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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgctgtattttagaggttttaaaagaatcatcctagttttgagaagttgaattttgtggtatttgagttcactgtgtaaatgaggattctgctgtaacagATTGGTCCTGCACAGATCGAAGCATTGTACCAATATTCCAAATTCCAGTTTGAGTGTGGAAACTACTCTGGTGCTGCTGACTATCTTTATCAATACAGAG

Basic information

species Glycine max
transcript GLYMA02G33770.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G33770.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G107893_T01 (Zea mays), 3'ss of exon 4
tgctgtattttaga---ggttttaaaagaat-catcctagttttgagaagttgaattttgtggtatttg--agttcactgtgtaaatgaggattctgctgtaacagATTGGTCCTGCACAGATCGAAGCATTGTACCAATATTCCAAATTCCAGTTTGAGTGTGGAAACTACTCTGGTGCTGCTGACTATCTTTATCAATACAGAG
      | || |||       || ||    | |||  |  ||   | |  |||  ||||||| || |||  | |  | ||   ||     |  | | |     ||||| |||||||  ||||| |||||  |||| || ||| ||||||| |||||||||||||| |||||||| || |||||||| || ||||| || ||  | |
--tcaaaattcagatggaacgttgaagctgtgcatttttattgctatagcttg--ttttgtgataattgctaatgaattgatcaatccttg--tttaccaatgcagATCGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTTGAGTGTGGTAACTACTCAGGGGCTGCTGATTACCTTTACCAGTATGGTG

upper sequence: GLYMA02G33770.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G151549_T02 (Zea mays), 3'ss of exon 1
--tgctgtattttagaggttttaaaagaatcatcctagttttgagaagttgaattttgtggtatttgagttcactgtgtaaatgaggattctgctgtaacagATTGGTCCTGCACAGATCGAAGCATTGTACCAATATTCCAAATTCCAGTTTGAGTGTGGAAACTACTCTGGTGCTGCTGACTATCTTTATCAATACAGAG
     |  |  | | | |||  |   |     |  |  ||   | |  |||  || ||    ||   | |  | ||   ||     |  | | |     ||||| |||||||  ||||| |||||  |||| || ||| ||||||| |||||||||||||| |||||||| || |||||||| || ||||| || ||  | |
caaaattcagatgaaacgttgaagctgtgcattttttattgctatagcttgttttgtgataaatgctaatgaattgatcaatccttg--tttaccaatgcagATCGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTTGAGTGTGGTAACTACTCAGGGGCTGCTGATTACCTTTACCAGTATCGTG

upper sequence: GLYMA02G33770.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G132144_T01 (Zea mays), 3'ss of exon 5
tgctgtattttagagg----ttttaaaagaatcatcctagttttgagaagttgaattttgtggtatttgagttcactgtgtaaatgaggattctgctgtaacagATTGGTCCTGCACAGATCGAAGCATTGTACCAATATTCCAAATTCCAGTTTGAGTGTGGAAACTACTCTGGTGCTGCTGACTATCTTTATCAATACAGAG
      | || ||| |     || ||      |||  |  ||   | |  |||  || ||    ||   | |  | ||   ||     |  | | |     ||||| |||||||  ||||| |||||  |||| || ||| ||||||| |||||||||||||| |||||||| || |||||||| || ||||| || ||  | |
--tcaaaattcagatgaaacgttgaagctgcgcatttttattgctatagcttgttttgtgataaatgctaatgaattgatcaatccttg--tttaccaatgcagATCGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTTGAGTGTGGTAACTACTCAGGGGCTGCTGATTACCTTTACCAGTATCGTG

upper sequence: GLYMA02G33770.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G038028_T01 (Zea mays), 3'ss of exon 6
tgctgtattttaga---ggttttaaaagaat-catcctagttttgagaagttgaattttgtggtatttgagttcactgtgtaaatgaggattctgctgtaacagATTGGTCCTGCACAGATCGAAGCATTGTACCAATATTCCAAATTCCAGTTTGAGTGTGGAAACTACTCTGGTGCTGCTGACTATCTTTATCAATACAGAG
      | || |||       || ||    | |||  |  ||   | |  |||  || ||    ||   | |  | ||   ||     |  | | |     ||||| |||||||  ||||| |||||  |||| || ||| ||||||| |||||||||||||| |||||||| || |||||||| || ||||| || ||  | |
--tcaaaattcagatgaaacgttgaagctgtgcatttttattgctatagcttgttttgtgataaatgctaatgaattgatcaatccttg--tttaccaatgcagATCGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTTGAGTGTGGTAACTACTCAGGGGCTGCTGATTACCTTTACCAGTATGGTG

upper sequence: GLYMA02G33770.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G038313_T01 (Zea mays), 3'ss of exon 1
-tgctgtattttagaggttttaaaagaatcatcctagttttgagaagttgaattttgtggtatttgagttcactgtgtaaatgaggattctgctgtaacagATTGGTCCTGCACAGATCGAAGCATTGTACCAATATTCCAAATTCCAGTTTGAGTGTGGAAACTACTCTGGTGCTGCTGACTATCTTTATCAATACAGAG
       | || ||| |   |     |    | |   |||   |   | |  | || ||   |    | | ||    |||||     ||   |  |  |||||||||||||  ||||| |||||  |||| || ||| ||||||| |||||||||||||| ||||||||  | |||||||| || || || || ||  | |
agatcaaaattcagatggaatgttgaagctgtgcacttttattgttatagcctcttctgtgctaaatgctaacgaactaaatccttgtttaacaatg-cagATTGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTTGAGTGTGGTAACTACTCCTGGGCTGCTGAGTACCTGTACCAGTATCGTG

upper sequence: GLYMA02G33770.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G105461_T01 (Zea mays), 3'ss of exon 2
tgctgtattttagaggttttaaaagaatcatcctagttttgagaagttgaattttgtggtatttgagttcac-tgtgtaaatgaggattctgctgtaacagATTGGTCCTGCACAGA-TCGAAGCATTGTACCAATATTCCAAATTCCAGTTTGAGTGTGGAAACTACTCTGGTGCTGCTGACTATCTTTATCAATACAGAG---------------
              ||     | ||  |||||  |   | |  |  |  |   |    | || ||        |||     |  |   | |  | | | | | |  |     | ||  | |||||  |||| || ||| ||||||| |||||||||||||| |||||||| || |||||||| || ||||| || ||  | |               
--------------ggcacagatagtctcatctca---tagtcagatccagcctctccgaatctggccaggtgtgttctggtttgctctatttttttatatacttatataatatagcCTTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTTGAGTGTGGTAACTACTCAGGGGCTGCTGATTACCTTTACCAGTATGGTGCTTTGTGCACAAACA

upper sequence: GLYMA02G33770.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G094083_T01 (Zea mays), 3'ss of exon 8
tgctgtattttaga---ggttttaaaagaat-catcctagttttgagaagttgaattttgtggtatttgagttcactgtgtaaatgaggattctgctgtaacagATTGGTCCTGCACAGATCGAAGCATTGTACCAATATTCCAAATTCCAGTTTGAGTGTGGAAACTACTCTGGTGCTGCTGACTATCTTTATCAATACAGAG
      | || |||       || ||    | |||  |  ||   | |  |||  || ||    ||   | |  | ||   ||     |  | | |     ||||| |||| ||  ||||| |||||  |||| || ||| || |||| |||||||||||||| |||||||| || |||||||| || ||||| || ||  | |
--tcaaaattcagatgaaacgttgaagctgtgcatttttattgctatagcttgttttgtgataaatgctaatgaattgatcaatccttg--tttaccaatgcagATCGGTCTTGACCAGATTGAAGCTCTGTATCAGTATGCCCAATTTCAGTTTGAGTGTGGTAACTACTCAGGGGCTGCTGATTACCTTTACCAGTATGGTG

upper sequence: GLYMA02G33770.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G57290.1 (Arabidopsis thaliana), 3'ss of exon 2
tgctgtattttagaggttttaaaagaatcatcct----agttttgagaag-ttgaattttgtg---gtatttgagttcactgtgtaaatgaggattc-tgctgtaacagATTGGTCCTGCACAGATCGAAGCATTGTACCAATATTCCAAATTCCAGTTTGAGTGTGGAAACTACTCTGGTGCTGCTGACTATCTTTATCAATACAGAG
 | |||  ||| || | || |   |  | ||  |    | | ||    || ||   ||||||    |||||   |  |||       ||  || ||  ||   || ||||||||||| |  ||||| || || |||||||| ||  |||| || |||||||| ||||| ||||| |||||||||||||| |||||||| || |||||  
-gttgtgatttggatgattaagttgtttaattttgtgaaatgttatccagatttggttttgtttgtgtattgtggaacacaaatcttatatggcttggtgtcttatcagATTGGTCCAGACCAGATTGAGGCTTTGTACCAGTACGCCAAGTTTCAGTTTGAATGTGGCAACTATTCTGGTGCTGCTGATTATCTTTACCAGTACAGGA

upper sequence: GLYMA02G33770.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv00s0252g00070.t01 (Vitis vinifera), 3'ss of exon 2
---tgctgtattttagaggttttaaaagaatcatcctagttttgagaagttgaattt-tgtggtatttgagttcactgtgtaaatgaggattctgctgtaacagATTGGTCCTGCACAGATCGAAGCATTGTACCAATATTCCAAATTCCAGTTTGAGTGTGGAAACTACTCTGGTGCTGCTGACTATCTTTATCAATACAGAG
   || | |  ||      || |     | |   |  | || |  |   |||  | | | |||  |   |    | | | |   |      | | ||| | |||||||| |  |  ||||| || ||||| || || ||| ||||||| |||||||| |||||||||||||||||||||||||| || || ||||| ||||| |
tcctgtttttgttgttgtattgttgctaatttgacagaattctaggtttttgggtctatttggcttacaaa---attatatcccttttttcttttctg-accagATTGGCCAGGAGCAGATAGAGGCATTATATCAGTATGCCAAATTTCAGTTTGAATGTGGAAACTACTCTGGTGCTGCTGATTACCTGTATCAGTACAGGG

upper sequence: GLYMA02G33770.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S73_26V6.1 (Physcomitrella patens), 3'ss of exon 2
------tgctgtattttagaggttttaaaagaatcatcctagttttgagaagttgaattttgtggtatttgagttcactgtgtaaatgaggattctgctgtaacagATTGGTCCTGCACAGATCGAAGCATTGTACCAATATTCCAAATTCCAGTTTGAGTGTGGAAACTACTCTGGTGCTGCTGACTATCTTTATCAATACAGAG
        |  |||   |  |  |||  | |  |   | |    |     |  ||| ||| | |||   ||| | ||  || | |||     |  |    |   |||| ||| |||  || || || ||  | ||||| ||| | || ||||||||||||||||||||||| || |||||  ||||||| || ||||| ||  |  
atcgaccaccttatgacatcgcatttccatgccttgccatctgctccgatatgtgactttggaggt--ctgactacatcgtatgaatt----tcttctctttgtagATCGGTTCTGATCAAATTGAGGCTCTTTACCAGTATGCGAAGTTCCAGTTTGAGTGTGGAAACTATTCAGGTGCCTCTGACTACCTCTATCAGTATCGCA

upper sequence: GLYMA02G33770.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S363_21V6.2 (Physcomitrella patens), 3'ss of exon 2
--tgctgtattttagaggttttaaaagaa--tcatcctagttttgagaagttga-attttgtggtatttgagttcactgtgtaaatgaggattctgctgtaacagATTGGTCCTGCACAGATCGAAGCATTGTACCAATATTCCAAATTCCAGTTTGAGTGTGGAAACTACTCTGGTGCTGCTGACTATCTTTATCAATACAGAG
  ||   ||| |   |  |   |    ||  || | |||  |  | |  | ||  |  || |    | |||       || |||||   |||| |    |   |||| ||| |||  || ||||| ||  |||| || ||| |||| |||||||||||||| ||||||||||| |||||  | ||||| || ||| | ||  | |
attgtaatatgtagcatatcgcatttcaacgtcttgctacctccgtgtggatgccacattataa-gtctgacagtttcgtctaaattgtgattgt----ttgtagATCGGTTCTGAGCAAATCGAGGCTCTGTATCAGTATGCCAAGTTCCAGTTTGAGTGCGGAAACTACTCGGGTGCATCCGACTACCTGTATGAGTATCGCG

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|209708048|gb|BW657090.1|BW657090
EST:     TCCGTGCCGACAAGCAGTACAATCTTCAGATGCTCAATGACCAATATCAG                         ATTGGTCCTGCACAGATCGAAGCATTGTACCAATATTCCAAATTCCAGTTT
genomic: TCCGTGCCGACAAGCAGTACAATCTTCAGATGCTCAATGACCGATATCAGgtttagggtt ... gctgtaacagATTGGTCCTGCACAGATCGAAGCATTGTACCAATATTCCAAATTCCAGTTT
EST: gi|209715150|gb|BW665625.1|BW665625
EST:     TCCGTGCCGACAAGCAGTACAATCTTCAGATGCTCAATGACCGATATCAG                         ATTGGTCCTGCACAGATCGAAGCATTGTACCAATATTCCAAATTCCAGTTT
genomic: TCCGTGCCGACAAGCAGTACAATCTTCAGATGCTCAATGACCGATATCAGgtttagggtt ... gctgtaacagATTGGTCCTGCACAGATCGAAGCATTGTACCAATATTCCAAATTCCAGTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgaattttgtggtatttgagttcactgtgtaaatgaggattctgctgtaacagATTGGTCCTGCACAGATCGAAGCATTGTACCAATATTCCAAATTCCAGTTTGAGTGTGGAAACTACTCTGGTGCTGCTGACTATCTTTATCAATACAGAG
                                         ttctgct  CT-rich tract
     attttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgctgtattttagaggttttaaaagaatcatcctagttttgagaagttgaattttgtggtatttgagttcactgtgtaaatgaggattctgctgtaacagATTGGTCCTGCACAGATCGAAGCATTGTACCAATATTCCAAATTCCAGTTTGAGTGTGGAAACTACTCTGGTGCTGCTGACTATCTTTATCAATACAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
tgctgta
- - - - - - - - - - aaaagaa
- - - - - - - - - - - - - - - - - - - - - - - - - -ttttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgtgta