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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgattacactttcggaagaaaattattccatagacacccatattttgctcaactagttctaattcttgtatggtatgtgatttgtttttctttttgtagTGGTTGAAGACATATTCAAGCGAAGGCAACCATTGCCCACCATGGATGCTATATACTTCATCCAGCCAACCAGAGAGAA

Basic information

species Glycine max
transcript GLYMA05G03970.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G03970.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G12360.1 (Arabidopsis thaliana), 3'ss of exon 3
------atgattacactttcggaagaaaatta-ttccatagacacccatattttgctcaactagttctaattcttgtatggtatgtgatttgtttttctttttgtagTGGTTGAAGACATATTCAAGCGAAGGCAACCATTGCCCACCATGGATGCTATATACTTCATCCAGCCAACCAGAGAGAA
      ||||    | ||| | |  ||   || |||||||     |  ||||| |    | ||  | ||||| | ||| | |||          | | | | ||||||||||||||||||||| |  ||||| |||||| | ||  | |||||||| |||||||||||||||||||| | ||||||
gtgagaatgaa-gtatttttgtacaaattctagttccatatgatactttatttgg---gaataact-taattgtcgtaagatat----------tatttctctgtagTGGTTGAAGACATATTTAGACGAAGACAACCACTTCCTTCAATGGATGCAATATACTTCATCCAGCCAACTAAAGAGAA

upper sequence: GLYMA05G03970.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv13s0019g05000.t01 (Vitis vinifera), 3'ss of exon 3
--atgattacactttcggaagaaaattattccatagacacccatattttgctcaactagttctaattcttgtatggtatgtgatttgtttttctttttgtagTGGTTGAAGACATATTCAAGCGAAGGCAACCATTGCCCACCATGGATGCTATATACTTCATCCAGCCAACCAGAGAGAA
   ||  |     |  |        ||| |  ||| | |||  | ||| |||       |||| ||  ||| ||| |||   |||| | ||||| | || |||||| ||||| |||| |||||||||||| ||||||||| | ||||| || ||||||||||| |||||||||| ||||||
gtgtgtgtgtgtgtgtgttttttttttaatatatatatacct-tttttcgctttttcttttctcatctttgaatg-tatcaaatttctatttctctgtgcagTGGTGGAAGATATATACAAGCGAAGGCAGCCATTGCCCTCAATGGACGCAATATACTTCATACAGCCAACCAAAGAGAA
















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|193417180|gb|FK384608.1|FK384608
EST:     AATGTCTCATTCTTGCAAGATGGCTGATATCACTGATGAAGGCGTTTCAT                         TGGTTGAAGACATATTCAAGCGAAGGCAACCATTGCCCACCATGGATGCTA
genomic: AATGTCTCATTCTTGCAAGATGGCTGATATCACTGATGAAGGCGTTTCATgtaagaatcc ... ctttttgtagTGGTTGAAGACATATTCAAGCGAAGGCAACCATTGCCCACCATGGATGCTA
EST: gi|193421450|gb|FK389623.1|FK389623
EST:     TTGTTCTCATTCTTGCAAGATGGCTGATATCACTGATGAAGGCGTTTCAT                         TGGTTGAAGACATATTCAAGCGAAGGCAACCATTGCCCACCATGGATGCTA
genomic: -TG-TCTCATTCTTGCAAGATGGCTGATATCACTGATGAAGGCGTTTCATgtaagaatcc ... ctttttgtagTGGTTGAAGACATATTCAAGCGAAGGCAACCATTGCCCACCATGGATGCTA
EST: gi|193343817|gb|FK311521.1|FK311521
EST:     ATTGTCTCATTCTTGCAAGATGGCTGATATCACTGATGAAGGCGTTTCAT                         TGGTTGAAGACATATTCAAGCGAAGGCAACCATTGCCCACCATGGATGCTA
genomic: A-TGTCTCATTCTTGCAAGATGGCTGATATCACTGATGAAGGCGTTTCATgtaagaatcc ... ctttttgtagTGGTTGAAGACATATTCAAGCGAAGGCAACCATTGCCCACCATGGATGCTA
EST: gi|193345000|gb|FK311626.1|FK311626
EST:     ATTGTCTCATTCTTGCAAGATGGCTGATATCACTGATGAAGGCGTTTCAT                         TGGTTGAAGACATATTCAAGCGAAGGCAACCATTGCCCACCATGGATGCTA
genomic: A-TGTCTCATTCTTGCAAGATGGCTGATATCACTGATGAAGGCGTTTCATgtaagaatcc ... ctttttgtagTGGTTGAAGACATATTCAAGCGAAGGCAACCATTGCCCACCATGGATGCTA
EST: gi|193421324|gb|FK388671.1|FK388671
EST:     ATTGTCTCATTCTTGCAAGATGGCTGATATCACTGATGAAGGCGTTTCAT                         TGGTTGAAGACATATTCAAGCGAAGGCAACCATTGCCCACCATGGATGCTA
genomic: A-TGTCTCATTCTTGCAAGATGGCTGATATCACTGATGAAGGCGTTTCATgtaagaatcc ... ctttttgtagTGGTTGAAGACATATTCAAGCGAAGGCAACCATTGCCCACCATGGATGCTA
EST: gi|193405470|gb|FK372105.1|FK372105
EST:     TGTTCTTCATTCTTGCAAGATGGCTGATATCACTGATGAAGGCGTTTCAT                         TGGTTGAAGACATATTCAAGCGAAGGCAACCATTGCCCACCATGGATGCTA
genomic: TG-TC-TCATTCTTGCAAGATGGCTGATATCACTGATGAAGGCGTTTCATgtaagaatcc ... ctttttgtagTGGTTGAAGACATATTCAAGCGAAGGCAACCATTGCCCACCATGGATGCTA
EST: gi|193349521|gb|FK318639.1|FK318639
EST:     ATTGTCTCATTCTTGCAAGATGGCTGATATCACTGATGAAGGCGTTTCAT                         TGGTTGAAGACATATTCAAGCGAAGGCAACCATTGCCCACCATGGATGCTA
genomic: A-TGTCTCATTCTTGCAAGATGGCTGATATCACTGATGAAGGCGTTTCATgtaagaatcc ... ctttttgtagTGGTTGAAGACATATTCAAGCGAAGGCAACCATTGCCCACCATGGATGCTA
EST: gi|193435828|gb|FK399432.1|FK399432
EST:     AATGTCTCATTCTTGCAAGATGGCTGATATCACTGATGAAGGCGTTTCAT                         TGGTTGAAGACATATTCAAGCGAAGGCAACCATTGCCCACCCATGGATGCT
genomic: AATGTCTCATTCTTGCAAGATGGCTGATATCACTGATGAAGGCGTTTCATgtaagaatcc ... ctttttgtagTGGTTGAAGACATATTCAAGCGAAGGCAACCATTGCCCACC-ATGGATGCT
EST: gi|193349384|gb|FK314106.1|FK314106
EST:     AATGTCTCATTCTTGCAAGATGGCTGATATCACTGATGAAGGCGTTTCAT                         TGGTTGAAGACATATTCAAGCGAAGGCAACCATTGCCCACCATGGATGCTA
genomic: AATGTCTCATTCTTGCAAGATGGCTGATATCACTGATGAAGGCGTTTCATgtaagaatcc ... ctttttgtagTGGTTGAAGACATATTCAAGCGAAGGCAACCATTGCCCACCATGGATGCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgctcaactagttctaattcttgtatggtatgtgatttgtttttctttttgtagTGGTTGAAGACATATTCAAGCGAAGGCAACCATTGCCCACCATGGATGCTATATACTTCATCCAGCCAACCAGAGAGAA
            ttctaat  putative branch site (score: 2)
                                    tttgtttttctttttg  putative PPT
                                   atttgtttttcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgattacactttcggaagaaaattattccatagacacccatattttgctcaactagttctaattcttgtatggtatgtgatttgtttttctttttgtagTGGTTGAAGACATATTCAAGCGAAGGCAACCATTGCCCACCATGGATGCTATATACTTCATCCAGCCAACCAGAGAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - -cactttc
- - - - - - - - aagaaaa
- - - - - - - - - - - - - - - - -gacaccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgtatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtatgtg