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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgaaaccacacacacactctctctgttcttgaattgattttgtgttttgaatgtgaattgagcttgttgttgttatagGAAGGCGAAGCTGTATCGGTTTGACAAGGAGGGGAACCAGTGGAAGGAGCGTGGCGGCGGGAACGTTAAGCTGCTGAAACATAAGGTCACCGGGAAGGTG

Basic information

species Glycine max
transcript GLYMA01G29410.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G29410.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os05g28290.1 (Oryza sativa), 3'ss of exon 1
--------------------gtacgaaaccacacacacactctctctgttcttgaa--ttgattttgtgttttgaatgtgaattgagcttgttg----------ttgtt-atagGAAGGCGAAGCTGTATCGGTTTGACAAGGAGGGGAACCAGTGGAAGGAGCGTGGCGGCGGGAACGTTAAGCTGCTGAAACATAAGGTCACCGGGAAGGTG
                       |     | | | |    |||| |   ||||| |  | |  |   | ||||   |  ||  ||     | ||          |||||   |||||||||||||| || ||||||||||||||||||||||||||||||||||| ||    || | ||| ||||| || || || ||||  | ||| ||||| 
gtgagccccccccgccgccgccgcttgctctctctcctcttctcccctctcttgtagctcgtgtgctttttttcggttcgatctggtggcgctgatccgcgcgattgtttgcagGAAGGCGAAGCTTTACCGGTTTGACAAGGAGGGGAACCAGTGGAAGGAGCGGGGGACGGGCACCGTCAAGCTCCTCAAGCACAAGGAGAACGGCAAGGTC

upper sequence: GLYMA01G29410.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os03g18180.1 (Oryza sativa), 3'ss of exon 1
gtacgaaaccacacacacactctctctgttcttgaattgattttgt---gttttgaatgtgaattga--gcttgttgttgtta---------tagGAAGGCGAAGCTGTATCGGTTTGACAAGGAGGGGAACCAGTGGAAGGAGCGTGGCGGCGGGAACGTTAAGCTGCTGAAACATAAGGTCACCGGGAAGGTG
||| |   || | | | | |||  ||    |  ||   ||| |      | |||||        |||   || ||| || ||           |||||| |||||||||| || || ||||||||||||||||| ||||||||| | |||  ||| |  || ||||||||||| || ||||  ||||| ||||| 
gtaagccgcctccccctccctcgatccagccccgatccgatctcccccggctttgatctgagcctgacgactcgttttttttggatttcccgcagGAAGTCGAAGCTGTACCGCTTCGACAAGGAGGGGAACCAATGGAAGGAGAGAGGCACCGGCACGGTGAAGCTGCTGAAGCACAAGGAGACCGGCAAGGTC

upper sequence: GLYMA01G29410.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G094388_T01 (Zea mays), 3'ss of exon 1
-------gtacgaaaccacacacacactctctctgttcttgaattgattttgtgttttgaatgtgaattgagcttgttgttgttat--agGAAGGCGAAGCTGTATCGGTTTGACAAGGAGGGGAACCAGTGGAAGGAGCGTGGCGGCGGGAACGTTAAGCTGCTGAAACATAAGGTCACCGGGAAGGTG
        | ||   || |    |  | | | |  | |  ||   ||||| |    |    |||  ||      ||  |  | | |  |||||||||||||| || ||||| ||||||||||||||||||||||| ||||| |||   || |  || |||||||| || || || | |||||  ||||| 
gtgaggcatccgcggccgcttcgattcccccccc-tccccgatccgattt-gcccatgtcttgttgatctgatgtgcggcggctgtgcagGAAGGCGAAGCTCTACCGGTTCGACAAGGAGGGGAACCAGTGGAAAGAGCGCGGCACAGGCACTGTGAAGCTGCTCAAGCACAAAGACACCGCCAAGGTC

upper sequence: GLYMA01G29410.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G078933_T01 (Zea mays), 3'ss of exon 1
-------gtacgaaaccacacacacactct---ctctgttcttgaattgattttgt--gttttgaatgtgaattgagcttgttgttgttat--agGAAGGCGAAGCTGTATCGGTTTGACAAGGAGGGGAACCAGTGGAAGGAGCGTGGCGGCGGGAACGTTAAGCTGCTGAAACATAAGGTCACCGGGAAGGTG
        | |    || |    |  |||    | |    |  ||   ||||  |   | |||   ||   ||    | ||| |  |||||  |||||||||||||| || ||||| |||||||||| |||||||||||| || ||||||   || |  || |||||||| || || ||||  ||||  ||||| 
gtgatgcatcctcggccgcttcgattctccccaccccaaccccgatccgattcggctaggttttgttgatcatctgacgtgtggcggttatgcagGAAGGCGAAGCTCTACCGGTTCGACAAGGAGGCGAACCAGTGGAAAGAACGTGGCACAGGCACTGTGAAGCTGCTTAAGCACAAGGAGACCGCCAAGGTC

upper sequence: GLYMA01G29410.1 (Glycine max), 3'ss of exon 1
lower sequence: AC213884.3_FGT001 (Zea mays), 3'ss of exon 1
---gtacgaaaccacacacacactctctctgttctt----gaattgattttgtgttttgaatgtgaattga-gcttgtt--gttgttatagGAAGGCGAAGCTGTATCGGTTTGACAAGGAGGGGAACCAGTGGAAGGAGCGTGGCGGCGGGAACGTTAAGCTGCTGAAACATAAGGTCACCGGGAAGGTG
      ||   || |   | |    ||  || || |    |  |    ||  | ||       ||| |||| |||  ||  | | ||  ||||||||||||||||| |||||||| || || |||||||| |||||||| || |||   || | ||| ||||| || ||  | ||||  ||||| ||||| 
gtgaggcgctgcccccttccccacttccttgctcatcgccgcgtgcggttgctcttccccgcttgatttgatgctgatttgggttttgcagGAAGGCGAAGCTGTACCGGTTTGATAAAGACGGGAACCAATGGAAGGAACGGGGCACGGGCACCGTCAAGCTTCTCAAGAACAAGGAGACCGGCAAGGTC

upper sequence: GLYMA01G29410.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S25_241V6.2 (Physcomitrella patens), 3'ss of exon 1
----------gtacgaaaccacacacacactctctctgttcttgaattgattttgt------gttttgaatgtgaattgagct-tgt-tgttgttat-agGAAGGCGAAGCTGTATCGGTTTGACAAGGAGGGGAACCAGTGGAAGGAGCGTGGCGGCGGGAACGTTAAGCTGCTGAAACATAAGGTCACCGGGAAGGTG
           |              ||  |   | || | ||| ||||| |  ||      ||||  |   || | ||| || ||| || | || | |||||||| ||||||||||||||||||||||| || |  || ||||| ||| | ||||  ||  | || ||| | ||  |||| |||   | |   ||||| 
agggctttggtttttcctttggggttaccttggttttgattttgtattgactacgtcagcatgtttatacgttggaatgaactgtgtgtgctattctcagGAAGGCTAAGCTGTATCGGTTTGACAAGGAAGGAACACAATGGAAAGAGAGGGGCGTTGGCCAAGTGAAGATTCTAGAACACAAGTCAAACAAAAAGGTT

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|298173186|gb|HO020170.1|HO020170
EST:     GAGGTCGCCGTCACCACCGGCGAGGAGGACGAGGATCCCATCCTTGACCT                         GAAGGCGAAGCTGTATCGGTTTGACAAGGAGGGGAACCAGTGGAAGGAGCG
genomic: GAGGTCGCCGTCACCACCGGCGAGGAGGACGAGGATCCCATCCTTGATCTgtacgaaacc ... gttgttatagGAAGGCGAAGCTGTATCGGTTTGACAAGGAGGGGAACCAGTGGAAGGAGCG
EST: gi|298164310|gb|HO013955.1|HO013955
EST:     GAGGTCGCCGTCACCACCGGCGAGGAGGACGAGGATCCCATCCTTGACCT                         GAAGGCGAAGCTGTATCGGTTTGACAAGGAGGGGAACCAGTGGAAGGAGCG
genomic: GAGGTCGCCGTCACCACCGGCGAGGAGGACGAGGATCCCATCCTTGATCTgtacgaaacc ... gttgttatagGAAGGCGAAGCTGTATCGGTTTGACAAGGAGGGGAACCAGTGGAAGGAGCG
EST: gi|213614876|gb|DB956984.1|DB956984
EST:     GAGGTCGCCGTCACCACCGGCGAGGAGGACGAGGATCCCATCCTTGACCT                         GAAGGCGGAGCTGTATCGGTTTGACAAGGAGGGGAACCAGTGGAAGGAGCG
genomic: GAGGTCGCCGTCACCACCGGCGAGGAGGACGAGGATCCCATCCTTGATCTgtacgaaacc ... gttgttatagGAAGGCGAAGCTGTATCGGTTTGACAAGGAGGGGAACCAGTGGAAGGAGCG
EST: gi|213592588|gb|DB961848.1|DB961848
EST:     GAGGTCGCCGTCACCACCGGCGAGGAGGACGAGGATCCCATCCTTGACCT                         GAAGGCGAAGCTGTATCGGTTTGACAAGGAGGGGAACCAGTGGAAGGAGCG
genomic: GAGGTCGCCGTCACCACCGGCGAGGAGGACGAGGATCCCATCCTTGATCTgtacgaaacc ... gttgttatagGAAGGCGAAGCTGTATCGGTTTGACAAGGAGGGGAACCAGTGGAAGGAGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttcttgaattgattttgtgttttgaatgtgaattgagcttgttgttgttatagGAAGGCGAAGCTGTATCGGTTTGACAAGGAGGGGAACCAGTGGAAGGAGCGTGGCGGCGGGAACGTTAAGCTGCTGAAACATAAGGTCACCGGGAAGGTG
        aattgat  putative branch site (score: 4)
        aattgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgaaaccacacacacactctctctgttcttgaattgattttgtgttttgaatgtgaattgagcttgttgttgttatagGAAGGCGAAGCTGTATCGGTTTGACAAGGAGGGGAACCAGTGGAAGGAGCGTGGCGGCGGGAACGTTAAGCTGCTGAAACATAAGGTCACCGGGAAGGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT