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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggttcttatggtttttacatgcttcattgcatttgcactttcttactgtctccttgaaagttctcacattcaattaaatttatttttcttcaaacatttttataggctattgttgttgtattgctatagGGTAATCTGGTAGCAAAAAAATCAACATTTCCTTCTGGAATCAAAGCTCTTGCAGATTATGTTCACAGCAAGGGTCTTAAGCTTGGAATTTATTCAGATG

Basic information

species Glycine max
transcript GLYMA09G40990.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G40990.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G146463_T01 (Zea mays), 3'ss of exon 5
gtatggttcttatggtttttacatgcttcattgcatttgcactttcttactgtctccttgaaagttctcacattcaattaaatttatttttcttcaaacatttttataggctattgttgttgtattgctatagGGTAATCTGGTAGCAAAAAAATCAACATTTCCTTCTGGAATCAAAGCTCTTGCAGATTATGTTCACAGCAAGGGTCTTAAGCTTGGAATTTATTCAGATG
   | || | || |  |  | | | | | |     |   || || ||| | ||        || ||||  || |   | ||     | ||| || ||      |  ||  | | |  || ||       | ||||  |  |||| || ||       ||||| || || |||||||| || || |||||||| |||||||||||||| ||||||||||| || || ||    |
--gtagtacgtacgagtgctgc-tacgtgaccttgtcgtcagttactttcagtt-------aaattcttgcact-gctgaagcacgtgtttgtttaagaggaatgctaatcgact--tgctg-------acagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTGGCAGATTACGTTCACAGCAAGGGGCTTAAGCTTGGCATCTACTCTTCCG

upper sequence: GLYMA09G40990.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G146463_T03 (Zea mays), 3'ss of exon 5
gtatggttcttatggtttttacatgcttcattgcatttgcactttcttactgtctccttgaaagttctcacattcaattaaatttatttttcttcaaacatttttataggctattgttgttgtattgctatagGGTAATCTGGTAGCAAAAAAATCAACATTTCCTTCTGGAATCAAAGCTCTTGCAGATTATGTTCACAGCAAGGGTCTTAAGCTTGGAATTTATTCAGATG
     || | || |  |  | | | | | |     |   || || ||| | ||        || ||||  || |   | ||     | ||| || ||      |  ||  | | |  || ||       | ||||  |  |||| || ||       ||||| || || |||||||| || || |||||||| |||||||||||||| ||||||||||| || || ||    |
-----gtacgtacgagtgctgc-tacgtgaccttgtcgtcagttactttcagtt-------aaattcttgcact-gctgaagcacgtgtttgtttaagaggaatgctaatcgact--tgctg-------acagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTGGCAGATTACGTTCACAGCAAGGGGCTTAAGCTTGGCATCTACTCTTCCG

upper sequence: GLYMA09G40990.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G08380.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatggttcttatggtttttacatgcttcattgcatttgcact-ttcttactgtctccttgaaagttctcacattcaattaaatttatttttcttcaaacatttttataggctattgttgttgtattgctatagGGTAATCTGGTAGCAAAAAAATCAACATTTCCTTCTGGAATCAAAGCTCTTGCAGATTATGTTCACAGCAAGGGTCTTAAGCTTGGAATTTATTCAGATG
                                | |||  ||   |||||  ||| |||| |     | |||  |    ||   | |    || | | |   ||| | |    ||    ||||       |  |||| | ||||||  |||| || ||||| || ||||||||||| |||||  |||| |||||||||||||| || || ||||||||||| ||||| |||||||
--------------------------------gtattatcataattctttgtgtttcctgg-----tttcatttcttgtt---tctgcagttttgctagattttatcttccttaactctgtt------ttccagGGAAGTCTGGTGCCAAAGAAGTCAACTTTCCCTTCTGGAATTAAAGCGGTTGCGGATTATGTTCACAGTAAAGGCCTTAAGCTTGGGATTTACTCAGATG

upper sequence: GLYMA09G40990.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv10s0071g01100.t01 (Vitis vinifera), 3'ss of exon 4
gtatggttcttatggtttttacatgcttcattgcatttgcactttcttactgtctccttgaaagttctcacattcaattaaatttatttttcttcaaacatttt-tataggctattgttgt-tgtattgctat-agGGTAATCTGGTAGCAAAAAAATCAACATTTCCTTCTGGAATCAAAGCTCTTGCAGATTATGTTCACAGCAAGGGTCTTAAGCTTGGAATTTATTCAGATG
||  |||| | ||  | ||||  |  |  ||| | || | | |   | |   ||    |    |||   | |  | |  |    | |   |    |  ||||   |||  ||  ||        | | | | | |||||| |||||| || || ||||| ||||| || || || || ||||||||||| || || || |||||||| ||||||||||| ||||| || || ||||
gt-cggttttaat--tctttattttttctatttcgttggtattcattgatattccaagttttggtttgaagaaactaggaggagtgtcactgcatattcattcagtatgtgcacttaaaaaacatttcgatttcagGGTACTCTGGTTGCTAAGAAATCCACATTCCCATCGGGCATTAAAGCTCTTGCGGACTACGTGCACAGCAAAGGTCTTAAGCTAGGAATCTACTCTGATG

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|213608125|gb|DB972593.1|DB972593
EST:     ATGATTGTTGGGCTGAATTAAATCGGGATGCTAAG                         GGTAATCTGGTAGCNNNNNNNTCAACATTTCCTTCTGGAATCAAAGCTCTT
genomic: ATGATTGTTGGGCTGAATTAAATCGGGATGCTAAGgtatggttct ... attgctatagGGTAATCTGGTAGCAAAAAAATCAACATTTCCTTCTGGAATCAAAGCTCTT
EST: gi|213595971|gb|DB966274.1|DB966274
EST:     ATGATTGTTGGGCTGAATTAAATCGGGATGCTAAG                         GGTAATCTGGTAGCNNNNNNNTCAACATTTCCTTCTGGAATCAAAGCTCTT
genomic: ATGATTGTTGGGCTGAATTAAATCGGGATGCTAAGgtatggttct ... attgctatagGGTAATCTGGTAGCAAAAAAATCAACATTTCCTTCTGGAATCAAAGCTCTT
EST: gi|193529172|gb|FK484363.1|FK484363
EST:     TTGTTGGGCTGAATTAAATCGGGATGCTAAG                         GGTAATCTGGTAGCAAAAAATTCAACGTTTCCTTCTGGAATCAAAGCTCTT
genomic: TTGTTGGGCTGAATTAAATCGGGATGCTAAGgtatggttct ... attgctatagGGTAATCTGGTAGCAAAAAAATCAACATTTCCTTCTGGAATCAAAGCTCTT
EST: gi|207805925|gb|GD779158.1|GD779158
EST:     TTGGGCTGAATTAAATCGGGATGCTAAG                         GGTAATCTGGTAGCAAAAAATTCAACGTTTCCTTCTGGAATCAAAGCTCTT
genomic: TTGGGCTGAATTAAATCGGGATGCTAAGgtatggttct ... attgctatagGGTAATCTGGTAGCAAAAAAATCAACATTTCCTTCTGGAATCAAAGCTCTT
EST: gi|213589246|gb|DB957778.1|DB957778
EST:     ATGATTGTTGGGCTGAATTAAATCGGGATGCTAAG                         GGTAATCTGGTAGCNNNNNNNNTCAACATTTCCTTCTGGAATCAAAGCTCT
genomic: ATGATTGTTGGGCTGAATTAAATCGGGATGCTAAGgtatggttct ... attgctatagGGTAATCTGGTAGCAAAAAAA-TCAACATTTCCTTCTGGAATCAAAGCTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaatttatttttcttcaaacatttttataggctattgttgttgtattgctatagGGTAATCTGGTAGCAAAAAAATCAACATTTCCTTCTGGAATCAAAGCTCTTGCAGATTATGTTCACAGCAAGGGTCTTAAGCTTGGAATTTATTCAGATG
     ttatttttcttcaaac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggttcttatggtttttacatgcttcattgcatttgcactttcttactgtctccttgaaagttctcacattcaattaaatttatttttcttcaaacatttttataggctattgttgttgtattgctatagGGTAATCTGGTAGCAAAAAAATCAACATTTCCTTCTGGAATCAAAGCTCTTGCAGATTATGTTCACAGCAAGGGTCTTAAGCTTGGAATTTATTCAGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG