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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgattattgagaagaaatagttgttgaaagaattttattatttttaatatctttgacttcaagtgatttaataaattcagtgatgatcagGAAGAAGGTGGTGAAGGTGCGCGAAACCGGCCAGCATGGGACAAGTGGTCAAATGATGGCACAGAAAGACAGGTAGCTAAGCTTATGGAAGAAAACGTTG

Basic information

species Glycine max
transcript GLYMA19G34360.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G34360.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g58330.1 (Oryza sativa), 3'ss of exon 6
---gtgattattgagaagaaatagttgttgaaagaattttattatttttaatatctt-tgacttcaagtgatttaataa------attcagtgatgatcagGAAGAAGGTGGTGAAGGTGCGCGAAACCGGCCAGCATGGGACAAGTGGTCAAATGATGGCACAGAAAGACAGGTAGCTAAGCTTATGGAAGAAAACGTTG
        |      ||| |||   | |||| ||   |||    | | |  | | |  |  |||   ||  || ||           |   |  |  | |||  ||||   | ||  ||| | | ||||  |     ||||| ||||||||||  ||||||||||||||||||||||| ||||| ||||||||| || | |
atcacaccttcactcaaggaatcaat-ttgagagtccttttccgtctctgctctttcatatcttttggttgttaaactgtatcttgctttattttcgttagGGGGAAGCAAGCGATAGTGGGGGCAACCAACAGATTTGGGAAAAGTGGTCAACGGATGGCACAGAAAGACAGGTAGCGAAGCTGATGGAAGAAGACATCG

upper sequence: GLYMA19G34360.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os07g08440.1 (Oryza sativa), 3'ss of exon 5
----gtgattattgagaagaaatagttgttgaaagaattttattatttt------taatatctttga-cttcaagtgatttaataaattcagtgatgatcagGAAGAAGGTGGTGAAGGTGCGCGAAACCGGCCAGCATGGGACAAGTGGTCAAATGATGGCACAGAAAGACAGGTAGCTAAGCTTATGGAAGAAAACGTTG
     || ||  |     |  | | |||||   |     || |   |         |||||| |||| ||| ||   |  |  |   || | ||   || |||  || |   ||||  ||| | | || |  |     ||||| ||||||||||  |||||||||||||  |||||||| ||||| ||||||||| || | |
aatcatgttttgtcttgtgccacatttgtttgcatgcccttgtccgtcagtcacacaatatcgttgatctttaaactaaatcttgc-ttgaatggc-attagGGGGAGGCAAGTGACAGTGGGAGCAAACAACAGATTTGGGAAAAGTGGTCAACCGATGGCACAGAAAAGCAGGTAGCGAAGCTGATGGAAGAAGACATCG

upper sequence: GLYMA19G34360.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G004356_T01 (Zea mays), 3'ss of exon 6
----gtgattattgagaagaaatagttgttgaaagaattttattattttta-atatctttgacttcaagtgatttaa--taaat-----tcagtgatgatcagGAAGAAGGTGGTGAAGGTGCGCGAAACCGGCCAGCATGGGACAAGTGGTCAAATGATGGCACAGAAAGACAGGTAGCTAAGCTTATGGAAGAAAACGTTG
    ||  | | |  ||| ||| | ||  |||  |   |||   ||    | || ||  |  ||    ||  || ||  |  ||     |  |   |  | |||  ||||   ||||  ||| | | || | ||     ||||| ||||||||||  || ||||||||||||||||| || ||||| ||||||||| || |||
ccttgttgtgactt-gaaaaaacaatt--tgactgtccttttccatcccgatatttccgtatctattggtcgttaaaattggatcttcctttggtttcgttagGGGGAAGCAAGTGATAGTGGGAGCAAACAGCAGATTTGGGAGAAGTGGTCAACGGACGGCACAGAAAGACAGGTCGCAAAGCTGATGGAAGAAGACATTG

upper sequence: GLYMA19G34360.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G03040.2 (Arabidopsis thaliana), 3'ss of exon 5
gtgattattgagaagaaatagtt-gttgaaagaattttattatttttaatatctttgacttcaagtgatttaataaattcagtgatgatcagGAAGAAGGTGGTGAAGGTGCGCGAAACCGGCCAGCATGGGACAAGTGGTCAAATGATGGCACAGAAAGACAGGTAGCTAAGCTTATGGAAGAAAACGTTG------------------
|| |  | |    ||| ||| ||  || ||| ||    |  | |||    ||  ||            |||  |  | | | |  || |  | || ||  |  |  |||   | ||  | |||| |  ||||| || |||||||| ||||| ||||| || || || |||||||| ||||||||||||||||                  
gttag-actagagagagatacttcattaaaaaaagaacagaactttggtaatggtt------------tttcttgcactgacttgtggt--gtaaaaactttcttcagG-ATGAGACGCAGGCC-GTGTGGGAGAAATGGTCAAACGATGGGACAGAGAGGCAAGTGGCTAAGCTGATGGAAGAAAACGTTGGAGCAGCGATGCAACTTT

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|254317152|gb|GR826097.1|GR826097
EST:     CCGGTGCAGTGGCACCACTGGTAACTGACATCCCATTATCATCAGTCGAG                         GAAGAAGGTGGTGAAAGGTGCGCGAAACCGGCCAGCATGGGACAAGTGGTC
genomic: CCGGTGCAGTGGCACCACTGGTAACTGACATCCCATTATCATCAGTCGAGgtgattattg ... tgatgatcagGAAGAAGGTGGTGAA-GGTGCGCGAAACCGGCCAGCATGGGACAAGTGGTC
EST: gi|19453220|gb|BM954630.1|BM954630
EST:     CCGGTGCAGTGGCACCACTGGTAACTGACATCCCATTATCATCAGTCGAG                         GAAGAAGGTGGTGAAGGTGCGCGAAACCGGCCAGCATGGGACAAGTGGTCA
genomic: CCGGTGCAGTGGCACCACTGGTAACTGACATCCCATTATCATCAGTCGAGgtgattattg ... tgatgatcagGAAGAAGGTGGTGAAGGTGCGCGAAACCGGCCAGCATGGGACAAGTGGTCA
EST: gi|21677257|gb|BQ629608.1|BQ629608
EST:     CCGGTGCAGTGGCACCACTGGTAACTGACATCCCATTATCATCAGTCGAG                         GAAGAAGGTGGTGAAGGTGCGCGAAACCGGCCAGCATGGGACAAGTGGTCA
genomic: CCGGTGCAGTGGCACCACTGGTAACTGACATCCCATTATCATCAGTCGAGgtgattattg ... tgatgatcagGAAGAAGGTGGTGAAGGTGCGCGAAACCGGCCAGCATGGGACAAGTGGTCA
EST: gi|21888332|gb|BQ741545.1|BQ741545
EST:     CCGGTGCAGTGGCACCACTGGTAACTGACATCCCATTATCATCAGTCGAG                         GAAGAAGGTGGTGAAGGTGCGCGAAACCGGCCAGCATGGGACAAGTGGTCA
genomic: CCGGTGCAGTGGCACCACTGGTAACTGACATCCCATTATCATCAGTCGAGgtgattattg ... tgatgatcagGAAGAAGGTGGTGAAGGTGCGCGAAACCGGCCAGCATGGGACAAGTGGTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattatttttaatatctttgacttcaagtgatttaataaattcagtgatgatcagGAAGAAGGTGGTGAAGGTGCGCGAAACCGGCCAGCATGGGACAAGTGGTCAAATGATGGCACAGAAAGACAGGTAGCTAAGCTTATGGAAGAAAACGTTG
                         aagtgatttaataaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgattattgagaagaaatagttgttgaaagaattttattatttttaatatctttgacttcaagtgatttaataaattcagtgatgatcagGAAGAAGGTGGTGAAGGTGCGCGAAACCGGCCAGCATGGGACAAGTGGTCAAATGATGGCACAGAAAGACAGGTAGCTAAGCTTATGGAAGAAAACGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA