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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actatatgtatagtccatgttaagaaggcaaaatgtctattgttcatcatttgtttagcacgttgtttacaaattacaagacttgacattcctgtttcagGGTTCATGGATAGTAAAGCAGAGTGTGGGAAAGAAGGCATGCCTAGTTGGTCAAGCACTGGAAATCAATTATTTCCAGGGAAGTAACTATTTGGAG

Basic information

species Glycine max
transcript GLYMA12G29750.1
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G29750.1 (Glycine max), 3'ss of exon 18
lower sequence: LOC_Os10g33930.1 (Oryza sativa), 3'ss of exon 7
actatatgtatagtccatgttaagaaggcaaaatgtctattgtt--catcatttgtttagcacgttgtttacaaattacaagacttgacattcctgtttcagGGTTCATGGATAGTAAAGCAGAGTGTGGGAAAGAAGGCATGCCTAGTTGGTCAAGCACTGGAAATCAATTATTTCCAGGGAAGTAACTATTTGGAG
            || | | ||  | |     |   |  ||| ||  ||   |||  |||| |  | | | |    |||       |     | | | ||||||| || |||||||||||||| |||||||||||||| || ||  | |||||||||||||| || |||||||||||||  ||||| || |||||||||
------------gtacctattctgcactaccagccttcattcttgtcaagctttacttagtaaat-gctgatggtttatcttcggtatatgtgccgcttcagGGGTCTTGGATAGTAAAGCAAAGTGTGGGAAAGAAAGCCTGTTTGGTTGGTCAAGCACTAGAGATCAATTATTTCCGTGGAAGCAATTATTTGGAG

upper sequence: GLYMA12G29750.1 (Glycine max), 3'ss of exon 18
lower sequence: GRMZM2G069976_T01 (Zea mays), 3'ss of exon 19
actatatgtatagtccatgttaagaaggcaaaatgtctattgttcatcatttgtttagcacgttgtttacaaattacaagacttgacattcctgt---ttcagGGTTCATGGATAGTAAAGCAGAGTGTGGGAAAGAAGGCATGCCTAGTTGGTCAAGCACTGGAAATCAATTATTTCCAGGGAAGTAACTATTTGGAG
       || |  |      |  ||     |  ||     | || | | | |  | || |   |||  | |  |||      |||  ||   |||   || |||| || ||||| || || ||||||||||| ||||| || ||| | ||||| |||||| | |||||||||||||| |  ||||| ||||||||||||
-------gtttgttttgcactttgagccttatttgatctgttttaagc-tgtactcagtaaactgtcaatatcttatt---tttggaatgtgtgtctatttagGGATCTTGGATTGTTAAACAGAGTGTGGGCAAGAAAGCTTGCTTGGTTGGACAAGCATTAGAAATCAATTATTTTCGTGGAAGAAACTATTTGGAG

upper sequence: GLYMA12G29750.1 (Glycine max), 3'ss of exon 18
lower sequence: AT2G28320.1 (Arabidopsis thaliana), 3'ss of exon 18
actatatgtatagtccatgttaagaaggcaaaatgtctattgttcatcatttgtttagcacgt-tgtttacaaattacaa--gacttgacattcctgtttcagGGTTCATGGATAGTAAAGCAGAGTGTGGGAAAGAAGGCATGCCTAGTTGGTCAAGCACTGGAAATCAATTATTTCCAGGGAAGTAACTATTTGGAG
            ||    || ||  |       | | || | || || |||||| |  |   |   || | |  | ||    |  ||| |  |    |||||||| || |||||||| ||||| |||||||||||||| ||||||||  |||||||||| ||||| ||||| || |||  |||||  |||||| | |||
------------gttggcgtaaaagattacctctatttagt-tttattatttgtctgtccaatgcattcatacctgacttttggtttggcgatat--tttcagGGCTCTTGGATAGTTAAGCAAAGTGTGGGAAAGAAAGCATGCCTTATTGGTCAAGCCCTGGAGATCAACTACTTCAGGGGAAAGAACTATATTGAG

upper sequence: GLYMA12G29750.1 (Glycine max), 3'ss of exon 18
lower sequence: Vv06s0004g02720.t01 (Vitis vinifera), 3'ss of exon 18
actatatgtatagtccatgttaagaaggcaaaatgtctat-tgttcatcatttgtttagcacgttgtttacaaattacaagact-tgacattcctgtttcagGGTTCATGGATAGTAAAGCAGAGTGTGGGAAAGAAGGCATGCCTAGTTGGTCAAGCACTGGAAATCAATTATTTCCAGGGAAGTAACTATTTGGAG
   | |  |||  |   | | || ||         | ||  | || |  |||   ||   |  | |  ||  |     | |||| | |  ||  | | |||||| || |||||||| |||||||| || |||||||| ||||||||||| |||||||| || ||||| ||||||||||| || |  ||||| ||||||
--aagacttattatttctttaaacaatattttgcttttaggtctttagaattgacttcaaatttggcgtaatataatgaggactgtaagcttaatttctcagGGGTCCTGGATAGTTAAGCAGAGCGTTGGAAAGAAAGCATGCCTAGTGGGTCAAGCGCTTGAAATTAATTATTTCCATGGGAAGAACTACTTGGAG

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|209712559|gb|BW653715.1|BW653715
EST:     ATGATGCCTTCAGAAATTCCAGATTTAAACTTATACCATACATATCTAAG                         GGTTCATGGATAGTAAAGCAGAGTGTGGGAAAGAAGGCATGCCTAGTTGGT
genomic: ATGATGCCTTCAGAAATTCCAGATTTAAACTTATACCATACATATCTAAGgtgagtaaaa ... cctgtttcagGGTTCATGGATAGTAAAGCAGAGTGTGGGAAAGAAGGCATGCCTAGTTGGT
EST: gi|22933067|gb|BU550206.1|BU550206
EST:     ATGATGCCTTCAGAAATTCCAGATTTAAACTTATACCATACATATNNAAG                         GGTTCATGGATAGTAAAGCAGAGTGTGGGAAAGAAGGCATGCCTAGTTGGT
genomic: ATGATGCCTTCAGAAATTCCAGATTTAAACTTATACCATACATATCTAAGgtgagtaaaa ... cctgtttcagGGTTCATGGATAGTAAAGCAGAGTGTGGGAAAGAAGGCATGCCTAGTTGGT
EST: gi|192327435|gb|FK018167.1|FK018167
EST:     ATGATGCCTTCAGAAATTCCAGATTTAAACTTATACCATACATATCTAAG                         GGTTCATGGATAGTAAAGCAGAGTGCGGGAAAGAAGGCATGCCTAGTTGGT
genomic: ATGATGCCTTCAGAAATTCCAGATTTAAACTTATACCATACATATCTAAGgtgagtaaaa ... cctgtttcagGGTTCATGGATAGTAAAGCAGAGTGTGGGAAAGAAGGCATGCCTAGTTGGT
EST: gi|209722676|gb|BW654683.1|BW654683
EST:     ATGATGCCTTCAGAAATTCCAGATTTAAACTTATACCATACATATCTAAG                         GGTTCATGGATAGTAAAGCAGAGTGTGGGAAAGAAGGCATGCCTAGTTGGT
genomic: ATGATGCCTTCAGAAATTCCAGATTTAAACTTATACCATACATATCTAAGgtgagtaaaa ... cctgtttcagGGTTCATGGATAGTAAAGCAGAGTGTGGGAAAGAAGGCATGCCTAGTTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcatttgtttagcacgttgtttacaaattacaagacttgacattcctgtttcagGGTTCATGGATAGTAAAGCAGAGTGTGGGAAAGAAGGCATGCCTAGTTGGTCAAGCACTGGAAATCAATTATTTCCAGGGAAGTAACTATTTGGAG
                                   acttgac  putative branch site (score: 4)
                                           ttcctgtttc  CT-rich tract
                 ttgtttacaaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actatatgtatagtccatgttaagaaggcaaaatgtctattgttcatcatttgtttagcacgttgtttacaaattacaagacttgacattcctgtttcagGGTTCATGGATAGTAAAGCAGAGTGTGGGAAAGAAGGCATGCCTAGTTGGTCAAGCACTGGAAATCAATTATTTCCAGGGAAGTAACTATTTGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - ccatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttgaca