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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaattataattgattttatttcatgtcacgcttttcctgttttggattgttcttacttagatattggtttgtttgcagCTCTGTGGATTTGGTTGTTAGTTGCTTGGGACTACACTGGACTAATGATCTGCCTGGAGCAATGATACAG

Basic information

species Glycine max
transcript GLYMA12G37130.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G37130.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os12g10200.1 (Oryza sativa), 3'ss of exon 2
---------gcaatta--taattgattttatttcatg--tcacgcttttcctgttt-tggattgttcttact----tagatattggtttg---tttgcagCTCTGTGGATTTGGTTGTTAGTTGCTTGGGACTACACTGGACTAATGATCTGCCTGGAGCAATGATACAG
          ||||||  || || |  | |    |||  || || | ||||| | |    |||| || |       |  || | | | ||   | || |||||   ||||  | |  | |||||  | || || || ||||| |||||||| ||||||||||||||||||
gcagttctcacaattatttagtttaagtcaaacaatgtttcccgatcttcctatctgcatattgctcatgtcattattaatgtggttatggtctctgaagCTCGCAGGATACGATAATAAGTTGTCTTGGGCTTCATTGGACAAATGATCTACCTGGAGCAATGATACAG

upper sequence: GLYMA12G37130.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G087692_T01 (Zea mays), 3'ss of exon 2
-------gcaattataat----tgattttatttcatgtcacgcttttcctgttttggattgttcttacttagatattggtt-tg---tttgcagCTCTGTGGATTTGGTTGTTAGTTGCTTGGGACTACACTGGACTAATGATCTGCCTGGAGCAATGATACAG
        || || |  |      |   || |    | ||| |    |   | ||| |   ||    | |  || | | |  ||   | || |||||   ||||||| |  | || ||  | ||||| || ||||| |||||||| ||||||||||||||||||
gagtgagtcagttgtcgtgtcacaagcataatcatagacacacaga-cagatcttgcaacatttactcattaatgtggttcatgggttctgaagctcacagGATTTGATAATGAGCTGTCTTGGACTTCATTGGACAAATGATCTACCTGGAGCAATGATACAG

upper sequence: GLYMA12G37130.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G087692_T02 (Zea mays), 3'ss of exon 2
gcaattataattgattttatt-tcatgtcacgcttttcctgttt------tggattgttcttac-----ttagatattggtttg----------tttgcagCTCTGTGGATTTGGTTGTTAGTTGCTTGGGACTACACTGGACTAATGATCTGCCTGGAGCAATGATACAG
 ||  ||| | ||| |   || || ||||||     |  |  |         ||  | |||| |     |||   |||  | ||          | || |||||   ||||||| |  | || ||  | ||||| || ||||| |||||||| ||||||||||||||||||
-catgtatgagtgagtcagttgtcgtgtcacaagcataatcatagacacacagacagatcttgcaacatttactcattaatgtggttcatgggttctgaagCTCACAGGATTTGATAATGAGCTGTCTTGGACTTCATTGGACAAATGATCTACCTGGAGCAATGATACAG

upper sequence: GLYMA12G37130.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0001g06830.t01 (Vitis vinifera), 3'ss of exon 4
--------------gcaattataattgattttatttcatgtcacgctt---ttcctgttttggattgttcttacttag---atattggtttgtt-tgcagCTCTGTGGATTTGGTTGTTAGTTGCTTGGGACTACACTGGACTAATGATCTGCCTGGAGCAATGATACAG
                 || |  ||  || |   ||||||| |    |   ||  ||||||   | |  ||    | |    |||| ||   ||    || ||| | ||| ||||  | || ||||||||||| || ||||| |||||||| |||||||| |||||||||
tgctcttcaatgccttcatcagtatgtatgtagattcatgtaaaaaatatgttgatgtttttattggcactctaatggcttgtatttgtaaattgcaaagTTCTCTAGATCTGGTAATCAGCTGCTTGGGACTCCATTGGACGAATGATCTTCCTGGAGCCATGATACAG

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|6846254|gb|AW348544.1|AW348544
EST:     GAGACCCACTTTCTTGTTGCTGNNNAAGAGTTTCTTCCTATCAAAGAAAG                         NNCTGTGGATTTGGTTGTTAGTTGCTTGGGACTACACTGGACTAATGATCT
genomic: GAGACCCACTTTCTTGTTGCTGACGAAGAGTTTCTTCCTATCAAAGAAAGgcaattataa ... ttgtttgcagCTCTGTGGATTTGGTTGTTAGTTGCTTGGGACTACACTGGACTAATGATCT
EST: gi|14012032|gb|BG726963.1|BG726963
EST:     GAGACCCACTTTCTTGTTGCTGACGAAGAGTTTCTTCCTATCAAAGAAAG                         CTCTGTGGATTTGGTTGTTAGTTGCTTGGGACTACACTGGACTAATGATCT
genomic: GAGACCCACTTTCTTGTTGCTGACGAAGAGTTTCTTCCTATCAAAGAAAGgcaattataa ... ttgtttgcagCTCTGTGGATTTGGTTGTTAGTTGCTTGGGACTACACTGGACTAATGATCT
EST: gi|192297062|gb|FG990333.1|FG990333
EST:     GAGACCCACTTTCTTGTTGCTGACGAAGAGTTTCTTCCTATCAAAGAAAG                         CTCTGTGGATTTGGTTGTTAGTTGCTTGGGACTACACTGGACTAATGATCT
genomic: GAGACCCACTTTCTTGTTGCTGACGAAGAGTTTCTTCCTATCAAAGAAAGgcaattataa ... ttgtttgcagCTCTGTGGATTTGGTTGTTAGTTGCTTGGGACTACACTGGACTAATGATCT
EST: gi|15200173|gb|BI424211.1|BI424211
EST:     GAGACCCACTTTCTTGTTGCTGACGAAGAGTTTCTTCCTATCAAAGAAAG                         CTCTGTGGATTTGGTTGTTAGTTGCTTGGGACTACACTGGACTAATGATCT
genomic: GAGACCCACTTTCTTGTTGCTGACGAAGAGTTTCTTCCTATCAAAGAAAGgcaattataa ... ttgtttgcagCTCTGTGGATTTGGTTGTTAGTTGCTTGGGACTACACTGGACTAATGATCT
EST: gi|51335049|gb|CO978915.1|CO978915
EST:     GAGACCCACTTTCTTGTTGCTGACGAAGAGTTTCTTCCTATCAAAGAAAG                         CTCTGTGGATTTGGTTGTTAGTTGCTTGGGACTACACTGGACTAATGATCT
genomic: GAGACCCACTTTCTTGTTGCTGACGAAGAGTTTCTTCCTATCAAAGAAAGgcaattataa ... ttgtttgcagCTCTGTGGATTTGGTTGTTAGTTGCTTGGGACTACACTGGACTAATGATCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtcacgcttttcctgttttggattgttcttacttagatattggtttgtttgcagCTCTGTGGATTTGGTTGTTAGTTGCTTGGGACTACACTGGACTAATGATCTGCCTGGAGCAATGATACAG
                          ttcttac  putative branch site (score: 2)
                                            tttgttt  putative PPT
                                 ttagatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaattataattgattttatttcatgtcacgcttttcctgttttggattgttcttacttagatattggtttgtttgcagCTCTGTGGATTTGGTTGTTAGTTGCTTGGGACTACACTGGACTAATGATCTGCCTGGAGCAATGATACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA