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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgtaagattcacgccattctgtgtttgatttcatcttccttcgattatgatttttacgaggtagtatgtgttttgtgtctttgcagTTTCACCAGTACCAGGTGGTCGGGAGGGCTCTCCCAACGGAAGCAGATCAGCATCCGAAGATCTACCGAATGAAGCTCTGGGCCACCAACGAGGTTCGCG

Basic information

species Glycine max
transcript GLYMA13G28830.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G28830.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S101_218V6.1 (Physcomitrella patens), 3'ss of exon 1
---------------gtgcgtaagattcacgccattctgtgtttgatttcatcttccttcgattatgatttttacgaggtagtatgtgttttgtgtctttgcagTTTCACCAGTACCAGGTGGTCGGGAGGGCTCTCCCAACGGAAGCAGATCAGCATCCGAAGATCTACCGAATGAAGCTCTGGGCCACCAACGAGGTTCGCG
               |   ||     |       | ||   ||| |   | |||  || ||  | |||||  |  ||    || ||||   | ||      ||||||||||||||||||||||| ||| |||| |||||||| |   |  || |   ||| |||  |||||| |||||  | ||||| || ||||| || ||||
gcgtcgagccggtaggaaagtggagattgaattgt-ctccatttaaaggcttctatctgcg--tgtgattactctgattgtgtttgtgcgct-tggtacaacagTTTCACCAGTACCAGGTGGTGGGGCGGGCCCTCCCAACAGCTACCAATGAAACTCCCAAGGCCTACCGCATGAAATTATGGGCGACGAACGAAGTGCGCG

upper sequence: GLYMA13G28830.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S184_111V6.1 (Physcomitrella patens), 3'ss of exon 1
--gtgcgtaagattcacgccattc---tgtgtttgatttcatcttccttcgattatgatttttacga----ggtagtatgtgttttg--tgtctttgcagTTTCACCAGTACCAGGTGGTCGGGAGGGCTCTCCCAACGGAAGCAGATCAGCATCCGAAGATCTACCGAATGAAGCTCTGGGCCACCAACGAGGTTCGCG
   ||     |  | | | | | |   ||   | |  | | | ||   || |      || ||  |     | | |      || ||  |||| |  ||||||||||||||||||||||| ||  |||| |||||||| |   |  || ||   || |||   ||||| |||||| | ||||| || || || || ||||
agttgtaggggtattatgtcgtgcacttgaagtgggatgcgtgttatctctacggctgttattgtggttttgatggctacgattatgcttgtcgtgacagTTTCACCAGTACCAGGTGGTGGGTCGGGCCCTCCCAACTGCTACCAATGAGACCCCCAAGGCATACCGCATGAAGTTGTGGGCGACGAATGAAGTGCGCG

upper sequence: GLYMA13G28830.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S74_193V6.2 (Physcomitrella patens), 3'ss of exon 1
-gtgcgtaa--gattcacgccattctgtgtttgatt--tcat-------cttccttcgattatgatttttacgaggtagtatgtgttttgtgtctttgcagTTTCACCAGTACCAGGTGGTCGGGAGGGCTCTCCCAACGGAAGCAGATCAGCATCCGAAGATCTACCGAATGAAGCTCTGGGCCACCAACGAGGTTCGCG
 |||  | |  | || | | ||   |  || |||    ||||       |||  ||  || ||  |        | | |      |||  | |  |  |||||||| || ||||||||||| ||| |||| || || || |   |  || ||   || |||   ||||| ||||||||||||||||||||||| || ||||
tgtgtatgattgtttgatgtcaccgta-gtatgacccatcatgcggtaacttgttttcatcattttccggttctgatcgctccaatttcttttggtatcagTTTCATCAATACCAGGTGGTTGGGCGGGCCCTTCCTACCGCGACCAATGAGACACCTAAGGCTTACCGCATGAAGCTCTGGGCCACCAACGAAGTGCGCG

upper sequence: GLYMA13G28830.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ38689 (Selaginella moellendorffii), 3'ss of exon 1
gtgcgtaagattcacgccattctgtgtttgatttcatcttccttcgattatgatttttacgaggtagtatgtgttttgtgtctttgcagTTTCACCAGTACCAGGTGGTCGGGAGGGCTCTCCCAACGGAAGCAGATCAGCATCCGAAGATCTACCGAATGAAGCTCTGGGCCACCAACGAGGTTCGCG
                         ||  || |||        ||||        |  |     |   ||   |    |    | ||||||||| |||||||||||||||||||| |||   || ||    |   || |||| || ||||| ||||| |||||||||||||||  | |||| || ||||
-------------------------gtaagaattcgca---gctcgagcgctcgatccatcgattg--atccctcccattgtctcgcagTTTCATCAGTACCAGGTGGTCGGGAGAGCTACTCCCACTCCCGACAATGAGCACCCAAAGATGTACCGGATGAAGCTCTGGGCCGGCGACGAAGTGCGCG

upper sequence: GLYMA13G28830.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ31458 (Selaginella moellendorffii), 3'ss of exon 1
gtgcgtaagattcacgccattctgtgtttgatttcatcttccttcgattatgatttttacgaggtagtatgtgttttgtgtctttgcagTTTCACCAGTACCAGGTGGTCGGGAGGGCTCTCCCAACGGAAGCAGATCAGCATCCGAAGATCTACCGAATGAAGCTCTGGGCCACCAACGAGGTTCGCG
                         ||  || |||        ||||        |  |     |   ||   |    |    | ||||||||||||||||||||||||||| || |||   || ||    |   || |||| || ||||| ||||| |||||||||||||||  | |||| || ||||
-------------------------gtaagaattcgca---gctcgagcgctcgatccatcgattg--atccctcccattgtctcgcagTTTCACCAGTACCAGGTGGTCGGAAGAGCTACTCCCACTCCCGACAATGAGCACCCAAAGATGTACCGGATGAAGCTCTGGGCCGGCGACGAAGTGCGCG

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|14991155|gb|BI316828.1|BI316828
EST:     AGAGAGTGTTCTTCGTTTGTTACCTTCTCTCAGAAATGGTTACGTTCAGG                         TTTCACCAGTACCAGGTGGTCGGGAGGGCTCTCCCAACGGAAGCAGATCAG
genomic: AGAGAGTGTTCTTCGTTTGCTACCTTCTCCCAGAAATGGTTACGTTCAGGgtgcgtaaga ... gtctttgcagTTTCACCAGTACCAGGTGGTCGGGAGGGCTCTCCCAACGGAAGCAGATCAG
EST: gi|193389576|gb|FK357177.1|FK357177
EST:     AGAGAGTGTTCTTCGTTTGCTACCTTCTCCCAGAAATGGTTACGTTCAGG                         TTTCACCAGTACCAGGTGGTCGGGAGGGCTCTCCCAACGGAAGCAGATCAG
genomic: AGAGAGTGTTCTTCGTTTGCTACCTTCTCCCAGAAATGGTTACGTTCAGGgtgcgtaaga ... gtctttgcagTTTCACCAGTACCAGGTGGTCGGGAGGGCTCTCCCAACGGAAGCAGATCAG
EST: gi|4395921|gb|AI494918.1|AI494918
EST:     AGAGAGTGTTCTTCGTTTGCTACCTTCTCCCAGAAATGGTTACGTTCAGG                         TTTCACCAGTACCAGGTGGTCGGGAGGGCTCTCCCAACGGAAGCAGATCAG
genomic: AGAGAGTGTTCTTCGTTTGCTACCTTCTCCCAGAAATGGTTACGTTCAGGgtgcgtaaga ... gtctttgcagTTTCACCAGTACCAGGTGGTCGGGAGGGCTCTCCCAACGGAAGCAGATCAG
EST: gi|207825851|gb|GD801034.1|GD801034
EST:     AGAGAGTGTTCTTCGTTTGCTACCTTCTCCCAGAAATGGTTACGTTCAGG                         TTTCACCAGTACCAGGTGGTCGGGAGGGCTCTCCCAACGGAAGCAGATCAG
genomic: AGAGAGTGTTCTTCGTTTGCTACCTTCTCCCAGAAATGGTTACGTTCAGGgtgcgtaaga ... gtctttgcagTTTCACCAGTACCAGGTGGTCGGGAGGGCTCTCCCAACGGAAGCAGATCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catcttccttcgattatgatttttacgaggtagtatgtgttttgtgtctttgcagTTTCACCAGTACCAGGTGGTCGGGAGGGCTCTCCCAACGGAAGCAGATCAGCATCCGAAGATCTACCGAATGAAGCTCTGGGCCACCAACGAGGTTCGCG
                                            tgtcttt  CT-rich tract
            attatgattttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgtaagattcacgccattctgtgtttgatttcatcttccttcgattatgatttttacgaggtagtatgtgttttgtgtctttgcagTTTCACCAGTACCAGGTGGTCGGGAGGGCTCTCCCAACGGAAGCAGATCAGCATCCGAAGATCTACCGAATGAAGCTCTGGGCCACCAACGAGGTTCGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC