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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgaaacaaatttgcgtactttgttgattgtatgcttttctagtgtaacttgtaaacctatgactggatttcttataattgtttgatgtgctttgagtggagggactaacattgcagctttatgacaaggttattccagACCAATATGTTAGCTGCTGGGCTTGCTGCTTCCAACCTAATTCTGTATGCATTTGTATATACACCCTTGAAGCAGATTCATCCCATAAATACATGGGTGG

Basic information

species Glycine max
transcript GLYMA20G38710.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G38710.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g34390.1 (Oryza sativa), 3'ss of exon 3
gtattgaaacaaatttgcgtactttgttgattgtatgcttttctagtgtaacttgtaaacctatgactggatttcttataattgtttgatgtgctttgagtggagggact-aacattgcagctttatgacaaggttattccagACCAATATGTTAGCTGCTGGGCTTGCTGCTTCCAACCTAATTCTGTATGCATTTGTATATACACCCTTGAAGCAGATTCATCCCATAAATACATGGGTGG
             || |   |   | ||   | | |   |    | ||| |  |||     ||  | ||  |||| | | | |  ||| | |  |     |       || ||||  | |   || || |||||||  | ||| | |||   || || |||||||| || ||||| || || |||||||||||||||||||| ||||| |||||||| || || ||  ||||||||||||| |
------------gttcgtacaagatcttctctatttatctgcaca-tgttatgtgttgtttta--aatgtgtttcgtttcagtagttggtatagtactgttattacatctgaacaccgtaaaattttggcaaggtttctgcagGCTAATGGCTTGGCGGCTGGGCTCGCAGCTTCTAATCTTATTCTGTATGCATTTGTATACACACCATTGAAGCAAATACACCCTGTAAATACATGGGTTG

upper sequence: GLYMA20G38710.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G162776_T02 (Zea mays), 3'ss of exon 3
gtattgaaacaaatttgcgtactttgttgatt--gtatgcttttctagtgtaacttgtaaacctatgactggatttcttataattgtttgatgtgctttgagtgga----gggactaacattgcagctttatgacaaggttattccagACCAATATGTTAGCTGCTGGGCTTGCTGCTTCCAACCTAATTCTGTATGCATTTGTATATACACCCTTGAAGCAGATTCATCCCATAAATACATGGGTGG
              |||| | || | |  |||   ||||  ||| || | || |||     | | |||    ||||  || || |||    |        ||| ||    || |||||   ||||      || |||||||  | ||| | |||   || || ||||||||||| ||||| |||||  ||||||| |||||||| ||||| || |||||||| || || ||  | ||||||||||| |
----------gttcttgctttctctttgcattcaatatgtatttatattctacctt-----cttttga---aatttacta-aactgtgaagtagatagaaagttgacactggaactaaacatgcaaaaaattggcaaggtttgtgcagGCTAATGGCTTGGCAGCTGGGCTTGCAGCTTCTAACCTTGTTCTGTACGCATTTGTTTATACGCCGTTGAAGCAAATACACCCTGTTAATACATGGGTTG

upper sequence: GLYMA20G38710.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G178859_T01 (Zea mays), 3'ss of exon 3
gtattgaaacaaatttgcgtactttgttgattgtatgcttttctag-tgtaacttgtaaacctatgactggatttcttataattgtttgatgtgctttgagtgga----gggactaacattgcagctttatgacaaggttattccagACCAATATGTTAGCTGCTGGGCTTGCTGCTTCCAACCTAATTCTGTATGCATTTGTATATACACCCTTGAAGCAGATTCATCCCATAAATACATGGGTGG
                  || ||| | |   | | ||| | | ||| || |  || ||  | |     || | ||     |  |||  | |   |    ||  ||    || |||||   ||||      || |||||||  | ||| | |||   || || ||||||||||| ||||| || ||  |||||||||||||||| ||||| || |||||||| || || ||  | ||||||||||| |
------------------gttctt-gctttctctttgcatctatagatgcatattcta--ctttcttttgaaatttactaagctgtgaggtagtcagaaagctgacactggaactaaacatgcaaaaaattggcaaggtttgtgcagGCTAATGGCTTGGCAGCTGGGCTTGCAGCTTCTAATCTTGTTCTGTATGCATTTGTGTATACGCCGTTGAAGCAAATACACCCTGTTAATACATGGGTTG

upper sequence: GLYMA20G38710.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G162776_T03 (Zea mays), 3'ss of exon 3
gtattgaaacaaatttgcgtactttgttgatt--gtatgcttttctagtgtaacttgtaaacctatgactggatttcttataattgtttgatgtgctttgagtgga----gggactaacattgcagctttatgacaaggttattccagACCAATATGTTAGCTGCTGGGCTTGCTGCTTCCAACCTAATTCTGTATGCATTTGTATATACACCCTTGAAGCAGATTCATCCCATAAATACATGGGTGG
              |||| | || | |  |||   ||||  ||| || | || |||     | | |||    ||||  || || |||    |        ||| ||    || |||||   ||||      || |||||||  | ||| | |||   || || ||||||||||| ||||| |||||  ||||||| |||||||| ||||| || |||||||| || || ||  | |||          
----------gttcttgctttctctttgcattcaatatgtatttatattctacctt-----cttttga---aatttacta-aactgtgaagtagatagaaagttgacactggaactaaacatgcaaaaaattggcaagGTTTGTGCAGGCTAATGGCTTGGCAGCTGGGCTTGCAGCTTCTAACCTTGTTCTGTACGCATTTGTTTATACGCCGTTGAAGCAAATACACCCTGTTAAT----------

upper sequence: GLYMA20G38710.1 (Glycine max), 3'ss of exon 3
lower sequence: AT2G44520.1 (Arabidopsis thaliana), 3'ss of exon 3
gtattgaaacaaatttgcgtactttgttgattgtatgcttttcta-gtgtaacttgtaaacctatgactggatttcttataattgtttgatgtgctttgagtggagggactaacattgcagctttatgacaaggttattccagACCAATATGTTAGCTGCTGGGCTTGCTGCTTCCAACCTAATTCTGTATGCATTTGTATATACACCCTTGAAGCAGATTCATCCCATAAATACATGGGTGG
                           ||| ||| || |||| ||  ||| | || |           ||  ||    ||   || ||||     | ||  |       ||||  ||     |  | |||||||||||| ||||| |||||||| |||||||| |||||  || |||| ||  | || ||||| ||||| ||||| || ||||||||  |||| || || ||||||||||| |
--------------------------gtgaatgtttgtttttttatatgtgatttct----------ttgttttatgaatgggtgattgagagattatggat-------ctaaacttttgcttccacgacaaggttattgcagACTAATATGTTGGCTGCTGGACTTGCATCTGCCAATCTTGTACTTTATGCGTTTGTTTATACTCCGTTGAAGCAACTTCACCCTATCAATACATGGGTTG

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|5820336|gb|AI988542.1|AI988542
EST:     GCTGGGCATCCTCTGTTGGATTAGCTGGTACGGCTCTACTAGCTACGCAG                         ACCAATATGTTAGCTGCTGGGCTTGCTGCTTCCAACCTAATTCTGTATGCA
genomic: GCTGGGCATCCTCTGTTGGATTAGCTGGTACGGCTCTACTAGCTACGCAGgtattgaaac ... gttattccagACCAATATGTTAGCTGCTGGGCTTGCTGCTTCCAACCTAATTCTGTATGCA
EST: gi|13252104|gb|BG363007.1|BG363007
EST:     GCTGGGCATCCTCTGTTGGATTAGCTGGTACGGCTCTACTAGCTACGCAG                         ACCAATATGTTAGCTGCTGGGCTTGCTGCTTCCAACCTAATTCTGTATGCA
genomic: GCTGGGCATCCTCTGTTGGATTAGCTGGTACGGCTCTACTAGCTACGCAGgtattgaaac ... gttattccagACCAATATGTTAGCTGCTGGGCTTGCTGCTTCCAACCTAATTCTGTATGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgtgctttgagtggagggactaacattgcagctttatgacaaggttattccagACCAATATGTTAGCTGCTGGGCTTGCTGCTTCCAACCTAATTCTGTATGCATTTGTATATACACCCTTGAAGCAGATTCATCCCATAAATACATGGGTGG
                   gactaac  putative branch site (score: 1)
                                              ttattcc  putative PPT
                      taacatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattgaaacaaatttgcgtactttgttgattgtatgcttttctagtgtaacttgtaaacctatgactggatttcttataattgtttgatgtgctttgagtggagggactaacattgcagctttatgacaaggttattccagACCAATATGTTAGCTGCTGGGCTTGCTGCTTCCAACCTAATTCTGTATGCATTTGTATATACACCCTTGAAGCAGATTCATCCCATAAATACATGGGTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT