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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTAACAGGTCTGCCATTAAATGAAGTTATTGGTACAATTTTGAAGGGAAAATGGGACAATAAGAGAACTGAGTTCTCTTTACCACCACTGATGAATCTTgtaagcaaacaatcagacctaaattcttacctagaaaaacctgttgtgaacttcaccaacttcttatttctttgacttctgtgaaatctggtgtactaacaagatgttgtcttatttag

Basic information

species Arabidopsis thaliana
transcript AT1G31910.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G31910.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA06G13260.1 (Glycine max), 5'ss of exon 7
AGTAACAGGTCTGCCATTAAATGAAGTTATTGGTACAATTTTGAAGGGAAAATGGGACAATAAGAGAACTGAGTTCTCTTTACCACCACTGATGAATCTTgtaagcaaac-aatcagacctaaattcttacctagaaaaacctgttgtgaac---ttcacca-acttcttatttctttgacttctgtgaaatctggtgtactaacaagatgttgtcttatttag
||  | ||   |||| ||    ||   |||   |  |||| | || ||||| |||||| || | | | |||||||||||||||||||  |||||| ||||||||||||   ||      |||  ||  |  ||  ||||    | | ||  |   | ||||   |  |   |  |||   |  || |    ||||||  |                        
AGATATAGCAGTGCCTTTGCCAGATAGTATCACTGAAATTATAAAAGGAAATTGGGACCATGACACAGCTGAGTTCTCTTTACCACCTTTGATGACTCTTgtaagcaacttaaattttgctacttttatgtcttaaaaatgtggctatgggcacttacaccctgccccacctcccttctccccctatctcttctggttga------------------------
















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|124768672|gb|EH858802.1|EH858802
EST:     ATGGGGACAATAAGAGAACTGAGTTCTCTTTACCACCACTGATGAATCTT                         TTCCTTGGAGAACCTGGAAGTGGTGGATCCTCCACACCATCAA
genomic: AT-GGGACAATAAGAGAACTGAGTTCTCTTTACCACCACTGATGAATCTTgtaagcaaac ... tcttatttagTTCCTTGGAGAACCTGGAAGTGGTGGATCCTCCACACCATCAA
EST: gi|125259324|gb|EL273409.1|EL273409
EST:     AATAAGAGAACTGAGTTCTCTTTACCACCACTGATGAATCTT                         TTCCTTGGAGAACCTGGAAGTGGTGGATCCTCCACACCATCAATGGTTAGG
genomic: AATAAGAGAACTGAGTTCTCTTTACCACCACTGATGAATCTTgtaagcaaac ... tcttatttagTTCCTTGGAGAACCTGGAAGTGGTGGATCCTCCACACCATCAATGGT-AGG
EST: gi|124771248|gb|EH861378.1|EH861378
EST:     AATAAGAGAACTGAGTTCTCTTTACCACCCACTGATGAATCTT                         TTCCTTGGAGAACCTGGAAGTGGTGGATCCTCCACAACCATCAATGGTAGG
genomic: AATAAGAGAACTGAGTTCTCTTTACCA-CCACTGATGAATCTTgtaagcaaac ... tcttatttagTTCCTTGGAGAACCTGGAAGTGGTGGATCCTCCACA-CCATCAATGGTAGG
EST: gi|125037276|gb|EL109545.1|EL109545
EST:     AATGGGACAATAAGAGAACTGAGTTCTCTTTACCACCACTGATGAATCTT                         TTCCTTGGAGAACCTGGAAGTGGTGGATCCTCCACACCATCAATGGTAGGT
genomic: AATGGGACAATAAGAGAACTGAGTTCTCTTTACCACCACTGATGAATCTTgtaagcaaac ... tcttatttagTTCCTTGGAGAACCTGGAAGTGGTGGATCCTCCACACCATCAATGGTAGGT
EST: gi|124960441|gb|EL035108.1|EL035108
EST:     AATAAGAGAACTGAGTTCTCTTTACCACCCACTGATGAATCTT                         TTCCTTGGAGAACCTGGAAGTGGTGGATCCTCCACACCATCAATGGTAGGT
genomic: AATAAGAGAACTGAGTTCTCTTTACCA-CCACTGATGAATCTTgtaagcaaac ... tcttatttagTTCCTTGGAGAACCTGGAAGTGGTGGATCCTCCACACCATCAATGGTAGGT
EST: gi|125197270|gb|EL212224.1|EL212224
EST:     TGATGAATCTT                         TTCCTTGGAGAACCTGGAAGTGGTGGATCCTCCACACCATCAATGGTAGGT
genomic: TGATGAATCTTgtaagcaaac ... tcttatttagTTCCTTGGAGAACCTGGAAGTGGTGGATCCTCCACACCATCAATGGTAGGT
EST: gi|124762696|gb|EH852826.1|EH852826
EST:     AATGGGACAATAAGAGAACTGAGTTCTCTTTACCACCACTGATGAATCTT                         TTCCTTGGAGAACCTGGAAGTGGTGG
genomic: AATGGGACAATAAGAGAACTGAGTTCTCTTTACCACCACTGATGAATCTTgtaagcaaac ... tcttatttagTTCCTTGGAGAACCTGGAAGTGGTGG
EST: gi|86070800|gb|DR366557.1|DR366557
EST:     TGATGAATCTT                         TTCCTTGGAGAACCTGGAAGTGGTGGATCCTCCACACCATCAATGGTAGGT
genomic: TGATGAATCTTgtaagcaaac ... tcttatttagTTCCTTGGAGAACCTGGAAGTGGTGGATCCTCCACACCATCAATGGTAGGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTAACAGGTCTGCCATTAAATGAAGTTATTGGTACAATTTTGAAGGGAAAATGGGACAATAAGAGAACTGAGTTCTCTTTACCACCACTGATGAATCTTgtaagcaaacaatcagacctaaattcttacctagaaaaacctgttgtgaacttcaccaacttcttatttctttgacttctgtgaaatctggtgtactaacaagatgttgtcttatttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA