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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtttgttgcatgttatgtagatttgtatgttcatagaaattgacgtgcttggttgaattaaatctaatgctgtgccaattattgctgctgttatacttagATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGAACTGAAATTGACCCTAGAACCCAAAGTTTTCTGACATGGGAAAGTTTGG

Basic information

species Glycine max
transcript GLYMA13G20790.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G20790.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g16900.3 (Oryza sativa), 3'ss of exon 3
gtttgttgcatgttatgtagatttgtatgttcatagaaattgacgtgcttggttgaattaaatctaatgctgtgccaattattgctgctgttatacttagATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGAACTGAAATTGACCCTAGAACCCAAAGTTTTCTGACATGGGAAAGTTTGG
    ||  || ||    |    |  |   |||  |  |  |  |  | |    || ||| | | ||     ||   || | || ||  || | |  | || ||||| | |  || |  || ||||||||||||||||| |||||||| || || ||| |||| || |||||  | ||||||||||| |||||||| ||||
----gtgccaagtgccttctgatcatgctttctgactatgtagctcgttcttatgtatttattatatcttagtttgaacttttccttttgctgt-ttcagGTATTCAATGTTGCAGGGGTACCAATAGAATGGGAAGAACACTATGTTGGTACAGAAGTTGATCCCAGAACAGAGAGTTTTCTGACTTGGGAAAGCTTGG

upper sequence: GLYMA13G20790.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g16900.1 (Oryza sativa), 3'ss of exon 2
-gtttgttgcatgttatgtagatttgtatgttcatagaaattgacgtgcttggttgaattaaatctaatgctgtgccaattattgctgctgttatacttagATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGAACTGAAATTGACCCTAGAACCCAAAGTTTTCTGACATGGGAAAGTTTGG
   | ||  || ||    |    |  |   |||  |  |  |  |  | |    || ||| | | ||     ||   || | || ||  || | |  | || ||||| | |  || |  || ||||||||||||||||| |||||||| || || ||| |||| || |||||  | ||||||||||| |||||||| ||||
aaatggtgccaagtgccttctgatcatgctttctgactatgtagctcgttcttatgtatttattatatcttagtttgaacttttccttttgctgt-ttcagGTATTCAATGTTGCAGGGGTACCAATAGAATGGGAAGAACACTATGTTGGTACAGAAGTTGATCCCAGAACAGAGAGTTTTCTGACTTGGGAAAGCTTGG

upper sequence: GLYMA13G20790.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G03290.1 (Arabidopsis thaliana), 3'ss of exon 1
------------------------------------gtttgttgcatgttatg--ta-gatttgtatgttc-atagaaattgacgtgcttggttgaattaaatctaatgctgtgccaattattgctgc-tgttatact----tagATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGAACTGAAATTGACCCTAGAACCCAAAGTTTTCTGACATGGGAAAGTTTGG
                                    |  |  || | || ||   || ||  |   ||||  || ||| ||     | |   |||    || ||      | ||   ||  ||  ||| | || ||||     || | ||   | |||||| ||| ||||| || |||||||| |||||||| || ||||| || || || ||||| || |||||  |||||||||||||| | |
gtccctcatcctaatctcttttctgcgcagaatttcgagttctggaagtcatagttacgagataattgtttgattgaattttgtacgataatttgtgggaattcggcaattttgttgatagtttttgcgttttgtactgatccagGTGTTTACAACAGCTGGTGTACCAATTGAGTGGGAAGAACACTATGTTGGGACTGAGATAGATCCGAGAACACAGAGTTTCTTGACATGGGAAAGTCTCG

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|213607679|gb|DB958698.1|DB958698
EST:     TCTTCCCCGGCGACGGCATCGGCCCCGAGATCGCCGAATCCGTCAAACAG                         ATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGA
genomic: TCTTCCCCGGCGACGGCATCGGCCCCGAGATCGCCGAATCCGTCAAACAGgttccttctt ... ttatacttagATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGA
EST: gi|254321136|gb|GR827585.1|GR827585
EST:     TCTTCCCCGGCGACGGCATCGGCCCCGAGATCGCCGAATCCGTCAAACAG                         ATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGA
genomic: TCTTCCCCGGCGACGGCATCGGCCCCGAGATCGCCGAATCCGTCAAACAGgttccttctt ... ttatacttagATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGA
EST: gi|24135690|gb|BU926200.1|BU926200
EST:     TCTTCCCCGGCGACGGCATCGGCCCCGAGATCGCCGAATCCGTCAAACAG                         ATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGA
genomic: TCTTCCCCGGCGACGGCATCGGCCCCGAGATCGCCGAATCCGTCAAACAGgttccttctt ... ttatacttagATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGA
EST: gi|19348449|gb|BM892981.1|BM892981
EST:     TCTTCCCCGGCGACGGCATCGGCCCCGAGATCGCCGAATCCGTCAAACAG                         ATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGA
genomic: TCTTCCCCGGCGACGGCATCGGCCCCGAGATCGCCGAATCCGTCAAACAGgttccttctt ... ttatacttagATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGA
EST: gi|209702312|gb|BW667500.1|BW667500
EST:     TCTTCCCCGGCGACGGCATCGGCCCCGAGATCGCCGAATCCGTCAAACAG                         ATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGA
genomic: TCTTCCCCGGCGACGGCATCGGCCCCGAGATCGCCGAATCCGTCAAACAGgttccttctt ... ttatacttagATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGA
EST: gi|298197822|gb|HO039361.1|HO039361
EST:     TCTTCCCCGGCGACGGCATCGGCCCCGAGATCGCCGAATCCGTCAAACAG                         ATATTCCAAGCAGCTGATGCCCCAATAGAATGGGAAGAGCACTGTGTAGGA
genomic: TCTTCCCCGGCGACGGCATCGGCCCCGAGATCGCCGAATCCGTCAAACAGgttccttctt ... ttatacttagATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcttggttgaattaaatctaatgctgtgccaattattgctgctgttatacttagATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGAACTGAAATTGACCCTAGAACCCAAAGTTTTCTGACATGGGAAAGTTTGG
                atctaat  putative branch site (score: 3)
       ttgaattaaatctaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgttgcatgttatgtagatttgtatgttcatagaaattgacgtgcttggttgaattaaatctaatgctgtgccaattattgctgctgttatacttagATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGAACTGAAATTGACCCTAGAACCCAAAGTTTTCTGACATGGGAAAGTTTGG

- - - -gcatgtt
- - - - - - - - - - - -tgtatgt
- - - - - - - - - - - - - - - - - - - - - - -tgcttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgctgc