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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctatccagtagcaactctaaatcaactttgtctctgttttttcttcctaactagtattttatttactaagtattttgttttctctgtaaaattctgcagAAGAAATGGATTGGGATAAAAATGGAATGGTTAACTTCAAGGAGTTTCTATTTGCTTTTACACGTTGGGTTGGAATTGATGAAGTTGACGATGAGGAAAA

Basic information

species Glycine max
transcript GLYMA08G33830.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G33830.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g10470.1 (Oryza sativa), 3'ss of exon 4
tctatccagtagcaactctaaatcaactttgtctctgttttttcttcctaactagtattttatttactaagtattttgttttctctgtaaaattctg-------cagAAGAAATGGATTGGGATAAAAATGGAATGGTTAACTTCAAGGAGTTTCTATTTGCTTTTACACGTTGGGTTGGAATTGATGAAGTTGACGATGAGGAAAA
           | || | |   |     | || || ||      |  |  |  |  |   ||   ||| |  ||  || |     |  |   || ||       |||| |||||||||||||| || ||||||| ||| | |||||||||||| || || |||||||| |||||||| || ||||||||    || ||||| ||  |
-----------gtaagttttcttttttgtggtatc-gtcacaaatctcacatgaacacagtacacactgacaatgatggtcctaatacactcttttggtggtcccagAGGAAATGGATTGGGACAAGAATGGAACGGTGACCTTCAAGGAGTTCCTCTTCGCTTTTACTCGTTGGGTGGGGATTGATGATAACGAAGATGACGACGA

upper sequence: GLYMA08G33830.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os06g40720.1 (Oryza sativa), 3'ss of exon 4
-tctatccagtagcaactctaaatcaactttgtctctgttttttcttcctaactagtattttatt-tactaagtattttgttttctctgtaaaattctgcagAAGAAATGGATTGGGATAAAAATGGAATGGTTAACTTCAAGGAGTTTCTATTTGCTTTTACACGTTGGGTTGGAATTGATGAAGTTGACGATGAGGAAAA
 | | || | ||| || ||||||      | |  |     ||  | ||      || |||   |  ||  | |||     || | | | |  |   |  |||| |||||||| ||||| || ||||||||||| | |||||| || ||||| ||||| || || || |||||||| ||||| |||  ||| || ||  |  |
atttctcta-tagtaa-tctaaaaatttctagattgacaattcccatcagtttcagaattaagtcctaacatgtaacactttctttttttgcatggcaccagAGGAAATGGACTGGGACAAGAATGGAATGGTGACCTTCAAAGAATTTCTGTTTGCATTCACTCGCTGGGTTGGGATTGACGAAAATGAGGACGACAATGA

upper sequence: GLYMA08G33830.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G006790_T01 (Zea mays), 3'ss of exon 3
tctatccagtagcaactctaaatcaactttg-tctctgttttttcttcctaactagtattttatttactaagtatt----ttgttttctctgtaaaattctgcagAAGAAATGGATTGGGATAAAAATGGAATGGTTAACTTCAAGGAGTTTCTATTTGCTTTTACACGTTGGGTTGGAATTGATGAAGTTGACGATGAGGAAAA
       ||||  ||  ||    ||    |  |  |||||  |  ||   |||| |  |   || | |  |||  |    ||    | ||| || |   |   ||| |||||||| ||||| || || |||||||| |  ||||||||||| || ||||| || || || ||||| ||||||||||||  ||| ||||| ||  |
-----gaagtataaaaacttgcacactcataattcctgttactgttttgaaacttgcgtcccatcttcccagtcctgacgtttacctttctttacatggcactagAGGAAATGGACTGGGACAAGAACGGAATGGTGACATTCAAGGAGTTCCTGTTTGCCTTCACTCGCTGGGTAGGAATTGATGAAAATGAGGATGAAGATGA

upper sequence: GLYMA08G33830.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv19s0015g01200.t01 (Vitis vinifera), 3'ss of exon 4
----tctatccagt-agcaactctaa--atcaactttgtctctgttttttcttcctaactagtattttattt-actaagtattttgttttctctgtaaaattctgcagAAGAAATGGATTGGGATAAAAATGGAATGGTTAACTTCAAGGAGTTTCTATTTGCTTTTACACGTTGGGTTGGAATTGATGAAGTTGACGATGAGGAAAA
      ||    || || | || | |  ||   ||    |    |    | ||  |   || || | ||||| |||  |  | ||||||| |        |  |||||| || |||||||||||||||||||||||||| ||||||||||||||||| |||||||| || ||||||||||| ||||| ||  |||| ||||| ||| |
tgccagtagatggttagaagctttgatgatttcctcgaacaggctccaatttttttccataataatctatttcacttggcctcttgttttat--------tattgcagAGGAGATGGATTGGGATAAAAATGGAATGGTGAACTTCAAGGAGTTTCTTTTTGCTTTCACCCGTTGGGTTGGGATTGACGATATTGAGGATGAAGAAGA

upper sequence: GLYMA08G33830.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S197_126V6.1 (Physcomitrella patens), 3'ss of exon 3
--------------tctatc-cagtagca-actctaaatcaactttgtctctgttttttcttcctaactagtattttatt-------tactaagtattttgttttctctgtaaaattctgcagAAGAAATGGATTGGGATAAAAATGGAATGGTTAACTTCAAGGAGTTTCTATTTGCTTTTACACGTTGGGTTGGAATTGATGAAGTTGACGATGAGGAAAA
               | | | || |  ||  |   |||| |  | ||   | |||||   || | |     | |  | |         ||| | ||      |         ||  | |||||| |||||||||||||||||| | || ||| | |  |||||||||||| |||| ||||||||    ||||| ||| ||||  | |  || || ||   |  
gtatgttactctttcccacctcactgtcatgcatcaaattatttctgcaaccgttttcaattgccattgcctttcctgtaaatgtgacactgactaaacgaatgcgaaccccaacatgtgcagAGGAAATGGATTGGGATAAAGACGGCATGATCACATTCAAGGAGTTTTTATTCGCTTTTACGGACTGGGTAGGACTTGAGAATGACGAAGAAGAAACAGG

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|18735235|gb|BM528647.1|BM528647
EST:     AACTACATCAGGGGAGCGTTCTTCTGGAAGAATAGCCATGAAAAGATTTG                         AAGAAATGGATTGGGATAAAAATGGAATGGTTAACTTCAAGGAGTTTCTAT
genomic: AACTACATCAGGGGAGCGTTCTTCTGGAAGAATAGCCATGAAAAGATTTGgtcagttatc ... aattctgcagAAGAAATGGATTGGGATAAAAATGGAATGGTTAACTTCAAGGAGTTTCTAT
EST: gi|18038716|gb|BM307010.1|BM307010
EST:     CTGGAAGAATAGCCATGAAAAGATTTG                         AAGAAATGGATTGGGATAAAAATGGAATGGTTAACTTCAAGGAGTTTCTAT
genomic: CTGGAAGAATAGCCATGAAAAGATTTGgtcagttatc ... aattctgcagAAGAAATGGATTGGGATAAAAATGGAATGGTTAACTTCAAGGAGTTTCTAT
EST: gi|254316174|gb|GR827711.1|GR827711
EST:     AACTACATCAGGGGAGCGTTCTTCTGGAAGAATAGCCATGAAAAGATTTG                         AAGAAATGGATTGGGATAAAAATGGAATGGTTAACTTCAAGGAGTTTCTAT
genomic: AACTACATCAGGGGAGCGTTCTTCTGGAAGAATAGCCATGAAAAGATTTGgtcagttatc ... aattctgcagAAGAAATGGATTGGGATAAAAATGGAATGGTTAACTTCAAGGAGTTTCTAT
EST: gi|207762743|gb|GD732974.1|GD732974
EST:     AACTACATCAGGGGAGCGTTCTTCTGGAAGAATAGCCATGAAAAGATTTG                         AAGAAATGGATTGGGATAAAAATGGAATGGTTAACTTCAAGGAGTTTCTAT
genomic: AACTACATCAGGGGAGCGTTCTTCTGGAAGAATAGCCATGAAAAGATTTGgtcagttatc ... aattctgcagAAGAAATGGATTGGGATAAAAATGGAATGGTTAACTTCAAGGAGTTTCTAT
EST: gi|13563522|gb|BG551742.1|BG551742
EST:     AACTACATCAGGGGAGCGTTCTTCTGGAAGAATAGCCATGAAAAGATTTG                         AAGAAATGGATTGGGATAAAAATGGAATGGTTAACTTCAAGGAGTTTCTAT
genomic: AACTACATCAGGGGAGCGTTCTTCTGGAAGAATAGCCATGAAAAGATTTGgtcagttatc ... aattctgcagAAGAAATGGATTGGGATAAAAATGGAATGGTTAACTTCAAGGAGTTTCTAT
EST: gi|14991862|gb|BI317535.1|BI317535
EST:     AACTACATCAGGGGAGCGTTCTTCTGGAAGAATAGCCATGAAAAGATTTG                         AAGAAATGGATTGGGATAAAAATGGAATGGTTAACTTCAAGGAGTTTCTAT
genomic: AACTACATCAGGGGAGCGTTCTTCTGGAAGAATAGCCATGAAAAGATTTGgtcagttatc ... aattctgcagAAGAAATGGATTGGGATAAAAATGGAATGGTTAACTTCAAGGAGTTTCTAT
EST: gi|192305727|gb|FG995697.1|FG995697
EST:     AACTACATCAGGGGAGCGTTTTTCTGGAAGAATAGCCATGAAAAGATTTG                         AAGAAATGGATTGGGATAAAAATGGAATGGTTAACTTCAAGGAGTTTCTAT
genomic: AACTACATCAGGGGAGCGTTCTTCTGGAAGAATAGCCATGAAAAGATTTGgtcagttatc ... aattctgcagAAGAAATGGATTGGGATAAAAATGGAATGGTTAACTTCAAGGAGTTTCTAT
EST: gi|22524377|gb|BU083188.1|BU083188
EST:     AACTACATCAGGGGAGCGTTCTTCTGGAAGAATAGCCATGAAAAGATTTG                         AAGAAATGGATTGGGATAAAAATGGAATGGTTAACTTCAAGGAGTTTCTAT
genomic: AACTACATCAGGGGAGCGTTCTTCTGGAAGAATAGCCATGAAAAGATTTGgtcagttatc ... aattctgcagAAGAAATGGATTGGGATAAAAATGGAATGGTTAACTTCAAGGAGTTTCTAT
EST: gi|13481965|gb|BG511308.1|BG511308
EST:     AACTACATCAGGGGAGCGTTCTTCTGGAAGAATAGCCATGAAAAGATTTG                         AAGAAATGGATTGGGATAAAAATGGAATGGTTAACTTCAAGGAGTTTCTAT
genomic: AACTACATCAGGGGAGCGTTCTTCTGGAAGAATAGCCATGAAAAGATTTGgtcagttatc ... aattctgcagAAGAAATGGATTGGGATAAAAATGGAATGGTTAACTTCAAGGAGTTTCTAT
EST: gi|7590643|gb|AW706391.1|AW706391
EST:     AACTACATCAGGGGAGCGTTCTTCTGGAAGAATAGCCATGAAAAGATTTG                         AAGAAATGGATTGGGATAAAAATGGAATGGTTAACTTCAAGGAGTTTCTAT
genomic: AACTACATCAGGGGAGCGTTCTTCTGGAAGAATAGCCATGAAAAGATTTGgtcagttatc ... aattctgcagAAGAAATGGATTGGGATAAAAATGGAATGGTTAACTTCAAGGAGTTTCTAT
EST: gi|19345846|gb|BM890726.1|BM890726
EST:     AACTACATCAGGGGAGCGTTCTTCTGGAAGAATAGCCATGAAAAGATTTG                         AAGAAATGGATTGGGATAAAAATGGAATGGTTAACTTCAAGGAGTTTCTAT
genomic: AACTACATCAGGGGAGCGTTCTTCTGGAAGAATAGCCATGAAAAGATTTGgtcagttatc ... aattctgcagAAGAAATGGATTGGGATAAAAATGGAATGGTTAACTTCAAGGAGTTTCTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctaactagtattttatttactaagtattttgttttctctgtaaaattctgcagAAGAAATGGATTGGGATAAAAATGGAATGGTTAACTTCAAGGAGTTTCTATTTGCTTTTACACGTTGGGTTGGAATTGATGAAGTTGACGATGAGGAAAA
 tcctaac  putative branch site (score: 1)
       tagtattttatttact  TA-rich tract