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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggggtgatgtgtagtttgtaaagatgatatatttcagtgggacatctgctgttttcttattgactcagttttttccttaccaatatgttttggctaacagCATTATAAGGGTGACATTTCGGAGTTGGAACTATACTTTGTTATAGTAAATAATGAATATGGAGAACAAACAGAGGAGGAACTGCTTCCCGGAGGAAGGA

Basic information

species Glycine max
transcript GLYMA17G04180.1
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G04180.1 (Glycine max), 3'ss of exon 19
lower sequence: LOC_Os05g06690.3 (Oryza sativa), 3'ss of exon 20
ggggtgatgtgtagttt-gtaaagatgatatatttcagtgggacatctgctgttttcttattgactcagttttttccttaccaatatgttttggctaacagCATTATAAGGGTGACATTTCGGAGTTGGAACTATACTTTGTTATAGTAAATAATGAATATGGAGAACAAACAGAGGAGGAACTGCTTCCCGGAGGAAGGA
|  | |   ||||  || | |    | |||  || || |    |||| | ||||   ||      |   |  |||  |   |  |   |||       ||||||||| | ||||| || ||| | |||||  ||||||||||||| || ||||| |||||||| |||||| | || || |||||||| || || || ||  
gaagcgcattgtatcttagcagctttaatac-ttacattacttcatcagatgttcattttgcacttttatgattttttactctctccttttacatcctcagCATTATGATGGTGATATCTCGCAATTGGAGTTATACTTTGTTATTGTGAATAACGAATATGGTGAACAATCTGAAGAAGAACTGCTCCCAGGTGGGAGAG

upper sequence: GLYMA17G04180.1 (Glycine max), 3'ss of exon 19
lower sequence: GRMZM2G034622_T01 (Zea mays), 3'ss of exon 4
ggggtgatgtgtagtttgtaaagatgatatatttcagtgggacatctgctgttttcttattgactcagttttttccttacc--aatatgttttggctaacagCATTATAAGGGTGACATTTCGGAGTTGGAACTATACTTTGTTATAGTAAATAATGAATATGGAGAACAAACAGAGGAGGAACTGCTTCCCGGAGGAAGGA
     | |||| |   |    | |||| | |  || | |         |   | |  | || | |  |    |  || | |    | | ||   | |  ||||||||||| ||||| || || |||||||||||||| |||||||| ||||||||||||||||| ||||||   || || ||||| || || || || ||| 
-catagctgtggatacta-ggatatgaaagaaatctgggaagttcaatccaatctaatgttaagtttgcccctaactgatctcgtttttttcctgttctcagCATTATAATGGTGATATCTCAGAGTTGGAACTATATTTTGTTATTGTAAATAATGAATATGGTGAACAATGTGAAGAAGAACTTCTCCCTGGTGGGAGGC

upper sequence: GLYMA17G04180.1 (Glycine max), 3'ss of exon 19
lower sequence: GRMZM2G101098_T01 (Zea mays), 3'ss of exon 4
ggggtgatgtgtagtttgtaaagatg-atatatttcagtgggacatctgctgttttcttat-tgac--tcagttttttcct-----taccaatatgttttggctaacagCATTATAAGGGTGACATTTCGGAGTTGGAACTATACTTTGTTATAGTAAATAATGAATATGGAGAACAAACAGAGGAGGAACTGCTTCCCGGAGGAAGGA
         |||| |||| | || ||   ||| |    |   |  |    |   |||  || |||   ||||||| | |||     |  || |   |||    |  |||||||| || ||||| || || ||||||||||| || |||||||| || |||||||||||||| ||||||   || || ||||| || || || || ||| 
--------ttgta-tttgcatagctgtggatactaggatacaaatttgagttcattccaatctgatgttcagtttgtccctactggtctcacttcttttccattctcagCATTACAATGGTGATATCTCAGAGTTGGAACTGTATTTTGTTATTGTGAATAATGAATATGGTGAACAATGTGAAGAAGAACTTCTCCCTGGTGGGAGGG

upper sequence: GLYMA17G04180.1 (Glycine max), 3'ss of exon 19
lower sequence: AT3G17205.1 (Arabidopsis thaliana), 3'ss of exon 19
ggggtgatgtgtagtttgtaaagatgatat--atttcagtgggacatctgctgttttcttattgactcagttt-tttccttaccaatatgttttggc--taacagCATTATAAGGGTGACATTTCGGAGTTGGAACTATACTTTGTTATAGTAAATAATGAATATGGAGAACAAACAGAGGAGGAACTGCTTCCCGGAGGAAGGA
       ||| ||  |    | ||| || |    |    |      | |  | ||| ||| ||  ||   |     |  |||   ||   || ||    |  |||| |||||||||||| || || || ||||| || |||||||||||  | |||||||||||||||||    |||||||| || || ||||| || ||     
-----tttgtttacctacctacgataattttggctcttttttttttttttttttttgcttcttagctttatacacctttttatgtattcattatgatatttgcagCGTTATAAGGGTGATATCTCAGACTTGGAGCTTTACTTTGTTATTTTGAATAATGAATATGGAGAGAGGACAGAGGAAGAGCTACTTCCAGGGGGCCAAG

upper sequence: GLYMA17G04180.1 (Glycine max), 3'ss of exon 19
lower sequence: Vv05s0077g00470.t01 (Vitis vinifera), 3'ss of exon 20
-ggggtgatgtgtagtttgtaaagatgatatatttcagtgggacatctgctgtt-ttcttattgactcagttttttccttaccaatatgttttggctaacagCATTATAAGGGTGACATTTCGGAGTTGGAACTATACTTTGTTATAGTAAATAATGAATATGGAGAACAAACAGAGGAGGAACTGCTTCCCGGAGGAAGGA
     ||     |  ||| | |  ||   | |    | || | | || | | || ||  ||||    ||   |  |  || || || | || || |   ||||||| | | |||||| | || || |||||||| || |||||||| |||||||||||||| || ||||||||||||||||| |||||||| |||||||  |
caaaatggaac-tcttttattaccatttgacaccctattgcgtcctcagttcttattactatttttgcacactcatt-ttgcctatttattgtgacctgcagCATTTTGAAGGTGACTTATCAGAATTGGAACTTTATTTTGTTATTGTAAATAATGAATACGGGGAACAAACAGAGGAGGAGCTGCTTCCTGGAGGAAAAA

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|27425262|gb|CA936782.1|CA936782
EST:     ACTTGCCTTCCTTGGACCCAGAATTATATCGTCATCTCTTTTTTCTTAAG                         CATTATAAGGGTGACATTTCGGAGTTGGAACTATACTTTGTTATAGTAAAT
genomic: ACTTGCCTTCCTTGGACCCAGAATTATATCGTCATCTCATTTTTCTTAAGgtaatgtcac ... tggctaacagCATTATAAGGGTGACATTTCGGAGTTGGAACTATACTTTGTTATAGTAAAT
EST: gi|151406815|gb|EV276630.1|EV276630
EST:     ACTTGCCTTCCTTGGACCCAGAATTATATCGTCATCTCATTTTTCTTAAG                         CATTATAAGGGTGACATTTCGGAGTTGGAACTATACTTTGTTATAGTAAAT
genomic: ACTTGCCTTCCTTGGACCCAGAATTATATCGTCATCTCATTTTTCTTAAGgtaatgtcac ... tggctaacagCATTATAAGGGTGACATTTCGGAGTTGGAACTATACTTTGTTATAGTAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgctgttttcttattgactcagttttttccttaccaatatgttttggctaacagCATTATAAGGGTGACATTTCGGAGTTGGAACTATACTTTGTTATAGTAAATAATGAATATGGAGAACAAACAGAGGAGGAACTGCTTCCCGGAGGAAGGA
                            tccttac  putative branch site (score: 2)
      ttttcttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggggtgatgtgtagtttgtaaagatgatatatttcagtgggacatctgctgttttcttattgactcagttttttccttaccaatatgttttggctaacagCATTATAAGGGTGACATTTCGGAGTTGGAACTATACTTTGTTATAGTAAATAATGAATATGGAGAACAAACAGAGGAGGAACTGCTTCCCGGAGGAAGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- ggtgatg
- - - - - - - - - - - - - - - - ttcagtg
- - - - - - - - - - - - - - - - - - - - - catctgc