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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccttaagaaaccttgtgtgtatctttgcagtctataatttattgtttagaaattcatttactattatcataattaaaaaattaatatatgctaatttcagTGGGGAGAGTATGGAGAATGCTTTGAGAGCATGCTGTAAAGGTATCAAGATTGGGAAAATTTTAATTCACAGAGAAGGTGACAATGGTCAGCAGG

Basic information

species Glycine max
transcript GLYMA18G08180.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G08180.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os11g16370.1 (Oryza sativa), 3'ss of exon 11
--------ccttaagaaaccttgtgtgtatctttgcagtctataatttattgtttagaaattcatttactattatcataattaaaaaattaatatatgctaatttcagTGGGGAGAGTATGGAGAATGCTTTGAGAGCATGCTGTAAAGGTATCAAGATTGGGAAAATTTTAATTCACAGAGAAGGTGACAATGGTCAGCAGG
         |||   |||  || ||| ||     ||  |  |||  |  |||  || |||| |||  |||||| |||  ||||      | | |  ||||  || |||||| ||||||||||||||||| ||| | ||||||||||||||||| || |||||||| ||| | |||||||||||||| ||||||||  | ||| 
attcaatttcttgttaaagattctgt-taataaagctcttcatacatccttgagtataaatacata-actattgtca--attattt--cttacaattgct--ttccagTGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGTAAAGGTATAAAAATTGGGAAGATTCTTATTCACAGAGAAGGAGACAATGGCAAACAG-

upper sequence: GLYMA18G08180.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os02g17320.2 (Oryza sativa), 3'ss of exon 11
---------ccttaagaaaccttgtgtgtatctttgcagtctataatttattgtttagaaattcatttactattatcataattaaaaaattaatatatgctaatttcagTGGGGAGAGTATGGAGAATGCTTTGAGAGCATGCTGTAAAGGTATCAAGATTGGGAAAATTTTAATTCACAGAGAAGGTGACAATGGTCAGCAGG
         ||||   ||   |  ||| ||     |||    |||| || |||  ||||||  |||     | |||  ||||||     ||  |  |   |   | |||||| ||||||||||||||||| ||| | |||||||| |||||||| || |||||||| ||| | |||||||| ||||| ||||||||  | ||| 
ggattcattccttgtcaagtatcttgt-tagtaaagcacatcataaatttttgaatagaaaggcata----actatgttaattat----tttctgcaacttctctccagTGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAATTGGGAAGATTCTTATTCACAGGGAAGGAGACAATGGCAAACAG-

upper sequence: GLYMA18G08180.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G169462_T01 (Zea mays), 3'ss of exon 10
-----ccttaagaaaccttgtgtgtatctt--tgcagtctataatttattgtttagaaattcatttactattatcataattaaaaaattaatatatgctaatttcagTGGGGAGAGTATGGAGAATGCTTTGAGAGCATGCTGTAAAGGTATCAAGATTGGGAAAATTTTAATTCACAGAGAAGGTGACAATGGTCAGCAGG
      |  ||   |||     || |      | || |  || | | ||       | ||  || |||| |       |  ||  | ||  || |      || |||||| || ||||||||||||||  |  | ||||||||||||||||| ||||||||||| ||| | |||||  | |||||||||||||| || ||| 
aacatgcacaattgacccctcatgcactagaattcaattcatcagtcatcacaagaacatctatgtactct-------acaaatgatttgctacaactggtttccagTGGCGAAAGTATGGAGAATGCACTACGTGCATGCTGTAAAGGTATAAAGATTGGGAAGATTCTTATTCATCGGGAAGGTGACAATGGACAACAG-

upper sequence: GLYMA18G08180.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G034143_T03 (Zea mays), 3'ss of exon 12
ccttaagaaaccttgtgtgtatctttgca-gtctataatttattgtttagaaattcatttactattatcataattaaaaaattaatatatgctaatttcagTGGGGAGAGTATGGAGAATGCTTTGAGAGCATGCTGTAAAGGTATCAAGATTGGGAAAATTTTAATTCACAGAGAAGGTGACAATGGTCAGCAGG
  | | | |      |     || |  || |   ||   | ||       |   |    ||   |   |      ||  | ||  || |      || |||||| || || ||||||||||| ||  ||||||||||||||||||| ||||||||||| ||| | |||||  | ||||| |||||||| || ||| 
-ttcatgcactagaattcaattcatcacaagaacatgtatgatcccccctatccttgaataaagtgtactctgcaaatgatttgctacaactgctttccagTGGCGAAAGCATGGAGAATGCGTTACGAGCATGCTGTAAAGGTATAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAG-

upper sequence: GLYMA18G08180.1 (Glycine max), 3'ss of exon 11
lower sequence: AT1G55810.1 (Arabidopsis thaliana), 3'ss of exon 11
ccttaagaaaccttgtgtgtatctttgcagtctataatttattgtttagaaattcatttactattatcataattaaaaaattaatatatg-ctaatttcagTGGGGAGAGTATGGAGAATGCTTTGAGAGCATGCTGTAAAGGTATCAAGATTGGGAAAATTTTAATTCACAGAGAAGGTGACAATGGTCAGCAGG
                             ||  | || | |  | ||| | | | ||    ||   |||  | || | ||| | | | |  || |    || || |||||||||||||| ||| | ||||||||||| ||||| ||||| |||||||| ||| | ||||| |||||||| ||||||||||| ||| 
-----------------------------gtaaagaaatca--gcttaaacactaata-gttaacgtcaatactatataatgattttgtctctgaacatagCGGTGAGAGTATGGAGAACGCTCTTAGAGCATGCTGCAAAGGCATCAAAATTGGGAAGATTCTGATTCATAGAGAAGGCGACAATGGTCAACAG-

upper sequence: GLYMA18G08180.1 (Glycine max), 3'ss of exon 11
lower sequence: AT4G26510.2 (Arabidopsis thaliana), 3'ss of exon 11
---ccttaagaaaccttgtgtgtatctt-tgcagtctataatttattgtttagaaattcatttactattatcataattaaaaaat--taatatatgctaatttcagTGGGGAGAGTATGGAGAATGCTTTGAGAGCATGCTGTAAAGGTATCAAGATTGGGAAAATTTTAATTCACAGAGAAGGTGACAATGGTCAGCAGG
   | ||   | | |||   | ||  || | || |    | ||     |       ||||| | | | | ||  |   |    ||  |  | |    ||||   ||||| ||||| ||||||||||| ||  ||||||| || |||||||||||||| ||||| ||  |||||||||||||||||||||||||||| ||| 
gtactttcctatatcttagctttagtttatacaataggaacttccccatcct----ttcatatcccactctctcaccaacttgatggtgttttgaaataatgctagTGGTGAGAGCATGGAGAATGCGTTACGAGCATGTTGCAAAGGTATCAAGATCGGGAAGATCCTAATTCACAGAGAAGGTGACAATGGTCAACAG-

upper sequence: GLYMA18G08180.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv19s0015g01730.t01 (Vitis vinifera), 3'ss of exon 11
----ccttaagaaaccttgtgtgtatctttgcagtctataatttattgtttagaaattcatttactattatcataattaaaaaattaatatatgctaatttcagTGGGGAGAGTATGGAGAATGCTTTGAGAGCATGCTGTAAAGGTATCAAGATTGGGAAAATTTTAATTCACAGAGAAGGTGACAATGGTCAGCAGG
        |||||         | || ||    ||     |   ||| | |     ||  | |  |    |     || ||  ||       | || ||  |||||| ||||||||||||||||||||| ||||||| || ||||||||||| |||||||| ||| | || || || ||||| || || ||||||||| 
aaaggaaaaagaagtgcaaaaagcatattcctggttatggacccattttctc----tttgtcttttgcattttggtttgaaccatcttctcttactgatgccagTGGTGAGAGTATGGAGAATGCTTTGCGAGCATGTTGCAAAGGTATCAAAATTGGGAAGATTCTTATCCATAGGGAAGGGGATAACGGTCAGCAG-

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|21602644|gb|BQ612975.1|BQ612975
EST:     ACTGGTGTTGATTTTTGTAAAAGGTTGTGTGGTGTCTCTGTTATCAGAAG                         TGGGGAGAGTATGGAGAATGCTTTGAGAGCATGCTGTAAAGGTATCAAGAT
genomic: ACTGGTGTTGATTTTTGTAAAAGGTTGTGTGGTGTCTCTGTTATCAGAAGgtattagtct ... ctaatttcagTGGGGAGAGTATGGAGAATGCTTTGAGAGCATGCTGTAAAGGTATCAAGAT
EST: gi|14125241|gb|BG789679.1|BG789679
EST:     ACTGGTGTTGATTTTTGTAAAAGGTTGTGTGGTGTCTCTGTTATCAGAAG                         TGGGGAGAGTATGGAGAATGCTTTGAGAGCATGCTGTAAAGGTATCAAGAT
genomic: ACTGGTGTTGATTTTTGTAAAAGGTTGTGTGGTGTCTCTGTTATCAGAAGgtattagtct ... ctaatttcagTGGGGAGAGTATGGAGAATGCTTTGAGAGCATGCTGTAAAGGTATCAAGAT
EST: gi|58019197|gb|CX705939.1|CX705939
EST:     ACTGGTGTTGATTTTTGTAAAAGGTTGTGTGGTGTCTCTGTTATCAGAAG                         TGGGGAGAGTATGGAGAATGCTTTGAGAGCATGCTGTAAAGGTATCAAGAT
genomic: ACTGGTGTTGATTTTTGTAAAAGGTTGTGTGGTGTCTCTGTTATCAGAAGgtattagtct ... ctaatttcagTGGGGAGAGTATGGAGAATGCTTTGAGAGCATGCTGTAAAGGTATCAAGAT
EST: gi|58018989|gb|CX705731.1|CX705731
EST:     ACTGGTGTTGATTTTTGTAAAAGGTTGTGTGGTGTCTCTGTTATCAGAAG                         TGGGGAGAGTATGGAGAATGCTTTGAGAGCATGCTGTAAAGGTATCAAGAT
genomic: ACTGGTGTTGATTTTTGTAAAAGGTTGTGTGGTGTCTCTGTTATCAGAAGgtattagtct ... ctaatttcagTGGGGAGAGTATGGAGAATGCTTTGAGAGCATGCTGTAAAGGTATCAAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagaaattcatttactattatcataattaaaaaattaatatatgctaatttcagTGGGGAGAGTATGGAGAATGCTTTGAGAGCATGCTGTAAAGGTATCAAGATTGGGAAAATTTTAATTCACAGAGAAGGTGACAATGGTCAGCAGG
                                           tgctaat  putative branch site (score: 2)
     aattcatttactatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccttaagaaaccttgtgtgtatctttgcagtctataatttattgtttagaaattcatttactattatcataattaaaaaattaatatatgctaatttcagTGGGGAGAGTATGGAGAATGCTTTGAGAGCATGCTGTAAAGGTATCAAGATTGGGAAAATTTTAATTCACAGAGAAGGTGACAATGGTCAGCAGG

- - aagaaacc
- - - - - - -tgtgtgt
- - - - - - - - - - - - -tgcagtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaat