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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgctcttcaacttcgatttcgcactcttttggttcaacattcttaacattttttttttggttcttatgttgttgtcttctgttgtgtaattgcagCCGCAAGGGGATTACATAGAGCGTCACAGAAGAGACTATGGCTACCGTCTTGATCACTTCGAGCGGAAGCGCAAGAAAGAGGCGCGTCAAGTTCACAAAC

Basic information

species Glycine max
transcript GLYMA10G10000.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G10000.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G06360.1 (Arabidopsis thaliana), 3'ss of exon 1
-----------------------gttcgctcttcaacttcgatttcgcactcttttggttcaacattcttaacatttttttttt----ggttcttatgttgttgtcttctgttgtgt-aattgcagCCGCAAGGGGATTACATAGAGCGTCACAGAAGAGACTATGGCTACCGTCTTGATCACTTCGAGCGGAAGCGCAAGAAAGAGGCGCGTCAAGTTCACAAAC
                         |   | |||  |||  |  |  |  |  |  | |  ||||   | | | ||||  | |       ||  | || | |  |||  || ||  | ||   ||||| || || |||||||||||    ||||| |      |||| || || || || ||||||||| | ||||||||||| ||||||||| |||||||||| |
gtacgttctccgccgccggagtaccttttttttcttcttacagctttcgtttctcagatataacagcttgagcgttttgatctctaacaatttctgtggtttcttctattggtggatgaaaaacagCCTCAGGGAGATTACATAGATTTGCACAGGAAGAGGAATGGATATCGCCTCGACCACTTCGAGAGAAAGCGCAAGAAGGAGGCGCGTGAAGTTCACAAGC

upper sequence: GLYMA10G10000.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv08s0105g00280.t01 (Vitis vinifera), 3'ss of exon 1
----------gttcgctcttcaacttcgatttcgc---actcttttggttcaacattcttaacattttttttttggttcttatgttgttgtcttctgttgtgtaattgcagCCGCAAGGGGATTACATAGAGCGTCACAGAAGAGACTATGGCTACCGTCTTGATCACTTCGAGCGGAAGCGCAAGAAAGAGGCGCGTCAAGTTCACAAAC
          ||| | | | |||     ||||| |   |   |||   | |||||   | |    ||| |  |||  | || || |  | | |  |||  | |  || ||||||||||| ||||||||||| | ||| || |    | ||||||| || | ||| || |||||||| ||||||||||||||||| ||| |||||||||| |
gttagtatccgtttg-tttccaaggaaaatttccctagaagatttatttccaacaaagtcagtgatttctgattgtattttgtggttgtttgtattgtcctctg-tttcagCCGCAAGGAGATTACATAGACCTTCATAGGAAGCGCCATGGCTATCGCCCTGACCATTTCGAGCGCAAGCGCAAGAAAGAGGCTCGTGAAGTTCACAAGC

upper sequence: GLYMA10G10000.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S136_220V6.1 (Physcomitrella patens), 3'ss of exon 1
gttcgctcttcaacttcgatttcgcactcttttggttcaacattcttaacattttttttttggttcttatgttgttgtcttctgtt---gtgtaattgcagCCGCAAGGGGATTACATAGAGCGTCACAGAAGAGACTATGGCTACCGTCTTGATCACTTCGAGCGGAAGCGCAAGAAAGAGGCGCGTCAAGTTCACAAAC
 ||     |  |   |   ||| |     |||   |      ||  ||| | ||  |||| |  |  | |||| ||   || ||||         |  |||||||| || ||| | || ||    ||  | |      |||| ||||| |  ||| |||||||  |||||||||||||||| |||||| ||||||| ||||
tttgaaggtgtagagtttgtttggttagttttgaatggtgagtttgtaa-acttacttttggtattctgtgttatttgtttttgtttccactgggtaacagCCGCAGGGAGATCATATTGACTTGCATCGCAAGCGTCATGGGTACCGACCGGATTACTTCGAAAGGAAGCGCAAGAAAGATGCGCGTGAAGTTCATAAAC

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|9987770|gb|BE661878.1|BE661878
EST:     CTCTTCGTCTTTCTCTGTTCTGAAACCACTACCGTTTCGTCGNCACCATG                         CCGCAAGGGGATTACATAGAGCGTCACAGAAGAGACTATGGCTACCGTCTT
genomic: CTCTTCGTCTTTCTCTGTTCTGAAACCACTACCGTTTCGTCGTCACCATGgttcgctctt ... gtaattgcagCCGCAAGGGGATTACATAGAGCGTCACAGAAGAGACTATGGCTACCGTCTT
EST: gi|15813808|gb|BI786083.1|BI786083
EST:     TCGTCGTCACCATG                         CCGCAAGGGGATTACATAGAGCGTCACAGAAGAGACTATGGCTACCGTCTC
genomic: TCGTCGTCACCATGgttcgctctt ... gtaattgcagCCGCAAGGGGATTACATAGAGCGTCACAGAAGAGACTATGGCTACCGTCTT
EST: gi|14205367|gb|BG839045.1|BG839045
EST:     CTCTTCGTCTTTCTCTGTTCTGAAACCACTACCGTTTCGTCGTCACCATG                         CCGCAAGGGGATTACATAGAGCGTCACAGAAGAGACTATGGCTACCGTCTT
genomic: CTCTTCGTCTTTCTCTGTTCTGAAACCACTACCGTTTCGTCGTCACCATGgttcgctctt ... gtaattgcagCCGCAAGGGGATTACATAGAGCGTCACAGAAGAGACTATGGCTACCGTCTT
EST: gi|151397650|gb|EV267523.1|EV267523
EST:     CTCTTCGTCTTTCTCTGTTCTGAAACCACTACCGTTTCGTCGTCACCATG                         CCGCAAGGGGATTACATAGAGCGTCACAGAAGAGACTATGGCTACCGTCTT
genomic: CTCTTCGTCTTTCTCTGTTCTGAAACCACTACCGTTTCGTCGTCACCATGgttcgctctt ... gtaattgcagCCGCAAGGGGATTACATAGAGCGTCACAGAAGAGACTATGGCTACCGTCTT
EST: gi|151408011|gb|EV277826.1|EV277826
EST:     GTTCTGAAACCACTCCCGCCTCGTCGTCACCATG                         CCGCAAGGGGATTACATAGAGCGTCACAGAAGAGACTATGGCTACCGTCTC
genomic: GTTCTGAAACCACTACCGTTTCGTCGTCACCATGgttcgctctt ... gtaattgcagCCGCAAGGGGATTACATAGAGCGTCACAGAAGAGACTATGGCTACCGTCTT
EST: gi|298177257|gb|HO023504.1|HO023504
EST:     CTCTTCGTCTTTCTCTGTTCTGAAACCACTACCGTTTCGTCGTCACCATG                         CCGCAAGGGGATTACATAGAGCGTCACAGAAGAGACTATGGCTACCGTCTT
genomic: CTCTTCGTCTTTCTCTGTTCTGAAACCACTACCGTTTCGTCGTCACCATGgttcgctctt ... gtaattgcagCCGCAAGGGGATTACATAGAGCGTCACAGAAGAGACTATGGCTACCGTCTT
EST: gi|14206051|gb|BG839729.1|BG839729
EST:     CTCTTCGTCTTTCTCTGTTCTGAAACCACTACCGTTTCGTCGTCACCATG                         CCGCAAGGGGATTACATAGNAGCGTCACAGAAGAGACTATGGCTACCGTCT
genomic: CTCTTCGTCTTTCTCTGTTCTGAAACCACTACCGTTTCGTCGTCACCATGgttcgctctt ... gtaattgcagCCGCAAGGGGATTACATAG-AGCGTCACAGAAGAGACTATGGCTACCGTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttaacattttttttttggttcttatgttgttgtcttctgttgtgtaattgcagCCGCAAGGGGATTACATAGAGCGTCACAGAAGAGACTATGGCTACCGTCTTGATCACTTCGAGCGGAAGCGCAAGAAAGAGGCGCGTCAAGTTCACAAAC
 tcttaac  putative branch site (score: 2)
       attttttttttggtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcgctcttcaacttcgatttcgcactcttttggttcaacattcttaacattttttttttggttcttatgttgttgtcttctgttgtgtaattgcagCCGCAAGGGGATTACATAGAGCGTCACAGAAGAGACTATGGCTACCGTCTTGATCACTTCGAGCGGAAGCGCAAGAAAGAGGCGCGTCAAGTTCACAAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG