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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatggtctatctgaatgagtaatgatattgctaataaaggcagtttataggttaatcttttgtaaaatcagtttaaaattgtatttacctttgtcatcatgtgtttgataattgcaattttactgaaaaagtgcttatggttggtttcttaattatcccaagcttatattgctttctctttatactgtagATATGTTGCAACTGCGGTGACTTCAGTTCATGAAATGGAGAATGGTTTCAATATATGGTCTTTCAATGGCAAGCATCTATATCGGATTCTGAAGGATCAC

Basic information

species Glycine max
transcript GLYMA07G14870.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G14870.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os10g41960.1 (Oryza sativa), 3'ss of exon 9
gtatatggtctatctgaatgagtaatgatattgctaataaaggcagtttataggttaatcttttgtaaaatcagtttaaaattgtatttacctttgtcatcatgtgtttgataattgcaattttactgaaaaagtgcttatggttggtttcttaattatcccaagcttatattgctttctctttatactgtagATATGTTGCAACTGCGGTGACTTCAGTTCATGAAATGGAGAATGGTTTCAATATATGGTCTTTCAATGGCAAGCATCTATATCGGATTCTGAAGGATCAC
                                                                                            ||| | || ||   | | |    ||  | |  ||     |||      |   | || | ||| |    | ||  | || |||   | | ||| |  |  |||||| ||||| |||| || || ||||| ||||||||||||||||||||| | ||||||||||||| ||||||||| || ||   | |    ||||| |||
-------------------------------------------------------------------------------------------tttttttataatacttctcactggtgtgactaaacaagttaagatggatttccttgtatgttagtggaactaaaatgatgttgggatttttttttgtt--agATATCTTGCATCTGCAGTTACCTCAGTCCATGAAATGGAGAATGGTTTCCAAATATGGTCTTTCAGTGGCAAGCAACTTTACAAGGTGTCAAAGGACCAC

upper sequence: GLYMA07G14870.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G174757_T01 (Zea mays), 3'ss of exon 9
gtatatggtctatctgaatgagtaatgatattgctaataaaggcagtttataggttaatcttttgtaaaatcagtttaaaattgtatttacctttgtcatcatgtgtttgataattgcaattttactgaaaaagtgcttatggttggtttcttaattatcccaagcttatattgctttctctttatactgtagATATGTTGCAACTGCGGTGACTTCAGTTCATGAAATGGAGAATGGTTTCAATATATGGTCTTTCAATGGCAAGCATCTATATCGGATTCTGAAGGATCAC
                                                                                      | ||  | |    |   |     |  | | |  ||  |         || |  || |       | ||| | | |  |  | || ||||     ||||   |   |||||| | || ||||| || || ||||||||||||||||||||||| ||  | |||||||| |||| |||||||||||| ||   | |    |||||||| 
-------------------------------------------------------------------------------------gtatatttctaaattttggccacagtcagtagtcatactgtgtcttgggtacccatagc------cctaaatgtactgaaatgattttgcaactccttttgtcc--agATATCTCGCGACTGCAGTTACCTCAGTTCATGAAATGGAGAATGGCTTTCAAATATGGTCCTTCAGTGGCAAGCATCTTTACAAGGTGTCAAAGGATCAT

upper sequence: GLYMA07G14870.1 (Glycine max), 3'ss of exon 9
lower sequence: AT5G27640.1 (Arabidopsis thaliana), 3'ss of exon 10
gtatatggtctatctgaatgagtaatgatattgctaataaaggcagtttataggttaatcttttgtaaaatcagtttaaaattgtatttacctttgtcatcatgtgtttgataattgcaattttactgaaaaagtgcttatggttggtttcttaattatcccaa--gcttatattgctttctctttatactgt----agATATGTTGCAACTGCGGTGACTTCAGTTCATGAAATGGAGAATGGTTTCAATATATGGTCTTTCAATGGCAAGCATCTATATCGGATTCTGAAGGATCAC
                                                                                                               |  |      || ||| ||  ||| ||| ||||||  ||  || || | ||||  ||| || ||| || | |||| |  | |    || || |||||||| || ||||| ||||| ||||| ||||||||||| ||||  |||||||||||||| || |     || || |||||  |||||||||| 
--------------------------------------------------------------------------------------------------------------gtcctactgtcttaactaaaccagtcctt-tggttg--tttctatttgttccaattgctgatgttgtttgcacttttttattttcaaagGTACGTTGCAACCGCAGTGACATCAGTCCATGAGATGGAGAATGGGTTCACCATATGGTCTTTCAACGGGATTATGCTTTACCGGATATTGAAGGATCAT

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|58020037|gb|CX706779.1|CX706779
EST:     ACTGCTGAACATTTTATGGCAACAGATATTGAATGGGATCCAACTGGAAG                         ATATGTTGCAACTGCGGTGACTTCAGTTCATGAAATGGAGAATGGTTTCAA
genomic: ACTGCTGAACATTTTATGGCAACAGATATTGAATGGGATCCAACTGGAAGgtatatggtc ... tatactgtagATATGTTGCAACTGCGGTGACTTCAGTTCATGAAATGGAGAATGGTTTCAA
EST: gi|12772952|gb|BG237879.1|BG237879
EST:     GCTGAACATTTGATGGCAACAGATATTGAATGGGATCCAACTGGAAG                         ATATGTTGCAACTGCGGTGACTTCAGTTCATGAAATGGAGAATGGTTTCAA
genomic: GCTGAACATTTTATGGCAACAGATATTGAATGGGATCCAACTGGAAGgtatatggtc ... tatactgtagATATGTTGCAACTGCGGTGACTTCAGTTCATGAAATGGAGAATGGTTTCAA
EST: gi|5688006|gb|AI941021.1|AI941021
EST:     ACTGCTGAACATTTTATGGCAACAGATATTGAATGGGATCCAACTGGAAG                         ATATGTTGCAACTGCGGTGACTTCAGTTCATGAAATGGAGAATGGTTTCAA
genomic: ACTGCTGAACATTTTATGGCAACAGATATTGAATGGGATCCAACTGGAAGgtatatggtc ... tatactgtagATATGTTGCAACTGCGGTGACTTCAGTTCATGAAATGGAGAATGGTTTCAA
EST: gi|58023617|gb|CX710358.1|CX710358
EST:     ACTGCTGAACATTTTATGGCAACAGATATTGAATGGGATCCAACTGGAAG                         ATATGTTGCAACTGCGGTGACTTCAGTTCATGAAATGGAGAATGGTTTCAA
genomic: ACTGCTGAACATTTTATGGCAACAGATATTGAATGGGATCCAACTGGAAGgtatatggtc ... tatactgtagATATGTTGCAACTGCGGTGACTTCAGTTCATGAAATGGAGAATGGTTTCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatggttggtttcttaattatcccaagcttatattgctttctctttatactgtagATATGTTGCAACTGCGGTGACTTCAGTTCATGAAATGGAGAATGGTTTCAATATATGGTCTTTCAATGGCAAGCATCTATATCGGATTCTGAAGGATCAC
           tcttaat  putative branch site (score: 3)
                               tattgctttctcttt  putative PPT
         tttcttaattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatggtctatctgaatgagtaatgatattgctaataaaggcagtttataggttaatcttttgtaaaatcagtttaaaattgtatttacctttgtcatcatgtgtttgataattgcaattttactgaaaaagtgcttatggttggtttcttaattatcccaagcttatattgctttctctttatactgtagATATGTTGCAACTGCGGTGACTTCAGTTCATGAAATGGAGAATGGTTTCAATATATGGTCTTTCAATGGCAAGCATCTATATCGGATTCTGAAGGATCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG