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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcaaaaactcttgttgagttgaaatagtctgtacttcaattattgagtctctgccactatacctaatccttgctctcattatccatcttttaaatgtaggTTGTTGAACTTGATTTTCTCTATCCTAGTGAGGGAATCCACAGGCGATGGGATAATGGTTATAGGATTACAGCAACTGCTGCTACATGGGATCAATCTGC

Basic information

species Glycine max
transcript GLYMA18G53810.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G53810.1 (Glycine max), 3'ss of exon 14
lower sequence: AT3G13670.1 (Arabidopsis thaliana), 3'ss of exon 14
gcaaaaactctt--gttgagttgaaatagtc---tgtacttcaattattgagtctctgccactatacctaatccttgctctcattatccatcttttaaatgtaggTTGTTGAACTTGATTTTCTCTATCCTAGTGAGGGAATCCACAGGCGATGGGATAATGGTTATAGGATTACAGCAACTGCTGCTACATGGGATCAATCTGC
|  | |  ||     |  || |||| |  |    | | ||||| || | ||      ||    ||  ||||| ||  || |  |     || | |    |  ||||||| |||||||||||||| ||||| ||||| || ||||||||||| ||||||  ||| |  || || ||| |||| || || |||   |||||| ||| 
gttagacttcaccgatatagatgaatttcttccgtttccttcagttttggatctgtcgcgttgatttctaattctc-ctgttttcgcttatatctcctctacagGTTGTGGAACTTGATTTTCTGTATCCAAGTGAAGGCATCCACAGGCGTTGGGATGGTGGATTCAGAATCACATCAACAGCAGCCACAACCGATCAAGCTG-

upper sequence: GLYMA18G53810.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv06s0004g01090.t01 (Vitis vinifera), 3'ss of exon 14
gcaaaaactcttgttgagttgaaata-gtctgtacttcaattattgagtctctgccactatacctaatccttgctctcattatccatcttttaaatg-------taggTTGTTGAACTTGATTTTCTCTATCCTAGTGAGGGAATCCACAGGCGATGGGATAATGGTTATAGGATTACAGCAACTGCTGCTACATGGGATCAATCTGC
       || || |    || || || |  || | |||| ||||   |  | |     | |   |     |   |||| || || | ||| | ||||       |||||||| || ||||||||||||||||| |||||||| ||||||||  | ||||| | ||||||| | || ||| |||| ||||| || ||||||||||||| 
------tctgttttatcatttaactatggttgcagttca-ttataatggttttagagttttggttttgattgtttctctttctctaacttgtcaatgacgttcatagGTTGTGGAGCTTGATTTTCTCTATCCAAGTGAGGGCATCCACAGAAGGTGGGACAGTGGTTATCGAATAACATCAACGGCTGCAACTTGGGATCAATCTG-
















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|298196558|gb|HO041301.1|HO041301
EST:     AAGTCGTTGGGGTGTTGTTATGTCGCGAAATGCCGGATTCAGTGATCAGG                         TTGTTGAACTTGATTTTCTCTATCCTAGTGAGGGAATCCACAGGCGATGGG
genomic: AAGTCGTTGGGGTGTTGTTATGTCGCGAAATGCCGGATTCAGTGATCAGGtttgctttat ... taaatgtaggTTGTTGAACTTGATTTTCTCTATCCTAGTGAGGGAATCCACAGGCGATGGG
EST: gi|15337953|gb|BI498609.1|BI498609
EST:     AAGTCGTTGGGGTGTTGTTATGTCGCGAAATGCCGGATTCAGTGATCAAG                         TTGTTGAACTTGATTTTCTCTATCCTAGTGAGGGAATC
genomic: AAGTCGTTGGGGTGTTGTTATGTCGCGAAATGCCGGATTCAGTGATCAGGtttgctttat ... taaatgtaggTTGTTGAACTTGATTTTCTCTATCCTAGTGAGGGAATC
EST: gi|58022100|gb|CX708841.1|CX708841
EST:     AAGTCGTTGGGGTGTTGTTATGTCGCGAAATGCCGGATTCAGTGATCAGG                         TTGTTGAACTTGATTTTCTCTATCCTAGTGAGGGAATCCACAGGCGATGGG
genomic: AAGTCGTTGGGGTGTTGTTATGTCGCGAAATGCCGGATTCAGTGATCAGGtttgctttat ... taaatgtaggTTGTTGAACTTGATTTTCTCTATCCTAGTGAGGGAATCCACAGGCGATGGG
EST: gi|10709803|gb|BF009527.1|BF009527
EST:     AAGTCGTTGGGGTGTTGTTATGTCGCGAAATGCCGGATTCAGTGATCAGG                         TTGTTGAACTTGATTTTCTCTATCCTAGTGAGGGAATCCACAGGCGATGGG
genomic: AAGTCGTTGGGGTGTTGTTATGTCGCGAAATGCCGGATTCAGTGATCAGGtttgctttat ... taaatgtaggTTGTTGAACTTGATTTTCTCTATCCTAGTGAGGGAATCCACAGGCGATGGG
EST: gi|13252748|gb|BG363651.1|BG363651
EST:     AAGTCGTTGGGGTGTTGTTATGTCGCGAAATGCCGGATTCAGTGATCAGG                         TTGTTGAACTTGATTTTCTCTATCCTAGTGAGGGAATCCACAGGCGATGGG
genomic: AAGTCGTTGGGGTGTTGTTATGTCGCGAAATGCCGGATTCAGTGATCAGGtttgctttat ... taaatgtaggTTGTTGAACTTGATTTTCTCTATCCTAGTGAGGGAATCCACAGGCGATGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtctctgccactatacctaatccttgctctcattatccatcttttaaatgtaggTTGTTGAACTTGATTTTCTCTATCCTAGTGAGGGAATCCACAGGCGATGGGATAATGGTTATAGGATTACAGCAACTGCTGCTACATGGGATCAATCTGC
               acctaat  putative branch site (score: 3)
                                    tccatctttt  putative PPT
                                       atcttttaaatgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaaaaactcttgttgagttgaaatagtctgtacttcaattattgagtctctgccactatacctaatccttgctctcattatccatcttttaaatgtaggTTGTTGAACTTGATTTTCTCTATCCTAGTGAGGGAATCCACAGGCGATGGGATAATGGTTATAGGATTACAGCAACTGCTGCTACATGGGATCAATCTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
-caaaaac
- - - - -cttgttg
- - - - - - - - - - - - - -tctgtac
- - - - - - - - - - - - - - - - - - - - - - - - ctctgcc