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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atacagtagcaactctaaatcaaccttctctttgttttttcttcctagctagtattttatttactaataagtattttgttttctctgcaaaattctgcagAAGAAATGGATTGGGATAAAAATGGAATGGTGAACTTCAAGGAGTTTCTATTTGCTTTTACACGTTGGGTTGGAATTGATGAAGTTGAGGACGAGGAAAA

Basic information

species Glycine max
transcript GLYMA16G16060.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G16060.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g10470.1 (Oryza sativa), 3'ss of exon 4
atacagtagcaactctaaatcaaccttctctttgttttttc-----ttcctagctagtattttatttactaataagtat----tttgttttctctgcaaaattctgcagAAGAAATGGATTGGGATAAAAATGGAATGGTGAACTTCAAGGAGTTTCTATTTGCTTTTACACGTTGGGTTGGAATTGATGAAGTTGAGGACGAGGAAAA
               ||| |   | || |  | || |  ||     |  |     |  |   ||   ||| | ||  ||     |  |   ||||           |||| |||||||||||||| || ||||||| ||||| |||||||||||| || || |||||||| |||||||| || ||||||||    || || || ||  |
--------------gtaagttttcttttttgtggtatcgtcacaaatctcacatgaacacagtacacactgacaatgatggtcctaatacactcttttggtggtcccagAGGAAATGGATTGGGACAAGAATGGAACGGTGACCTTCAAGGAGTTCCTCTTCGCTTTTACTCGTTGGGTGGGGATTGATGATAACGAAGATGACGACGA

upper sequence: GLYMA16G16060.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os06g40720.1 (Oryza sativa), 3'ss of exon 4
---atacagtagcaactctaaatcaaccttctctttgttttttcttcctagctagtattttatttactaataagtattttgttttctctgcaaaattctgcagAAGAAATGGATTGGGATAAAAATGGAATGGTGAACTTCAAGGAGTTTCTATTTGCTTTTACACGTTGGGTTGGAATTGATGAAGTTGAGGACGAGGAAAA
      |  ||| || ||||||  ||  |     |||    |||     || |      |||  | |||| | |||     || | | |    |   |  |||| |||||||| ||||| || ||||||||||||| |||||| || ||||| ||||| || || || |||||||| ||||| |||  |||||||||  |  |
atttctctatagtaa-tctaaa--aatttctagattgacaattcccatcagtttcagaattaagtcctaacatgtaacactttctttttttgcatggcaccagAGGAAATGGACTGGGACAAGAATGGAATGGTGACCTTCAAAGAATTTCTGTTTGCATTCACTCGCTGGGTTGGGATTGACGAAAATGAGGACGACAATGA

upper sequence: GLYMA16G16060.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G006790_T01 (Zea mays), 3'ss of exon 3
atacagtagcaactctaaatcaaccttc-tctttgttttttcttcctagctagtattttatttactaa---taagtattttgttttctctgcaaaattctgcagAAGAAATGGATTGGGATAAAAATGGAATGGTGAACTTCAAGGAGTTTCTATTTGCTTTTACACGTTGGGTTGGAATTGATGAAGTTGAGGACGAGGAAAA
    ||||  ||  ||    ||  | |  |   ||||  |  ||   | || |  |   || | |  |         |||   ||||| | ||     ||  ||| |||||||| ||||| || || ||||||||||  ||||||||||| || ||||| || || || ||||| ||||||||||||  |||||| || ||  |
--gaagtataaaaacttgcacactcataattcctgttactgttttgaaacttgcgtcccatcttcccagtcctgacgtttacctttctttacatggcact--agAGGAAATGGACTGGGACAAGAACGGAATGGTGACATTCAAGGAGTTCCTGTTTGCCTTCACTCGCTGGGTAGGAATTGATGAAAATGAGGATGAAGATGA

upper sequence: GLYMA16G16060.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G142693_T02 (Zea mays), 3'ss of exon 4
-----atacagtagcaactctaaatcaaccttctctttgttttttcttcctagctagtattttatttactaataagtattttgttttctctgcaaaattctgcagAAGAAATGGATTGGGATAAAAATGGAATGGTGAACTTCAAGGAGTTTCTATTTGCTTTTACACGTTGGGTTGGAATTGATGAAGTTGAGGACGAGGAAAA
      |||  |  |     ||   |       |    | ||    | ||| | ||   || ||| |         |||||   |   |  |  ||    | |||| |||||||||||||| || ||||| |  |||| ||||||||| || || ||||||||||| || ||||| || || ||| | |  || || || ||  |
cgtcggtacgttttccttcttatgccctgtgggtacccgattgccatccctggatatgtttatatgtttgccctgatattt-actactttggtgaa----tacagAGGAAATGGATTGGGACAAGAATGGCACAGTGACCTTCAAGGAATTCCTTTTTGCTTTTACTCGCTGGGTGGGGATCGATAATGAAGACGATGATGATGA

upper sequence: GLYMA16G16060.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G26470.1 (Arabidopsis thaliana), 3'ss of exon 4
atacagtagcaactctaaatcaaccttctctttgttttttcttcctagctagtatt-ttatttactaa--taagtattttgttttctctgcaaaattctgcagAAGAAATGGATTGGGATAAAAATGGAATGGTGAACTTCAAGGAGTTTCTATTTGCTTTTACACGTTGGGTTGGAATTGATGAAGTTGAGGACGAGGAAAA
                   | |  |||    |   |   ||||| |  | ||  || || || ||| |   ||| || ||| |||   | |     |||||||| |||||||| ||||| || || ||||||||||||||||| |||||||| || || ||||| |  |||||||| || |||||   ||| || || ||| |
-----------------gtttattcttaaactccctccctcttcttctcaagctttcttcttcactgaaccaagaatattgattttgattcctgtgtctgcagAGGAAATGGACTGGGACAAGAACGGAATGGTGAACTTCAAAGAGTTTCTCTTCGCATTTACGCAGTGGGTTGGGATAGATGAGAATGAAGAAGAAGAAGA

upper sequence: GLYMA16G16060.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv19s0015g01200.t01 (Vitis vinifera), 3'ss of exon 4
atacagtagcaactctaaatcaaccttctctttgttttttcttcctagctagtattttatttactaataag-tattttgttt----tctctgcaaaattctgcagAAGAAATGGATTGGGATAAAAATGGAATGGTGAACTTCAAGGAGTTTCTATTTGCTTTTACACGTTGGGTTGGAATTGATGAAGTTGAGGACGAGGAAAA
       || |    |   |  |   | |  |  |||  ||   |  |||   ||||| ||   ||||||  |||||   ||    |||      | |  |||||| || |||||||||||||||||||||||||||||||||||||||||||| |||||||| || ||||||||||| ||||| ||  ||||||| || ||| |
---tgccagtaga--tggttagaagctttgatgatttcctcgaacaggctccaatttttttccataataatctatttcacttggcctcttgttttattattgcagAGGAGATGGATTGGGATAAAAATGGAATGGTGAACTTCAAGGAGTTTCTTTTTGCTTTCACCCGTTGGGTTGGGATTGACGATATTGAGGATGAAGAAGA

upper sequence: GLYMA16G16060.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S197_126V6.1 (Physcomitrella patens), 3'ss of exon 3
-------atacagtagcaactctaaatcaaccttctctttgttttttc-----ttcctagctagtattttatttactaataagtattttgttttctc------tgcaaaattc------tgcagAAGAAATGGATTGGGATAAAAATGGAATGGTGAACTTCAAGGAGTTTCTATTTGCTTTTACACGTTGGGTTGGAATTGATGAAGTTGAGGACGAGGAAAA
       |  |  |  || |||    |||  | ||   || ||| | |     ||   |  |   |||   ||| ||  ||| | |     |  ||       ||| ||   |      |||||| |||||||||||||||||| | || ||| | |  |||||||||||| |||| ||||||||    ||||| ||| ||||  | |  || || ||   |  
gtatgttactctttcccacctcactgtcatgcatcaaattatttctgcaaccgttttcaattgccattgcctttcctg-taaatgtgacactgactaaacgaatgcgaaccccaacatgtgcagAGGAAATGGATTGGGATAAAGACGGCATGATCACATTCAAGGAGTTTTTATTCGCTTTTACGGACTGGGTAGGACTTGAGAATGACGAAGAAGAAACAGG

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|17964764|gb|BM271494.1|BM271494
EST:     AACTACATCAGGGGAGCGTTCTTCTGGAAGAATAGCCATGAAAAGATTTG                         AAGAAATGGATTGGGATAAAAATGGAATGGTGAACTTCAAGGAGTTTCTAT
genomic: AACTACATCAGGGGAGCGTTCTTCTGGAAGAATAGCCATGAAAAGATTTGgtcagttgtc ... aattctgcagAAGAAATGGATTGGGATAAAAATGGAATGGTGAACTTCAAGGAGTTTCTAT
EST: gi|254348670|gb|GR852349.1|GR852349
EST:     AACTACATCAGGGGAGCGTTCTTCTGGAAGAATAGCCATGAAAAGATTTG                         AAGAAATGGATTGGGATAAAAATGGAATGGTGAACTTCAAGGAGTTTCTAT
genomic: AACTACATCAGGGGAGCGTTCTTCTGGAAGAATAGCCATGAAAAGATTTGgtcagttgtc ... aattctgcagAAGAAATGGATTGGGATAAAAATGGAATGGTGAACTTCAAGGAGTTTCTAT
EST: gi|208315057|gb|GE115737.1|GE115737
EST:     GGAAGAATAGCCATGAAAAAGATTTG                         AAGAAATGGATTGGGATAAAAATGGAATGGTGAACTTCAAGGAGTTTCTAT
genomic: GGAAGAATAGCCATG-AAAAGATTTGgtcagttgtc ... aattctgcagAAGAAATGGATTGGGATAAAAATGGAATGGTGAACTTCAAGGAGTTTCTAT
EST: gi|16341888|gb|BI967483.1|BI967483
EST:     AACTACATCAGGGGAGCGTTCTTCTGGAAGAATAGCCATGAAAAGATTTG                         AAGAAATGGATTGGGATAAAAATGGAATGGTGAACTTCAAGGAGTTTCTAT
genomic: AACTACATCAGGGGAGCGTTCTTCTGGAAGAATAGCCATGAAAAGATTTGgtcagttgtc ... aattctgcagAAGAAATGGATTGGGATAAAAATGGAATGGTGAACTTCAAGGAGTTTCTAT
EST: gi|7796463|gb|AW781860.1|AW781860
EST:     AACTACATCAGGGGAGCGTTCTTCTGGAAGAATAGCCATGAAAAGATTTG                         AAGAAATGGATTGGGATAAAAATGGAATGGTGAACTTCAAGGAGTTTCTAT
genomic: AACTACATCAGGGGAGCGTTCTTCTGGAAGAATAGCCATGAAAAGATTTGgtcagttgtc ... aattctgcagAAGAAATGGATTGGGATAAAAATGGAATGGTGAACTTCAAGGAGTTTCTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagctagtattttatttactaataagtattttgttttctctgcaaaattctgcagAAGAAATGGATTGGGATAAAAATGGAATGGTGAACTTCAAGGAGTTTCTATTTGCTTTTACACGTTGGGTTGGAATTGATGAAGTTGAGGACGAGGAAAA
                tactaat  putative branch site (score: 1)
     agtattttatttacta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atacagtagcaactctaaatcaaccttctctttgttttttcttcctagctagtattttatttactaataagtattttgttttctctgcaaaattctgcagAAGAAATGGATTGGGATAAAAATGGAATGGTGAACTTCAAGGAGTTTCTATTTGCTTTTACACGTTGGGTTGGAATTGATGAAGTTGAGGACGAGGAAAA

- - - - -caactct
- - - - - - - - - - - -ccttctc
- - - - - - - - - - - - - - - - - - - ttcttcc