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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taatactgacagccctcttactgaatgctatttcttcctttgcccaccggcatttacattctaaaagtattagaagttctaactaatttctcatgttcagGTATTGAACAATAATGCTGGATCTGGATATGAAGCTCCCGAAGTTGGCTTGTCTGGTCATTATACTCTTAAGAGTGATGTTTATAGCTTTGGAGTTGTCA

Basic information

species Glycine max
transcript GLYMA07G05230.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G05230.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os10g25090.1 (Oryza sativa), 3'ss of exon 13
----------------------------------------------------------------------taatactgacagccctcttactgaatg--ctatttcttcctttgccca-ccggcat-ttacattctaaaagtattag-aagttctaactaatttctcatgttcagGTATTGAACAATAATGCTGGATCTGGATATGAAGCTCCCGAAGTTGGCTTGTCTGGTCATTATACTCTTAAGAGTGATGTTTATAGCTTTGGAGTTGTCA------
                                                                      ||| |  |  | |     | |||||||   |  |||||   |||   | ||   || |||||    | | |  |||  |  || |   |  || |  ||        || |       ||   || |||||||||   || || ||||||| | || |||| || ||||| || |||||||||||||||||||||||||||||||      
gtaaaactcaaatcattttgctccaacaaacatatatattttcaattgtaaagaaatttatggtcttacttaaaaaaggaaacttaagttctgaatggattggttcttttcttgagtatccaagatgttacacaacatatggcttaccatatttttcatgtttccaaataaatctcaatagGCTTCAGATCAGGGTTCTGGATATAGTGCCCCTGAAGTTGACATGACTGGGCAGTATACCCTCAAGAGTGATGTTTATAGCTTTGGAGTTGTCATGCTGG

upper sequence: GLYMA07G05230.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G330907_T01 (Zea mays), 3'ss of exon 13
taatac-tgacagccctcttactgaatgctatttcttcctttgcccaccggc--atttac-attctaaaagtattagaagttctaactaatttctcatgttcagGTATTGAACAATAATGCTGGATCTGGATATGAAGCTCCCGAAGTTGGCTTGTCTGGTCATTATACTCTTAAGAGTGATGTTTATAGCTTTGGAGTTGTCA------
  |||| | |    | |||     | |  ||  |   | ||    ||| |||  ||| || ||  | | ||| ||  |      ||  || |   | |||  ||| |    |  | | ||| ||||      |    || || ||||| | | || | ||||| || || || |||||||||||||| ||||||||||||||||      
-tatacatcatcatcatctacgcaattcttacctagcctttcagacactggctgattaaccatcttcatagtgttgca---ctaaataaaataaacttgtgtagGCAGCAGAACAAAGTGCCGGAT------ACACTGCCCCAGAAGTGGACATGACCGGTCAGTACACCCTCAAGAGTGATGTTTACAGCTTTGGAGTTGTCATGCTTG
















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|193694233|gb|FK629881.1|FK629881
EST:     CTCATCTTTCTGACAGTGGATTGGCAAGCTATATTCCAAATGCAAACCAG                         GTATTAAACAATAATGCTGGATCTGGATATGAAGCTCCCGAAGTTGGTTTG
genomic: CTCATCTTTCCGACAGTGGATTGGCAAGCTATATTCCAAATGCAAACCAGgtgactttag ... tcatgttcagGTATTGAACAATAATGCTGGATCTGGATATGAAGCTCCCGAAGTTGGCTTG
EST: gi|10709647|gb|BF009371.1|BF009371
EST:     CTCATCTTTCCGACAGTGGATTGGCAAGCTATATTCCAAATGCAAACCAN                         GTATTGAACAATAATGCTGGATCTGGATATGAAGCTCCCGAAGTTGGCTTG
genomic: CTCATCTTTCCGACAGTGGATTGGCAAGCTATATTCCAAATGCAAACCAGgtgactttag ... tcatgttcagGTATTGAACAATAATGCTGGATCTGGATATGAAGCTCCCGAAGTTGGCTTG
EST: gi|208078027|gb|GD875321.1|GD875321
EST:     CTATATTCCAAATGCAAACCAG                         GTATTGAACAATAATGCTGGATCTGGATATGAAGCTCCCGAAGTTGGCTTG
genomic: CTATATTCCAAATGCAAACCAGgtgactttag ... tcatgttcagGTATTGAACAATAATGCTGGATCTGGATATGAAGCTCCCGAAGTTGGCTTG
EST: gi|7029604|gb|AW459321.1|AW459321
EST:     CTCATCTTTCCGACAGTGGATTGGCAAGCTATATTCCAAATGCAAACCAG                         GTATTGAACAATAATGCTGGATCTGGATATGAAGCTCCCGATGTTGGCTTG
genomic: CTCATCTTTCCGACAGTGGATTGGCAAGCTATATTCCAAATGCAAACCAGgtgactttag ... tcatgttcagGTATTGAACAATAATGCTGGATCTGGATATGAAGCTCCCGAAGTTGGCTTG
EST: gi|298175534|gb|HO018245.1|HO018245
EST:     CTCATCTTTCCGACAGTGGATTGGCAAGCTATATTCCAAATGCAAACCAG                         GTATTGAACAATAATGCTGGATCTGGATATGAAGCTCCCGAAGTTGGCTTG
genomic: CTCATCTTTCCGACAGTGGATTGGCAAGCTATATTCCAAATGCAAACCAGgtgactttag ... tcatgttcagGTATTGAACAATAATGCTGGATCTGGATATGAAGCTCCCGAAGTTGGCTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accggcatttacattctaaaagtattagaagttctaactaatttctcatgttcagGTATTGAACAATAATGCTGGATCTGGATATGAAGCTCCCGAAGTTGGCTTGTCTGGTCATTATACTCTTAAGAGTGATGTTTATAGCTTTGGAGTTGTCA
                                         tttctcat  CT-rich tract
      atttacattctaaaag  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taatactgacagccctcttactgaatgctatttcttcctttgcccaccggcatttacattctaaaagtattagaagttctaactaatttctcatgttcagGTATTGAACAATAATGCTGGATCTGGATATGAAGCTCCCGAAGTTGGCTTGTCTGGTCATTATACTCTTAAGAGTGATGTTTATAGCTTTGGAGTTGTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- -tactgac
- - - - - - ccctctt
- - - - - - - - - - - gaatgct
- - - - - - - - - - - - - - - - - - -ctttgcc
- - - - - - - - - - - - - - - - - - - - - - caccggc
- - - - - - - - - - - - - - - - - - - - - - - - - - - tacattc