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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgaatattcgagagatttttctttacatataggcttgattaggggatcttaccctctaaaattcttgaacacttgcagGATGGACGTATCAGCTACGATGAATTTGTTGCTATGATGAAAACTGGAACAGATTGGAGAAAAGCATCAAGGCATTACTCACGTGGAAGATTCAATAGCT

Basic information

species Glycine max
transcript GLYMA07G18310.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G18310.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g61590.1 (Oryza sativa), 3'ss of exon 6
gtgtgaatattcgagagatttttctttacat--ataggcttgattaggggatcttaccctctaaa--------attcttgaacacttgcagGATGGACGTATCAGCTACGATGAATTTGTTGCTATGATGAAAACTGGAACAGATTGGAGAAAAGCATCAAGGCATTACTCACGTGGAAGATTCAATAGCT
|||   |||||   ||       | ||   |   ||   | | | |     | ||    ||||||         || |        ||||||||||    || ||||| || |||||||| || |||||||| || || |||||||||||||| || ||  ||||||||||  | ||||||||||| ||| 
gtgatgatatttctgaatacaaccattcttttggtaatatcgttcaaaacttttttttatctaaataacatatgttttcttttcactgcagGATGGCAAGATTAGCTATGACGAATTTGTAGCAATGATGAAGACGGGCACAGATTGGAGAAAGGCGTCCCGGCATTACTCTAGAGGAAGATTCAACAGCC

upper sequence: GLYMA07G18310.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os05g39090.1 (Oryza sativa), 3'ss of exon 6
gtgtgaatattcgagagatttttctttacatataggctt--gattaggggatcttaccctctaaaattcttgaacacttg--cagGATGGACGTATCAGCTACGATGAATTTGTTGCTATGATGAAAACTGGAACAGATTGGAGAAAAGCATCAAGGCATTACTCACGTGGAAGATTCAATAGCT
|||   ||   | |  | |  |       |||||  ||   |||     |   ||||     |||  | | || |  ||   ||||||||    || ||||| || ||||| || || |||||||| ||||| |||||||||||||| || ||| ||||||| ||| | ||| | ||||| ||| 
gtgatgattcactaatgctggtagcaatgatataacctccagatcttatgcctttacttaacaaacatttcgatcgtttattcagGATGGCAAAATTAGCTATGAAGAATTCGTAGCAATGATGAAGACTGGCACAGATTGGAGAAAGGCGTCACGGCATTATTCAAGAGGACGTTTCAACAGCC

upper sequence: GLYMA07G18310.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G030673_T01 (Zea mays), 3'ss of exon 6
----------gtgtgaatattcgagagatttttct-ttacatataggcttgattaggggatcttaccctctaaaattcttga-acacttgcagGATGGACGTATCAGCTACGATGAATTTGTTGCTATGATGAAAACTGGAACAGATTGGAGAAAAGCATCAAGGCATTACTCACGTGGAAGATTCAATAGCT
               ||    |  |||||   |||  | | |  |    | ||||     |   |  | | | ||   |||       ||||||||||    || |||||||| |||||||| || |||||||| ||||||||||||||||| || || ||  ||||||| ||| | ||  | ||||||||| 
gttaacggttcacctaaggcccctgagatagctctgctgccttcaaatctcattaattatttcaagtcgcaataacctttgttgtttctgcagGATGGTAAAATTAGCTACGAAGAATTTGTAGCGATGATGAAGACTGGAACAGATTGGAGGAAGGCGTCGCGGCATTATTCAAGAGGGCGCTTCAATAGCC

upper sequence: GLYMA07G18310.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G51850.1 (Arabidopsis thaliana), 3'ss of exon 6
-----------------------gtgtgaatattcgagagatttttctttacatataggcttgattaggggatcttaccctctaaaattcttgaacacttgcagGATGGACGTATCAGCTACGATGAATTTGTTGCTATGATGAAAACTGGAACAGATTGGAGAAAAGCATCAAGGCATTACTCACGTGGAAGATTCAATAGCT
                            |  |    ||||| | |  ||    || |    |   |   || |  | ||    |    | ||  ||| |   |||||||  | || |||||||| || ||||  || ||||||||||| ||||| ||||||||||| || ||  | ||||||||| | || |||||||||||| 
agagagttcacttctcatatcgttaaacagaaccttagagactatagttagtgtaaaaatgtttcttctgg-ttgtgcctgacatggatttttgacatt---agGATGGGAGAATAAGCTACGAAGAGTTTGCGGCAATGATGAAAACAGGAACGGATTGGAGAAAGGCGTCTCGTCATTACTCAAGAGGGAGATTCAATAGCC

upper sequence: GLYMA07G18310.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv08s0105g00390.t01 (Vitis vinifera), 3'ss of exon 6
gtgtgaatattcgagagatttttctttacatataggcttgattaggggatcttacc---ctctaaaattcttgaacacttgcagGATGGACGTATCAGCTACGATGAATTTGTTGCTATGATGAAAACTGGAACAGATTGGAGAAAAGCATCAAGGCATTACTCACGTGGAAGATTCAATAGCT
  || || || | ||   |||  | | |  |  |   |     ||  |||  ||     || ||   || |   ||| | |||||||||    || || || ||||||||||  |||||||||||||||||||||||||||||||| || || |||||||| ||| | || |||||||| ||  
--gtaaagatcc-agtagtttgccatcaactcgattttcatccagcagattataaatgactttatttttgtcttacaat-gcagGATGGGAAAATTAGTTATGATGAATTTGCGGCTATGATGAAAACTGGAACAGATTGGAGAAAGGCTTCTAGGCATTATTCAAGAGGGAGATTCAACAGTC

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|254318198|gb|GR832366.1|GR832366
EST:     ACTGTACAGATGTAGCGAATGACATTTTCCTAGAAGTAGACACGGACAAG                         GATGGACGTATCAGCTACGATGAATTTGTTGCTATGATGAAAACTGGAACA
genomic: ACTGTACAGATGTAGCGAATGACATTTTCCTAGAAGTAGACACGGACAAGgtgtgaatat ... acacttgcagGATGGACGTATCAGCTACGATGAATTTGTTGCTATGATGAAAACTGGAACA
EST: gi|7284239|gb|AW596835.1|AW596835
EST:     ACTGTACAGATGTAGCGAATGACATTTTCCTAGAAGTAGACACGGACAAG                         GATGGACGTATCATCTACGAT
genomic: ACTGTACAGATGTAGCGAATGACATTTTCCTAGAAGTAGACACGGACAAGgtgtgaatat ... acacttgcagGATGGACGTATCAGCTACGAT
EST: gi|6912801|gb|AW394285.1|AW394285
EST:     ACTGTACAGATGTAGCGAATGACATTTTCCTAGAAGTAGACACGGACAAG                         GATGGACGTATCAGCTACGATGAATTTGTTGCTATGATGAAAACTGGAACA
genomic: ACTGTACAGATGTAGCGAATGACATTTTCCTAGAAGTAGACACGGACAAGgtgtgaatat ... acacttgcagGATGGACGTATCAGCTACGATGAATTTGTTGCTATGATGAAAACTGGAACA
EST: gi|51344853|gb|CO985586.1|CO985586
EST:     ACTGTACAGATGTAGCGAATGACATTTTCCTAGAAGTAGACACGGACAAG                         GATGGACGTATCAGCTACGATGAATTTGTTGCTATGATGAAAACTGGAACA
genomic: ACTGTACAGATGTAGCGAATGACATTTTCCTAGAAGTAGACACGGACAAGgtgtgaatat ... acacttgcagGATGGACGTATCAGCTACGATGAATTTGTTGCTATGATGAAAACTGGAACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacatataggcttgattaggggatcttaccctctaaaattcttgaacacttgcagGATGGACGTATCAGCTACGATGAATTTGTTGCTATGATGAAAACTGGAACAGATTGGAGAAAAGCATCAAGGCATTACTCACGTGGAAGATTCAATAGCT
                              ctctaaa  putative branch site (score: 3)
                                 taaaattctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgaatattcgagagatttttctttacatataggcttgattaggggatcttaccctctaaaattcttgaacacttgcagGATGGACGTATCAGCTACGATGAATTTGTTGCTATGATGAAAACTGGAACAGATTGGAGAAAAGCATCAAGGCATTACTCACGTGGAAGATTCAATAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA