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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgtgtttttttctttcatgtatgtggtttaaagttttgttttacttgggtatcataatgaatggtcttatattatttatcaattattatatatatgttctttgacatatttatagGTTAGTCTGATTCAAATCCCCAGCAAAGTGGAACTCAGGCAGAAAAACCTTTTCAGTGTCAGTGACTGCAAGATGTACTGGCAAAGCAATGGAGACTACC

Basic information

species Glycine max
transcript GLYMA03G00470.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G00470.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os10g41960.1 (Oryza sativa), 3'ss of exon 8
gtaagtgtgtttttttctttcatgtatgtggtttaaagttttgttttacttgggtatcataatgaatggtcttatattatttatcaattattatatatatgttctttgacatatttatagGTTAGTCTGATTCAAATCCCCAGCAAAGTGGAACTCAGGCAGAAAAACCTTTTCAGTGTCAGTGACTGCAAGATGTACTGGCAAAGCAATGGAGACTACC
                       ||| |||      | |||| | |   |      |  | | |||    | |  | || |  | ||   | | || |||  | |||     ||| | |||| || ||  | ||||| ||  |||||| ||| ||  |||||||||||||||||||||||||||| ||||||||||||||||| | || |||||| || |
-----------------------gtaagtgc-----aattttctgtgcttcatcccttttgaggaagttccgtcaactaatggtgaagactaaaatctataattttt-----attgaaagGTGAGCCTTGTGCAAATTCCTGGCAAAGAGGAGCTGCGGCAGAAAAACCTTTTCAGTGTCAGTGATTGCAAGATGTACTGGCAGAACAGTGGAGAATATC

upper sequence: GLYMA03G00470.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G174757_T01 (Zea mays), 3'ss of exon 8
gtaagtgtgtttttttctttcatgtatgtggtttaaagttttgttttacttgggtatcataatgaatggtcttatattatttatcaattatta-tatatatgttctttgacatatttatagGTTAGTCTGATTCAAATCCCCAGCAAAGTGGAACTCAGGCAGAAAAACCTTTTCAGTGTCAGTGACTGCAAGATGTACTGGCAAAGCAATGGAGACTACC
                          ||  |  |||| || ||    |  |   | | |||    ||| |  |  | ||  ||   || |    || |  || |||||    | || | |||| |||||  | ||||||||  |||||| ||| ||  | |||||||||||||||||||||||||| || |||||||| ||||||| || |||||| || |
-------------------------gtg-agcataaatttgtggaacagatacctcttatacc--atgtttattcaataactaatgataaaggctaaaattgatcttt--tctgttgaaagGTGAGTCTAGTGCAAATCCCTGGCAAAGAGGAGCTGCGACAGAAAAACCTTTTCAGTGTCAGTGATTGTAAGATGTATTGGCAAAACAGTGGAGAATATC

upper sequence: GLYMA03G00470.1 (Glycine max), 3'ss of exon 8
lower sequence: AT5G25780.1 (Arabidopsis thaliana), 3'ss of exon 8
gtaagtgtgtttttttctttcatgtatgtggtttaaagttttgttttacttgggtatcataatgaatggtcttatattatttatcaattattatatatatgttctttgacata----tttatagGTTAGTCTGATTCAAATCCCCAGCAAAGTGGAACTCAGGCAGAAAAACCTTTTCAGTGTCAGTGACTGCAAGATGTACTGGCAAAGCAATGGAGACTACC
    || ||||| |||  ||  | |||||   | |||           |   | || |  ||| |     | |   || | |  || || || | ||| |     |||| ||     | |  |||||  |||  | |||||||| || || || || || |||||||| || || |||||||| || |||||||||||||||||||| || | |||||| || |
----gtatgtttcttttatttct-tatgtaaatgaaaa---------gccctgatacctcaataatcttccgt---ttctctgccagttgttttgtatttacatgttgatatcccattcttcagGTTGCTCTAGTCCAAATCCCGAGTAAGGTAGAGCTGAGGCAGAAGAATCTCTTCAGTGTGAGCGACTGCAAGATGTACTGGCAGAGTAGTGGAGAGTATC

upper sequence: GLYMA03G00470.1 (Glycine max), 3'ss of exon 8
lower sequence: AT5G27640.1 (Arabidopsis thaliana), 3'ss of exon 9
gtaagtgtgtttttttctttcatgtatgtggtttaaagttttgttttacttgggtatcataatgaatggtcttatattatttatcaattattatatatatgttctttgacatatttatagGTTAGTCTGATTCAAATCCCCAGCAAAGTGGAACTCAGGCAGAAAAACCTTTTCAGTGTCAGTGACTGCAAGATGTACTGGCAAAGCAATGGAGACTACC
||| || |  | || | | | |||||  ||    |||| | ||  |  | |   | |  |  ||  |       |  | |||   |||||  || |  || | | ||        |  |||||   ||  | |||||||| ||||| ||||| || |||||||| || || |||||||| || |||||||||||||||||||| || | |||||| || |
gtatgt-ttctattatttctgatgtacatga---aaagctctgaat--ccttaatttgcttctgtttctctgcctggtgttttgaaattac-atgttgatatccctt-------cttcagGTTGCCCTAGTCCAAATCCCGAGCAAGGTGGAGCTGAGGCAGAAGAATCTCTTCAGTGTGAGCGACTGCAAGATGTACTGGCAGAGTAGTGGAGAGTATC

upper sequence: GLYMA03G00470.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S138_36V6.1 (Physcomitrella patens), 3'ss of exon 6
----------------------------gtaagtgtgtttttttctttcatgtatgtggttta--aagttttg------ttttacttgggtatcataatgaatggtcttatattatttatcaattattatatatatgttctttgacatatttatagGTTAGTCTGATTCAAATCCCCAGCAAAGTGGAACTCAGGCAGAAAAACCTTTTCAGTGTCAGTGACTGCAAGATGTACTGGCAAAGCAATGGAGACTACC
                            ||| ||    |    | |  |||   ||  ||||    || |  |      ||||| ||||  ||| | ||| |||    | |   | | || | |     |   || |   |    |||  ||  |||||||  || |    || || |||| || |||| |  | ||||| ||||| ||||| |||||||||||||||||||| |||||||||||||| || ||| 
gtgggtttcgaactggctctttgattatgtatgtaatctacggtgtggcattcctgaagtttgttgaggtgcgacaaaattttatttggccatcttcatgtatgcaactctgaaaataataagtcggagtgcttacggcttgctgcatcctt-cagGTTAGCTTGGTGTCCATTCCTAGCAGAGAGGAATTGCGACAGAAGAACCTCTTCAGCGTCAGTGACTGCAAGATGTATTGGCAAAGCAATGGCGAGTACT

upper sequence: GLYMA03G00470.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S130_248V6.2 (Physcomitrella patens), 3'ss of exon 6
-----------------gtaagtgtgtttttttctttcatgtatg--tggtttaaagttttgttttacttgggtatcataatgaatggtct--tatattatt----tatcaattattatatata-tgttctttgacatatttatagGTTAGTCTGATTCAAATCCCCAGCAAAGTGGAACTCAGGCAGAAAAACCTTTTCAGTGTCAGTGACTGCAAGATGTACTGGCAAAGCAATGGAGACTACC
                  |   | || | |||| ||||||   ||  |  |    |  ||| ||| |    | || |||| ||  ||  ||  |  || |      ||   |  || ||  | | || | | ||  || |||  |||| |||||  |    || ||||||| ||  ||  |  | || || ||||||||||| || ||||||||||| ||||| ||||||||||| || || ||| 
gtgagtttttaccccctttctatttgatattttgtttcatacttgggtaatccggaacttt-tttgaggacgatagcatattgtttgacctcctgcatgaaggcaatactgaaaataatggacaatgatttgtggtatcttt-cagGTGAGTCTTGTGTCTATTCCCAGCAGAGAAGAGTTGCGTCAAAAGAACCTTTTCAGCGTGAGTGACTGCAAAATGTATTGGCAAAGCAACGGTGAGTACT

upper sequence: GLYMA03G00470.1 (Glycine max), 3'ss of exon 8
lower sequence: EFJ13839 (Selaginella moellendorffii), 3'ss of exon 8
gtaagtgtgtttttttctttcatgtatgtggtttaaagttttgttttacttgggtatcataatgaatggtcttatattatttatcaat-tattatatatatgttctttgacatatttatagGTTAGTCTGATTCAAATCCCCAGCAAAGTGGAACTCAGGCAGAAAAACCTTTTCAGTGTCAGTGACTGCAAGATGTACTGGCAAAGCAATGGAGACTACC
                                                              |   |  |  | | | |||| || |  | | |  |   |     |||||   |  | ||||||| ||| ||||||| ||  |||  |  ||||| |||||||| |||||||||||||||||||||||||||||||||||||||||||| |||||||| |
-------------------------------------------------------------gtatgtatttgtgtttgatttctctacatgtgacctggtttgctcttgact--tcaacagGTTAGCCTGGTTCAAATTCCTGGCAGGGAAGAACTGAGGCAGAAGAACCTTTTCAGTGTCAGTGACTGCAAGATGTACTGGCAAAGCAACGGAGACTATC

upper sequence: GLYMA03G00470.1 (Glycine max), 3'ss of exon 8
lower sequence: EFJ12681 (Selaginella moellendorffii), 3'ss of exon 8
gtaagtgtgtttttttctttcatgtatgtggtttaaagttttgttttacttgggtatcataatgaatggtcttatattatttatcaattattatatatatgttctttgacatatttatagGTTAGTCTGATTCAAATCCCCAGCAAAGTGGAACTCAGGCAGAAAAACCTTTTCAGTGTCAGTGACTGCAAGATGTACTGGCAAAGCAATGGAGACTACC
                                                              |   |  |  | | | |||| || |  ||   |  |   ||  |    |  |  | |||| || ||| ||||||| ||  |||  |  ||||| |||||||| |||||||||||||||||||||||||||||||||||||||||||| |||||||| |
-------------------------------------------------------------gtatgtatttgtgtttgatttctctac-atgtgacctggtttgctctcaacttcaacagGTCAGCCTGGTTCAAATTCCTGGCAGGGAAGAACTGAGGCAGAAGAACCTTTTCAGTGTCAGTGACTGCAAGATGTACTGGCAAAGCAACGGAGACTATC

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|213614289|gb|DB964949.1|DB964949
EST:     TTATTGCTCTTTTTGTTCCTGAGATGGGAGGTGGTAACCAGCCTGCCAGG                         GTTAGTCTGATTCAAATCCCCAGCAAAGAGGAACTCAGGCAGAAAAACCTT
genomic: TTATTGCTCTTTTTGTTCCTGAGATGGGAGGTGGTAACCAGCCTGCCAGGgtaagtgtgt ... atatttatagGTTAGTCTGATTCAAATCCCCAGCAAAGTGGAACTCAGGCAGAAAAACCTT
EST: gi|254329399|gb|GR838952.1|GR838952
EST:     TTATTGCTCTTTTTGTTCCTGAGATGGGAGGTGGTAACCAGCCTGCCAGG                         GTTAGTCTGATTCAAATCCCCAGCAAAGTGGAACTCAGGCAGAAAAACCTT
genomic: TTATTGCTCTTTTTGTTCCTGAGATGGGAGGTGGTAACCAGCCTGCCAGGgtaagtgtgt ... atatttatagGTTAGTCTGATTCAAATCCCCAGCAAAGTGGAACTCAGGCAGAAAAACCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggtcttatattatttatcaattattatatatatgttctttgacatatttatagGTTAGTCTGATTCAAATCCCCAGCAAAGTGGAACTCAGGCAGAAAAACCTTTTCAGTGTCAGTGACTGCAAGATGTACTGGCAAAGCAATGGAGACTACC
                                      ctttgac  putative branch site (score: 4)
      ttatattatttatcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgtgtttttttctttcatgtatgtggtttaaagttttgttttacttgggtatcataatgaatggtcttatattatttatcaattattatatatatgttctttgacatatttatagGTTAGTCTGATTCAAATCCCCAGCAAAGTGGAACTCAGGCAGAAAAACCTTTTCAGTGTCAGTGACTGCAAGATGTACTGGCAAAGCAATGGAGACTACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA