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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgattgattcctattgatgccaatgaacacaaatgctagtaagtataaaatttactctattgtaagagtgtttaacaaattccctttctatgctttcagGTTCCCTTCTTCTCACAGATGGATGATCAGCTTCTGGATGCAATATGTGAGCGGCTGGTATCGTCTCTGAGCACTCAAGGCACCTACATTGTTCGTGAGG

Basic information

species Glycine max
transcript GLYMA04G24950.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G24950.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os02g54760.1 (Oryza sativa), 3'ss of exon 6
atgattgattcctattgatgccaatgaacacaaatgctagtaagtataaaatttactctattg-taagagtgtttaacaaattccctttctatgctttcagGTTCCCTTCTTCTCACAGATGGATGATCAGCTTCTGGATGCAATATGTGAGCGGCTGGTATCGTCTCTGAGCACTCAAGGCACCTACATTGTTCGTGAGG
 |  || |     ||  ||  |   |   |   |  |||  | || |    | ||||  |  | |  |    |||      | ||      |   ||||||||||| |||||||| ||||||||  |||| ||| |||| || || |||||||| || ||||| ||  || |||| || ||||| |||||||| |||||||
tttttttaaaaaaatgcatttcttgggcaatttacacta-caggtttgccttatacttgaccggtgtgctaattttgtctttacctaccacaatatttcagGTTCCTTTCTTCTCCCAGATGGACAATCAACTTTTGGACGCCATCTGTGAGCGTCTTGTATCATCGTTGTGCACACAGGGCACATACATTGTCCGTGAGG

upper sequence: GLYMA04G24950.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os06g08850.1 (Oryza sativa), 3'ss of exon 6
atgattgattcctattgatgccaatgaacacaaatgctagtaagtataaaatttactctattg--taagagtgtttaacaaattccctttctatgctt--tcagGTTCCCTTCTTCTCACAGATGGATGATCAGCTTCTGGATGCAATATGTGAGCGGCTGGTATCGTCTCTGAGCACTCAAGGCACCTACATTGTTCGTGAGG
 |  |  ||| | ||| |||   |  |   ||  || |||| ||      |  | || |||    ||    |  | | |||  |  | | |     |   | |||| || || ||||| |||||||||| ||| ||||||||||| || |||||||| || ||||| ||  |||||||    ||||| |||||||| ||||| |
-ttgtc-attgccattaatgt--agcatttcatttgatagtgagatctcgacattctatatcacttactgattctcaccaatctttcataccgcaatgcattagGTCCCTTTTTTCTCCCAGATGGATGGTCAACTTCTGGATGCCATCTGTGAGCGTCTTGTATCTTCCTTGAGCACAGTGGGCACATACATTGTCCGTGAAG

upper sequence: GLYMA04G24950.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G005791_T01 (Zea mays), 3'ss of exon 5
atgattgattcctattgatgccaatgaacacaaatgc-tagtaagtataaaatttactctatt----gtaagagtgtttaacaaattcc-ctttctat-gc----tttcagGTTCCCTTCTTCTCACAGATGGATGATCAGCTTCTGGATGCAATATGTGAGCGGCTGGTATCGTCTCTGAGCACTCAAGGCACCTACATTGTTCGTGAGG
         |||| |||   ||  |||| |  | ||| | |||| | | || |  ||  |  |      |  | ||  |   ||||  | |||| ||| ||    || |||||||| || ||||| |||||||||||||||||||| ||||| || |||||||| || ||||| || ||| ||||  ||||||| |||||||| |||||||
--------atcct-ttgccccc--tgaaaaagattgcatcgtaaatttgaactacacattgctttctacataattgcatggtaaatctcgctttgtatcgcaatgttgcagGTTCCTTTTTTCTCCCAGATGGATGATCAGCTTCTTGATGCCATCTGTGAGCGTCTTGTATCATCACTGTGCACAAAAGGCACATACATTGTCCGTGAGG

upper sequence: GLYMA04G24950.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G436583_T01 (Zea mays), 3'ss of exon 1
----------------------------------------------------------------------------------atgattgattcctattgatgccaatga-acacaaatgctagtaagtataa-aatttactctattgtaag-agtgtt--taacaaattccctttctatgc----tttcagGTTCCCTTCTTCTCACAGATGGATGATCAGCTTCTGGATGCAATATGTGAGCGGCTGGTATCGTCTCTGAGCACTCAAGGCACCTACATTGTTCGTGAGG
                                                                                   | ||  |||  |   |    || ||   | |   |    |  ||| | |  | | ||   |   | || ||||||  | ||  | ||  ||     ||     | ||||| ||  | ||||| |||||||| ||||||||||| || || ||||| ||||| |||||||||||  |||||||  | ||||| |||||||| || || |
gtaaatcagcttactacctttgctctctcgtttttttattggtcagcaacagagttagtaacttagtagtgctagttgaattcttatccatttgtgaggtgatcagtggcgcgcctctaacggctagtcttacgaataacctgaccatgagtagtgttacttacttaatcttttatatcgcaatgctgcagGTCCCACTTTTCTCCCAGATGGACGATCAGCTTCTAGACGCCATATGCGAGCGCCTGGTATCGTCCTTGAGCACAGAGGGCACATACATTGTCCGAGAAG

upper sequence: GLYMA04G24950.1 (Glycine max), 3'ss of exon 6
lower sequence: AT4G30360.1 (Arabidopsis thaliana), 3'ss of exon 5
atgattgattcctattgatgccaatgaacacaaatgctagtaagtataaaatttactctattgtaagagtgtttaacaaattccctttctatgcttt-cagGTTCCCTTCTTCTCACAGATGGATGATCAGCTTCTGGATGCAATATGTGAGCGGCTGGTATCGTCTCTGAGCACTCAAGGCACCTACATTGTTCGTGAGG
                        | |       |  |  |  || |   ||       || ||   | | ||     || | |  |  |      | ||||| || || ||||| || |||||||||||||| || ||||| ||||||||||| ||||| || |||||| | ||| |||| || ||| |||| ||||| |
-----------------------gtaagtttttctattgatttgttt---atcctacaaatggttcaacttttaggttaactactatcttgaatcatgcagGTCCCATTTTTCTCTCAAATGGATGATCAGCTGCTTGATGCGATATGTGAGCGCCTGGTTTCTTCTCTGTGTACTGAAGGGACTTACCTTGTACGTGAAG

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|7924955|gb|AW830981.1|AW830981
EST:     ATCTTCGCCGTGATATACAGCGGCATTTGTGCTTAGACCTTGTTAGAAGA                         GTTCCCTTCTTCTCACAGATGGATGATCAGCTTCTGGATGCAATATGTGAG
genomic: ATCTTCGCCGTGATATACAGCGGCATTTGTGCTTAGACCTTGTTAGAAGAgtatgatttc ... atgctttcagGTTCCCTTCTTCTCACAGATGGATGATCAGCTTCTGGATGCAATATGTGAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataaaatttactctattgtaagagtgtttaacaaattccctttctatgctttcagGTTCCCTTCTTCTCACAGATGGATGATCAGCTTCTGGATGCAATATGTGAGCGGCTGGTATCGTCTCTGAGCACTCAAGGCACCTACATTGTTCGTGAGG
                         gtttaac  putative branch site (score: 3)
                                   ttccctttctatgctt  putative PPT
                          tttaacaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgattgattcctattgatgccaatgaacacaaatgctagtaagtataaaatttactctattgtaagagtgtttaacaaattccctttctatgctttcagGTTCCCTTCTTCTCACAGATGGATGATCAGCTTCTGGATGCAATATGTGAGCGGCTGGTATCGTCTCTGAGCACTCAAGGCACCTACATTGTTCGTGAGG

- - -tgattcc
- - - - - - - -tgatgcc
- - - - - - - - - - - aatgaac
- - - - - - - - - - - - - - - caaatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gagtgtt