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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcatgaatatttgataaaagtgttattgtgctgttgagtcagtatgattgactattgttggtaagttttgactgccttggtatatgtcttgtgtgaacagGAACGTGAGAATCCTACATTGACAGAGTGGGATCGCTTTGCTCATAGAGAATATATTAGGCTTTCTATGGAAGAAGATGTAGAGGATGCCTCTAACGGTA

Basic information

species Glycine max
transcript GLYMA03G41180.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G41180.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os10g33680.1 (Oryza sativa), 3'ss of exon 11
gtgcatgaatatttgataaaagtgttattgtgctgttgagtcagtatgattgactattgttggtaagttttgactgccttggtatatgtcttgtgtgaacagGAACGTGAGAATCCTACATTGACAGAGTGGGATCGCTTTGCTCATAGAGAATATATTAGGCTTTCTATGGAAGAAGATGTAGAGGATGCCTCTAACGGTA
                | |        |  |||  |  || ||||   ||| ||| ||  |  |     |  ||    | | |     | || | |   ||||||||||| ||||| || || || ||||||||||| || || |||||||| ||||||||  | || |||||||||||||  || ||||| || || || |
---------------gtgatcacaacttcttgccataaag-cagtg-aattcactgttaatcatctaaat-aacaagttggatcatctttttattt---cagGAACGTGAAAATCCAACTTTAACCGAGTGGGATCGGTTCGCACATAGAGAGTATATTAGATTGTCCATGGAAGAAGATGGTGAAGATGCTTCAAATGGAA

upper sequence: GLYMA03G41180.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G148323_T01 (Zea mays), 3'ss of exon 11
gtgcatgaatatttgataaaagtgttattgtgctgttgagtcagtat--gattgactattgttggtaagttttgactgccttggtatatgtcttgtgtgaacagGAACGTGAGAATCCTACATTGACAGAGTGGGATCGCTTTGCTCATAGAGAATATATTAGGCTTTCTATGGAAGAAGATGTAGAGGATGCCTCTAACGGTA
                       || ||| |  |  | | | |   |  ||||  ||        | |  ||  |     ||||   |||| |  |      |||||||||| ||||| ||  | || |||||||| || ||||| |||||||||||||||||  | || |||||||||||||  |||||||| || || || |
-----------------------gtgattataatccttaataaactttagatttgctgccaagtattaagttaaataa--ttggctaatgtttaatt---gtagGAACGTGAAAATCCAACTCTAACTGAGTGGGACCGGTTTGCACATAGAGAATATATTAGATTGTCCATGGAAGAAGATGGTGAGGATGCTTCAAATGGAA

upper sequence: GLYMA03G41180.1 (Glycine max), 3'ss of exon 11
lower sequence: AT5G28900.1 (Arabidopsis thaliana), 3'ss of exon 11
gtgcatgaatatttgataaaagtgttattgtgctgttgagtcagtatgattgactattgttggtaagttttgactgccttggtatatgtcttgtgtgaacagGAACGTGAGAATCCTACATTGACAGAGTGGGATCGCTTTGCTCATAGAGAATATATTAGGCTTTCTATGGAAGAAGATGTAGAGGATGCCTCTAACGGTA
|| | | |  || | ||       |||   ||||  |   |||         || |      |    || | ||     |     |||||    |  ||||||| || ||||| |||||||||||||| ||||| || ||||| |||||||| ||||||||||| || |||||||||||||| || ||||| ||||| || |
gtac-taatcatctaat-------ttaccttgctacttcttcac--------accaccacatgcgtcttataacatttcta----atgtcaaacggaaacagGAGCGAGAGAACCCTACATTGACAGATTGGGACCGTTTTGCACATAGAGAGTATATTAGGCTATCAATGGAAGAAGATGTTGAAGATGCATCTAATGGAA

upper sequence: GLYMA03G41180.1 (Glycine max), 3'ss of exon 11
lower sequence: AT5G28850.1 (Arabidopsis thaliana), 3'ss of exon 10
gtgcatgaatatttgataaaagtgttattgtgctgttgagtcagtatgattgactattgttggtaagttttgactgccttggtatatgtcttgtgtgaacagGAACGTGAGAATCCTACATTGACAGAGTGGGATCGCTTTGCTCATAGAGAATATATTAGGCTTTCTATGGAAGAAGATGTAGAGGATGCCTCTAACGGTA
  | |  | |    | |  |  |   |   |||||||   |    |  || | |   | ||   |  |||  |            |||||    |  ||||||| || ||||| || ||||||||||| ||||| || ||||| |||||||| |||||| |||| || |||||||||||||| || ||||| || || || |
--gtactactccacgtttgatattcaaccttgctgttttcttgacacaatgggc--ctcttataacatttcaa------------atgtcaaacgaaaacagGAGCGCGAGAACCCGACATTGACAGACTGGGACCGTTTTGCACATAGAGAGTATATTCGGCTATCAATGGAAGAAGATGTTGAAGATGCATCCAATGGAA

upper sequence: GLYMA03G41180.1 (Glycine max), 3'ss of exon 11
lower sequence: AT1G54450.1 (Arabidopsis thaliana), 3'ss of exon 10
gtgcatgaatatttgataaaagtgttattgtgctgttgagtcag-tatgattgactattgttggtaagttttgactgccttggtatatgtcttgtgtgaacagGAACGTGAGAATCCTACATTGACAGAGTGGGATCGCTTTGCTCATAGAGAATATATTAGGCTTTCTATGGAAGAAGATGTAGAGGATGCCTCTAACGGTA
         |||   | || |  || |   | |  |  ||  || |||   |   ||| |     |  | || | | |      ||   |      |  | |||| || |  ||||| |||| ||||||||||||||| |||||||||||||||||||||||||| || |||||||||||||| || ||||| ||||| || |
--------gtatcacaaaatatagtaa--ataccttaaagctagctatacatacttatag-----agatattcatttctcaatgattgattgctgatacatagGAGCGCGCAAATCCGACATGGACAGAGTGGGATCGTTTTGCTCATAGAGAATATATTAGGCTATCAATGGAAGAAGATGTCGAAGATGCTTCTAATGGAA

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|15000873|gb|BI321687.1|BI321687
EST:     GTGACCCATTTTTGATTCGTCAG                         GAACGTGAGAATCCTACGTTGACAGAGTGGGATCGCTTTGCTCATAGAGAA
genomic: GTGACCCATTTTTGATTCGTCAGgtgcatgaat ... gtgtgaacagGAACGTGAGAATCCTACATTGACAGAGTGGGATCGCTTTGCTCATAGAGAA
EST: gi|17023595|gb|BM094629.1|BM094629
EST:     TGAATAAGTTCATGGCCTTTGAAACTCGTGACCCATTTTTGATTCGTCAG                         GAACGTGAGAATCCTACATTGACAGAGTGGGATCGCTTTGCTCATAGAGAA
genomic: TGAATAAGTTCATGGCCTTTGAAACTCGTGACCCATTTTTGATTCGTCAGgtgcatgaat ... gtgtgaacagGAACGTGAGAATCCTACATTGACAGAGTGGGATCGCTTTGCTCATAGAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattgactattgttggtaagttttgactgccttggtatatgtcttgtgtgaacagGAACGTGAGAATCCTACATTGACAGAGTGGGATCGCTTTGCTCATAGAGAATATATTAGGCTTTCTATGGAAGAAGATGTAGAGGATGCCTCTAACGGTA
                    ttttgac  putative branch site (score: 3)
                taagtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcatgaatatttgataaaagtgttattgtgctgttgagtcagtatgattgactattgttggtaagttttgactgccttggtatatgtcttgtgtgaacagGAACGTGAGAATCCTACATTGACAGAGTGGGATCGCTTTGCTCATAGAGAATATATTAGGCTTTCTATGGAAGAAGATGTAGAGGATGCCTCTAACGGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG