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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatatacctgttgagttgtatgcctgaactggagaatttggattttctatttctattcattgttgttctcctctaattaaattgttagatatgaatttagGTACAAGAAGCTGCAGATTGCTTGGGTGCTGACTGTGTGCCTCGATATGTTGAGATGAAGCAGATGGGGAACTTTGATGTTGAAACTCTCTTCAAACAAT

Basic information

species Glycine max
transcript GLYMA12G09100.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G09100.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os11g05260.1 (Oryza sativa), 3'ss of exon 6
-tatatacctgttgagttgtatgcctgaactggagaatttggatt--ttctatttctattcattgttgtt-ctcctctaattaaattgttagata-tgaatt-tagGTACAAGAAGCTGCAGATTGCTTGGGTGCTGACTGTGTGCCTCGATATGTTGAGATGAAGCAGATGGGGAACTTTGATGTTGA-AACTCTCTTCAAACAAT
 ||  ||| |  |||   || ||    |  || | | ||| |     | |  | ||  || |||||| || |     | ||  ||   |   | | |||||| ||||| ||||| |||||||||||||| |||||||||||||||||||| ||||| || |||||| |  ||    |  | ||  ||||  |  |  | ||||||| 
gtaactacattctgaa--gtctgaacaatttgcaaagtttagtccaatgcattatcgttttattgttattacctgcttgatctaaccatagtagagtgaattgtagGTTCAAGAGGCTGCAGATTGCTTAGGTGCTGACTGTGTGCCTCGTTATGTGGAAATGAAGAAACTGCTAGAACTAGAAATTGATGATGCCTTCCAAACAA-

upper sequence: GLYMA12G09100.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv06s0061g01340.t01 (Vitis vinifera), 3'ss of exon 7
-----------------------tatatacctgttgagttgtatgcctgaactggagaatttggattttctatttctattcattgttgttctcctctaattaaattgttagatatgaatttagGTACAAGAAGCTGCAGATTGCTTGGGTGCTGACTGTGTGCCTCGATATGTTGAGATGAAGCAGATGGGGAACTTTGATGTTGAAACTCTCTTCAAACAAT
                        ||   | | |     |  ||       |||  ||| |  || | || | ||| | |         ||| || || |  || || | ||  ||  | ||||| ||||||||||||||||||||||| ||||| ||||||||||| ||||||||||||||||| |||  | || ||||| ||||||   |  |    ||||
gtaagatcatcctcaatgttcttgatcatcatataacaattcatattctttctgttgaaat--gagtatcaaattccactgcagagctctctact-tattccaactggttgacttgcttatagGTGCAAGAAGCTGCAGATTGCTTGGGGGCTGATTGTGTGCCTCGCTATGTTGAGATGAAGCAAATGCAGGACCTTGATCTTGAAAAAATACTTGGGCAAT
















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|8670367|gb|BE191474.1|BE191474
EST:     TTAGCAGTCCTAACAAAGCTTGTGTTGGGACAGCCACGATCATCTCCCAG                         GTACAAGAAGCTGCAGATTGCTTGGGTGCTGACTGTGTGCCTCGATATGTT
genomic: TTAGCAGTCCTAACAAAGCTTGTGTTGGGACAGCCACGATCATCTCCCAGgtaggctcac ... atgaatttagGTACAAGAAGCTGCAGATTGCTTGGGTGCTGACTGTGTGCCTCGATATGTT
EST: gi|17519519|gb|BM188561.1|BM188561
EST:     TTAGCAGTCCTAACAAAGCTTGTGTTGGGACAGCCACGATCATCTCCCAG                         GTACAAGAAGCTGCAGATTGCTTGGGTGCTGACTGTGTGCCTCGATATGTT
genomic: TTAGCAGTCCTAACAAAGCTTGTGTTGGGACAGCCACGATCATCTCCCAGgtaggctcac ... atgaatttagGTACAAGAAGCTGCAGATTGCTTGGGTGCTGACTGTGTGCCTCGATATGTT
EST: gi|51335983|gb|CO979849.1|CO979849
EST:     TTAGCAGTCCTAACAAAGCTTGTGTTGGGACAGCCACGATCATNNCCCAG                         GTACAAGAAGCTGCAGATTGCTTGGGTGCTGACTGTGTGCCTCGATATGTT
genomic: TTAGCAGTCCTAACAAAGCTTGTGTTGGGACAGCCACGATCATCTCCCAGgtaggctcac ... atgaatttagGTACAAGAAGCTGCAGATTGCTTGGGTGCTGACTGTGTGCCTCGATATGTT
EST: gi|120497211|gb|EH225378.1|EH225378
EST:     TTAGCAGTCCTAACAAAGCTTGTGTTGGGACAGCCACGATCATCTCCCAG                         GTACAAGAAGCTGCAGATTGCTTGGGTGCTGACTGTGTGCCTCGATATGTT
genomic: TTAGCAGTCCTAACAAAGCTTGTGTTGGGACAGCCACGATCATCTCCCAGgtaggctcac ... atgaatttagGTACAAGAAGCTGCAGATTGCTTGGGTGCTGACTGTGTGCCTCGATATGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctatttctattcattgttgttctcctctaattaaattgttagatatgaatttagGTACAAGAAGCTGCAGATTGCTTGGGTGCTGACTGTGTGCCTCGATATGTTGAGATGAAGCAGATGGGGAACTTTGATGTTGAAACTCTCTTCAAACAAT
                         ctctaat  putative branch site (score: 3)
                          tctaattaaattgtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatatacctgttgagttgtatgcctgaactggagaatttggattttctatttctattcattgttgttctcctctaattaaattgttagatatgaatttagGTACAAGAAGCTGCAGATTGCTTGGGTGCTGACTGTGTGCCTCGATATGTTGAGATGAAGCAGATGGGGAACTTTGATGTTGAAACTCTCTTCAAACAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - cctgttg
- - - - - - - - -gtatgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcctct