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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtctattgcgttttttttttttggtctccactctgctgtgattgttctgtactaaccttttgcttgatttctatgactttgctactgaaaaatatgaagGTATGCCTCAGAGGGACCACTGAAAGGTATCCTTGGGTACACAGACGAGGATGTTGTCTCTAATGACTTTGTTGGTGATTCAAG

Basic information

species Glycine max
transcript GLYMA03G22790.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G22790.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os02g07490.1 (Oryza sativa), 3'ss of exon 11
gtatgtctattgcgttttttttttttggtctccactctgctgtgattgttctgtac-taaccttttgcttgatttctatgactttgctactgaaaaatatg---aagGTATGCCTCAGAGGGACCACTGAAAGGTATCCTTGGGTACACAGACGAGGATGTTGTCTCTAATGACTTTGTTGGTGATTCAAG
      ||   |   |    || |   ||||  |   | |||||||    |||||  |||| || ||  |  ||| |  || ||| ||  | |    | ||    |||   || ||||||||  ||||||||||||| || || |||||||| |||||||| || || |||||||| ||||||||| ||||
-----actgcggtcatgcacttgtaccgtctgaagatt-ctgtgatgtgcctgtatgtaacattgtgaatcttttatcaga-tttactcataagctgtgtgtttcagGGCAGCATCAGAGGGTGCACTGAAAGGTATTCTAGGTTACACAGATGAGGATGTGGTTTCCAATGACTTCGTTGGTGATGCAAG

upper sequence: GLYMA03G22790.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G104632_T01 (Zea mays), 3'ss of exon 11
gtatgt-ctattgcgtttttttt----ttttggtctccactctgctgtgattgttctgtactaaccttttgcttgatttctatgactttgctactgaaaaatatgaagGTATGCCTCAGAGGGACCACTGAAAGGTATCCTTGGGTACACAGACGAGGATGTTGTCTCTAATGACTTTGTTGGTGATTCAAG
|| ||| ||  |||  | ||  |    |||  |     |      ||||  | || |  || |||||   |      ||  |  |  ||  |  |        |  |||   || ||||||||  |||| |||||||| ||||| |||||||||||||||||||| || ||||| |||||||||||||||||
gtgtgttctgatgcactattcctaagatttatgcagagagaaccatgtgcatattatcgaccaacctacagtggatcttacacaatctttttttt--------ttcagGACGGCATCAGAGGGTGCACTCAAAGGTATTCTTGGCTACACAGACGAGGATGTTGTTTCCAATGATTTTGTTGGTGATTCAAG

upper sequence: GLYMA03G22790.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G051004_T01 (Zea mays), 3'ss of exon 11
--gtatgtctattgcgttttttttttttggtctccactctgctgtgattgttctgt-actaaccttttgcttgat-ttctatgactttgctactgaaaaatatgaagGTATGCCTCAGAGGGACCACTGAAAGGTATCCTTGGGTACACAGACGAGGATGTTGTCTCTAATGACTTTGTTGGTGATTCAAG
  |     || | |  ||  |    ||||  |      |  |  ||    |  |   |   | | |  | | ||| || |    | |  ||  |      |   | ||   || ||||||||  |||| |||||||| ||||| |||||||||||||| ||||| || ||||| |||||||||||||| ||
gtgctctgctgtggtattcctaagatttgtgcagagagcaaccatgcgcatattaccagccatcctacggtggatcttatgcagcatatctttt------ttccagGGCG-GCATCAGAGGGTGCACTCAAAGGTATTCTTGGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAG

upper sequence: GLYMA03G22790.1 (Glycine max), 3'ss of exon 11
lower sequence: AT1G79530.1 (Arabidopsis thaliana), 3'ss of exon 11
gtatgtctattgcgttttttttttttgg-------tctccactctgctgtgattgttctgtactaaccttttgcttgatttctatgactttgctactgaaaaatatga-agGTATGCCTCAGAGGGACCACTGAAAGGTATCCTTGGGTACACAGACGAGGATGTTGTCTCTAATGACTTTGTTGGTGATTCAAG
|||||  |  |    |||| ||    |        ||  ||        | || |||   |    | || ||  |    |   |||  ||    |   |||  | | | ||| |||||||||| ||||| || ||||| || || ||||||||||| || ||||| ||||| ||||| || || |||||||||||
gtatgcttcctaaaattttattgcccgaccagatatcgtcatcgaaacattatcgtttaatgtagaactcttaataacctctcatggttta---atgtaaacctctaacagGCATGCCTCAGAAGGACCTCTTAAAGGCATTCTCGGGTACACAGATGAAGATGTCGTCTCCAATGATTTCGTCGGTGATTCAAG

upper sequence: GLYMA03G22790.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv19s0085g00600.t01 (Vitis vinifera), 3'ss of exon 11
-----gtatgtctattgcgttttttttttttggtctccactctg-ctgtgattgttctgtactaaccttttgcttgatttcta--tgactttgctactgaaaaata----tgaagGTATGCCTCAGAGGGACCACTGAAAGGTATCCTTGGGTACACAGACGAGGATGTTGTCTCTAATGACTTTGTTGGTGATTCAAG
      | | ||| |  |  | | | | | |      |  |||  || | ||      ||| | |  | |  |   || |  |  | |  || ||  |  ||  |     | |||||||||||||||||| ||| |||| ||||| ||||| ||||| || |||||||||||||| ||||| ||||||||||| |||||
gtatactctctctctctctctctctctctctatctatctatctatctatcatgcccaagta-tgatttatcccaaaatattaaaattatctttctctttgaatttccaactaaagGTATGCCTCAGAGGGGCCATTGAAGGGTATTCTTGGATACACGGATGAGGATGTTGTCTCCAATGATTTTGTTGGTGACTCAAG

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|151403747|gb|EV273557.1|EV273557
EST:     TGCCGGCTTAAGAAGAATGCTTCCTATGAAGATGTTAAAGCAGCAATAAA                         GTATGCCTCAGAGGGACCACTGAAAGGTATCCTTGGGTACACAGACGAGGA
genomic: TGCCGGCTTAAGAAGAATGCTTCCTATGAAGATGTTAAAGCAGCAATAAAgtatgtctat ... aaatatgaagGTATGCCTCAGAGGGACCACTGAAAGGTATCCTTGGGTACACAGACGAGGA
EST: gi|17022180|gb|BM093214.1|BM093214
EST:     TGCCGGCTTAAGAAGAATGCTTCCTATGAAGATGTTAAAGCAGCAATAAA                         GTATGCCTCAGAGGGACCACTGAAAGGTATCCTTGGGTACACAGACGAGGA
genomic: TGCCGGCTTAAGAAGAATGCTTCCTATGAAGATGTTAAAGCAGCAATAAAgtatgtctat ... aaatatgaagGTATGCCTCAGAGGGACCACTGAAAGGTATCCTTGGGTACACAGACGAGGA
EST: gi|193539491|gb|FK494751.1|FK494751
EST:     TGCCGGCTTAAGAAGAATGCTTCCTATGAAGATGTTAAAGCAGCAATAAA                         GTATGCCTCAGAGGGACCACTGAAAGGTATCCTTGGGTACACAGACGAGGA
genomic: TGCCGGCTTAAGAAGAATGCTTCCTATGAAGATGTTAAAGCAGCAATAAAgtatgtctat ... aaatatgaagGTATGCCTCAGAGGGACCACTGAAAGGTATCCTTGGGTACACAGACGAGGA
EST: gi|15589578|gb|BI674194.1|BI674194
EST:     TGCCGGCTTAAGAAGAATGCTTCCTATGAAGATGTTAAAGCAGCAATAAA                         GTATGCCTCAGAGGGACCACTGAAAGGTATCCTTGGGTACACAGACGAGGA
genomic: TGCCGGCTTAAGAAGAATGCTTCCTATGAAGATGTTAAAGCAGCAATAAAgtatgtctat ... aaatatgaagGTATGCCTCAGAGGGACCACTGAAAGGTATCCTTGGGTACACAGACGAGGA
EST: gi|51334832|gb|CO978698.1|CO978698
EST:     TGCCGGCTTAAGAAGAATGCTTCCTATGAAGATGTTAAAGCAGCAATAAA                         GTATGCCTCAGAGGGACCACTGAAAGGTATCCTTGGGTACACAGACGAGGA
genomic: TGCCGGCTTAAGAAGAATGCTTCCTATGAAGATGTTAAAGCAGCAATAAAgtatgtctat ... aaatatgaagGTATGCCTCAGAGGGACCACTGAAAGGTATCCTTGGGTACACAGACGAGGA
EST: gi|22927146|gb|BU544285.1|BU544285
EST:     NNCCGGCTTAAGAAGAATGCTTCCTATGAAGATGTTAAAGCAGCAATAAA                         GTATGCCTCAGAGGGACCACTGAAAGGTATCCTTGGGTACACAGACGAGGA
genomic: TGCCGGCTTAAGAAGAATGCTTCCTATGAAGATGTTAAAGCAGCAATAAAgtatgtctat ... aaatatgaagGTATGCCTCAGAGGGACCACTGAAAGGTATCCTTGGGTACACAGACGAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctgtactaaccttttgcttgatttctatgactttgctactgaaaaatatgaagGTATGCCTCAGAGGGACCACTGAAAGGTATCCTTGGGTACACAGACGAGGATGTTGTCTCTAATGACTTTGTTGGTGATTCAAG
                                           aaaaatatgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtctattgcgttttttttttttggtctccactctgctgtgattgttctgtactaaccttttgcttgatttctatgactttgctactgaaaaatatgaagGTATGCCTCAGAGGGACCACTGAAAGGTATCCTTGGGTACACAGACGAGGATGTTGTCTCTAATGACTTTGTTGGTGATTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG