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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtcttattttgcaattgcattgaagtcttggagcattctggtcctattcctatattccctaaataggaaataatattttttttattaacgtcagAGGAACAAAGCTCCATATGAGCAAGCAATTCCATTACTTATGCCTCAGCATCATATGGTTATTCCACATTACTTGGGAAGAAGCAGAGAGATACAGATTG

Basic information

species Glycine max
transcript GLYMA09G04620.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G04620.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os01g20860.1 (Oryza sativa), 3'ss of exon 9
gttagtcttattttgcaattgcattgaagtcttggagcattctggtcctattcctatattccctaaataggaaataatattttttttattaacgtcagAGGAACAAAGCTCCATATGAGCAAGCAATTCCATTACTTATGCCTCAGCATCATATGGTTATTCCACATTACTTGGGAAGAAGCAGAGAGATACAGATTG
                       |     |  |||   ||  |  ||  || |||||   |  | ||   || |    | | || |         |||||||||||||| ||| |||||||||||||||| ||| | |||||||| ||||| ||||| ||||| |||||| |||| | || || |||   | |    |
----------------------gtatgtttactggttaatattactc--atccctatcaccgttgaaattgacaactcaatcttatg--------cagAGGAACAAAGCACCAAATGAGCAAGCAATTCCCTTATTGATGCCTCAACATCACATGGTAATTCCCCATTACATGGGTAAAATCAAAGAATCAAATGAGG

upper sequence: GLYMA09G04620.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os05g29050.1 (Oryza sativa), 3'ss of exon 10
gttagtcttattttgcaattgcattgaagtcttggagcattctggtcctattcctatattccctaaataggaaataatattttttttattaacgtcagAGGAACAAAGCTCCATATGAGCAAGCAATTCCATTACTTATGCCTCAGCATCATATGGTTATTCCACATTACTTGGGAAGAAGCAGAGAGATACAGATTG
          |||  |  || ||||| |  ||     |||  | ||| |   | |   |    ||||||  |||||   |||||||         |||||||||||||||||  ||||||||| |||||| || || |||||||| || || ||||| ||||||||||||  ||| | | ||  ||| ||  | | ||
---------gtttgtcttttccattgcatact-----catcatagtcttccccttcattattgtaaata--aaataccttttttttc--------cagAGGAACAAAGCTCCCAATGAGCAAGGAATTCCCTTGCTGATGCCTCATCACCACATGGTAATTCCACATTACAAGGGCATAGGCCAAGAAATTAATAGTG

upper sequence: GLYMA09G04620.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G066485_T01 (Zea mays), 3'ss of exon 10
gttagtcttattttgcaattgcattgaagtcttggagcattctggtcctattcctatattccctaaataggaaataatattttttttattaacgtcagAGGAACAAAGCTCCATATGAGCAAGCAATTCCATTACTTATGCCTCAGCATCATATGGTTATTCCACATTACTTGGGAAGAAGCAGAGAGATACAGATTG
                       |||    |||  | | || |||||   ||   |||      ||   | |||  | ||| ||||| ||    ||||||||||||||||| | |||||||||||||||| ||||| ||||||||  | || ||||| |||||||| |||  ||| ||||||| ||| | | |   ||
----------------------gttg----cttatatccttgtggtctgcttatcataga----aagcggtaaacta-attgtttttttttctttcagAGGAACAAAGCTCTAAATGAGCAAGCAATTCCCTTACTGATGCCTCATTACCACATGGTAATTCCACACTACAAGGGTAGAAGCAAAGAAACAAATGATG

upper sequence: GLYMA09G04620.1 (Glycine max), 3'ss of exon 11
lower sequence: AT3G16785.1 (Arabidopsis thaliana), 3'ss of exon 11
gttagtcttattttgcaattgcattgaagtcttggagcattctggtcctattcctatattccctaaataggaaataatattttttttattaacgtcagAGGAACAAAGCTCCATATGAGCAAGCAATTCCATTACTTATGCCTCAGCATCATATGGTTATTCCACATTACTTGGGAAGAAGCAGAGAGATACAGATTG
                  |  |    |  ||||  |   |  |    || ||  | | | |  | | ||    |  |||    || | ||    |||||| |||||||| ||||||||| |  |||||||  | ||||||||||| ||||| |||||||| || || ||| |||||||       |||  | | ||||
----------------gttcacccatacttctttaactttcttctatctgtttgtttttcctgttattaccgtaacataaccattgtgtt--tttcagAGAAACAAAGCACCATATGAGGATTCAATTCCGCTTCTTATGCCTCAACATCACATGGTTATACCCCACTACATGGGAAGGCAAGAGGAGTCAGACATTG

upper sequence: GLYMA09G04620.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv05s0077g01830.t01 (Vitis vinifera), 3'ss of exon 12
gttagtcttattttgcaattgcattgaagtcttggagcattctggtcctattcctatattccctaaataggaaataatattttttttattaacgtcagAGGAACAAAGCTCCATATGAGCAAGCAATTCCATTACTTATGCCTCAGCATCATATGGTTATTCCACATTACTTGGGAAGAAGCAGAGAGATACAGATTG
       | || |    | | |||   | ||        ||||      | |   |||  || |  ||   ||   |    |  |||  |     ||||| || ||||||||| ||||||||||||||||| |||||||||||||||| || ||||| |||||||||||| ||||||| |||||||||||  || |||
-----gttgatgtcttcactacat---actccctagttcttctttcaaaagtataataaaccttttatctcaatacaagcatacttttctg----cagAGAAATAAAGCTCCAAATGAGCAAGCAATTCCACTACTTATGCCTCAGCAGCACATGGTCATTCCACATTACATGGGAAGGAGCAGAGAGATGGAGGTTG

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|51343297|gb|CO984030.1|CO984030
EST:     GTGACATTGCTAGGCACTTTGTTCAGCGATGGAATTATGCCAAG                         AGGAACAAAGCTCCATATGAGCAAGCAATTCCATTACTTATGCCTCAGCAT
genomic: GTGACATTGCTAGGCACTTTGTTCAGCGATGGAATTATGCCAAGgttagtctta ... ttaacgtcagAGGAACAAAGCTCCATATGAGCAAGCAATTCCATTACTTATGCCTCAGCAT
EST: gi|23062044|gb|BU578493.1|BU578493
EST:     AGGCACTTTGTTCAGCGATGGAATTATGCCAAG                         AGGAACAAAGCTCCATATGAGCAAGCAATTCCATTACTTATGCCTCAGCAT
genomic: AGGCACTTTGTTCAGCGATGGAATTATGCCAAGgttagtctta ... ttaacgtcagAGGAACAAAGCTCCATATGAGCAAGCAATTCCATTACTTATGCCTCAGCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtcctattcctatattccctaaataggaaataatattttttttattaacgtcagAGGAACAAAGCTCCATATGAGCAAGCAATTCCATTACTTATGCCTCAGCATCATATGGTTATTCCACATTACTTGGGAAGAAGCAGAGAGATACAGATTG
                                           tattaac  putative branch site (score: 1)
                                    ttttttttatt  CT-rich tract
           tatattccctaaatag  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtcttattttgcaattgcattgaagtcttggagcattctggtcctattcctatattccctaaataggaaataatattttttttattaacgtcagAGGAACAAAGCTCCATATGAGCAAGCAATTCCATTACTTATGCCTCAGCATCATATGGTTATTCCACATTACTTGGGAAGAAGCAGAGAGATACAGATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC