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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTATAAAAGAGTGGACAGCATGGGACATTGCCAGACGTGCTGCATTTGCATTTTTTGGTATTTTTGCTGGGACTGAAGAGAATCCCGAGTTCATCCAGTgtacgataattttatctcatcatgcgttttacttgaaattgtttcatttctggctttctaaatcaaaatatttggttcatgatggcag

Basic information

species Glycine max
transcript GLYMA04G41080.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G41080.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os09g36040.1 (Oryza sativa), 5'ss of exon 4
CTTATAAAAGAGTGGACAGCATGGGACATTGCCAGACGTGCTGCATTTGCATTTTTTGGTATTTTTGCTGGGACTGAAGAGAATCCCGAGTTCATCCAGTgtacgataattttatct-catcatgcgttttacttgaaattgtttcatttctggctttcta-aatcaaaatatttggttcatgatggcag----------
 | ||||| || |||||||||||||| ||||| ||||| || ||||||||||| ||||| || ||| |||| || ||||||||||| |||||||| ||  ||| | || |||  |||   |  ||| |  |  ||     | |   |  || |  |||  | |    |     |||  |  |  |  ||           
TTGATAAAGGAATGGACAGCATGGGATATTGCAAGACGGGCAGCATTTGCATTCTTTGGCATATTTTCTGGAACAGAAGAGAATCCTGAGTTCATACAAAgtatggtagtttattctgttttctgcttcatggttactcatatactacctccgttttttaatagatgacgccgttgactttttctcacatgtttgaccat

upper sequence: GLYMA04G41080.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G052610_T02 (Zea mays), 5'ss of exon 4
CTTATAAAAGAGTGGACAGCATGGGACATTGCCAGACGTGCTGCATTTGCATTTTTTGGTATTTTTGCTGGGACTGAAGAGAATCCCGAGTTCATCCAGTgtacgataattttatctcatcatgcgttttacttgaaattgtttcatttctggctttcta--aatcaaaa--tatttggttcatgatggcag
 | || || || |||||||| ||||| ||||| || ||||| || ||||| || || || || |||||||| || ||||||||||| |||||||| ||| ||| | ||        |  |  |||  |||| ||     |   ||||      |  |  |  || || ||   |   | ||     | |   
TTAATCAAGGAATGGACAGCGTGGGATATTGCGAGGCGTGCAGCGTTTGCGTTCTTCGGCATATTTGCTGGAACAGAAGAGAATCCTGAGTTCATACAGAgtatggtagcaaacattgctgctgctgtttaattagtgattactcatcatcaacgatacagtaaccagaaggcacacgctttgccttag---

upper sequence: GLYMA04G41080.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G052610_T01 (Zea mays), 5'ss of exon 4
CTTATAAAAGAGTGGACAGCATGGGACATTGCCAGACGTGCTGCATTTGCATTTTTTGGTATTTTTGCTGGGACTGAAGAGAATCCCGAGTTCATCCAGTgtacgataattttatctcatcatgcgttttacttgaaattgtttcatttctggctttcta--aatcaaaa--tatttggttcatgatggcag--
 | || || || |||||||| ||||| ||||| || ||||| || ||||| || || || || |||||||| || ||||||||||| |||||||| ||| ||| | ||        |  |  |||  |||| ||     |   ||||      |  |  |  || || ||   |   | ||     | |     
TTAATCAAGGAATGGACAGCGTGGGATATTGCGAGGCGTGCAGCGTTTGCGTTCTTCGGCATATTTGCTGGAACAGAAGAGAATCCTGAGTTCATACAGAgtatggtagcaaacattgctgctgctgtttaattagtgattactcatcatcaacgatacagtaaccagaaggcacacgctttgccttagtgcag

upper sequence: GLYMA04G41080.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv16s0098g01280.t01 (Vitis vinifera), 5'ss of exon 4
CTTATAAAAGAGTGGACAGCATGGGACATTGCCAGACGTGCTGCATTTGCATTTTTTGGTATTTTTGCTGGGACTGAAGAGAATCCCGAGTTCATCCAGTgtacgataattttatctcatcatgcgttttact-tgaaattgtttc------atttctggctttctaa-atcaaaatatttggt-tcatgatggcag
|||||||| || |||||||| ||||||||||| || ||||||||||||||||||||||| || ||||| || || |||||||| || |||||||| ||  |||   |  | ||| || ||||||| ||    | |   |||| |||      |||  ||| ||   |  | | |||| | |||| ||||| |  |||
CTTATAAAGGAATGGACAGCGTGGGACATTGCTAGGCGTGCTGCATTTGCATTTTTTGGCATATTTGCAGGCACAGAAGAGAACCCAGAGTTCATGCAAAgtatattgttcttacctaatcatgctttgagttgttggattgcttctggataattcatggtttgggattaactaaatgtatggtatcatgctaacag

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|31310357|gb|CD395560.1|CD395560
EST:     ATTTTTTGGTATTTTTGCTGGGACTGAAGAGAATCCCGAGTTCATCCAGT                         CTGTTGAAGCAAAATTAGATAAAAATGCAAAGATAATAGTAGCTTGCTCAG
genomic: ATTTTTTGGTATTTTTGCTGGGACTGAAGAGAATCCCGAGTTCATCCAGTgtacgataat ... atgatggcagCTGTTGAAGCAAAATTAGATAAAAATGCAAAGATAATAGTAGCTTGCTCAG
EST: gi|31305694|gb|CD390897.1|CD390897
EST:     ATTTTTTGGTATTTTTGCTGGGACTGAAGAGAATCCCGAGTTCATCCAGT                         CTGTTGAAGCAAAATTAGATAAAAATGCAAAGATAATAGTAGCTTGCTCAG
genomic: ATTTTTTGGTATTTTTGCTGGGACTGAAGAGAATCCCGAGTTCATCCAGTgtacgataat ... atgatggcagCTGTTGAAGCAAAATTAGATAAAAATGCAAAGATAATAGTAGCTTGCTCAG
EST: gi|22524166|gb|BU082977.1|BU082977
EST:     ATTTTTTGGTATTTTTGCTGGGACTGAAGAGAATCCCGAGTTCATCCAGT                         CTGTTGAAGCAAAATTAGATAAAAATGCAAAGATAATAGTAGCTTGCTCAG
genomic: ATTTTTTGGTATTTTTGCTGGGACTGAAGAGAATCCCGAGTTCATCCAGTgtacgataat ... atgatggcagCTGTTGAAGCAAAATTAGATAAAAATGCAAAGATAATAGTAGCTTGCTCAG
EST: gi|17963446|gb|BM270195.1|BM270195
EST:     ATTTTTTGGTATTTTTGCTGGGACTGAAGAGAATCCCGAGTTCATCCAGT                         CTGTTGAAGCAAAATTAGATAAAAATGCA
genomic: ATTTTTTGGTATTTTTGCTGGGACTGAAGAGAATCCCGAGTTCATCCAGTgtacgataat ... atgatggcagCTGTTGAAGCAAAATTAGATAAAAATGCA
EST: gi|31309501|gb|CD394704.1|CD394704
EST:     ATTTTTTGGTATTTTTGCTGGGACTGAAGAGAATCCCGAGTTCATCCAGT                         CTGTTGAAGCCAAATTAGATATAAATGCAAAGATAATAGTAGCTTGCTCAG
genomic: ATTTTTTGGTATTTTTGCTGGGACTGAAGAGAATCCCGAGTTCATCCAGTgtacgataat ... atgatggcagCTGTTGAAGCAAAATTAGATAAAAATGCAAAGATAATAGTAGCTTGCTCAG
EST: gi|192321025|gb|FK013513.1|FK013513
EST:     ATTTTTTGGTATTTTTGCTGGGACTGAAGAGAATCCCGAGTTCATCCAGT                         CTGTTGAAGCAAAATTAGATAAAAATGCAAAGATAATAGTAGCTTGCTCAG
genomic: ATTTTTTGGTATTTTTGCTGGGACTGAAGAGAATCCCGAGTTCATCCAGTgtacgataat ... atgatggcagCTGTTGAAGCAAAATTAGATAAAAATGCAAAGATAATAGTAGCTTGCTCAG
EST: gi|31471152|gb|CD413180.1|CD413180
EST:     ATTTTTTGGTATTTTTGCTGGGACTGAAGAGAATCCCGAGTTTATCCAGT                         CTGTTGAAGCAAAATTAGATAAAAATGCAAAGATAATAGTAGCTTGCTCAG
genomic: ATTTTTTGGTATTTTTGCTGGGACTGAAGAGAATCCCGAGTTCATCCAGTgtacgataat ... atgatggcagCTGTTGAAGCAAAATTAGATAAAAATGCAAAGATAATAGTAGCTTGCTCAG
EST: gi|17964473|gb|BM271208.1|BM271208
EST:     NNNNNNNGGTATTTTTGCTGGGACTGAAGAGAATCC-GAGTTCATCCAGT                         CTGTTGAAGCAAAATTAGATAAAAATGCAAAGATAATAGTAGCTTGCTCAG
genomic: TTTTTT-GGTATTTTTGCTGGGACTGAAGAGAATCCCGAGTTCATCCAGTgtacgataat ... atgatggcagCTGTTGAAGCAAAATTAGATAAAAATGCAAAGATAATAGTAGCTTGCTCAG
EST: gi|151402507|gb|EV272320.1|EV272320
EST:     ATTTTTTGGTATTTTTGCTGGGACTGAAGAGAATCCCGAGTTCATCCAGT                         CTGTTGAAGCAAAATTAGATAAAAATGCAAAGATAATAGTAGCTTGCTCAG
genomic: ATTTTTTGGTATTTTTGCTGGGACTGAAGAGAATCCCGAGTTCATCCAGTgtacgataat ... atgatggcagCTGTTGAAGCAAAATTAGATAAAAATGCAAAGATAATAGTAGCTTGCTCAG
EST: gi|31474466|gb|CD416494.1|CD416494
EST:     ATTTTTTGGTATTTTTGCTGGGACTGAAGAGAATCCCGAGTTCATCCAGT                         CTGTTGAAGCAAAATTAGATAAAAATGCAAAGATAATAGTAGCTTGCTCAG
genomic: ATTTTTTGGTATTTTTGCTGGGACTGAAGAGAATCCCGAGTTCATCCAGTgtacgataat ... atgatggcagCTGTTGAAGCAAAATTAGATAAAAATGCAAAGATAATAGTAGCTTGCTCAG
EST: gi|17963465|gb|BM270214.1|BM270214
EST:     ATTTTTTGGTATTTTTGCTGGGACTGAAGAGAATCCCGAGTTCATCCAGT                         CTGTTGAAGCAAA
genomic: ATTTTTTGGTATTTTTGCTGGGACTGAAGAGAATCCCGAGTTCATCCAGTgtacgataat ... atgatggcagCTGTTGAAGCAAA
EST: gi|15589894|gb|BI674510.1|BI674510
EST:     ATTTTTTGGTATTTTTGCTGGGACTGAAGAGAATCCCGAGTTCATCCAGT                         CTGTTGAAGCAAAATTAGATAAAAATGCAAAGATAATAGTAGCTTGCTCAG
genomic: ATTTTTTGGTATTTTTGCTGGGACTGAAGAGAATCCCGAGTTCATCCAGTgtacgataat ... atgatggcagCTGTTGAAGCAAAATTAGATAAAAATGCAAAGATAATAGTAGCTTGCTCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTATAAAAGAGTGGACAGCATGGGACATTGCCAGACGTGCTGCATTTGCATTTTTTGGTATTTTTGCTGGGACTGAAGAGAATCCCGAGTTCATCCAGTgtacgataattttatctcatcatgcgttttacttgaaattgtttcatttctggctttctaaatcaaaatatttggttcatgatggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA