATCGTGGAAAG
                                                                |||||||| | |     |     | | |       |  ||   |   |  |||   |||| |    |    |   |||| |    ||||  |  |    |   ||||||| ||||| |||||| ||||||||||||| ||||||||||| || || ||  | |||||||| || ||||| ||||| |||
gtacgtagttaccccctacatacatacgttggttcattgatgtgatctgtggattgggttcctctatcctctgcctgccctcgatctcctcttttgtggatgtggggaacaaaacctaccttgctttcttttctcatcagtttgt----atttcaattctacttctctgcagATTTTTGTTATGTGGCTGGACTTCGTCACCTACTTGCACCATCACGGCCACAACGACAAGCTGCCCTGGTACCGTGGCAAG

upper sequence: AT5G05580.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G128971_T03 (Zea mays), 3'ss of exon 1
------gtatcctctacttctgtacctctccgtttcagacaaacttgattatgtattcctttgttgcctcagatgtgaaggtgtttattggaattttcaaacacaattaatgcagATATTTGTAATGTGGTTGGACTTCGTCACTTACTTGCACCACCATGGACATGAAGACAAGCTCCCTTGGTATCGTGGAAAG
      |   | |   || || | |  | |   ||| |  |||   ||| || |       || || ||     |||  | |||  |||    ||           |   ||||| |||||||    ||| ||||  | ||||| ||||||||||| ||||| || ||||||||||| || ||||| |||||||||
gtaagagcggcatgccctcctcttcggcccaacttctgcaaaaaaagataatttgaatgggtggtgtct-----gtggtgctgtaaatttatgttcctgc---tggtgtgtgcagGTATTTGTTGCTTGGCTGGATATGGTCACATACTTGCACCATCATGGCCACGAAGACAAGCTTCCCTGGTACCGTGGAAAG

upper sequence: AT5G05580.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv13s0067g01120.t01 (Vitis vinifera), 3'ss of exon 5
gtatcctctacttctgtacctctccgtttcagacaaacttgattatgtattcctttgttgcctcagatgtgaaggtgtttattggaattttcaaaca-caattaatgcagATATTTGTAATGTGGTTGGACTTCGTCACTTACTTGCACCACCATGGACATGAAGACAAGCTCCCTTGGTATCGTGGAAAG
               || |    | |||||    |   ||  || | |  |    |||||  |      ||    |  | |    |  ||| ||||  | || ||||||||| || || ||||||||||| || || ||||||||||| |||||||| |||||||| ||||| ||||||||||||||||||
---------------gt-cagtgcagtttc--ttagtttttgttgttttcttggctgttgagttcatgttggttttactcagctaagctttgaaacttccatgaatgcagATTTTCGTCATGTGGTTGGATTTAGTGACTTACTTGCATCACCATGGCCATGAAGAGAAGCTTCCTTGGTATCGTGGAAAG

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|125270461|gb|EL284546.1|EL284546
EST:     CAAACTATATGGCATCCCTTATTGG                         ATATTTGTAATGTGGTTGGACTTCGTCACTTACTTGCACCACCATGGACAT
genomic: CAAACTATATGGCATCCCTTATTGGgtatcctcta ... attaatgcagATATTTGTAATGTGGTTGGACTTCGTCACTTACTTGCACCACCATGGACAT
EST: gi|125023034|gb|EL095303.1|EL095303
EST:     TCAAACTATATGGCATCCCTTATTGG                         ATATTTGTAATGTGGTTGGACTTCGTCACTTACTTGCACCACCATGGACA
genomic: TCAAACTATATGGCATCCCTTATTGGgtatcctcta ... attaatgcagATATTTGTAATGTGGTTGGACTTCGTCACTTACTTGCACCACCATGGACA
EST: gi|124969980|gb|EL043842.1|EL043842
EST:     TTGTCATGGGTCCAATCCAGATGCTCAAACTATATGGCATCCCTTATTGG                         ATATTTGTAATGTGGTTGGACTTCGT
genomic: TTGTCATGGGTCCAATCCAGATGCTCAAACTATATGGCATCCCTTATTGGgtatcctcta ... attaatgcagATATTTGTAATGTGGTTGGACTTCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttgcctcagatgtgaaggtgtttattggaattttcaaacacaattaatgcagATATTTGTAATGTGGTTGGACTTCGTCACTTACTTGCACCACCATGGACATGAAGACAAGCTCCCTTGGTATCGTGGAAAG
                                            aattaat  putative branch site (score: 3)
                       tttattggaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcctctacttctgtacctctccgtttcagacaaacttgattatgtattcctttgttgcctcagatgtgaaggtgtttattggaattttcaaacacaattaatgcagATATTTGTAATGTGGTTGGACTTCGTCACTTACTTGCACCACCATGGACATGAAGACAAGCTCCCTTGGTATCGTGGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT