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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttgtcaccctttctgtctttatgtatttcttttttacttcaatttctcctcatgcctttgctccaaggtggcttttagtatctgctcggaggaattcagttgtaaatgaaggtaagattcggtgttactttattggcttgttcctgacatattttgaacagGAATTTAGTGATCCTCGAGATGCTGATGATGCTAGATACAACCTGGATGGTCGTGATGTTGAAGGAAGTCGTATTATTGTGGAATTTGCCAAGGGG

Basic information

species Glycine max
transcript GLYMA03G33270.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G33270.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G099186_T03 (Zea mays), 3'ss of exon 4
gtaagttgtcaccctttctgtctttatgtatttcttttttacttcaatttctcctcatgcctttgctccaaggtggcttttagtatctgctcggaggaattcagttgtaaatgaaggtaagattcggtgttactttattggcttgttcctgacatattttgaacagGAATTTAGTGATCCTCGAGATGCTGATGATGCTAGATACAACCTGGATGGTCGTGATGTTGAAGGAAGTCGTATTATTGTGGAATTTGCCAAGGGG
                                                             |||  |   || |  ||  || |||       ||  ||  || || |   || | || | ||||    ||| ||| |  | |  ||  |||    |    |||||||||| ||||| || || ||||||||||||||    |||||||| |||||  | || || || ||||| ||||||||||| |||||||| || || 
---------------------------------------------------------gatttttaatgttagcttactcgtattatggaaattgaaaaaaacatttattt-tgcacgtgacattct---ttattttgtccgatgttt--tgat---tgcaaaacagGAATTCAGTGACCCCCGTGATGCTGATGATGCGCAGTACAACCTAGATGGCAGGGAAGTCGATGGAAGCCGTATTATTGTTGAATTTGCTAAAGGA

upper sequence: GLYMA03G33270.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv08s0040g02860.t01 (Vitis vinifera), 3'ss of exon 1
gtaagttgtcaccctttctgtctttatgtatttcttttttacttcaatttctcctcatgcctttgctccaaggtggcttttagtatctgctcggaggaattcagttgtaaatgaaggta---agattcg-gtgttactttattggcttgttcctgacatattttgaacagGAATTTAGTGATCCTCGAGATGCTGATGATGCTAGATACAACCTGGATGGTCGTGATGTTGAAGGAAGTCGTATTATTGTGGAATTTGCCAAGGGG
||| ||  ||| || ||   | || || |||||||||  |  |||      | || |||  | ||    |   |   | |   ||| |      || | |    || || |||  | ||   | ||  | |  |  | || || | |  | |     || || |  ||||||||| |||||||| ||||||||||||||||| ||||| ||| |  |||| || ||| |||| ||||||||||| |||||||||||||| || |||
gtatgt-atcaaccatt---tgttcatctatttctttcctttttct-cccttgcttatggttatgg---agtatttttctccttatttatctatagaagtcacattatagatggtgttacacaaatatgagcatcccgttgttcgttcttgcacttaattttatctacagGAATTCAGTGATCCCCGAGATGCTGATGATGCAAGATATAACTTAAATGGACGAGATTTTGATGGAAGTCGTATCATTGTGGAATTTGCGAAAGGG
















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|254344581|gb|GR855452.1|GR855452
EST:     GAAGAATGATTTCGCCTTTGTT                         GAATTTAGTGATCCTCGAGATGCTGATGATGCTAGATACAACCTGGATGGT
genomic: GAAGAATGATTTCGCCTTTGTTgtaagttgtc ... ttttgaacagGAATTTAGTGATCCTCGAGATGCTGATGATGCTAGATACAACCTGGATGGT
EST: gi|192331339|gb|FK023808.1|FK023808
EST:     AGTTCGAGGCGTAGATATGAAGAATGATTTCGTCTTTGTT                         GAATTTAGTGATCCTCGAGATGCTGATGATGCTAGATACAACCTGGATGGT
genomic: AGTTCGAGGCGTAGATATGAAGAATGATTTCGCCTTTGTTgtaagttgtc ... ttttgaacagGAATTTAGTGATCCTCGAGATGCTGATGATGCTAGATACAACCTGGATGGT
EST: gi|151411040|gb|EV280851.1|EV280851
EST:     AGTTCGAGGCGTAGATATGAAGAATGATTTCGCCTTTGTT                         GAATTTAGTGATCCTCGAGATGCTGATGATGCTAGATACAACCTGGATGGT
genomic: AGTTCGAGGCGTAGATATGAAGAATGATTTCGCCTTTGTTgtaagttgtc ... ttttgaacagGAATTTAGTGATCCTCGAGATGCTGATGATGCTAGATACAACCTGGATGGT
EST: gi|26058479|gb|CA801393.1|CA801393
EST:     AGTTCGAGGCGTAGATATGAAGAATGATTTCGCCTTTGTT                         GAATTTAGTGATCCTCGAGATGCTGATGATGCTAGATACAACCTGGATGGT
genomic: AGTTCGAGGCGTAGATATGAAGAATGATTTCGCCTTTGTTgtaagttgtc ... ttttgaacagGAATTTAGTGATCCTCGAGATGCTGATGATGCTAGATACAACCTGGATGGT
EST: gi|120529026|gb|EH257160.1|EH257160
EST:     AGTTCGAGGCGTAGATATGAAGAATGATTTCGCCTTTGTT                         GAATTTAGTGATCCTCGAGATGCTGATGATGCTAGATACAANCTGGATGGT
genomic: AGTTCGAGGCGTAGATATGAAGAATGATTTCGCCTTTGTTgtaagttgtc ... ttttgaacagGAATTTAGTGATCCTCGAGATGCTGATGATGCTAGATACAACCTGGATGGT
EST: gi|254332768|gb|GR846599.1|GR846599
EST:     AGTTCGAGGCGT--ATATGAAGAATGATTTCGCCTTTGTT                         GAATTTAGTGATCCTCGAGATGCTGATGATGCTAGATACAACCTGGATGGT
genomic: AGTTCGAGGCGTAGATATGAAGAATGATTTCGCCTTTGTTgtaagttgtc ... ttttgaacagGAATTTAGTGATCCTCGAGATGCTGATGATGCTAGATACAACCTGGATGGT
EST: gi|120534327|gb|EH262460.1|EH262460
EST:     AGTTCGAGGCGTAGATATGAAGAATGATTTCGCCTTTGTT                         GAATTTAGTGATCCTCGAGATGCTGATGATGCTAGATACAACCTGGATGGT
genomic: AGTTCGAGGCGTAGATATGAAGAATGATTTCGCCTTTGTTgtaagttgtc ... ttttgaacagGAATTTAGTGATCCTCGAGATGCTGATGATGCTAGATACAACCTGGATGGT
EST: gi|192320086|gb|FK014170.1|FK014170
EST:     AGTTCGAGGCGTAGATATGAAGAATGATTTCGCCTTTGTT                         GAATTTAGTGATCCTCGAGATGCTGATGATGCTAGATACAACCTGGATGGT
genomic: AGTTCGAGGCGTAGATATGAAGAATGATTTCGCCTTTGTTgtaagttgtc ... ttttgaacagGAATTTAGTGATCCTCGAGATGCTGATGATGCTAGATACAACCTGGATGGT
EST: gi|192299767|gb|FG993317.1|FG993317
EST:     AGTTCGAGGCGTAGATATGAAGAATGATTTCGCCTTTGTT                         GAATTTAGTGATCCTCGAGATGCTGATGATGCTAGATACAACCTGGATGGT
genomic: AGTTCGAGGCGTAGATATGAAGAATGATTTCGCCTTTGTTgtaagttgtc ... ttttgaacagGAATTTAGTGATCCTCGAGATGCTGATGATGCTAGATACAACCTGGATGGT
EST: gi|192328414|gb|FK020125.1|FK020125
EST:     AGTTCGAGGCGTAGATATGAAGAATGATTTCGCCTTTGTT                         GAATTTAGTGATCCTCGAGATGCTGATGATGCTAGATACAACCTGGATGGT
genomic: AGTTCGAGGCGTAGATATGAAGAATGATTTCGCCTTTGTTgtaagttgtc ... ttttgaacagGAATTTAGTGATCCTCGAGATGCTGATGATGCTAGATACAACCTGGATGGT
EST: gi|7146149|gb|AW508071.1|AW508071
EST:     AGTTCGAGGCGTAGATATGAAGAATGATTTCGCCTTTGTT                         GAATTTAGTGATCCTCGAGATGCTGATGATGCTAGATACAACCTGGATGGT
genomic: AGTTCGAGGCGTAGATATGAAGAATGATTTCGCCTTTGTTgtaagttgtc ... ttttgaacagGAATTTAGTGATCCTCGAGATGCTGATGATGCTAGATACAACCTGGATGGT
EST: gi|7692902|gb|AW761001.1|AW761001
EST:     AGTTCGAGGCGTAGATATGAAGAATGATTTCGCCTTTGTT                         GAATTTAGTGATCCTCGAGATGCTGATGATGCTAGATACAACCTGGATGGT
genomic: AGTTCGAGGCGTAGATATGAAGAATGATTTCGCCTTTGTTgtaagttgtc ... ttttgaacagGAATTTAGTGATCCTCGAGATGCTGATGATGCTAGATACAACCTGGATGGT
EST: gi|151398264|gb|EV268142.1|EV268142
EST:     AGTTCGAGGCGTAGATATGAAGAATGATTTCGCCTTTGTT                         GAATTTAGTGATCCTCGAGATGCTGATGATGCTAGATACAACCTGGATGGT
genomic: AGTTCGAGGCGTAGATATGAAGAATGATTTCGCCTTTGTTgtaagttgtc ... ttttgaacagGAATTTAGTGATCCTCGAGATGCTGATGATGCTAGATACAACCTGGATGGT
EST: gi|193440148|gb|FK408535.1|FK408535
EST:     AGTTCGAGGCGTAGATATGAAGAATGATTTCGCTTTTGTT                         GATTTTAGTGAT
genomic: AGTTCGAGGCGTAGATATGAAGAATGATTTCGCCTTTGTTgtaagttgtc ... ttttgaacagGAATTTAGTGAT
EST: gi|16347699|gb|BI973294.1|BI973294
EST:     AGTTCGAGGCGTAGATATGAAGAATGATTTCGTCTTTGTT                         GAATTTAGTGATCCTCGAGATGCTGATGATGCTAGATACAACCTGGATGGT
genomic: AGTTCGAGGCGTAGATATGAAGAATGATTTCGCCTTTGTTgtaagttgtc ... ttttgaacagGAATTTAGTGATCCTCGAGATGCTGATGATGCTAGATACAACCTGGATGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaggtaagattcggtgttactttattggcttgttcctgacatattttgaacagGAATTTAGTGATCCTCGAGATGCTGATGATGCTAGATACAACCTGGATGGTCGTGATGTTGAAGGAAGTCGTATTATTGTGGAATTTGCCAAGGGG
                                   tcctgac  putative branch site (score: 2)
                  ttactttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttgtcaccctttctgtctttatgtatttcttttttacttcaatttctcctcatgcctttgctccaaggtggcttttagtatctgctcggaggaattcagttgtaaatgaaggtaagattcggtgttactttattggcttgttcctgacatattttgaacagGAATTTAGTGATCCTCGAGATGCTGATGATGCTAGATACAACCTGGATGGTCGTGATGTTGAAGGAAGTCGTATTATTGTGGAATTTGCCAAGGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA