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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgagatgacaggtggtggcagtttgaatttgcatatttcgctacgtctctaacgaacaaagctataataactactctctttttcctcttaaacatttcagGTAATGGATGTCTTCAACAAAATATCAGAACTCTTCCCTGGAGTAGGTTCACCTTGATGCATTTGTGTGTTGTTGCTGTTTTCTGGGTCAAGTTATGCAT

Basic information

species Glycine max
transcript GLYMA11G31810.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G31810.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv18s0041g01360.t01 (Vitis vinifera), 3'ss of exon 13
--------------------------------------------------------------------------------------cgagatgacaggt--ggtggcagtttgaatttgcatatttcgctacgtctctaacgaacaaagctataataactactctctttttcctcttaaacatttcagGTAATGGATGTCTTCAACAAAATATCAGAACTCTTCCCTGGAGTA---GGTTCACCTTGATGCAT-----TTGTGTGTTGTTGCTGTTTTCTGGGTCAAGTTATGCAT
                                                                                        ||   |    |    |   |  ||||          || |||    ||    |   |  || |||  |    | | |  | |   || |  | || |||||| |||||||| |||||||||||||| ||||||||||| ||||||   ||| ||||||||  | |     |  |     | |||  |||| | || | ||        
gtaagtctcaaattttatccaacttgtttaattgtgatcatagtgatgcttgttctgcacgttcacattcaaatcatttatgccattaaggccatttttttattaatatattgagccccttggatttgcttttgcttctgcctgc--agttatccttttaaatgtaatatgtatcattta-atctcagGTTATGGATGTTTTCAACAAAATATCGGAACTCTTCCCCGGAGTATCAGGTCCACCTTGAGTCTTATAGCTCATCCACAGCTGCACTTTTTTTGGGCTAG--------
















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|5753420|gb|AI960707.1|AI960707
EST:     AAATACCAAAACGATAAGGAG                         GTAATGGATGTCTTCAACAAAATATCAGAACTCTTCCCTGGAGTAGGTTCA
genomic: AAATACCAAAACGATAAGGAGgtatgctgat ... aacatttcagGTAATGGATGTCTTCAACAAAATATCAGAACTCTTCCCTGGAGTAGGTTCA
EST: gi|10253974|gb|BE821684.1|BE821684
EST:     TAAATACCAAAACGATAAGGAG                         GTAATGGATGTCTTCAACAAAATATCAGAACTCTTCCCTGGAGTAGGTTCA
genomic: TAAATACCAAAACGATAAGGAGgtatgctgat ... aacatttcagGTAATGGATGTCTTCAACAAAATATCAGAACTCTTCCCTGGAGTAGGTTCA
EST: gi|27424818|gb|CA936338.1|CA936338
EST:     TGTTCGCAGAATCCAATGAATATTACTAAATACCAAAACGATAAGGAG                         GTAATGGATGTCTTCAACAAAATATCAGAACTCTTCCCTGGAGTAGGTTCA
genomic: TGTTCGCAGAATCCAATGAATATTACTAAATACCAAAACGATAAGGAGgtatgctgat ... aacatttcagGTAATGGATGTCTTCAACAAAATATCAGAACTCTTCCCTGGAGTAGGTTCA
EST: gi|192305890|gb|FG995776.1|FG995776
EST:     AATATTACTAAATACCAAAACGATAAGGAG                         GTAATGGATGTCTTCAACAAAATATCAGAACTCTTCCCTGGAGTAGGTTCA
genomic: AATATTACTAAATACCAAAACGATAAGGAGgtatgctgat ... aacatttcagGTAATGGATGTCTTCAACAAAATATCAGAACTCTTCCCTGGAGTAGGTTCA
EST: gi|15813419|gb|BI785694.1|BI785694
EST:     TGTTCGCATAATCCAATGAATATTACTAAATACCAAAACGATAAGGAG                         GTAATGGATGTCTTCAACAAAATATCAGAACTCTTCCCTGGAGTAGGTTCA
genomic: TGTTCGCAGAATCCAATGAATATTACTAAATACCAAAACGATAAGGAGgtatgctgat ... aacatttcagGTAATGGATGTCTTCAACAAAATATCAGAACTCTTCCCTGGAGTAGGTTCA
EST: gi|51342536|gb|CO983519.1|CO983519
EST:     TGTTCGCAGAATCCAATGAATATTACTAAATACCAAAACGATAAGGAG                         GTAATGGATGTCTTCAACAAAATATCAGAACTCTTCCCTGGAGTAGGTTCA
genomic: TGTTCGCAGAATCCAATGAATATTACTAAATACCAAAACGATAAGGAGgtatgctgat ... aacatttcagGTAATGGATGTCTTCAACAAAATATCAGAACTCTTCCCTGGAGTAGGTTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctctaacgaacaaagctataataactactctctttttcctcttaaacatttcagGTAATGGATGTCTTCAACAAAATATCAGAACTCTTCCCTGGAGTAGGTTCACCTTGATGCATTTGTGTGTTGTTGCTGTTTTCTGGGTCAAGTTATGCAT
                   taataac  putative branch site (score: 1)
                         ctactctctttttcct  CT-rich tract
                 tataataacta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgagatgacaggtggtggcagtttgaatttgcatatttcgctacgtctctaacgaacaaagctataataactactctctttttcctcttaaacatttcagGTAATGGATGTCTTCAACAAAATATCAGAACTCTTCCCTGGAGTAGGTTCACCTTGATGCATTTGTGTGTTGTTGCTGTTTTCTGGGTCAAGTTATGCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - ggtggtg
- - - - - - - - - - - - - - -tgcatat
- - - - - - - - - - - - - - - - - - - - - - - - - - - aacaaagc