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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaataacaacacacattcatatcttccatttccaaagttgatgtacataagattgttcttaggctgatattacttccttttgttatgttagATCTTCCGGGGACTTGCTTACATTCACAATGTTGCTGGAGTTTGTCACAGAGATCTAAAGCCTCAAAATCTTCTG

Basic information

species Arabidopsis thaliana
transcript AT4G18710.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G18710.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA05G29200.1 (Glycine max), 3'ss of exon 3
gtaataacaacacacattcatatcttccatttccaaagttgatgtacataagattgttcttaggctgatattacttccttttgttatgttagATCTTCCGGGGACTTGCTTACATTCACAATGTTGCTGGAGTTTGTCACAGAGATCTAAAGCCTCAAAATCTTCTG
           |  | |  |  | |    |     |    | | |   |     | |||  |  ||||||    |   |  ||      ||||| ||| |||| || ||||| || |||| |||| |||||||||| ||||||||| | |||||||||||| | |||
---------gtatgcctcaaagtttcgggtgattgagaaggttctgtttttatcttttcacatcctgatacaggtctgtggtgcacatatagATTTTCAGGGGGCTGGCTTATATCCACACTGTTCCTGGAGTTTGCCACAGAGATTTGAAGCCTCAAAATATACTG

upper sequence: AT4G18710.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G12370.1 (Glycine max), 3'ss of exon 4
gtaataacaacacacattcatatcttccatttccaaagttgatgtacataagattgttcttaggctgatattacttccttttgttatgttagATCTTCCGGGGACTTGCTTACATTCACAATGTTGCTGGAGTTTGTCACAGAGATCTAAAGCCTCAAAATCTTCTG
           |  | |  |  | ||   |     |    | | |   |     | |||  |  ||||||        |  ||      ||||| ||| | || || ||||| || |||| |||| |||||||||| ||||||||| | |||||||||||| | |||
---------gtatgcctcaaattttttggtgattgagaaggttctgtttttatcttttcacattctgatacgggcctgtggtgcacatatagATTTTCAGTGGGCTGGCTTATATCCACACTGTTCCTGGAGTTTGCCACAGAGATTTGAAGCCTCAAAATATACTG
















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|124896861|gb|EH973075.1|EH973075
EST:     GTGCAAACCAAAGAATGCCTCTTGTCTATGTTAAACTTTACATGTATCAG                         ATCTTCCGGGGACTTGCTT
genomic: GTGCAAACCAAAGAATGCCTCTTGTCTATGTTAAACTTTACATGTATCAGgtaataacaa ... gttatgttagATCTTCCGGGGACTTGCTT
EST: gi|86056751|gb|DR352508.1|DR352508
EST:     GTGCAAACCAAAGAATGCCTCTTGTCTATGTTAAACTTTACATGTATCAG                         ATCTTCCGGGGACTTGCTTACATTCACAATGNNNNCTGGAGTTTGTCACAG
genomic: GTGCAAACCAAAGAATGCCTCTTGTCTATGTTAAACTTTACATGTATCAGgtaataacaa ... gttatgttagATCTTCCGGGGACTTGCTTACATTCACAATGTTG-CTGGAGTTTGTCACAG
EST: gi|124832488|gb|EH916927.1|EH916927
EST:     GTGCAAACCAAAGAATGCCTCTTGTCTATGTTAAACTTTACATGTATCAG                         ATCTTCCGGGGACTTGCTTACATT
genomic: GTGCAAACCAAAGAATGCCTCTTGTCTATGTTAAACTTTACATGTATCAGgtaataacaa ... gttatgttagATCTTCCGGGGACTTGCTTACATT
EST: gi|125059616|gb|EL128293.1|EL128293
EST:     TGTTAAACTTTACATGTATCAG                         ATCTTCCGGGGACTTGCTTACATTCACAATGTTGCTGGAGTTTGTCACAGA
genomic: TGTTAAACTTTACATGTATCAGgtaataacaa ... gttatgttagATCTTCCGGGGACTTGCTTACATTCACAATGTTGCTGGAGTTTGTCACAGA
EST: gi|124788256|gb|EH877935.1|EH877935
EST:     GTGCAAACCAAAGAATGCCTCTTGTCTATGTTAAACTTTACATGTATCAG                         ATCTTCCGGGGACTTGCTTACATTCACAAT
genomic: GTGCAAACCAAAGAATGCCTCTTGTCTATGTTAAACTTTACATGTATCAGgtaataacaa ... gttatgttagATCTTCCGGGGACTTGCTTACATTCACAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgatgtacataagattgttcttaggctgatattacttccttttgttatgttagATCTTCCGGGGACTTGCTTACATTCACAATGTTGCTGGAGTTTGTCACAGAGATCTAAAGCCTCAAAATCTTCTG
                         ggctgat  putative branch site (score: 4)
                                 ttacttccttttgtt  CT-rich tract
                              atattactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaataacaacacacattcatatcttccatttccaaagttgatgtacataagattgttcttaggctgatattacttccttttgttatgttagATCTTCCGGGGACTTGCTTACATTCACAATGTTGCTGGAGTTTGTCACAGAGATCTAAAGCCTCAAAATCTTCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC