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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgattcgactgcgcaattgcaaaatgcgaaaactctttggtttttctcgtgttttgactttttcgatactgttgcttattacttttttcgaaatcgcagGGTTATGCGGCGAGGGAGTTTGCCAAACAGGGCGTTAAGCCAGGGGAGTTGGCTATCATTTCGAAAGAAGCG

Basic information

species Glycine max
transcript GLYMA10G07820.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G07820.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os09g39380.1 (Oryza sativa), 3'ss of exon 1
-ttgattcgactgcg--caattgcaaaatgcgaaaactctttggtttttctcgtgttttgactttttcgatactgttgcttattacttttttcg-aaatcgcagGGTTATGCGGCGAGGGAGTTTGCCAAACAGGGCGTTAAGCCAGGGGAGTTGGCTATCATTTCGAAAGAAGCG
 || |||||  ||    |  ||     ||          |  || | |  |||    |    ||||||    ||||| || ||| || | |    |  | |||||| ||||||||  ||||||| ||||| ||||| ||||||||||||||| | || ||||| || || || || 
attcattcgcttggatccttttatttgatcttggtctgttccggatctcgtcgaaagtacggtttttc----ctgttcctaatttctctctgaatattttgcagGGATATGCGGCACGGGAGTTCGCCAAGCAGGGTGTTAAGCCAGGGGAGCTCGCCATCATCTCCAAGGAGGCC

upper sequence: GLYMA10G07820.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv08s0007g03610.t01 (Vitis vinifera), 3'ss of exon 1
ttgattcgactgcgcaattgcaaaatgcgaaaactctttggtttttctcgtgttttgactttttcgatactgttgcttattacttttttcgaaatcgcagGGTTATGCGGCGAGGGAGTTTGCCAAACAGGGCGTTAAGCCAGGGGAGTTGGCTATCATTTCGAAAGAAGCG
  ||  |  |   |    | | |  ||  | |     |    | |    |     |   ||||   ||  ||      ||   | |||  |   |  ||||| ||||| || |||||||||||||| || || ||||||||||||||  |||| || ||||| ||||| |||
aggaaccagccttgtctattctatgtgttatattatgtgcagtataaatgccacatattttttgttatcttgactaaaatgtttgtttatgtgctttcagGGATATGCAGCTAGGGAGTTTGCCAAGCAAGGGGTTAAGCCAGGGGAACTGGCAATTATTTCCAAAGAGGCG
















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|209718426|gb|BW666238.1|BW666238
EST:     CAATGGCGAAAACCTTCAAATACATCATCCTCGGTGGAGGAGTTTCCGCT                         GGTTATGCGGCGAGGGAGTTTGCCAAACAGGGCGTTAAGCCAGGGGAGTTG
genomic: CAATGGCGAAAACCTTCAAATACATCATCCTCGGTGGAGGAGTTTCCGCTgttagttcca ... gaaatcgcagGGTTATGCGGCGAGGGAGTTTGCCAAACAGGGCGTTAAGCCAGGGGAGTTG
EST: gi|209707196|gb|BW656814.1|BW656814
EST:     CAATGGCGAAAACCTTCAAATACATCATCCTCGGTGGAGGAGTTTCCGCT                         GGTTATGCGGCGAGGGAGTTTGCCAAACAGGGCGTTAAGCCAGGGGAGTTG
genomic: CAATGGCGAAAACCTTCAAATACATCATCCTCGGTGGAGGAGTTTCCGCTgttagttcca ... gaaatcgcagGGTTATGCGGCGAGGGAGTTTGCCAAACAGGGCGTTAAGCCAGGGGAGTTG
EST: gi|213595751|gb|DB955927.1|DB955927
EST:     CAATGGCGAAAACCTTCAAATACATCATCCTCGGTGGAGGAGTTTCCGCT                         GGTTATGCGGCGAGGGAGTTTGCCAAACAGGGCGTTAAGCCAGGGGAGTTG
genomic: CAATGGCGAAAACCTTCAAATACATCATCCTCGGTGGAGGAGTTTCCGCTgttagttcca ... gaaatcgcagGGTTATGCGGCGAGGGAGTTTGCCAAACAGGGCGTTAAGCCAGGGGAGTTG
EST: gi|209697959|gb|BW673018.1|BW673018
EST:     CAATGGCGAAAACCTTCAAATACATCATCCTCGGTGGAGGAGTTTCCGCT                         GGTTATGCGGCGAGGGAGTTTGCCAAACAGGGCGTTAAGCCAGGGGAGTTG
genomic: CAATGGCGAAAACCTTCAAATACATCATCCTCGGTGGAGGAGTTTCCGCTgttagttcca ... gaaatcgcagGGTTATGCGGCGAGGGAGTTTGCCAAACAGGGCGTTAAGCCAGGGGAGTTG
EST: gi|213615151|gb|DB963363.1|DB963363
EST:     CAATGGCGAAAACCTTCAAATACATCATCCTCGGTGGAGGAGTTTCCGCT                         GGTTATGCGGCGAGGGAGTTTGCCAAACAGGGCGTTAAGCCAGGGGAGTTG
genomic: CAATGGCGAAAACCTTCAAATACATCATCCTCGGTGGAGGAGTTTCCGCTgttagttcca ... gaaatcgcagGGTTATGCGGCGAGGGAGTTTGCCAAACAGGGCGTTAAGCCAGGGGAGTTG
EST: gi|192327629|gb|FK021306.1|FK021306
EST:     CAATGGCGAAAACCTTCAAATACATCATCCTCGGTGGAGGAGTTTCCGCT                         GGTTATGCGGCGAGGGAGTTTGCCAAACAGGGCGTTAAGCCAGGGGAGTTG
genomic: CAATGGCGAAAACCTTCAAATACATCATCCTCGGTGGAGGAGTTTCCGCTgttagttcca ... gaaatcgcagGGTTATGCGGCGAGGGAGTTTGCCAAACAGGGCGTTAAGCCAGGGGAGTTG
EST: gi|209697684|gb|BW655585.1|BW655585
EST:     CAATGGCGAAAACCTTCAAATACATCATCCTCGGTGGAGGAGTTTCCGCT                         GGTTATGCGGCGAGGGAGTTTGCCAAACAGGGCGTTAAGCCAGGGGAGTTG
genomic: CAATGGCGAAAACCTTCAAATACATCATCCTCGGTGGAGGAGTTTCCGCTgttagttcca ... gaaatcgcagGGTTATGCGGCGAGGGAGTTTGCCAAACAGGGCGTTAAGCCAGGGGAGTTG
EST: gi|254340648|gb|GR854376.1|GR854376
EST:     CAATGGCGAAAACCTTCAAATACATCATCCTCGGTGGAGGAGTTTCCGCT                         GGTTATGCGGCGAGGGAGTTTGCCAAACAGGGCGTTAAGCCAGGGGAGTTG
genomic: CAATGGCGAAAACCTTCAAATACATCATCCTCGGTGGAGGAGTTTCCGCTgttagttcca ... gaaatcgcagGGTTATGCGGCGAGGGAGTTTGCCAAACAGGGCGTTAAGCCAGGGGAGTTG
EST: gi|209701293|gb|BW653036.1|BW653036
EST:     CAATGGCGAAAACCTTCAAATACATCATCCTCGGTGGAGGAGTTTCCGCT                         GGTTATGCGGCGAGGGAGTTTGCCAAACAGGGCGTTAAGCCAGGGGAGTTG
genomic: CAATGGCGAAAACCTTCAAATACATCATCCTCGGTGGAGGAGTTTCCGCTgttagttcca ... gaaatcgcagGGTTATGCGGCGAGGGAGTTTGCCAAACAGGGCGTTAAGCCAGGGGAGTTG
EST: gi|192300239|gb|FG989361.1|FG989361
EST:     CAATGGCGAAAACCTTCAAATACATCATCCTCGGTGGAGGAGTTTCCGCT                         GGTTATGCGGCGAGGGAGTTTGCCAAACAGGGCGTTAAGCCAGGGGAGTTG
genomic: CAATGGCGAAAACCTTCAAATACATCATCCTCGGTGGAGGAGTTTCCGCTgttagttcca ... gaaatcgcagGGTTATGCGGCGAGGGAGTTTGCCAAACAGGGCGTTAAGCCAGGGGAGTTG
EST: gi|21676903|gb|BQ629254.1|BQ629254
EST:     CAATGGCGAAAACCTTCAAATACATCATCCTCGGTGGAGGAGTTTCCGCT                         GGTTATGCGGCGAGGGAGTTTGCCAAACAGGGCGTTAAGCCAGGGGAGTTG
genomic: CAATGGCGAAAACCTTCAAATACATCATCCTCGGTGGAGGAGTTTCCGCTgttagttcca ... gaaatcgcagGGTTATGCGGCGAGGGAGTTTGCCAAACAGGGCGTTAAGCCAGGGGAGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcgtgttttgactttttcgatactgttgcttattacttttttcgaaatcgcagGGTTATGCGGCGAGGGAGTTTGCCAAACAGGGCGTTAAGCCAGGGGAGTTGGCTATCATTTCGAAAGAAGCG
       ttttgac  putative branch site (score: 3)
                                     cttttttcg  putative PPT
                               ttattactttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgattcgactgcgcaattgcaaaatgcgaaaactctttggtttttctcgtgttttgactttttcgatactgttgcttattacttttttcgaaatcgcagGGTTATGCGGCGAGGGAGTTTGCCAAACAGGGCGTTAAGCCAGGGGAGTTGGCTATCATTTCGAAAGAAGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - cgactgc
- - - - - - - caattgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgttgc