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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatatctaaggcgccttttctgcttctcttagatgggtgtgaataacattatgattttgggcgatcttagcttgaagtacatttccaattatcttgcagGTGGTCAGGTTGTTACCTTCAGCCAAGTTGTTCTTGAAGTTATGAGGCATCTTGAAGGAGCTTATGCCCTTATTTTCAAAAGTCTACATTATCCTAATGA

Basic information

species Glycine max
transcript GLYMA09G38460.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G38460.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os12g03720.2 (Oryza sativa), 3'ss of exon 3
ttatatctaaggcgccttttctgcttctcttagatgggtgtgaataacattatgattttgggcgatcttagcttgaagtacatttccaattatcttgcagGTGGTCAGGTTGTTACCTTCAGCCAAGTTGTTCTTGAAGTTATGAGGCATCTTGAAGGAGCTTATGCCCTTATTTTCAAAAGTCTACATTATCCTAATGA------
|  ||   ||  |              ||    |   |  |  |||   |  |  |  ||  | |  |    || | | |  |||  | |  | |  |||||| |      || || || |||||||||||| | ||||| |||||||| ||||||||||| || || ||||| || ||||| | ||| || || |||||      
tcttacaaaattcaaaaggaaaagaaatcggtaactagattctatatgttggtcttactgtactagttctagttaaggcaactttttattattttctcagGTGAT------GTGACATTTAGCCAAGTTGTTATGGAAGTCATGAGGCAGCTTGAAGGAGCCTACGCACTTATCTTTAAAAGCCCACACTACCCCAATGAATTGAT

upper sequence: GLYMA09G38460.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os11g03900.1 (Oryza sativa), 3'ss of exon 3
ttatatctaaggcgccttttctgcttctcttagatgggtgtgaataacattatgattttgggcgatcttagcttgaagtacatttccaattatcttg-cagGTGGTCAGGTTGTTACCTTCAGCCAAGTTGTTCTTGAAGTTATGAGGCATCTTGAAGGAGCTTATGCCCTTATTTTCAAAAGTCTACATTATCCTAATGA------
|  ||   ||  |              |     |   |  |  |||   |  |  |  ||  | |  |    || | | | | ||  |||||| ||  |||||| |      || || || |||||||||||| | ||||| |||||||| ||||||||||| || || || || || ||||| | ||| || || |||||      
tcttacaaaattcaaaaggaaaagaaattggtaactagattctatatgttggtcttactgttctagttctagttaaggca-acttttaattattttctcagGTGAT------GTGACATTTAGCCAAGTTGTTATGGAAGTCATGAGGCAGCTTGAAGGAGCCTACGCACTCATCTTTAAAAGCCCACACTACCCCAATGAATTGAT

upper sequence: GLYMA09G38460.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G005849_T02 (Zea mays), 3'ss of exon 3
ttatatctaaggcgccttttctgcttctcttagatgggtgtgaataacattatgattttgggcgatcttagcttgaagtacatttccaattatcttgcagGTGGTCAGGT--TGTTACCTTCAGCCAAGTTGTTCTTGAAGTTATGAGGCATCTTGAAGGAGCTTATGCCCTTATTTTCAAAAGTCTACATTATCCTAATGA------
      |  |   | | ||   || |  |  | ||   |     | ||   |    ||  | |     |   | | ||| | || |  ||||| || ||  |  ||||||  ||| || || |||||||||||| | ||||| |||||||| ||||||||||| || || ||||| || ||||| |  || ||||| |||||      
-----gcagaatagtcattatcgcattaca-aaataattcattctgactgaacccattatgacttctatttatggcagtcccttac--attatttttcacttcctcagGTGATGTGACGTTTAGCCAAGTTGTTATGGAAGTCATGAGGCAGCTTGAAGGAGCCTACGCACTTATCTTTAAAAGCCCGCACTATCCCAATGAATTGAT

upper sequence: GLYMA09G38460.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G24090.1 (Arabidopsis thaliana), 3'ss of exon 3
-ttatatctaaggcgccttttctgcttctcttagatgggtgtgaataacattatgattttgggcgatcttagcttgaagtacatttccaattatcttgcagGTGGTCAGGTTGTTACCTTCAGCCAAGTTGTTCTTGAAGTTATGAGGCATCTTGAAGGAGCTTATGCCCTTATTTTCAAAAGTCTACATTATCCTAATGA
 | ||   ||  | || |     | ||        ||| |||   | |  |  | | | ||  |  | | |    ||  |  |||||  ||    ||| |||||| ||   |||||| ||| |  |||||||  ||||||| |||||||||||||||||||||||||| ||||| || |||||    |||||||| |||||
gtaatgcttattgtgcatg---agatttgaagtagtggttgttt-tgatttagttagtatgctcattttcatggggatatctatttcttat-gctttgtagGTGGACAAACTGTTACATTCTGTGAAGTTGTGTTTGAAGTGATGAGGCATCTTGAAGGAGCTTATGCTCTTATATTTAAAAGCTGGCATTATCCGAATGA

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|298174041|gb|HO017377.1|HO017377
EST:     CATTCCCAAGCTTGCAAAGTTTGTTTATGACAAGGCGAATGAAGCAGCCG                         GTGGTCAGGTTGTTACCTTCAGCCAAGTTGTTCTTGAAGTTATGAGGCATC
genomic: CATTCCCAAGCTTGCAAAGTTTGTTTATGACAAGGCGAATGAAGCAGCCGgtaatttttt ... tatcttgcagGTGGTCAGGTTGTTACCTTCAGCCAAGTTGTTCTTGAAGTTATGAGGCATC
EST: gi|298173459|gb|HO016795.1|HO016795
EST:     CATTCCCAAGCTTGCAAAGTTTGTTTATGACAAGGCGAATGAAGCAGCCG                         GTGGTCAGGTTGTTACCTTCAGCCAAGTTGTTCTTGAAGTTATGAGG
genomic: CATTCCCAAGCTTGCAAAGTTTGTTTATGACAAGGCGAATGAAGCAGCCGgtaatttttt ... tatcttgcagGTGGTCAGGTTGTTACCTTCAGCCAAGTTGTTCTTGAAGTTATGAGG
EST: gi|208121058|gb|GD915267.1|GD915267
EST:     CATTCCCAAGCTTGCAAAGTTTGTTTATGACAAGGCGAATGAAGCAGCCG                         GTGGTCAGGTTGTTACCTTCAGCCAAGTTGTTCTTGAAGTTATGAGGCATC
genomic: CATTCCCAAGCTTGCAAAGTTTGTTTATGACAAGGCGAATGAAGCAGCCGgtaatttttt ... tatcttgcagGTGGTCAGGTTGTTACCTTCAGCCAAGTTGTTCTTGAAGTTATGAGGCATC
EST: gi|213620145|gb|DB965423.1|DB965423
EST:     CATTCCCAAGCTTGCAAAGTTTGTTTATGACAAGGCGAATGAAGCAGCCG                         GTGGTCAGGTTGTTACCTTCAGCCAAGTTGTTCTTGAAGTTATGAGGCATC
genomic: CATTCCCAAGCTTGCAAAGTTTGTTTATGACAAGGCGAATGAAGCAGCCGgtaatttttt ... tatcttgcagGTGGTCAGGTTGTTACCTTCAGCCAAGTTGTTCTTGAAGTTATGAGGCATC
EST: gi|209696470|gb|BW664019.1|BW664019
EST:     CATTCCCAAGCTTGCAAAGTTTGTTTATGACAAGGCGAATGAAGCAGCCG                         GTGGTCAGGTTGTTACCTTCAGCCAAGTTGTTCTTGAAGTTATGAGGCATC
genomic: CATTCCCAAGCTTGCAAAGTTTGTTTATGACAAGGCGAATGAAGCAGCCGgtaatttttt ... tatcttgcagGTGGTCAGGTTGTTACCTTCAGCCAAGTTGTTCTTGAAGTTATGAGGCATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacattatgattttgggcgatcttagcttgaagtacatttccaattatcttgcagGTGGTCAGGTTGTTACCTTCAGCCAAGTTGTTCTTGAAGTTATGAGGCATCTTGAAGGAGCTTATGCCCTTATTTTCAAAAGTCTACATTATCCTAATGA
 gaataac  putative branch site (score: 2)
                                            ttatctt  putative PPT
     tatgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatatctaaggcgccttttctgcttctcttagatgggtgtgaataacattatgattttgggcgatcttagcttgaagtacatttccaattatcttgcagGTGGTCAGGTTGTTACCTTCAGCCAAGTTGTTCTTGAAGTTATGAGGCATCTTGAAGGAGCTTATGCCCTTATTTTCAAAAGTCTACATTATCCTAATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - -gcctttt
- - - - - - - - - - ctgcttc
- - - - - - - - - - - - - - - - - -gggtgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcttgaa