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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgttcagcaattgctgtatgttttcttcagtttcactgcagtagtgaaatctaagttgcattgatgttgctcactttattattattattttttgttcagGACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGCAGACAAGCTTCGGCCTATATCTGCGATGCAGGGGAAGAATTAGTGGCATTGCGGAAGAAGC

Basic information

species Glycine max
transcript GLYMA10G30220.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G30220.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G454952_T01 (Zea mays), 3'ss of exon 13
--ttgttcagcaattgctgtatgttttcttcagttt-cactgcagtagtgaaatctaagttgcattgatgttgctcactt-tattattattattttttgttcagGACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGCAGACAAGCTTCGGCCTATATCTGCGATGCAGGGGAAGAATTAGTGGCATTGCGGAAGAAGC
    ||      |     | ||||||| |||    |    ||||  |   |||  |  || |    ||  | |  || |  | |||||  |  | |   | ||||||||||| |||||||||||||| |||||  | || ||||| | | | |||||||| ||||||| ||| ||||| ||  |  ||||  | || |||||||
tggcgtctgaacaccttggaatgtttttttcctcctatcttgcaacatgcaaacatcggtag----gacatggtacattggtcttatttgtgctgtacatgcagGACTACATTGACAGCATGGAAGGAGCAACTCTCTCCGGCAGGCGAACGTCGGCCTACATCTGCGGTGCCGGGGAGGAGCTGCTGGCCCTCCGAAAGAAGC

upper sequence: GLYMA10G30220.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv14s0030g01740.t01 (Vitis vinifera), 3'ss of exon 13
----------------------------------------------------------------------------------ttgttcagcaa--ttgctgtatgttttctt---cagtttcactgcagtagtgaaatctaagttgcattgatgttgc-tcactttattat-tattattttttgttcagGACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGCAGACAAGCTTCGGCCTATATCTGCGATGCAGGGGAAGAATTAGTGGCATTGCGGAAGAAGC
                                                                                  |||   || ||  |  |   |||  ||  |   || | | | |    ||||    |     |  |||| |   | | ||| |     || | ||     |||| ||||| ||||| ||||| |||||||| |||||| |||| ||||| ||| |||| |||||||| ||||| || |||||||||||||  ||| ||| ||| ||||
gtaatttttgccttaacttcatccactcactgataatactgtttggttaccaaactgtcctgcatttccaccagcatttaatttgaaaagaaaaatgacataatggattaatatacattcttaataagctagttgggtggctttctcattcacaattcatcattgggacatgtgtttgggcttgtacagGATTACATTGACAGTATGGAAGGAGCAACCCTGTCAGGCAGGCAAACTTCAGCCTATATTTGCGACGCGGGGGAAGAATTAGCAGCACTGCAGAAAAAGC
















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|9899120|gb|BE608147.1|BE608147
EST:     AAAAGACACCAGTGAGGAATTTCTTTCTTGCTGGCTCTTACACAAAGCAG                         GACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGCAGACAAGCTTCG
genomic: AAAAGACACCAGTGAGGAATTTCTTTCTTGCTGGCTCTTACACAAAGCAGgtagcacctt ... ttttgttcagGACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGCAGACAAGCTTCG
EST: gi|8825652|gb|BE209445.1|BE209445
EST:     AAAAGACACCAGTGAGGAATTTCTTTCTTGCTGGCTCTTACACAAAGCAG                         GACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGCAGACAAGCTTCG
genomic: AAAAGACACCAGTGAGGAATTTCTTTCTTGCTGGCTCTTACACAAAGCAGgtagcacctt ... ttttgttcagGACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGCAGACAAGCTTCG
EST: gi|209729713|gb|BW669813.1|BW669813
EST:     AAAAGACACCAGTGAGGAATTTCTTTCTTGCTGGCTCTTACACAAAGCAG                         GACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGCAGACAAGCTTCG
genomic: AAAAGACACCAGTGAGGAATTTCTTTCTTGCTGGCTCTTACACAAAGCAGgtagcacctt ... ttttgttcagGACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGCAGACAAGCTTCG
EST: gi|192309148|gb|FG999081.1|FG999081
EST:     AAAAGACACCAGTGAGGAATTTCTTCCTTGCTGGCTCTTACACAAAGCAG                         GACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGCAGACAAGCTTCG
genomic: AAAAGACACCAGTGAGGAATTTCTTTCTTGCTGGCTCTTACACAAAGCAGgtagcacctt ... ttttgttcagGACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGCAGACAAGCTTCG
EST: gi|209702721|gb|BW652764.1|BW652764
EST:     AAAAGACACCAGTGAGGAATTTCTTTCTTGCTGGCTCTTACACAAAGCAG                         GACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGCAGACAAGCTTCG
genomic: AAAAGACACCAGTGAGGAATTTCTTTCTTGCTGGCTCTTACACAAAGCAGgtagcacctt ... ttttgttcagGACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGCAGACAAGCTTCG
EST: gi|151411529|gb|EV281340.1|EV281340
EST:     AAAAGACACCAGTGAGGAATTTCTTTCTTGCTGGCTCTTACACAAAGCAG                         GACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGCAGACAAGCTTCG
genomic: AAAAGACACCAGTGAGGAATTTCTTTCTTGCTGGCTCTTACACAAAGCAGgtagcacctt ... ttttgttcagGACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGCAGACAAGCTTCG
EST: gi|209717714|gb|BW671532.1|BW671532
EST:     AAAAGACACCAGTGAGGAATTTCTTTCTTGCTGGCTCTTACACAAAGCAG                         GACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGCAGACAAGCTTCG
genomic: AAAAGACACCAGTGAGGAATTTCTTTCTTGCTGGCTCTTACACAAAGCAGgtagcacctt ... ttttgttcagGACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGCAGACAAGCTTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaatctaagttgcattgatgttgctcactttattattattattttttgttcagGACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGCAGACAAGCTTCGGCCTATATCTGCGATGCAGGGGAAGAATTAGTGGCATTGCGGAAGAAGC
                       tgctcac  putative branch site (score: 2)
                                           ttttttgttc  putative PPT
                          tcactttattattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgttcagcaattgctgtatgttttcttcagtttcactgcagtagtgaaatctaagttgcattgatgttgctcactttattattattattttttgttcagGACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGCAGACAAGCTTCGGCCTATATCTGCGATGCAGGGGAAGAATTAGTGGCATTGCGGAAGAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - tgctgta
- - - - - - - - - - - - - - - - - cactgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - agttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatgttg