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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagagtttttgttctgaatttttaacattttagtctagtttttttctaatcctaataatattcttttttggttcttgtagTGCAGCACATGATGTATGGCTTTGGAGATGATCCTAAT

Basic information

species Glycine max
transcript GLYMA10G00360.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G00360.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g23630.1 (Oryza sativa), 3'ss of exon 2
--gtaagagtttttgttctgaatttttaacattttagtctagtttttttctaatcctaataatat-tcttttttggttcttgtagTGCAGCACATGATGTATGGCTTTGGAGATGATCCTAAT
       | | ||| |||| || |||     |  |  | |  ||    |    |  | ||  |   | |||    ||||||| |||||||||||||||||| || ||||| |||||||| |||
gtacggcactgttttttctaaactttagtactgctgctgttcttcgaattcgttgtttatgctgcatttttccccgttcttgcagTGCAGCACATGATGTACGGATTTGGGGATGATCCAAAT

upper sequence: GLYMA10G00360.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G081012_T01 (Zea mays), 3'ss of exon 1
---------------------------------gtaagagtttttgttctgaatttttaacattttagtcta-----gtttttttctaatccta------ataatat--tcttttttg--gttcttgtagTGCAGCACATGATGTATGGCTTTGGAGATGATCCTAAT
                                  ||    || ||||||||    ||   ||||  | ||       | |  |    |||  ||      ||| |||  | ||| |||  ||||||| |||||| |||||||||||||||||||| |||||||| |||
gtaagggacgcttactcattactgggcaaatttttagcctttgttgttctgtcacttaggcattcaattcagttgctgctcatcctcaattttatgtgttatagtataatttttgttgacgttcttgcagTGCAACACATGATGTATGGCTTTGGGGATGATCCAAAT
















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|15662367|gb|BI699738.1|BI699738
EST:     ACCATCAGAAACTTCGTCTAAGCGCAAAAGAGGAGTTTTCCAAAAAGAAT                         TGCAGCACATGATGTATGGCTTTGGAGATGATCCTAAT
genomic: ACCATCAGAAACTTCGTCTAAGCGCAAAAGAGGAGTTTTCCAAAAAGAATgtaagagttt ... gttcttgtagTGCAGCACATGATGTATGGCTTTGGAGATGATCCTAAT
EST: gi|298181114|gb|HO022553.1|HO022553
EST:     ACCATCAGAAACTTCGTCTAAGCGCAAAAGAGGAGTTTTCCAAAAAGAAT                         TGCAGCACATGATGTATGGCTTTGGGGATGATCCTAAT
genomic: ACCATCAGAAACTTCGTCTAAGCGCAAAAGAGGAGTTTTCCAAAAAGAATgtaagagttt ... gttcttgtagTGCAGCACATGATGTATGGCTTTGGAGATGATCCTAAT
EST: gi|22928089|gb|BU545228.1|BU545228
EST:     ACCATCAGAAACTTNNNNNAAGCGCAAAAGAGGAGTTTTCCAAAAAGAAT                         TGCAGCACATGATGTATGGCTTTGGAGATGATCCTAAT
genomic: ACCATCAGAAACTTCGTCTAAGCGCAAAAGAGGAGTTTTCCAAAAAGAATgtaagagttt ... gttcttgtagTGCAGCACATGATGTATGGCTTTGGAGATGATCCTAAT
EST: gi|192296855|gb|FG990231.1|FG990231
EST:     ACCATCAGAAACTTCGTCTAAGCGCAAAAGAGGAGTTTTCCAAAAAGAAT                         TGCAGCACATGATGTATGGCTTTGGAGATGATCCTAAT
genomic: ACCATCAGAAACTTCGTCTAAGCGCAAAAGAGGAGTTTTCCAAAAAGAATgtaagagttt ... gttcttgtagTGCAGCACATGATGTATGGCTTTGGAGATGATCCTAAT
EST: gi|209723100|gb|BW662476.1|BW662476
EST:     ACCATCAGAAACTTCGTCTAAGCGCAAAAGAGGAGTTTTCCAAAAAGAAT                         TGCAGCACATGATGTATGGCTTTGGAGATGATCCTAAT
genomic: ACCATCAGAAACTTCGTCTAAGCGCAAAAGAGGAGTTTTCCAAAAAGAATgtaagagttt ... gttcttgtagTGCAGCACATGATGTATGGCTTTGGAGATGATCCTAAT
EST: gi|192314957|gb|FK010775.1|FK010775
EST:     ACCATCAGAAACTTCGTCTAAGCGCAAAAGAGGAGTTTTCCAAAAAGAAT                         TGCAGCACATGATGTATGGCTTTGGAGATGATCCTAAT
genomic: ACCATCAGAAACTTCGTCTAAGCGCAAAAGAGGAGTTTTCCAAAAAGAATgtaagagttt ... gttcttgtagTGCAGCACATGATGTATGGCTTTGGAGATGATCCTAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattttagtctagtttttttctaatcctaataatattcttttttggttcttgtagTGCAGCACATGATGTATGGCTTTGGAGATGATCCTAAT
                        tcctaat  putative branch site (score: 2)
                                   ttcttttttggttctt  putative PPT
          tagtttttttctaatc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagagtttttgttctgaatttttaacattttagtctagtttttttctaatcctaataatattcttttttggttcttgtagTGCAGCACATGATGTATGGCTTTGGAGATGATCCTAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG