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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtccttttggacctgatgttgtttttgtaatcagttagtattgaaggaaaatttttgtttgttgacttgtaacccagctgcctaacttgaaacttatttggttttcagGTATGTATGGGAATCAAAAGCTGATGGAGCATTCGCTATTTCAGAAGATACATGGAATGAACCACTTGGACGAGGAACTGAGATTAGATTACACCTCAAG

Basic information

species Glycine max
transcript GLYMA14G40320.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G40320.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os06g50300.1 (Oryza sativa), 3'ss of exon 6
gtaagtccttttggacctgatgttgtttttgtaatcagttagtattgaaggaaaatttttgtttgttgacttgtaacccagctgcctaacttgaaact----tatttggttttcagGTATGTATGGGAATCAAAAGCTGATGGAGCATTCGCTATTTCAGAAGATACATGGAATGAACCACTTGGACGAGGAACTGAGATTAGATTACACCTCAAG
||||| |      ||  | |    |  |   || |  |||  |  |  |      ||||  ||   || | ||  | ||  || | |    ||    |    | |||   |   ||| |||| ||||| || |||||||||||| |||||||||| || || ||||||||||||||||| || || || |||||||| || ||| | ||||||   
gtaagacaccactgaaat-acagcggctacatattgtgtttttggttcatcttc-ttttccttcactggcatgacaacctacttcatgttctgctgttgcactttttctctgatagGCATGTCTGGGAGTCCAAAGCTGATGGATCATTCGCTATCTCTGAGGATACATGGAATGAACCCCTGGGCCGTGGAACTGAAATAAGACTGCACCTCCGA

upper sequence: GLYMA14G40320.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G141931_T02 (Zea mays), 3'ss of exon 6
gtaagtccttttggacctgatgttgtttttgtaatcagttagtattgaaggaaaatttttgtttgttgacttgtaacccagctgcctaacttgaaacttatttggttttcagGTATGTATGGGAATCAAAAGCTGATGGAGCATTCGCTATTTCAGAAGATACATGGAATGAACCACTTGGACGAGGAACTGAGATTAGATTACACCTCAAG
||||| | ||   | |       ||||||| |  ||| ||    ||||         |||   | || ||||||  | ||      |    |   |||        ||| |||||||| ||||||||||||||||||||| |||| || || || || |||||||||||||| || ||||| || ||||||||||| ||||| || ||    
gtaagacattgctggc-------tgtttttttgttcatttc---ttga---------tttacctatttacttgtgtcacattattgtggtgttgcactc-------ttttagGTATGTGTGGGAATCAAAAGCTGATGGATCATTTGCCATCTCTGAGGATACATGGAATGAGCCCCTTGGCCGTGGAACTGAGATAAGATTGCATCTGCGA

upper sequence: GLYMA14G40320.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G399073_T03 (Zea mays), 3'ss of exon 6
gtaagtccttttggacctgatgttgtttttgtaatcagttagtattgaaggaaaatttttgtttgttgacttgtaacccagctgcctaacttgaaacttatttggttttcagGTATGTATGGGAATCAAAAGCTGATGGAGCATTCGCTATTTCAGAAGATACATGGAATGAACCACTTGGACGAGGAACTGAGATTAGATTACACCTCAAG
||||||          ||| || | |||||||  ||| ||    ||            ||  || |   ||||   | | |     ||  |||   ||    |   ||| || ||||| ||||||||||||||||||||| | || ||||| || || ||||||||||||||||| ||||| || ||||| ||||| |||||||| ||    
gtaagttaccg-----ctgctgctttttttgt--tcatttctcgtt------------ttacttatgtgcttgcctcacgg-----tattttggtgctgtact--cttttagATATGTTTGGGAATCAAAAGCTGATGGATCGTTTGCTATCTCCGAGGATACATGGAATGAACCCCTTGGCCGTGGAACCGAGATAAGATTACATCTGCGA

upper sequence: GLYMA14G40320.1 (Glycine max), 3'ss of exon 6
lower sequence: AT4G24190.2 (Arabidopsis thaliana), 3'ss of exon 6
gtaagtccttttggacctgatgttgtttttgtaatcagttagtattgaaggaaaatttttgtttgttgacttgtaacccagctgcctaacttgaaacttatttggttttcagGTATGTATGGGAATCAAAAGCTGATGGAGCATTCGCTATTTCAGAAGATACATGGAATGAACCACTTGGACGAGGAACTGAGATTAGATTACACCTCAAG
||||||   ||| ||   |   ||  ||| | |||    | ||    | | |||||  |||             | |    |||  ||||||      | ||  |||||||||||||||||||||||||| ||| | ||   ||| ||| |||| || |||||||||||||| || |||||||| ||||| |||||||||||||| || | |
gtaagttgatttaga---gggctttgtttggcaatatacttgtgggcatgtaaaatcattga----------aaagcttttctga-taactt-----cttttccgttttcagGTATGTATGGGAATCAAAGGCTAACGGTAAATTTGCTGTTTCCGAGGATACATGGAATGAGCCTCTTGGACGTGGAACCGAGATTAGATTACATCTTAGG

upper sequence: GLYMA14G40320.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 6
gtaagtccttttggacctgatgttgtttttgtaatcagttagtattgaaggaaaatttttgtttgttgacttgtaacccagctgcctaacttgaaacttatttggttttc-----agGTATGTATGGGAATCAAAAGCTGATGGAGCATTCGCTATTTCAGAAGATACATGGAATGAACCACTTGGACGAGGAACTGAGATTAGATTACACCTCAAG
|| || ||| ||| |  |  | || | |||    |   ||| ||||         ||||| |||||  ||  |      |      |   ||||   | |||    ||||     |||||||||||||| || |||||||||||||| || || ||||| || |||  ||||||||||||||| ||||| ||||||||||| ||||| || ||||  
gtgag-cctcttgaagattttattttattttatttttattattattt--------tttttttttgtgaaccagaggttta-tgaaatggattgatgatcattcaaatttccattcagGTATGTATGGGAGTCTAAAGCTGATGGAGCTTTTGCAATTTCTGAGGATGTATGGAATGAACCACTCGGACGTGGAACTGAGATCAGATTGCATCTCAGA

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|57574607|gb|CX547582.1|CX547582
EST:     -TGNTGGCCGACTATGTCGAAGTTATTAGCAAGAATAACGATGATAAGCA                         GTATGTATGGGAATCAAAAGCTGATGGAGCATTCGCTATTTCAGAAGATAC
genomic: TTG-TGGCCGACTATGTCGAAGTTATTAGCAAGAATAACGATGATAAGCAgtaagtcctt ... tggttttcagGTATGTATGGGAATCAAAAGCTGATGGAGCATTCGCTATTTCAGAAGATAC
EST: gi|193378478|gb|FK343783.1|FK343783
EST:     CTTGTGGCCGACTATGTCGAAGTTATTAGCAAGAATAACGATGATAAGCA                         GTATGTATGGGAATCAAAAGCTGATGGAGCATTCGCTATTTCAGAAGATAC
genomic: CTTGTGGCCGACTATGTCGAAGTTATTAGCAAGAATAACGATGATAAGCAgtaagtcctt ... tggttttcagGTATGTATGGGAATCAAAAGCTGATGGAGCATTCGCTATTTCAGAAGATAC
EST: gi|163922973|gb|EH039569.1|EH039569
EST:     CTTGTGGCCGACTATGTCGAAGTTATTAGCAAGAATAACGATGATAAGCA                         GTATGTATGGGAATCAGAAGCTGATGGAGCATTCGCTATTTCGGAAGATAC
genomic: CTTGTGGCCGACTATGTCGAAGTTATTAGCAAGAATAACGATGATAAGCAgtaagtcctt ... tggttttcagGTATGTATGGGAATCAAAAGCTGATGGAGCATTCGCTATTTCAGAAGATAC
EST: gi|254328195|gb|GR835160.1|GR835160
EST:     CTTGTGGCCGACTATGTCGAAGTTATTAGCAAGAATAACGATGATAAGCA                         GTATGTATGGGAATCAAAAGCTGATGGAGCATTCGCTATTTCAGAAGATAC
genomic: CTTGTGGCCGACTATGTCGAAGTTATTAGCAAGAATAACGATGATAAGCAgtaagtcctt ... tggttttcagGTATGTATGGGAATCAAAAGCTGATGGAGCATTCGCTATTTCAGAAGATAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtttgttgacttgtaacccagctgcctaacttgaaacttatttggttttcagGTATGTATGGGAATCAAAAGCTGATGGAGCATTCGCTATTTCAGAAGATACATGGAATGAACCACTTGGACGAGGAACTGAGATTAGATTACACCTCAAG
                          gcctaac  putative branch site (score: 2)
                                       cttattt  putative PPT
                                    aaacttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtccttttggacctgatgttgtttttgtaatcagttagtattgaaggaaaatttttgtttgttgacttgtaacccagctgcctaacttgaaacttatttggttttcagGTATGTATGGGAATCAAAAGCTGATGGAGCATTCGCTATTTCAGAAGATACATGGAATGAACCACTTGGACGAGGAACTGAGATTAGATTACACCTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA