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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acaaatatttgtgttttttttttttttcacgttagtttggtcttgtgagttgtgattgaattagtgcaatctgatagaggcagtgtcccatttcttacagGGAGAACCTTTGTGTGTCTTCTATTCTCGTTATGGCATATGCAAATTTGGCCCAAGTTGCAAGTTTGACCACCCAATGGAAATTTTCTCTCATAATATCT

Basic information

species Glycine max
transcript GLYMA10G31370.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G31370.2 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os11g28270.1 (Oryza sativa), 3'ss of exon 6
acaaatatttgtgttttttttttttttcacgttagtttggt-cttgtga-gttgtgattgaattagtgcaatctgatagag-gcagtgtcccatttcttacagGGAGAACCTTTGTGTGTCTTCTATTCTCGTTATGGCATATGCAAATTTGGCCCAAGTTGCAAGTTTGACCACCCAATGGAAATTTTCTCTCATAATATCT
     |  |  ||   | ||        |    |  |   | | |   |  | |    || |  ||||    || ||     |     |     | ||| |||||||| ||  | ||    ||||||||||| |||||||| ||||| ||||| || | |||||| ||||| || ||||||| || | |     ||  | || 
---gtttatcatgcaatgttcaaaaccgataaaacataaatacatacaatatagaagatggacaagtgttgcctaatcctctgtttctttttcctgcttgcagGGAGAGCCCATATGCACATTCTATTCTCGCTATGGCATCTGCAAGTTTGGTCCGAATTGCAAATTTGATCATCCAATGGGAACTGTGATGTATGGTCTCG

upper sequence: GLYMA10G31370.2 (Glycine max), 3'ss of exon 5
lower sequence: AT3G02830.1 (Arabidopsis thaliana), 3'ss of exon 6
acaaatatttgtgttttttttttttttcacgttagtttggtcttgtgagttgtgattgaattagtgca--atctgatagaggcagtgtcccatttcttacagGGAGAACCTTTGTGTGTCTTCTATTCTCGTTATGGCATATGCAAATTTGGCCCAAGTTGCAAGTTTGACCACCCAATGGAAATTTTCTCTCATAATATCT
         |  | |       || | ||   |   |||||  |      |  |||| |||   ||||   | ||||        | || ||    | | |||||||||| |||||||| |||||| | || ||||| || ||||||||||| ||||| || || ||||| |||||||||  | | ||| |  |  | | | 
--------gtaagctcaaagacttgtgcataattacttggttct-----cttcgattaaatctctgcattgtttgattttttttctttctcaaaa-tgatagGGAGAACCGTTGTGTGTGTTCTATACACGCTATGGAATCTGCAAATTTGGTCCAAGCTGTAAATTTGATCACCCAATGCGAGTATTCACATACGACAACA

upper sequence: GLYMA10G31370.2 (Glycine max), 3'ss of exon 5
lower sequence: AT5G16540.3 (Arabidopsis thaliana), 3'ss of exon 4
acaaatatttgtgttttttttttttttcacgttagtttggtcttgtgagttgtgattgaattagtgcaatctgatagaggca-gtgtcccatttcttacagGGAGAACCTTTGTGTGTCTTCTATTCTCGTTATGGCATATGCAAATTTGGCCCAAGTTGCAAGTTTGACCACCCAATGGAAATTTTCTCTCATAATATCT
                  |    |  | |      |  | |  | |   || |  |   |||| ||   | || || |  |  ||  |   |||   ||||||||||||  |||| || ||||||||||| ||||| || ||||| ||||| ||||| || || ||||| ||||| |||  | | ||| || | || | | 
-----------------gtaagctaataaaagacttcagattctttcctttatagtctcatta-tgtggtttggtaaattcttgttgctggtttgaaacagGGAGAACCACTGTGCGTGTTCTATTCTCGGTATGGGATCTGCAAGTTTGGTCCAAGCTGTAAATTTGATCACCCGATGCGAGTCTTCACTTACAACAACA

upper sequence: GLYMA10G31370.2 (Glycine max), 3'ss of exon 5
lower sequence: AT5G16540.2 (Arabidopsis thaliana), 3'ss of exon 5
----acaaatatttgtgttttttttttttttcacgttagtttggtcttgtgagttgtgattgaattagtgcaatctgatagaggca-gtgtcccatttcttacagGGAGAACCTTTGTGTGTCTTCTATTCTCGTTATGGCATATGCAAATTTGGCCCAAGTTGCAAGTTTGACCACCCAATGGAAATTTTCTCTCATAATATCT
     |     |||  |     |    |  | |      |  | |  | |   || |  |   |||| ||   | || || |  |  ||  |   |||   ||||||||||||  |||| || ||||||||||| ||||| || ||||| ||||| ||||| || || ||||| ||||| |||  | | ||| || | || | | 
gttggccttcctttacgcccggtaagctaataaaagacttcagattctttcctttatagtctcatta-tgtggtttggtaaattcttgttgctggtttgaaacagGGAGAACCACTGTGCGTGTTCTATTCTCGGTATGGGATCTGCAAGTTTGGTCCAAGCTGTAAATTTGATCACCCGATGCGAGTCTTCACTTACAACAACA

upper sequence: GLYMA10G31370.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv04s0023g00370.t01 (Vitis vinifera), 3'ss of exon 6
acaaatatttgtgttttttttttttttcacgttagtttggtcttgtgagttgtgattgaattagtgc--aatctgatagaggcagtgtcccatttcttacagGGAGAACCTTTGTGTGTCTTCTATTCTCGTTATGGCATATGCAAATTTGGCCCAAGTTGCAAGTTTGACCACCCAATGGAAATTTTCTCTCATAATATCT
|| |  ||   |   | |  ||    |   |||  | || | |   ||||  |  |  | ||| |    ||| |||| ||    || |    |||   ||||||||||||||||||  | || |||||||||||||| || ||||||||||| ||||||||||||||||||||||| |||| ||| ||| |  | ||| | |
accataatgcataaatgtacttcaactttggttgctctgatata--gagtccttgtctagttatttataaatttgatggatctggtttttatttttcaacagGGAGAACCTTTGTGCATTTTTTATTCTCGTTATGGGATCTGCAAATTTGGTCCAAGTTGCAAGTTTGACCACCCTATGGGAATCTTCGCATACAATCTGT

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|13312087|gb|BG405738.1|BG405738
EST:     TTCCTGCTCCTAACTGTGTCTTGAGTCCCATAGGCCTTGCTTTACGTTCT                         GGAGAACCTTTGTGTGTCTTCTATTCTCGTTATGGCATATGCAAATTTGGC
genomic: TTCCTGCTCCTAACTGTGTCTTGAGTCCCATAGGCCTTCCTTTACGTCCTgtaagttggg ... tttcttacagGGAGAACCTTTGTGTGTCTTCTATTCTCGTTATGGCATATGCAAATTTGGC
EST: gi|10843882|gb|BF067236.1|BF067236
EST:     TTCCTGCTCCTAACTGTGTCTTGAGTTCCATAGGCCTTCCTTTACGTACT                         GGAGAACCTTTGTGTGTCTTCTATTCTCGTTATGGCATATGCAAATTTTGG
genomic: TTCCTGCTCCTAACTGTGTCTTGAGTCCCATAGGCCTTCCTTTACGTCCTgtaagttggg ... tttcttacagGGAGAACCTTTGTGTGTCTTCTATTCTCGTTATGGCATATGCAAATTT-GG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgagttgtgattgaattagtgcaatctgatagaggcagtgtcccatttcttacagGGAGAACCTTTGTGTGTCTTCTATTCTCGTTATGGCATATGCAAATTTGGCCCAAGTTGCAAGTTTGACCACCCAATGGAAATTTTCTCTCATAATATCT
                       atctgat  putative branch site (score: 4)
                                        tcccatttctt  putative PPT
         attgaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acaaatatttgtgttttttttttttttcacgttagtttggtcttgtgagttgtgattgaattagtgcaatctgatagaggcagtgtcccatttcttacagGGAGAACCTTTGTGTGTCTTCTATTCTCGTTATGGCATATGCAAATTTGGCCCAAGTTGCAAGTTTGACCACCCAATGGAAATTTTCTCTCATAATATCT

- - - -tttgtgt
- - - - - - - - - - - - - - - - - - - - tcttgtg
- - - - - - - - - - - - - - - - - - - - - - - -agttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcaatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtccca