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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtttcttgcatattcactttagcatatttcatggctgtacatagccctttgtcatgattttgtggtatcttaatgcagAAAAGGGTACTACTGTTTTTGGGCAGAAACTCCGTGAGCAAGTTGAGGAACGACTTGACTTTTATGACAAGGGAGTTGCCCCTCGCAAGAACATAGATGT

Basic information

species Glycine max
transcript GLYMA17G13770.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G13770.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g22880.1 (Oryza sativa), 3'ss of exon 6
gtttgtttcttgcatattcactttagcatatttcatggctgtacatagccctttgtcatga-------ttttgtggtatctt--aatgcagAAAAGGGTACTACTGTTTTTGGGCAGAAACTCCGTGAGCAAGTTGAGGAACGACTTGACTTTTATGACAAGGGAGTTGCCCCTCGCAAGAACATAGATGT
    |||  ||||||| |    ||  ||  ||  ||| |      |  |   || |  |||       |  ||   ||| ||  ||| ||||    | |||  | || |||||||| || || ||||||||||||||||| ||  | ||||| ||||||||||| ||||| ||||| || ||| | |||||
----gttagttgcatagttctgtttccaatttgtatgtccactagttactgcttttgctgaaagaacttgctgccatattttggaattcagAGTCAGCTACCGCAGTCTTTGGGCAAAAGCTTCGTGAGCAAGTTGAGGAGCGGTTAGACTTCTATGACAAGGGTGTTGCACCTCGTAAAAACCTTGATGT

upper sequence: GLYMA17G13770.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G12860.1 (Arabidopsis thaliana), 3'ss of exon 6
--gtttgtttcttgcatattcactttagca------tatttcatggctg-tacatagccctttgtcatgattttgtggtatct---taatgcagAAAAGGGTACTACTGTTTTTGGGCAGAAACTCCGTGAGCAAGTTGAGGAACGACTTGACTTTTATGACAAGGGAGTTGCCCCTCGCAAGAACATAGATGT
    |  | |   | || | |    ||  |      | |||    | || | | | |   ||    |  |  |  ||||   |   | ||||||| ||  | ||||| | ||| ||  |||||||  | || ||||| |||||| ||||||||||||||||||| || |||||||| || |||||  | |||||
gtaataatctagagaatgtcctgaataagagagaggtgtttgggagatgatgcgttgttattaactacaaaatcatggtggttgtgttatgcagATAACAGCACTACAGCTTTCGGTGAGAAACTAAGGGAACAAGTAGAGGAAAGACTTGACTTTTATGACAAAGGTGTTGCCCCACGTAAGAATGTTGATGT

upper sequence: GLYMA17G13770.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G56110.1 (Arabidopsis thaliana), 3'ss of exon 6
------gtttg---tttcttgcatattcactttagcatatttcatg-gctgtacatagccctttgtcatgattttgtggtatcttaatgcagAAAAGGGTACTACTGTTTTTGGGCAGAAACTCCGTGAGCAAGTTGAGGAACGACTTGACTTTTATGACAAGGGAGTTGCCCCTCGCAAGAACATAGATGT
       | ||    | |||| | |     ||| |  |||    |  | |||  | ||   |   | ||| |    || | || || ||||||    |  ||||||| ||||||  |||| || || || |||||||||||| | || || ||||||||||| || |||||||| ||||||||| | |||||
gtaaaaatctgaaactccttgaagaagagttttggattatgaattctgttgtgaa-agtgttaaattatg-tgccctgatgtccta-tgcagATGGTGCAACTACTGCTTTTGGTGAGAAGCTTCGCGAACAAGTTGAGGAAAGGCTAGAATTTTATGACAAAGGTGTTGCCCCACGCAAGAACGTGGATGT

upper sequence: GLYMA17G13770.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv17s0000g01720.t01 (Vitis vinifera), 3'ss of exon 6
----gtttgt-----ttcttgcatattcactttagcatatttcatggctgtacatagccctttgtc--atgattttgtggta------tcttaatgcagAAAAGGGTACTACTGTTTTTGGGCAGAAACTCCGTGAGCAAGTTGAGGAACGACTTGACTTTTATGACAAGGGAGTTGCCCCTCGCAAGAACATAGATGT
    |||| |     |||||  ||  ||| ||   ||| | |||||| ||     | |  ||| ||  || | ||||| | |      |||   |||||| |     || || ||||||||| ||||||||||||| ||||||||||| ||||| || ||||||||||||||| |||| ||||| || ||||| |||||
gtaagtttctataaattcttatatggtcattt---catttctcatggatg---gcaactttttatctgataaatttgttgcacaatcttctgtgtgcagAGAGTAACACCACGGTTTTTGGGGAGAAACTCCGTGAACAAGTTGAGGAGCGACTCGAATTTTATGACAAGGGAATTGCACCTCGGAAAAACATTGATGT

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|208242900|gb|GE041534.1|GE041534
EST:     TTATCTTGCAAACAAATGCTCAATTGCATCACGGATTGACTGCTTTTCTG                         AAAAGGGTACTACTGTTTTTGGGTCAGAAACTCCGTGAGCAAGTTGAGGAA
genomic: TTATCTTGCAAACAAATGCTCAATTGCATCACGGATTGACTGCTTTTCTGgtttgtttct ... cttaatgcagAAAAGGGTACTACTGTTTTTGGG-CAGAAACTCCGTGAGCAAGTTGAGGAA
EST: gi|193491563|gb|FK457417.1|FK457417
EST:     TTATCTTGCAAACAAATGCTCAATTGCATCACGGATTGACTGCTTTTCTG                         AAAAGGGTACTACTGTTTTTGGGCAGAAACTCCGTGAGCAAGTTGAGGAAC
genomic: TTATCTTGCAAACAAATGCTCAATTGCATCACGGATTGACTGCTTTTCTGgtttgtttct ... cttaatgcagAAAAGGGTACTACTGTTTTTGGGCAGAAACTCCGTGAGCAAGTTGAGGAAC
EST: gi|208070598|gb|GD867579.1|GD867579
EST:     TTATCTTGCAAACAAATGCTCAATTGCATCACGGATTGACTGCTTTTCTG                         AAAAGGGTACTACTGTTTTTGGGCAGAAACTACCGTGAGCAAGTT
genomic: TTATCTTGCAAACAAATGCTCAATTGCATCACGGATTGACTGCTTTTCTGgtttgtttct ... cttaatgcagAAAAGGGTACTACTGTTTTTGGGCAGAAACT-CCGTGAGCAAGTT
EST: gi|208310697|gb|GE104265.1|GE104265
EST:     TTATCTTGCAAACAAATGCTCAATTGCATCACGGATTGACTGCTTTTCTG                         AAAAGGGTACTACTGTTTTTGGGCAGAAAACTACCGTGAGCAAGTT
genomic: TTATCTTGCAAACAAATGCTCAATTGCATCACGGATTGACTGCTTTTCTGgtttgtttct ... cttaatgcagAAAAGGGTACTACTGTTTTTGGGCAGAAA-CT-CCGTGAGCAAGTT
EST: gi|208091684|gb|GD885417.1|GD885417
EST:     TTATCTTGCAAACAAATGCTCAATTGCATCACGGATTGACTGCTTTTCTG                         AAAAGGGTACTACTGTTTTTGGGCAGAAACTCCGTGAGCAAGTTGAGGAAC
genomic: TTATCTTGCAAACAAATGCTCAATTGCATCACGGATTGACTGCTTTTCTGgtttgtttct ... cttaatgcagAAAAGGGTACTACTGTTTTTGGGCAGAAACTCCGTGAGCAAGTTGAGGAAC
EST: gi|193461357|gb|FK428070.1|FK428070
EST:     TTATCTTGCAAACAAATGCTCAATTGCATCACGGATTGACTGCTCTTCTG                         AAAAGGGTACTACTGTTTTTGGGCAGAAACT
genomic: TTATCTTGCAAACAAATGCTCAATTGCATCACGGATTGACTGCTTTTCTGgtttgtttct ... cttaatgcagAAAAGGGTACTACTGTTTTTGGGCAGAAACT
EST: gi|207805279|gb|GD777285.1|GD777285
EST:     TTATCTTGCAAACAAATGCTCAATTGCATCACGGATTGACTGCTTTTCTG                         AAAAGGGTACTACTGTTTTTGGGCAGAAACTCCGTGAGCAAGTTGAGGAAC
genomic: TTATCTTGCAAACAAATGCTCAATTGCATCACGGATTGACTGCTTTTCTGgtttgtttct ... cttaatgcagAAAAGGGTACTACTGTTTTTGGGCAGAAACTCCGTGAGCAAGTTGAGGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatttcatggctgtacatagccctttgtcatgattttgtggtatcttaatgcagAAAAGGGTACTACTGTTTTTGGGCAGAAACTCCGTGAGCAAGTTGAGGAACGACTTGACTTTTATGACAAGGGAGTTGCCCCTCGCAAGAACATAGATGT
                                            tcttaat  putative branch site (score: 3)
                                          tatcttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtttcttgcatattcactttagcatatttcatggctgtacatagccctttgtcatgattttgtggtatcttaatgcagAAAAGGGTACTACTGTTTTTGGGCAGAAACTCCGTGAGCAAGTTGAGGAACGACTTGACTTTTATGACAAGGGAGTTGCCCCTCGCAAGAACATAGATGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC