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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atattgtattgtgtacataacatactatgttcaacatcactttaaatctgtttgtaaaccaatgatgctgattctcattatcactttgatccctttgtagATGTCACGGAGCCTTTATTGATCGAGGTTGATCAGATCTACCATCTTGCATGCCCTGCCTCTCCTATTTTCTACAAATACAATCCAGTAAAG

Basic information

species Glycine max
transcript GLYMA13G40960.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G40960.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 3
atattgtattgtgtacataacatactatgttcaacatcactttaaatctgtttgt-aaaccaatgatgctgattctcattatcactttgatccctttgtagATGTCACGGAGCCTTTATTGATCGAGGTTGATCAGATCTACCATCTTGCATGCCCTGCCTCTCCTATTTTCTACAAATACAATCCAGTAAAG
    | || | | | | |||       |  ||||  | |||| | |    ||    ||| |||||    | || |||||| |   | ||||   ||   |||||| || || ||| | ||  ||||||||||||| ||||||||| | ||||| || || ||||| ||||||||||||||||| || || |||
---gtatagtatcttcttaat------taatcaaacttacttaatactcattaaccaaaacaatg-cattaatactcattct---tgtgattttttc--agATGTGACTGAACCTCTTTTCGTCGAGGTTGATCAAATCTACCATTTAGCATGTCCCGCTTCTCCAATTTTCTACAAATACAACCCCGTTAAG

upper sequence: GLYMA13G40960.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G59290.2 (Arabidopsis thaliana), 3'ss of exon 3
atattgtattgtgtacataacatactatgttcaacatcactttaaatctgtttgtaa-accaatgatgctgattctcattatcactttgatccctttgtagATGTCACGGAGCCTTTATTGATCGAGGTTGATCAGATCTACCATCTTGCATGCCCTGCCTCTCCTATTTTCTACAAATACAATCCAGTAAAG
 ||| || | | | ||      |    |||| | | ||   ||     |||    || | | || ||  ||||    |||   | ||||  |  |    |||||| || |||||||| |||||||||||||||| ||| ||||||||||| || |||||||||||||| |||||||||||||| || || |||
gtatggtctcgag-actctcagtttgttgttaagcgtcttcttgttcatgtcaacaagatccatcatcgtgatctctatttggaatttgggctttaaacagATGTTACCGAGCCTTTGTTGATCGAGGTTGATCGGATTTACCATCTTGCTTGTCCTGCCTCTCCTATCTTCTACAAATACAACCCTGTTAAG

upper sequence: GLYMA13G40960.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 4
atattgtattgtg--tacataacatactatgttcaacatcactttaaatctgtttgtaaaccaatgatgctgattctcattatcactttgatccctttgtagATGTCACGGAGCCTTTATTGATCGAGGTTGATCAGATCTACCATCTTGCATGCCCTGCCTCTCCTATTTTCTACAAATACAATCCAGTAAAG--------
 ||| || |||    |   |  | |  |   | | |       |  ||| |   |||       |  |    |||   ||| |   ||||     ||   |||||||||||||||  | |||||||||||||||||||| |||||||||||||| ||||| |||||||| |||||||| ||||| || || |||        
gtatggttttgaaattctctggcttgttgc-tgctattgagaatggaatattcctgtcttttgttc-tatccatttatattttggttttgggt--ttaacagATGTCACGGAGCCACTTTTGATCGAGGTTGATCAGATTTACCATCTTGCATGTCCTGCTTCTCCTATCTTCTACAAGTACAACCCTGTGAAGACAATCAA

upper sequence: GLYMA13G40960.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 4
atattgtattgtgtacataacatacta--tgttcaacatc--actttaaatct--gtttgtaaaccaatgatgctgattctcattatcactttgatccctttgtagATGTCACGGAGCCTTTATTGATCGAGGTTGATCAGATCTACCATCTTGCATGCCCTGCCTCTCCTATTTTCTACAAATACAATCCAGTAAAG
    |   ||  |  || ||   || |  |||| | | |   |   ||| ||   ||||     | ||||||  |   | | |||     |||  || |||   ||||||||| ||||| || ||||| ||||||||| |||| ||||| |||||||| || || ||||||||||| || ||| ||||||| ||||||
----tcagttaagatcacaatgaaccacttgttaatcttttaatgataattcacagtttcatttctaatgat--tagcttttattccatattttttctcttcacagATGTCACTGAGCCATTGTTGATTGAGGTTGATAAGATATACCACCTTGCATGTCCCGCTTCTCCTATTTTTTATAAACACAATCCTGTAAAG

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|151406393|gb|EV276208.1|EV276208
EST:     CAACCTCAAAAAATGGATAGGTCATCCAAGATTTGAGCTTATCCGTCATG                         ATGTCACGGAGCCTTTATTGATCGAGGTTGATCAGATCTACCATCTTGCAT
genomic: CAACCTCAAAAAATGGATAGGTCATCCAAGATTTGAGCTTATCCGTCATGgtatagtcta ... ccctttgtagATGTCACGGAGCCTTTATTGATCGAGGTTGATCAGATCTACCATCTTGCAT
EST: gi|151404362|gb|EV274172.1|EV274172
EST:     CAACCTCAAAAAATGGATAGGTCATCCAAGATTTGAGCTTATCCGTCATG                         ATGTCACGGAGCCTTTATTGATCGAGGTTGATCAGATCTACCATCTTGCAT
genomic: CAACCTCAAAAAATGGATAGGTCATCCAAGATTTGAGCTTATCCGTCATGgtatagtcta ... ccctttgtagATGTCACGGAGCCTTTATTGATCGAGGTTGATCAGATCTACCATCTTGCAT
EST: gi|213590294|gb|DB963857.1|DB963857
EST:     CAACCTCAAAAAATGGATAGGTCATCCAAGATTTGAGCTTATCCGTCATG                         ATGTCACGGAGCCTTTATTGATCGAGGTTGATCAGATCTACCATCTTGCAT
genomic: CAACCTCAAAAAATGGATAGGTCATCCAAGATTTGAGCTTATCCGTCATGgtatagtcta ... ccctttgtagATGTCACGGAGCCTTTATTGATCGAGGTTGATCAGATCTACCATCTTGCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctgtttgtaaaccaatgatgctgattctcattatcactttgatccctttgtagATGTCACGGAGCCTTTATTGATCGAGGTTGATCAGATCTACCATCTTGCATGCCCTGCCTCTCCTATTTTCTACAAATACAATCCAGTAAAG
                                            tccctttgt  CT-rich tract
     tttgtaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atattgtattgtgtacataacatactatgttcaacatcactttaaatctgtttgtaaaccaatgatgctgattctcattatcactttgatccctttgtagATGTCACGGAGCCTTTATTGATCGAGGTTGATCAGATCTACCATCTTGCATGCCCTGCCTCTCCTATTTTCTACAAATACAATCCAGTAAAG

- - - - -tgtgtac
- - - - - - - - - - - - - - - - -acatcac
- - - - - - - - - - - - - - - - - - - - - - - - tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgct