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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtatacacatgttctgatgttcatatgcattgtggctgttcatgatgaatggttttcgatttcttcgcgcagATGACTGGGAAGGACAAAGATTACAGATATATGGCCACATCTGATTTGCTCAATGAGTTGAGCAAAGCAACGTTTAAGGCCGATGCTGATCTGGAGGTCA

Basic information

species Glycine max
transcript GLYMA07G40230.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G40230.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G168629_T05 (Zea mays), 3'ss of exon 2
---------gtatgtatacacatgttctgatgttca--tatgcattgtggctgttcatgatgaatggttttcgatttcttcgcgcagATGACTGGGAAGGACAAAGATTACAGATATATGGCCACATCTGATTTGCTCAATGAGTTGAGCAAAGCAACGTTTAAGGCCGATGCTGATCTGGAGGTCA
           |   ||  |||||   |   |||||  ||||||| ||      |  | | | |   | ||  ||  ||  || |||||||| ||||| || ||||| |||||||||||||| ||||| ||| |||| | ||| ||||  |||| ||  || || || |||   || || |||   |
gtaacccctaaactaatgtacatgaaattgggttcaactatgcatcgttttgacttttaaagcactttgttaaatgcct--gcacagATGACAGGGAAAGATAAAGACTACAGATATATGGCAACATCAGATCTGCTTAGTGAATTGAATAAAGAAAGCTTCAAAGCTGATCAAGACCTTGAGCCAA

upper sequence: GLYMA07G40230.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G02560.1 (Arabidopsis thaliana), 3'ss of exon 2
---------------gtatgtatacacatgttctgatgttcatatgcattgtggctgttcatgatgaatg-gttttcgatttcttcgcgcagATGACTGGGAAGGACAAAGATTACAGATATATGGCCACATCTGATTTGCTCAATGAGTTGAGCAAAGCAACGTTTAAGGCCGATGCTGATCTGGAGGTCA
               || | ||   |    |  |  ||||  |  | || ||  |  ||  | ||   ||  ||| | ||   |||    ||||||| || || || |||||||||||||| ||||| || ||||||||||| ||||||||||  || |   | |||||   |||    ||  |||      
gtcttttcatcatctgtttctaattaagcttaattttgtttttgagtatagtcaccttttctcattgctgtatttactatagTTTC----AGATGACGGGTAAAGATAAAGATTACAGATACATGGCAACCTCTGATTTGCTTAATGAGTTGAATAAGGATTCCTTTAAAATCGACCTGGACTTGG------

upper sequence: GLYMA07G40230.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G02560.2 (Arabidopsis thaliana), 3'ss of exon 2
---------------gtatgtatacacatgttctgatgttcatatgcattgtggctgttcatgatgaatg-gttttcgatttcttcgcgcagATGACTGGGAAGGACAAAGATTACAGATATATGGCCACATCTGATTTGCTCAATGAGTTGAGCAAAGCAACGTTTAAGGCCGATGCTGATCTGGAGGTCA
               || | ||   |    |  |  ||||  |  | || ||  |  ||  | ||   ||  ||| | ||   |||    ||||||| || || || |||||||||||||| ||||| || ||||||||||| ||||||||||  || |   | |||||   |||    ||  ||||||| |
gtcttttcatcatctgtttctaattaagcttaattttgtttttgagtatagtcaccttttctcattgctgtatttactatagtttc----agATGACGGGTAAAGATAAAGATTACAGATACATGGCAACCTCTGATTTGCTTAATGAGTTGAATAAGGATTCCTTTAAAATCGACCTGGACTTGGAGGTGA

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|213610988|gb|DB970915.1|DB970915
EST:     AAACTTGTGGAAACATGTACAACCTAGCTTTGACTAGCATACTAGAAAAG                         ATGACTGGGAAGGACAAAGATTACAGATATATGGCCACATCTGATTTGCTC
genomic: AAACTTGTGGAAACATGGCCAATCTAGCTTTGACTAGCATACTAGAAAAGgtatgtatac ... cttcgcgcagATGACTGGGAAGGACAAAGATTACAGATATATGGCCACATCTGATTTGCTC
EST: gi|208148790|gb|GD945436.1|GD945436
EST:     AAACTTGTGGAAACATGGCCAATCTAGCTTTGACTAGCATACTAGAAAAG                         ATGACTGGGAAGGACAAAGATTACAGATATAT
genomic: AAACTTGTGGAAACATGGCCAATCTAGCTTTGACTAGCATACTAGAAAAGgtatgtatac ... cttcgcgcagATGACTGGGAAGGACAAAGATTACAGATATAT
EST: gi|213600096|gb|DB964302.1|DB964302
EST:     AAACTTGTGGAAACATGGCCAATCTAGCTTTGACTAGCATACTAGAAAAG                         ATGACTGGGAAGGACAAAGATTACAGATATATGGCCACATCTGATTTGCTC
genomic: AAACTTGTGGAAACATGGCCAATCTAGCTTTGACTAGCATACTAGAAAAGgtatgtatac ... cttcgcgcagATGACTGGGAAGGACAAAGATTACAGATATATGGCCACATCTGATTTGCTC
EST: gi|213613547|gb|DB963263.1|DB963263
EST:     AAACTTGTGGAAACATGGCCAATCTAGCTTTGACTAGCATACTAGAAAAG                         ATGACTGGGAAGGACAAAGATTACAGATATATGGCCACATCTGATTTGCTC
genomic: AAACTTGTGGAAACATGGCCAATCTAGCTTTGACTAGCATACTAGAAAAGgtatgtatac ... cttcgcgcagATGACTGGGAAGGACAAAGATTACAGATATATGGCCACATCTGATTTGCTC
EST: gi|209717236|gb|BW657705.1|BW657705
EST:     AAACTTGTGGAAACATGGCCAATCTAGCTTTGACTAGCATACTAGAAAAG                         ATGACTGGGAAGGACAAAGATTACAGATATATGGCCACATCTGATTTGCTC
genomic: AAACTTGTGGAAACATGGCCAATCTAGCTTTGACTAGCATACTAGAAAAGgtatgtatac ... cttcgcgcagATGACTGGGAAGGACAAAGATTACAGATATATGGCCACATCTGATTTGCTC
EST: gi|213619876|gb|DB971135.1|DB971135
EST:     AAACTTGTGGAAACATGGCCAACCTAGCTTTGACTAGCATACTAGAAAAG                         ATGACTGGGAAGGACAAAGATTACAGATATATGGCCACATCTGATTTGCTC
genomic: AAACTTGTGGAAACATGGCCAATCTAGCTTTGACTAGCATACTAGAAAAGgtatgtatac ... cttcgcgcagATGACTGGGAAGGACAAAGATTACAGATATATGGCCACATCTGATTTGCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttcatatgcattgtggctgttcatgatgaatggttttcgatttcttcgcgcagATGACTGGGAAGGACAAAGATTACAGATATATGGCCACATCTGATTTGCTCAATGAGTTGAGCAAAGCAACGTTTAAGGCCGATGCTGATCTGGAGGTCA
                                   ttttcgatttcttc  CT-rich tract
                                         atttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtatacacatgttctgatgttcatatgcattgtggctgttcatgatgaatggttttcgatttcttcgcgcagATGACTGGGAAGGACAAAGATTACAGATATATGGCCACATCTGATTTGCTCAATGAGTTGAGCAAAGCAACGTTTAAGGCCGATGCTGATCTGGAGGTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG