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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccctaagaaaccttgtgtgtctctctgcagtttataatttattgttaagaaattcattttctgttatcataattaataatttaatatatgctcatttcagTGGGGAGAGTATGGAGAATGCTTTGAGAGCATGCTGTAAAGGTATAAAGATTGGGAAAATTTTAATTCACAGAGAAGGTGACAATGGTCAGCAG

Basic information

species Glycine max
transcript GLYMA08G45270.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G45270.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os11g16370.1 (Oryza sativa), 3'ss of exon 11
--------ccctaagaaaccttgtgtgtctctctgcagtttataatttattgttaagaaattcattttctgttatcataattaataatttaatatatgctcatttcagTGGGGAGAGTATGGAGAATGCTTTGAGAGCATGCTGTAAAGGTATAAAGATTGGGAAAATTTTAATTCACAGAGAAGGTGACAATGGTCAGCAG
         | |   |||  || ||| |      ||  || |||  |  |||   | |||| |||        |  ||  | ||| ||||  || |    | || |||||| ||||||||||||||||| ||| | |||||||||||||||||||| |||||||| ||| | |||||||||||||| ||||||||  | |||
attcaatttcttgttaaagattctgt-taataaagctcttcatacatccttgagtataaatacata-------actattgtcaattatttcttacaattgctttccagTGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGTAAAGGTATAAAAATTGGGAAGATTCTTATTCACAGAGAAGGAGACAATGGCAAACAG

upper sequence: GLYMA08G45270.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os02g17320.2 (Oryza sativa), 3'ss of exon 11
---------ccctaagaaaccttgtgtgtctctctgcagtttataatttattgttaagaaattcattttctgttatcataattaataatttaatatatgctcatttcagTGGGGAGAGTATGGAGAATGCTTTGAGAGCATGCTGTAAAGGTATAAAGATTGGGAAAATTTTAATTCACAGAGAAGGTGACAATGGTCAGCAG
         || |   ||   |  ||| |      |||  | |||| || |||   |||||  |||        |  ||  ||||| ||||  |  |   ||  | |||||| ||||||||||||||||| ||| | |||||||| ||||||||||| |||||||| ||| | |||||||| ||||| ||||||||  | |||
ggattcattccttgtcaagtatcttgt-tagtaaagcacatcataaatttttgaatagaaaggcata-------actatg-ttaattattttctgcaacttctctccagTGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAATTGGGAAGATTCTTATTCACAGGGAAGGAGACAATGGCAAACAG

upper sequence: GLYMA08G45270.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G169462_T01 (Zea mays), 3'ss of exon 10
-----ccctaa--gaaaccttgtgtgtctctctgcagtttataatttattgttaagaaattcattttctgttatcataattaataatttaatatatgctcatttcagTGGGGAGAGTATGGAGAATGCTTTGAGAGCATGCTGTAAAGGTATAAAGATTGGGAAAATTTTAATTCACAGAGAAGGTGACAATGGTCAGCAG
      |  ||  ||  |||  ||        | || || || | | ||    |  | ||  || | || |       |  ||| ||||  || |      || |||||| || ||||||||||||||  |  | ||||||||||||||||||||||||||||| ||| | |||||  | |||||||||||||| || |||
aacatgcacaattgacccctcatgcactagaattcaattcatcagtcatcacaagaacatctatgtactct-------acaaatgatttgctacaactggtttccagTGGCGAAAGTATGGAGAATGCACTACGTGCATGCTGTAAAGGTATAAAGATTGGGAAGATTCTTATTCATCGGGAAGGTGACAATGGACAACAG

upper sequence: GLYMA08G45270.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G034143_T03 (Zea mays), 3'ss of exon 12
ccctaagaaaccttgtgtgtctctctgca-gtttataatttattgttaagaaattcattttctgttatcataattaataatttaatatatgctcatttcagTGGGGAGAGTATGGAGAATGCTTTGAGAGCATGCTGTAAAGGTATAAAGATTGGGAAAATTTTAATTCACAGAGAAGGTGACAATGGTCAGCAG
    | | |      |     ||    || |   ||   | ||       |   |    |   ||   |      ||| ||||  || |    | || |||||| || || ||||||||||| ||  ||||||||||||||||||||||||||||||| ||| | |||||  | ||||| |||||||| || |||
-ttcatgcactagaattcaattcatcacaagaacatgtatgatcccccctatccttgaataaagtgtactctgcaaatgatttgctacaactgctttccagTGGCGAAAGCATGGAGAATGCGTTACGAGCATGCTGTAAAGGTATAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAG

upper sequence: GLYMA08G45270.1 (Glycine max), 3'ss of exon 11
lower sequence: AT1G55810.1 (Arabidopsis thaliana), 3'ss of exon 11
ccctaagaaaccttgtgtgtctctctgcagtttataatttattgttaagaaattcattttctgttatcataat-taataatttaatatatgctcatttcagTGGGGAGAGTATGGAGAATGCTTTGAGAGCATGCTGTAAAGGTATAAAGATTGGGAAAATTTTAATTCACAGAGAAGGTGACAATGGTCAGCAG
                             ||  | || | |   | || |     | ||   || |  |  || |||| ||||  | | ||  |||   || || |||||||||||||| ||| | ||||||||||| ||||| || || |||||||| ||| | ||||| |||||||| ||||||||||| |||
-----------------------------gtaaagaaatcagcttaaacactaatagttaacgtcaatactatataatgattttgtctctgaacat---agCGGTGAGAGTATGGAGAACGCTCTTAGAGCATGCTGCAAAGGCATCAAAATTGGGAAGATTCTGATTCATAGAGAAGGCGACAATGGTCAACAG

upper sequence: GLYMA08G45270.1 (Glycine max), 3'ss of exon 11
lower sequence: AT4G26510.2 (Arabidopsis thaliana), 3'ss of exon 11
ccctaagaaaccttgtgtgtctct-ctgcagtttataattta-----ttgttaagaaattcattttctgttatcataattaataatt--taatatatgctcatttcagTGGGGAGAGTATGGAGAATGCTTTGAGAGCATGCTGTAAAGGTATAAAGATTGGGAAAATTTTAATTCACAGAGAAGGTGACAATGGTCAGCAG
      | |   |  | | |||   ||  ||||||||   ||     ||    |    ||||| | |   | ||  |   | |   |  |  | |    | ||   ||||| ||||| ||||||||||| ||  ||||||| || |||||||| ||||| ||||| ||  |||||||||||||||||||||||||||| |||
------gtactttcctatatcttagctttagtttatacaataggaacttccccatcctttcatatcccactctctcaccaacttgatggtgttttgaaataatgctagTGGTGAGAGCATGGAGAATGCGTTACGAGCATGTTGCAAAGGTATCAAGATCGGGAAGATCCTAATTCACAGAGAAGGTGACAATGGTCAACAG

upper sequence: GLYMA08G45270.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv19s0015g01730.t01 (Vitis vinifera), 3'ss of exon 11
----ccctaagaaaccttgtgtgtctctctgcagtttataatttattgttaagaaattcattttctgttatcataatt--aataatttaatatatgctcatttcagTGGGGAGAGTATGGAGAATGCTTTGAGAGCATGCTGTAAAGGTATAAAGATTGGGAAAATTTTAATTCACAGAGAAGGTGACAATGGTCAGCAG
        |||||         |  | |     |||    |   ||| |       ||  | || ||  ||  |  ||  ||  || |  | | | || ||  |||||| ||||||||||||||||||||| ||||||| || |||||||| || |||||||| ||| | || || || ||||| || || |||||||||
aaaggaaaaagaagtgcaaaaagcatattcctggttatggacccattttctc----tttgtcttttgc-attttggtttgaaccatcttctct-tactgatgccagTGGTGAGAGTATGGAGAATGCTTTGCGAGCATGTTGCAAAGGTATCAAAATTGGGAAGATTCTTATCCATAGGGAAGGGGATAACGGTCAGCAG

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|31311442|gb|CD396645.1|CD396645
EST:     TGTGGTGTCTCTGTTATCAGAAG                         TGGGGAGAGTATGGAGAATGCTTTGAGAGCATGCTGTAAAGGTATAAAGAT
genomic: TGTGGTGTCTCTGTTATCAGAAGgtattagtct ... ctcatttcagTGGGGAGAGTATGGAGAATGCTTTGAGAGCATGCTGTAAAGGTATAAAGAT
EST: gi|13240468|gb|BG359777.1|BG359777
EST:     ACTGGTGTTGATTTTTGTAAAAGGTTGTGTGGTGTCTCTGTTATCAGAAG                         TGGGGAGAGTATGGAGAATGCTTTGAGAGCATGCTGTAAAGGTATAAAGAT
genomic: ACTGGTGTTGATTTTTGTAAAAGGTTGTGTGGTGTCTCTGTTATCAGAAGgtattagtct ... ctcatttcagTGGGGAGAGTATGGAGAATGCTTTGAGAGCATGCTGTAAAGGTATAAAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taagaaattcattttctgttatcataattaataatttaatatatgctcatttcagTGGGGAGAGTATGGAGAATGCTTTGAGAGCATGCTGTAAAGGTATAAAGATTGGGAAAATTTTAATTCACAGAGAAGGTGACAATGGTCAGCAG
                                             ctcatttc  CT-rich tract
     aattcattttctgtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccctaagaaaccttgtgtgtctctctgcagtttataatttattgttaagaaattcattttctgttatcataattaataatttaatatatgctcatttcagTGGGGAGAGTATGGAGAATGCTTTGAGAGCATGCTGTAAAGGTATAAAGATTGGGAAAATTTTAATTCACAGAGAAGGTGACAATGGTCAGCAG

- - aagaaacc
- - - - - - -tgtgtgt
- - - - - - - - - - - ctctgca