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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttatttccttcagatttatttttgcttaatcgtttacttaaactctctacttctgtacttcttgtaagatgaaagtaatttttcacaaatactatgtagGGTGGAGAAGAGGACAATTTTGCTATTGTGTTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAGCGTGACTTTGAGGAGAATGGATCAA

Basic information

species Glycine max
transcript GLYMA20G24070.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 3'ss of exon 7
cttatttccttcagatttattt--ttgcttaatcgtttacttaaactctctacttctgtacttcttgtaagatgaa-agtaatttttcacaaatactatgtagGGTGGAGAAGAGGACAATTTTGCTATTGTGTTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAGCGTGACTTTGAGGAGAATGGATCAA
 |  | | ||  |||   ||||   || | | |  ||| | |  |  |   | || || |   ||       ||   | |   |  | ||   || | |  ||||||| ||||| ||||| |||||||| |||||||| ||||||||||| || ||||| || || || || ||||| ||||| ||||| ||||| || ||||
atggtatgctgtagagcaatttacctgttcatttttttccatggagac---atttttgcatcgctgaatcactgcttatttgctgattacttttaatctccagGGTGGTGAAGATGACAACTTTGCTATCGTGTTTGCTGCTATGGGAGTGAATATGGAAACAGCCCAATTCTTCAAACGTGATTTTGAAGAGAACGGGTCAA

upper sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G094497_T01 (Zea mays), 3'ss of exon 7
cttatttccttcagatttatttttgctta----atcgtttact--taaactctctacttctgtacttcttgtaagatgaaagtaatttttcacaaatactatgtagGGTGGAGAAGAGGACAATTTTGCTATTGTGTTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAGCGTGACTTTGAGGAGAATGGATCAA
     | |  | || |  |  ||    |     || || || |  |  |  || ||| | | ||  | | |    || |  |    |  |       ||  || ||||||| ||||| ||||| ||||||||||||||||| ||||||||||| |||||||| || || || || ||||| ||||| ||||| |||||||| || |
-----tactgtaaggtcaacattcatatggagcattgtgtattaatgtatgctttacatgtctaaatatggcttaatcactgcttctgatttttgtaacc-tgcagGGTGGTGAAGATGACAACTTTGCTATTGTGTTTGCTGCTATGGGAGTGAACATGGAAACAGCTCAATTCTTCAAACGTGATTTTGAAGAGAATGGTTCCA

upper sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G181151_T02 (Zea mays), 3'ss of exon 7
cttatttccttcagatttatttttgcttaatcgtttacttaaactctctacttctgtacttcttg-taagatgaaagtaatttttcacaaat-acta--tgtagGGTGGAGAAGAGGACAATTTTGCTATTGTGTTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAGCGTGACTTTGAGGAGAATGGATCAA
    || |  | || |  |  |||   |    | ||   ||  |        | |  |  ||||  ||||    |   | |  |||  |  | | ||  || ||||||| ||||| ||||| ||||||||||||||||| ||||||||||| |||||||| || || || || ||||| ||||| ||||| ||||| || || |
----ttcctgtgaggtcaacatttatatggaggattgtgtattcatgtatgctttacatgtcttaataaggcttagtcactggttctgattttattacctgcagGGTGGTGAAGATGACAACTTTGCTATTGTGTTTGCTGCTATGGGAGTGAACATGGAAACAGCTCAATTCTTCAAACGTGATTTTGAAGAGAACGGTTCCA

upper sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 8
lower sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 8
cttatttccttcagatttatttttgcttaatcgtttacttaaactctctacttctgtact-tcttgtaagatgaaagtaatttttcacaaatactatgtagGGTGGAGAAGAGGACAATTTTGCTATTGTGTTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAGCGTGACTTTGAGGAGAATGGATCAA
||  |||  ||  |    || |    | | | | | | ||      |    |  |||| | |     |  || | | |  |   |       | | || ||  |   || || || || || || |||||||| ||||| ||||| || ||||||||||||||||| ||||| || ||||| || |||||||||||||| |
ctcctttgatttggtaaaatctacaatgagttggt-agttgtgtaatgccataatgtattataaaacagtatcacattggtccatttatgtgaatttgcagCATCAGGAGGATGATAACTTCGCCATTGTGTTCGCAGCAATGGGTGTGAACATGGAGACTGCACAATTTTTTAAACGTGATTTCGAGGAGAATGGATCGA

upper sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 7
cttatttccttcagatttatttttgcttaatcgtttacttaaactctctac---ttctgtacttcttgtaagatgaaagtaatttttcacaaatactatgtagGGTGGAGAAGAGGACAATTTTGCTATTGTGTTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAGCGTGACTTTGAGGAGAATGGATCAA
  | ||   |    ||||||||    || ||  | |  |    || | ||    || || ||||  | | ||||   |  | ||||  ||   ||   || ||| ||  ||||||||||| ||||| ||||| ||||||||||||||||| ||||||||||||||||||||||| || ||||| || ||||| ||||||||||
gatgttaaatgaccatttatttcctttttattttattttctttctttttatcaattttgaacttgctatgagat---atcatttttctacttttaacttgcagGATGTGGAAGAGGACAACTTTGCCATTGTTTTTGCAGCTATGGGAGTAAACATGGAGACTGCACAGTTTTTTAAACGTGATTTCGAGGAAAATGGATCAA

upper sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 7
cttatttccttcagatttatttttgcttaatcgtttacttaaactctctacttctgtacttcttgtaagatgaaagtaatttttcacaaatactat--gtagGGTGGA---GAAGAGGACAATTTTGCTATTGTGTTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAGCGTGACTTTGAGGAGAATGGATCAA
| ||   | ||     || | || | ||  | | | || |   || |   | |       || ||    |||| |  |  | ||  |   | |  |    ||| || |   |  || ||||||||   |||||| ||||||||||||||||||||||||||||| ||    || ||||| ||||| || ||||| || || |   
cctaag-catttgttcttttattggtttggttgat-accttttctataagcgtggaaggctcctgagtaatgataaaatgtgttggcgtgttccttcgacagGATGAACACGGCGAAGACAATTTCTGTATTGTTTTTGCAGCTATGGGAGTTAACATGGAGACAGCTACCTTCTTCAAACGTGATTTCGAGGAAAACGGGT---

upper sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 8
lower sequence: EFJ11911 (Selaginella moellendorffii), 3'ss of exon 6
cttatttccttcagatttatttttgcttaatcgtttacttaaactctctacttctgtacttcttgtaagatgaaagtaatttttcacaaatactatgtagGGTGGAGAAGAGGACAATTTTGCTATTGTGTTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAGCGTGACTTTGAGGAGAATGGATCAA
                        |   ||| |||| |     |  |   ||||||| ||  |  | |||   | | | ||| |  |      |||  || |||  |  || ||||| ||||| || || |||||||||||||| || ||||||||||||||||||||||||||  | || |||||||| |||||||| |
------------------------gtacaattgttttc-----cgtttatcttctgt-ctgttgttgagactgatg-agtttctttcg-----tatccagCGTGATGTTGAAGACAACTTTGCAATCGTCTTTGCAGCTATGGGTGTGAACATGGAGACTGCACAGTTTTTCAAAAGGGATTTTGAGGAAAATGGATCGA

upper sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 8
lower sequence: EFJ13375 (Selaginella moellendorffii), 3'ss of exon 6
cttatttccttcagatttatttttgcttaatcgtttacttaaactctctacttctgtacttcttgtaagatgaaagtaatttttcacaaatactatgtagGGTGGAGAAGAGGACAATTTTGCTATTGTGTTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAGCGTGACTTTGAGGAGAATGGATCAA
                                   |||||    | ||   || | | ||   |||  | ||| | | ||   |  |   |  |||  || |||  |  || ||||| ||||| || || |||||||||||||| || ||||||||||||||||||||||||||  | || |||||||| |||||||| |
----------------------------------gtacttttgttttccgtttatcttctgtctgtt-gttgagactgatgagtttctt-tcgtatccagCGTGATGTTGAAGACAACTTTGCAATCGTCTTTGCAGCTATGGGTGTGAACATGGAGACTGCACAGTTTTTCAAAAGAGATTTTGAGGAAAATGGATCGA

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|16279439|gb|BI943437.1|BI943437
EST:     GTCAGGCTGGCTTAATCAAGCGACTAGAGAAATCTGATAATCTTCTTGAG                         GGTGGAGAAGAGGACAATTTTGCTATTGTGTTTGCAGCTATGGGAGTTAAC
genomic: GTCAGGCTGGCTTAGTCAAGCGACTAGAGAAATCTGATAATCTTCTTGAGgtatagcgga ... tactatgtagGGTGGAGAAGAGGACAATTTTGCTATTGTGTTTGCAGCTATGGGAGTTAAC
EST: gi|151411391|gb|EV281202.1|EV281202
EST:     GTCAGGCTGGCTTAGTCAAGCGACTAGAGAAATCTGATAATCTTCTTGAG                         GGTGGAGAAGAGGACAATTTTGCTATTGTGTTTGCAGCTATGGGAGTTAAC
genomic: GTCAGGCTGGCTTAGTCAAGCGACTAGAGAAATCTGATAATCTTCTTGAGgtatagcgga ... tactatgtagGGTGGAGAAGAGGACAATTTTGCTATTGTGTTTGCAGCTATGGGAGTTAAC
EST: gi|23729967|gb|BU763089.1|BU763089
EST:     GTCAGGCTGGCTTAGTCAAGCGACTAGAGAAATCTGATAATCTTCTTGAG                         GGTGGAGAAGAGGACAATTTTGCTATTGTATTTGCAGCTATGGGAGTTAAC
genomic: GTCAGGCTGGCTTAGTCAAGCGACTAGAGAAATCTGATAATCTTCTTGAGgtatagcgga ... tactatgtagGGTGGAGAAGAGGACAATTTTGCTATTGTGTTTGCAGCTATGGGAGTTAAC
EST: gi|16279488|gb|BI943462.1|BI943462
EST:     GTCAGGCTGGCTTAGTCAAGCGACTAGAGAAATCTGATAATCTTCTTGAG                         GGTGGAGAAGAGGACAATTTTGCTATTGTGTTTGCAGCTATGGGAGTTAAC
genomic: GTCAGGCTGGCTTAGTCAAGCGACTAGAGAAATCTGATAATCTTCTTGAGgtatagcgga ... tactatgtagGGTGGAGAAGAGGACAATTTTGCTATTGTGTTTGCAGCTATGGGAGTTAAC
EST: gi|193680305|gb|FK624813.1|FK624813
EST:     GTCAGGCTGGCTTAGTCAAGCGACTAGAGAAATCTGATAATCTTCTTGAG                         GGTGGAGAAGAGGACAATTTTGCTATTGTGTTTGCAGCTATGGGAGTTAAC
genomic: GTCAGGCTGGCTTAGTCAAGCGACTAGAGAAATCTGATAATCTTCTTGAGgtatagcgga ... tactatgtagGGTGGAGAAGAGGACAATTTTGCTATTGTGTTTGCAGCTATGGGAGTTAAC
EST: gi|19346883|gb|BM891771.1|BM891771
EST:     GATAATCTTCTTGAG                         GGTGGAGAAGAGGACAATTTTGCTATTGTGTTTGCAGCTATGGGAGTTAAC
genomic: GATAATCTTCTTGAGgtatagcgga ... tactatgtagGGTGGAGAAGAGGACAATTTTGCTATTGTGTTTGCAGCTATGGGAGTTAAC
EST: gi|16279486|gb|BI943461.1|BI943461
EST:     GTCAGGCTGGCTTAGTCAAGCGACTAGAGAAATCTGATAATCTTCTTGAG                         GGTGGAGAAGAGGACAATTTTGCTATTGTGTTTGCAGCTATGGGAGTTAAC
genomic: GTCAGGCTGGCTTAGTCAAGCGACTAGAGAAATCTGATAATCTTCTTGAGgtatagcgga ... tactatgtagGGTGGAGAAGAGGACAATTTTGCTATTGTGTTTGCAGCTATGGGAGTTAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctacttctgtacttcttgtaagatgaaagtaatttttcacaaatactatgtagGGTGGAGAAGAGGACAATTTTGCTATTGTGTTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAGCGTGACTTTGAGGAGAATGGATCAA
                               taatttttcacaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttatttccttcagatttatttttgcttaatcgtttacttaaactctctacttctgtacttcttgtaagatgaaagtaatttttcacaaatactatgtagGGTGGAGAAGAGGACAATTTTGCTATTGTGTTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAGCGTGACTTTGAGGAGAATGGATCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA