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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cccaaactggtgtttagttcgtctttgaggggtgatgtatcatacagttccagtagttaagtaatgatggccttattgtttctggaaaccatttccgcagAGTTCGAGGCGTAGATATGAAGAATGATTTCGCCTTTGTT

Basic information

species Glycine max
transcript GLYMA03G33270.1
intron # 2
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 2
lower sequence: GRMZM2G175419_T02 (Zea mays), 3'ss of exon 3
----------cccaaactggtgtttagttcgtctttgaggggtgatgtatcatacagttccagtagttaagtaatg--------atggccttattgtttctggaaaccatttccgcagAGTTCGAGGCGTAGATATGAAGAATGATTTCGCCTTTGTT
          |||    ||   | |  ||     |||  |  ||||| |      ||||   ||| || |||| |          |   |||||||||| ||| ||||||||||||||| ||||||  || ||  |||||  ||| |  || ||  ||
gtgaagggcgcccttggtgtaatcttattgactgttgtaga-tgatgaagttgcaagttaatgtatttgagtacttcgactcacgtcagcttattgtttgtggcaaccatttccgcagAATTCGAGAAGTGGAGTTGAAGCGTGACTATGCATTCATT

upper sequence: GLYMA03G33270.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G175419_T01 (Zea mays), 3'ss of exon 2
cccaaactggtgtttagttcgtctttgaggggtgatgtatcatacagttccagtagttaagtaatgatggccttattgtttctggaaaccatttccgcagAGTTCGAGGCGTAGATATGAAGAATGATTTCGCCTTTGTT
   || ||  |     |||     |   |  ||      | |     ||  |||| ||         |   |||||||||| ||| ||||||||||||||| ||||||  || ||  |||||  ||| |  || ||  ||
tgtaatcttattgactgttgtagatgatgaagttgcaagttaatgtatttgagtacttcgactcacgtcagcttattgtttgtggcaaccatttccgcagAATTCGAGAAGTGGAGTTGAAGCGTGACTATGCATTCATT
















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|193711520|gb|FK642985.1|FK642985
EST:     TCGAGGACTCGTTCCCGTGACCTGGAGCGTGTCTTCAGCAGATATGGAAG                         AGTTCGAGGCGTAGATATGAAGAA
genomic: TCGAGGACTCGTTCCCGTGACCTGGAGCGTGTCTTCAGCAGATATGGAAGgtaattttcc ... atttccgcagAGTTCGAGGCGTAGATATGAAGAA
EST: gi|192331339|gb|FK023808.1|FK023808
EST:     TCGAGGACTCGTTCCCGTGACCTGGAGCGTGTCTTCAGCAGATATGGAAG                         AGTTCGAGGCGTAGATATGAAGAATGATTTCGTCTTTGTT
genomic: TCGAGGACTCGTTCCCGTGACCTGGAGCGTGTCTTCAGCAGATATGGAAGgtaattttcc ... atttccgcagAGTTCGAGGCGTAGATATGAAGAATGATTTCGCCTTTGTT
EST: gi|151411040|gb|EV280851.1|EV280851
EST:     TCGAGGACTCGTTCCCGTGACCTGGAGCGTGTCTTCAGCAGATATGGAAG                         AGTTCGAGGCGTAGATATGAAGAATGATTTCGCCTTTGTT
genomic: TCGAGGACTCGTTCCCGTGACCTGGAGCGTGTCTTCAGCAGATATGGAAGgtaattttcc ... atttccgcagAGTTCGAGGCGTAGATATGAAGAATGATTTCGCCTTTGTT
EST: gi|26058479|gb|CA801393.1|CA801393
EST:     TCGAGGACTCGTTCCCGTGACCTGGAGCGTGTCTTCAGCAGATATGGAAG                         AGTTCGAGGCGTAGATATGAAGAATGATTTCGCCTTTGTT
genomic: TCGAGGACTCGTTCCCGTGACCTGGAGCGTGTCTTCAGCAGATATGGAAGgtaattttcc ... atttccgcagAGTTCGAGGCGTAGATATGAAGAATGATTTCGCCTTTGTT
EST: gi|120529026|gb|EH257160.1|EH257160
EST:     TCGAGGACTCGTTCCCGTGACCTGGAGCGTGTCTTCAGCAGATATGGAAG                         AGTTCGAGGCGTAGATATGAAGAATGATTTCGCCTTTGTT
genomic: TCGAGGACTCGTTCCCGTGACCTGGAGCGTGTCTTCAGCAGATATGGAAGgtaattttcc ... atttccgcagAGTTCGAGGCGTAGATATGAAGAATGATTTCGCCTTTGTT
EST: gi|254332768|gb|GR846599.1|GR846599
EST:     TCGAGGACTCGTTCCCGTGACCTGGAGCGTGTCTTCAGCAGATATGGAAG                         AGTTCGAGGCGT--ATATGAAGAATGATTTCGCCTTTGTT
genomic: TCGAGGACTCGTTCCCGTGACCTGGAGCGTGTCTTCAGCAGATATGGAAGgtaattttcc ... atttccgcagAGTTCGAGGCGTAGATATGAAGAATGATTTCGCCTTTGTT
EST: gi|120534327|gb|EH262460.1|EH262460
EST:     TCGAGGACTCGTTCCCGTGACCTGGAGCGTGTCTTCAGCAGATATGGAAG                         AGTTCGAGGCGTAGATATGAAGAATGATTTCGCCTTTGTT
genomic: TCGAGGACTCGTTCCCGTGACCTGGAGCGTGTCTTCAGCAGATATGGAAGgtaattttcc ... atttccgcagAGTTCGAGGCGTAGATATGAAGAATGATTTCGCCTTTGTT
EST: gi|192320086|gb|FK014170.1|FK014170
EST:     TCGAGGACTCGTTCCCGTGACCTGGAGCGTGTCTTCAGCAGATATGGAAG                         AGTTCGAGGCGTAGATATGAAGAATGATTTCGCCTTTGTT
genomic: TCGAGGACTCGTTCCCGTGACCTGGAGCGTGTCTTCAGCAGATATGGAAGgtaattttcc ... atttccgcagAGTTCGAGGCGTAGATATGAAGAATGATTTCGCCTTTGTT
EST: gi|192299767|gb|FG993317.1|FG993317
EST:     TCGAGGACTCGTTCCCGTGACCTGGAGCGTGTCTTCAGCAGATATGGAAG                         AGTTCGAGGCGTAGATATGAAGAATGATTTCGCCTTTGTT
genomic: TCGAGGACTCGTTCCCGTGACCTGGAGCGTGTCTTCAGCAGATATGGAAGgtaattttcc ... atttccgcagAGTTCGAGGCGTAGATATGAAGAATGATTTCGCCTTTGTT
EST: gi|192328414|gb|FK020125.1|FK020125
EST:     TCGAGGACTCGTTCCCGTGACCTGGAGCGTGTCTTCAGCAGATATGGAAG                         AGTTCGAGGCGTAGATATGAAGAATGATTTCGCCTTTGTT
genomic: TCGAGGACTCGTTCCCGTGACCTGGAGCGTGTCTTCAGCAGATATGGAAGgtaattttcc ... atttccgcagAGTTCGAGGCGTAGATATGAAGAATGATTTCGCCTTTGTT
EST: gi|7146149|gb|AW508071.1|AW508071
EST:     TCGAGGACTCGTTCCCGTGACCTGGAGCGTGTCTTCAGCAGATATGGAAG                         AGTTCGAGGCGTAGATATGAAGAATGATTTCGCCTTTGTT
genomic: TCGAGGACTCGTTCCCGTGACCTGGAGCGTGTCTTCAGCAGATATGGAAGgtaattttcc ... atttccgcagAGTTCGAGGCGTAGATATGAAGAATGATTTCGCCTTTGTT
EST: gi|7692902|gb|AW761001.1|AW761001
EST:     TCGAGGACTCGTTCCCGTGACCTGGAGCGTGTCTTCAGCAGATATGGAAG                         AGTTCGAGGCGTAGATATGAAGAATGATTTCGCCTTTGTT
genomic: TCGAGGACTCGTTCCCGTGACCTGGAGCGTGTCTTCAGCAGATATGGAAGgtaattttcc ... atttccgcagAGTTCGAGGCGTAGATATGAAGAATGATTTCGCCTTTGTT
EST: gi|151398264|gb|EV268142.1|EV268142
EST:     TCGAGGACTCGTTCCCGTGACCTGGAGCGTGTCTTCAGCAGATATGGAAG                         AGTTCGAGGCGTAGATATGAAGAATGATTTCGCCTTTGTT
genomic: TCGAGGACTCGTTCCCGTGACCTGGAGCGTGTCTTCAGCAGATATGGAAGgtaattttcc ... atttccgcagAGTTCGAGGCGTAGATATGAAGAATGATTTCGCCTTTGTT
EST: gi|193440148|gb|FK408535.1|FK408535
EST:     TCGAGGACTCGTTCCCGTGACCTGGAGCGTGTCTTCAGCAGATATGGAAG                         AGTTCGAGGCGTAGATATGAAGAATGATTTCGCTTTTGTT
genomic: TCGAGGACTCGTTCCCGTGACCTGGAGCGTGTCTTCAGCAGATATGGAAGgtaattttcc ... atttccgcagAGTTCGAGGCGTAGATATGAAGAATGATTTCGCCTTTGTT
EST: gi|16347699|gb|BI973294.1|BI973294
EST:     TCGAGGACTCGTTCCCGTGACCTGGAGCGTGTCTTCAGCAGATATGGAAG                         AGTTCGAGGCGTAGATATGAAGAATGATTTCGTCTTTGTT
genomic: TCGAGGACTCGTTCCCGTGACCTGGAGCGTGTCTTCAGCAGATATGGAAGgtaattttcc ... atttccgcagAGTTCGAGGCGTAGATATGAAGAATGATTTCGCCTTTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttccagtagttaagtaatgatggccttattgtttctggaaaccatttccgcagAGTTCGAGGCGTAGATATGAAGAATGATTTCGCCTTTGTT
                                           ccatttcc  CT-rich tract
           ttaagtaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cccaaactggtgtttagttcgtctttgaggggtgatgtatcatacagttccagtagttaagtaatgatggccttattgtttctggaaaccatttccgcagAGTTCGAGGCGTAGATATGAAGAATGATTTCGCCTTTGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
-ccaaact
- - - - ggtgttt
- - - - - - - - - - - - -tgagggg
- - - - - - - - - - - - - - - - tgatgta
- - - - - - - - - - - - - - - - - - - -tcataca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatggc