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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatactactatttttggttagaattcagataaggaaaacgtttattatcttgactgctacttatatagcttgcctgtgtagtaactgttatccgttaaagcagaagtcttctaattattgttgtgtcatgttgcgtctcccttgtttgtgatttcaatccagGCTTGGATGGCTTATTCGTTTCATTAGTCACTCAGTCATATCTGGATTTACAAGTGCTTCGGCCATTGTGATTGGGTTATCTCAAATAAAATATTTCCTG

Basic information

species Arabidopsis thaliana
transcript AT5G13550.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G13550.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G068212_T01 (Zea mays), 3'ss of exon 3
gtaatactactatttttggttagaattcagataaggaaaacgtttattatcttgactgctacttatatagcttgcctgtgtagtaactgttatccgttaaagcagaagtcttctaattattgttgtgtcatgttgcgtctcccttgtttgtgatttcaatccagGCTTGGATGGCTTATTCGTTTCATTAGTCACTCAGTCATATCTGGATTTACAAGTGCTTCGGCCATTGTGATTGGGTTATCTCAAATAAAATATTTCCTG
                                                           || ||   ||  |||   ||  |  || |        ||         ||  |||   |     ||||| |     | | ||   ||||| |  |||  || ||||||||| ||||| |||||||||||||| || || || |||||||| || || |  ||||| |||||||| ||||| ||||| || ||||| |||||| | 
---------------------------------------------------------aatattttcttaatttgatagtagaacaaatacacaatcttggtatgcttgttctctg--tgagaatgtgtaac----catttcatatgttt-tattttgtatacagGCTTGGTTGGCTCATTCGTTTCATTAGCCATTCTGTAATATCTGGGTTCACTACAGCTTCAGCCATTGTTATTGGTTTATCCCAGATAAAGTATTTCTTA

upper sequence: AT5G13550.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA02G10590.1 (Glycine max), 3'ss of exon 3
gtaatactactatttttggttagaattcagataaggaaaacgtttattatcttgactgctacttatatagct-tgcctgtgtagtaactgttatccgttaaagcagaagtcttct----aattattgttgtgtcatgttgcgtctcccttgtttgtgatttcaatccagGCTTGGATGGCTTATTCGTTTCATTAGTCACTCAGTCATATCTGGATTTACAAGTGCTTCGGCCATTGTGATTGGGTTATCTCAAATAAAATATTTCCTG
                                                               |||||   | |||  |   || |      |||    ||| | ||| | ||      |   ||| |   |  |   | | | | | |  ||| || |  || | |||||||||||||||||||||||||||||| || ||||| |||||||| |||||||  ||||| || ||||| ||||| |||||||||  |||||| ||| ||
---------------------------------------------------------------tatatgattctgctggctcagcactcagcatc----aaacctgaattttttatgaaagggattttaaggataacctacatatacttgttttttggt--catttcagGCTTGGATGGCTTATTCGTTTCATTAGCCATTCAGTGATATCTGGCTTTACAACCGCTTCAGCTATTGTCATTGGTTTATCTCAAGCAAAATACTTCTTG

upper sequence: AT5G13550.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA18G52270.1 (Glycine max), 3'ss of exon 3
gtaatactactatttttggttagaattcagataaggaaaacgtttattatcttgactgctacttatatagcttgcctgtgtagtaactgttatccgttaaagcagaagtcttct----aattattgttgtgtcatgttgcgtctcccttgtttgtgatttcaatccagGCTTGGATGGCTTATTCGTTTCATTAGTCACTCAGTCATATCTGGATTTACAAGTGCTTCGGCCATTGTGATTGGGTTATCTCAAATAAAATATTTCCTG
                                                               |||||   |   |||     | |    |     | ||  | ||| | ||      |   ||| |   |  |   |  ||   | |   || || ||    | ||||||||||||||| |||||||||||||| || ||||| || ||||| ||||||| |||||| || ||||| ||||| |||||||||   ||||| ||| ||
---------------------------------------------------------------tatatgatt---ctgcaggctcagcactcagtttcaagcctgaattttttatgaaagggattttaacgataacctatgtacacttgtcttttggttct--ttcagGCTTGGATGGCTGATTCGTTTCATTAGCCATTCAGTGATTTCTGGCTTTACAACTGCTTCAGCTATTGTCATTGGTTTATCTCAAGCGAAATACTTCTTG

upper sequence: AT5G13550.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv13s0019g00010.t01 (Vitis vinifera), 3'ss of exon 3
gtaatactactatttttggttagaattcagataaggaaaacgtttattatcttgactgctacttatatagcttgcctgtgtagtaactgttatccgttaaagcagaagtcttctaattattgttgtgtcatgttgcgtctcccttgtttgtgatttcaatccagGCTTGGATGGCTTATTCGTTTCATTAGTCACTCAGTCATATCTGGATTTACAAGTGCTTCGGCCATTGTGATTGGGTTATCTCAAATAAAATATTTCCTG
                                                            | || ||         ||  || |  || |  |    | |  |  || | |      | |  ||  |  |      |   | |   |||    || |  || |||||||||||||||||||||||||| |||||||| || || ||||| ||||| |  ||||| || ||||||||||  |||||||||  ||| |||||||||
------------------------------------------------------------atttgtactagaaatttgcatattttctatcttttaattattctcaaatttctgtgatgtcatttagaaagaaaatgatgcaccctttt----ttcctttctagGCTTGGATGGCTTATTCGTTTCATCAGTCACTCTGTGATTTCTGGGTTTACGACAGCTTCAGCAATTGTGATTGCCTTATCTCAAGCAAAGTATTTCCTG

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|116420139|gb|EG462731.1|EG462731
EST:     TTGTTGGCGCTTTTAGTTGGAATCTTGGAGTGCATCATGGGGCTCTTAAG                         GCTTGGATGGCTTATTCGTTTCATTAGTCACTCAGTCATATCTGGATTTAC
genomic: TTGTTGGCGCTTTTAGTTGGAATCTTGGAGTGCATCATGGGGCTCTTAAGgtaatactac ... ttcaatccagGCTTGGATGGCTTATTCGTTTCATTAGTCACTCAGTCATATCTGGATTTAC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttctaattattgttgtgtcatgttgcgtctcccttgtttgtgatttcaatccagGCTTGGATGGCTTATTCGTTTCATTAGTCACTCAGTCATATCTGGATTTACAAGTGCTTCGGCCATTGTGATTGGGTTATCTCAAATAAAATATTTCCTG
 ttctaat  putative branch site (score: 2)
     aattattgtt  TA-rich tract