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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgatttcttttcttgctttgcatttttgggttttttgcctggtttggcaattatgttatgatttgatggtatccactgctaatttccttgtaacttgcagATTTTATGTGGCAGAGGTCCTACTGGCTTTGGAGTATCTTCACATGCTTGGGATTGTCTACCGTGACCTTAAGCCAGAAAATGTTCTTGTTAGGGATGAT

Basic information

species Glycine max
transcript GLYMA15G12760.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G12760.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os09g08420.1 (Oryza sativa), 3'ss of exon 2
-tgatttcttttcttgctttgcatttttgggtt-ttttgcctggtttggcaattatgttatgatttgatggtatccactgctaatttccttgtaacttgcagATTTTATGTGGCAGAGGTCCTACTGGCTTTGGAGTATCTTCACATGCTTGGGATTGTCTACCGTGACCTTAAGCCAGAAAATGTTCTTGTTAGGGATGAT
 ||  | |  |  ||   | | ||  | | ||  |  | |      | ||     | | |     | ||| |      || |   ||  || |   |||||| ||||||||||| ||||| || || ||| | || || || || |||||||| ||  | || || |||||||||||||||||||||||||| || || |||
gtgtctgccctggttttctggtatcatggagtgatagtactaaaccttgctcaagtctaagagagtcatgttgatgtttggttgattaattct--tttgcagGTTTTATGTGGCTGAGGTGCTTCTTGCTCTAGAATACCTGCATATGCTTGGCATCATATATCGGGACCTTAAGCCAGAAAATGTTCTTGTGAGAGAAGAT

upper sequence: GLYMA15G12760.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os08g38320.2 (Oryza sativa), 3'ss of exon 2
tgatttcttttcttgctttgcatttttgggttttttgcctggtttggcaattatgttatgatt----tgatggtatccactgctaatttccttgtaacttgcagATTTTATGTGGCAGAGGTCCTACTGGCTTTGGAGTATCTTCACATGCTTGGGATTGTCTACCGTGACCTTAAGCCAGAAAATGTTCTTGTTAGGGATGAT
 |||   || |  |    |   |  ||   | ||||    |  |||  |   |||  |||| |    | || | | |   || | || || | |||  || ||| || |||||||||||||| || || || || || || || || |||||||||||| | |||||||| || || ||||||||||| |||||  |||| |||
-gatcaattgttgtttgctaactcattaattctttttggcgtcttgaaaggcatgg-atgactcttctcattgaaacttttggtgatctcttggta--tttcagGTTCTATGTGGCAGAGGTTCTTCTTGCATTAGAATACCTGCATATGCTTGGGATTATATACCGTGATCTGAAACCAGAAAATGTCCTTGTCCGGGAGGAT

upper sequence: GLYMA15G12760.1 (Glycine max), 3'ss of exon 2
lower sequence: AC217842.3_FGT001 (Zea mays), 3'ss of exon 1
tgatttcttttcttgctttgcatttttgggttttttgcctggtttggcaattatgttatgatttgatggtatccactg-ctaatttccttgt-----aacttgcagATTTTATGTGGCAGAGGTCCTACTGGCTTTGGAGTATCTTCACATGCTTGGGATTGTCTACCGTGACCTTAAGCCAGAAAATGTTCTTGTTAGGGATGAT
    |  ||  | || |  ||     ||  | |  || |    || |||| |     | |  || ||   ||| |    || || |     |     ||  ||||| |||||||| |||||||| || || ||| |||| || || ||||||||||| ||  | ||||||||| | |||||||| ||||||||||| ||||| |||
---atatttagcatgataggctgccctgattgtcatgtca---tttgcaactgcaagaagccttaatcaaatctatgaacttatgttgacatcaaaaaatatgcagGTTTTATGTAGCAGAGGTGCTTCTTGCTCTGGAATACCTGCACATGCTTGGTATCATATACCGTGACTTAAAGCCAGAGAATGTTCTTGTGAGGGAAGAT

upper sequence: GLYMA15G12760.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G026065_T01 (Zea mays), 3'ss of exon 2
--tgatttcttttcttgctttgcatttttgg-gttttttgcctggtttggcaattatgttatgatttgatggtatccactgctaatttccttgtaacttgcagATTTTATGTGGCAGAGGTCCTACTGGCTTTGGAGTATCTTCACATGCTTGGGATTGTCTACCGTGACCTTAAGCCAGAAAATGTTCTTGTTAGGGATGAT
  |     || ||  |    |  |||| ||   || | || ||   ||   ||  |  |||  |||   ||| ||  | |    | | |||||    || ||| || |||||||||||||| || || || ||||| || || || |||||||||||| | |||||||| ||||| ||||||||||| || ||| |||| |||
tttctgacctatttataaactagatttgtgctattatctgtcttcattaa-aacgacttta-aattatttggcattgattatctaataccttgatgttt-cagGTTCTATGTGGCAGAGGTACTCCTTGCATTGGAATACCTGCATATGCTTGGGATTATATACCGTGATCTTAAACCAGAAAATGTCCTCGTTCGGGAAGAT

upper sequence: GLYMA15G12760.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G47750.1 (Arabidopsis thaliana), 3'ss of exon 2
------------------------------------------tgatttcttttcttgctttgcatttttgggttttt-----------tgcctggtttggcaattatgttatgatttgatggt-atc-cactgctaatttccttgtaactt----gcagATTTTATGTGGCAGAGGTCCTACTGGCTTTGGAGTATCTTCACATGCTTGGGATTGTCTACCGTGACCTTAAGCCAGAAAATGTTCTTGTTAGGGATGAT
                                          ||||||  | || |  ||   | | ||||||   |           | |    || |||             | | ||  | ||| ||||    ||||  || | | |     ||||||||||  | ||||||    |  | |||||||| || || ||||||||||||||||| || || || |||||||| ||||| ||||| ||| | || || 
gtgagtcatttttccttcgtctgtcaagattagcatttcctttgattt--tatcgtatttcaaagtattgggtagatgacaaaagacatactcatttcggctgaagcagagcattcttattctcatctcactaaagattttgttttcaatgtgtggcagATTTTACATAGCAGAGTCATTGTTAGCTTTGGAATACCTGCACATGCTTGGGATTGTGTATCGAGATCTTAAGCCTGAAAACGTTCTAGTTCGAGAAGAC

upper sequence: GLYMA15G12760.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv10s0116g00440.t01 (Vitis vinifera), 3'ss of exon 1
-tgatttcttttcttgctttgcatttttgggttttttgcctggtttggcaattatgttatgatttgatggtatccactgctaatttc-cttgtaacttgcagATTTTATGTGGCAGAGGTCCTACTGGCTTTGGAGTATCTTCACATGCTTGGGATTGTCTACCGTGACCTTAAGCCAGAAAATGTTCTTGTTAGGGATGAT
 | |||           | | || |      |      |    |||  |  | |  ||   ||||||     |  | ||  | |||  | | | || |||||||||||||| |||||||||||  | ||| | || || || ||||||||||||||||||||||| || |||||||| ||||||||||| || |||||||| 
gttattgggggctcaagtcttcaatcagctctgcaagacaaaatttatctttcacctttgtatttgaaat--ttgattgtaatttttacctttcacctgcagATTTTATGTAGCAGAGGTCCTCTTAGCTCTAGAATACCTCCACATGCTTGGGATTGTCTACCGAGATCTTAAGCCGGAAAATGTTCTGGTGAGGGATGAC

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|7326763|gb|AW620561.1|AW620561
EST:     ACTCTTAGGCAGAAGCAACCAGGGAAGCATTTTCCTGAGCAGGCAGTAAA                         ATTTTATGTGGCAGAGGTCCTACTGGCTTTGGAGTATCTTCACATGCTTGG
genomic: ACTCTTAGGCAGAAGCAACCAGGGAAGCATTTTCCTGAGCAGGCAGTAAAgtatgtttta ... taacttgcagATTTTATGTGGCAGAGGTCCTACTGGCTTTGGAGTATCTTCACATGCTTGG
EST: gi|11687345|gb|BF594985.1|BF594985
EST:     ACTCTTAGGCAGAAGCAACCAGGGAAGCATTTTCCTGAGCAGGCAGTAAA                         ATTTTATGTGGCAGAGGTCCTACTGGCTTTGGAGTATCTTCACATGCTTGG
genomic: ACTCTTAGGCAGAAGCAACCAGGGAAGCATTTTCCTGAGCAGGCAGTAAAgtatgtttta ... taacttgcagATTTTATGTGGCAGAGGTCCTACTGGCTTTGGAGTATCTTCACATGCTTGG
EST: gi|254326530|gb|GR841122.1|GR841122
EST:     ACTCTTAGGCAGAAGCAACCAGGGAAGCATTTTCCTGAGCAGGCAGTAAA                         ATTTTATGTGGCAGAGGTCCTACTGGCTTTGGAGTATCTTCACATGCTTGG
genomic: ACTCTTAGGCAGAAGCAACCAGGGAAGCATTTTCCTGAGCAGGCAGTAAAgtatgtttta ... taacttgcagATTTTATGTGGCAGAGGTCCTACTGGCTTTGGAGTATCTTCACATGCTTGG
EST: gi|9564501|gb|BE474010.1|BE474010
EST:     ACTCTTAGGCAGAAGCAACCAGGGAAGCATTTTCCTGAGCAGGCAGTAAA                         ATTTTATGTGGCAGAGGTCCTACTGGCTTTGGAGTATCTTCACATGCTTGG
genomic: ACTCTTAGGCAGAAGCAACCAGGGAAGCATTTTCCTGAGCAGGCAGTAAAgtatgtttta ... taacttgcagATTTTATGTGGCAGAGGTCCTACTGGCTTTGGAGTATCTTCACATGCTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggcaattatgttatgatttgatggtatccactgctaatttccttgtaacttgcagATTTTATGTGGCAGAGGTCCTACTGGCTTTGGAGTATCTTCACATGCTTGGGATTGTCTACCGTGACCTTAAGCCAGAAAATGTTCTTGTTAGGGATGAT
                                          ttgtaac  putative branch site (score: 2)
                                     tttccttgt  CT-rich tract
     ttatgttatgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgatttcttttcttgctttgcatttttgggttttttgcctggtttggcaattatgttatgatttgatggtatccactgctaatttccttgtaacttgcagATTTTATGTGGCAGAGGTCCTACTGGCTTTGGAGTATCTTCACATGCTTGGGATTGTCTACCGTGACCTTAAGCCAGAAAATGTTCTTGTTAGGGATGAT

- - - - -ttcttgc
- - - - - - - - - tgcattt
- - - - - - - - - - - - - - - - ttttgcc
- - - - - - - - - - - - - - - - - - - - ggtttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgttatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatggta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cactgct