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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctataatgtaaagtcttaaatcatttggcaggagcttgtctacatttgtgctgatattttctttttgctcctttattgaacactattttttgttatcagCTTCAAATGGGAACATTACAGAGCCGTTTGGATGCTGACTTTCTCCTATCTCATATGTGCTCTGTCAAGTTTAAGGAATGGATAGTTGTCCTGGCTACTC

Basic information

species Glycine max
transcript GLYMA18G47050.1
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G47050.1 (Glycine max), 3'ss of exon 20
lower sequence: LOC_Os02g54500.1 (Oryza sativa), 3'ss of exon 19
-gctataatgtaaagtcttaaatcatttggcaggagcttgtctacatttgtgctgatattttctttttgctcctttattgaacactattttttgttatcagCTTCAAATGGGAACATTACAGAGCCGTTTGGATGCTGACTTTCTCCTATCTCATATGTGCTCTGTCAAGTTTAAGGAATGGATAGTTGTCCTGGCTACTC
  ||  |      ||     |||      | |  | || |   | |||  |       ||   | |||| ||   | |  ||    || || || |  |||||||||||||  ||  | || || ||  | |||||||| || || ||  |||| ||||| ||||||||||||||||||||||| ||||| || || ||| 
cactcaatacctgagcaaccaatataccagaacaatctcgctgatattattatctgccttggatctttgttctcatttataat-tgatattctgatgacagCTTCAAATGGACACTCTTCAAAGTCGGCTTGATGCTGAGTTCCTTCTTGCTCACATGTGTTCTGTCAAGTTTAAGGAATGGATTGTTGTGCTAGCAACTT

upper sequence: GLYMA18G47050.1 (Glycine max), 3'ss of exon 20
lower sequence: GRMZM2G475867_T01 (Zea mays), 3'ss of exon 19
--------------------------------------------------------gctataatgtaaagtc-------ttaaatcatttggcaggagctt-----gtctacatttg--tgctgatattttctttttgctcctttattga-acactattttttgttatcagCTTCAAATGGGAACATTACAGAGCCGTTTGGATGCTGACTTTCTCCTATCTCATATGTGCTCTGTCAAGTTTAAGGAATGGATAGTTGTCCTGGCTACTC
                                                          |||| | | | | |       |  |  ||| ||     |   |     || | ||| ||  |  ||| | || ||| |        | |||  |  ||  ||| || |  ||||| |||||||  ||| | || |||||  | ||||| || || || ||| |||||||||| || |||||||||||||||||||| || || || |||||| 
gttctggtcaatatatcacaaagtttatgatttattatgcttatcattattaatttattatattctcatgcccctttggtccatccatatgaataaaatatttttggttttcatctgcttcttgaaacttacttatcatgtacatgttggtattctgatttctgatgacagCTCCAAATGGATACACTGCAAAGCCGACTTGATGCAGAGTTCCTTCTAGCTCATATGTGTTCAGTCAAGTTTAAGGAATGGATCGTGGTGCTAGCTACTT

upper sequence: GLYMA18G47050.1 (Glycine max), 3'ss of exon 20
lower sequence: GRMZM2G052750_T02 (Zea mays), 3'ss of exon 19
------------------------------------------------------gctataatgtaaagtcttaaatcatttggcaggagcttgtctacatttgtgctgatattttctttttg--ctcct------ttattgaacac-tattttttgttat--------cagCTTCAAATGGGAACATTACAGAGCCGTTTGGATGCTGACTTTCTCCTATCTCATATGTGCTCTGTCAAGTTTAAGGAATGGATAGTTGTCCTGGCTACTC
                                                        ||| |  |   ||  |   ||||    |       |||| | |    ||  |   ||||  ||||   |||||      ||||| | ||  ||  ||||| |||        ||||| |||||||  ||| | || || ||  | ||||| || || || ||| |||||||||| || |||||||||||||||||||| || || || |||||| 
gttctggtcaatatatcacaaagttttatggtttattctgcttatcggtgtaaatttattacatctggttgtttctcatgcccctttgttctgtccatacgaatgaagtagttttggttttaatctccttgaaacttatttatcatgtacattttggtattctgatgacagCTCCAAATGGATACACTGCAAAGTCGACTTGATGCAGAGTTCCTTCTAGCTCATATGTGTTCAGTCAAGTTTAAGGAATGGATCGTGGTGCTAGCTACTT

upper sequence: GLYMA18G47050.1 (Glycine max), 3'ss of exon 20
lower sequence: Vv15s0046g01890.t01 (Vitis vinifera), 3'ss of exon 20
-gctataatgtaaagtcttaaatcatttggcaggagcttgtctacatttgtgctgatattttctttttgctcctttattgaacactattttttgttatcagCTTCAAATGGGAACATTACAGAGCCGTTTGGATGCTGACTTTCTCCTATCTCATATGTGCTCTGTCAAGTTTAAGGAATGGATAGTTGTCCTGGCTACTC
 | | |    |||| | |  | |  |  |||| |      | |  |||| |  |  | |||    |||  |   || |     | | |||  | || ||||||| ||||||| ||  | ||||||||  ||||||| || || ||  |  |||||||||||||||| |||||||| || ||||||||||||||||||||||
agatttttgataaattttggagtattgaggcaagcatgactgttaatttctttttttttttgacctttatttgatt-tgatttattgtttcatattttcagCTTGAAATGGGTACGCTGCAGAGCCGGCTGGATGCAGAGTTCCTTTTGGCTCATATGTGCTCTGTTAAGTTTAAAGAGTGGATAGTTGTCCTGGCTACTC

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|12772054|gb|BG236981.1|BG236981
EST:     GTGCTCGGTTGGAGAATTTTGCTTCTGGGCTTGAACTAATAAGCCAAAAG                         CTTCAAATGGGAACATTACAGAGCCGTTGGGATGCTGACTGTCTCCTATCT
genomic: GTGCTCGGTTGGAGAATTTTGCTTCTGGGCTTGAACTAATAAGCCAAAAGgtttaagatt ... ttgttatcagCTTCAAATGGGAACATTACAGAGCCGTTTGGATGCTGACTTTCTCCTATCT
EST: gi|11688934|gb|BF596672.1|BF596672
EST:     GTGCTCGGTTGGAGAATTTTGCTTCTGGGCTTGAACTAATAAGCCAAAAG                         CTTCAAATGGGAACATTACAGAGCCGTTTGGATGCTGACTTTCTCCTATCT
genomic: GTGCTCGGTTGGAGAATTTTGCTTCTGGGCTTGAACTAATAAGCCAAAAGgtttaagatt ... ttgttatcagCTTCAAATGGGAACATTACAGAGCCGTTTGGATGCTGACTTTCTCCTATCT
EST: gi|22522775|gb|BU081586.1|BU081586
EST:     GTGCTCGGTTGGAGAATTTTGCTTCTGGGCTTGAACTAATAAGCCAAAAG                         CTTCAAATGGGAACATTACAGAGCCGTTTGGATGCTGACTTTCTCCTACCT
genomic: GTGCTCGGTTGGAGAATTTTGCTTCTGGGCTTGAACTAATAAGCCAAAAGgtttaagatt ... ttgttatcagCTTCAAATGGGAACATTACAGAGCCGTTTGGATGCTGACTTTCTCCTATCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtgctgatattttctttttgctcctttattgaacactattttttgttatcagCTTCAAATGGGAACATTACAGAGCCGTTTGGATGCTGACTTTCTCCTATCTCATATGTGCTCTGTCAAGTTTAAGGAATGGATAGTTGTCCTGGCTACTC
    tgctgat  putative branch site (score: 3)
                                      ctatttttt  putative PPT
       tgatattttcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctataatgtaaagtcttaaatcatttggcaggagcttgtctacatttgtgctgatattttctttttgctcctttattgaacactattttttgttatcagCTTCAAATGGGAACATTACAGAGCCGTTTGGATGCTGACTTTCTCCTATCTCATATGTGCTCTGTCAAGTTTAAGGAATGGATAGTTGTCCTGGCTACTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - gcttgtc
- - - - - - - - - - - - - - - - - - - - - - -tttgtgc