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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgctagttattcttgtttgacgaattcataatagttggtttcattttaccatttgactttgaagacacaagtaagtgtttgcttctgttattctgtagATGCTGATATGGAGGACTATGGATTTGAGTACTCAGATGAGGAGCAAGAGGAACAGGATGTTGATATTGAGAATCAATATTACAATTCAAAAG

Basic information

species Glycine max
transcript GLYMA03G00670.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G00670.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G132804_T01 (Zea mays), 3'ss of exon 1
----tttgctagttatt-cttgtttgacgaattcataatagttggtttcattttaccatttgactttgaagacacaagtaagtgtttgcttctgttattctg--tagATGCTGATATGGAGGACTATGGATTTGAGTACTCAGATGAGGAGCAAGAGGAACAGGATGTTGATATTGAGAATCAATATTACAATTCAAAAG
    |  | |   |    || ||  |   |||||   ||  || ||  | | ||  | |  |     ||  |      |   || |      ||||||  ||  ||||||| |||||||||||||| || || ||||||||||| |||||||  ||||| |||||||| ||||| ||||| || |||||||| || ||||
gtaatccgatccctccgactcgtgggctaaattctctattatttgtggcttgttctcttgcg-----gagaattttttttcttgatcatggatgttatggtgattagATGCGGATATGGAGGACTACGGGTTCGAGTACTCAGACGAGGAGCCGGAGGAGCAGGATGTCGATATCGAGAACCAGTATTACAACTCTAAAG

upper sequence: GLYMA03G00670.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G079196_T01 (Zea mays), 3'ss of exon 1
---tttgctagttattcttgtttgacgaattcataatagttggtttcattttaccatttgactttgaagacacaagtaagtgtttgcttctgttattctg--tagATGCTGATATGGAGGACTATGGATTTGAGTACTCAGATGAGGAGCAAGAGGAACAGGATGTTGATATTGAGAATCAATATTACAATTCAAAAG
    | ||      | |   |    ||  |  ||  |  |   ||||  |||||   ||    ||| ||| |    |   || |||    ||||||  ||  ||||||| || ||||||||||| || || |||||||| || || ||||  ||||| |||||||| || |||||||| || |||||||| || ||||
gtaatcgcgccccctccaattcgtgcgcttcgattttcctatatttctgtttacttgttc-tattgcagatatttttcc-tgattgtggatgttatggtgattagATGCGGACATGGAGGACTACGGGTTCGAGTACTCTGACGAAGAGCCGGAGGAGCAGGATGTCGACATTGAGAACCAGTATTACAACTCCAAAG

upper sequence: GLYMA03G00670.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv08s0040g00430.t01 (Vitis vinifera), 3'ss of exon 1
-----tttgctagttattcttgtttgacgaattcataatagttggtttcattttaccatttgactttgaagacacaagtaagtgtttgcttctgttattctgtagATGCTGATATGGAGGACTATGGATTTGAGTACTCAGATGAGGAGCAAGAGGAACAGGATGTTGATATTGAGAATCAATATTACAATTCAAAAG
      |||  |||     || |||  |  || ||  ||  ||  ||| ||| |   ||      || |  | |  | |  |  ||    | ||  ||||||||||||| || |||||||| |||||||||||||||||||| |||||||  ||||| ||||||||||||||||||||||||||||||||||| ||||
gtatccttgaaagtgcaaattctttctctcataca-gatgcttaattt-attctgtaatggtttgttaataaaatgatttggaatt---ctttggcattctgtagATGCAGACATGGAGGATTATGGATTTGAGTACTCAGAAGAGGAGCCTGAGGAGCAGGATGTTGATATTGAGAATCAATATTACAATTCTAAAG

upper sequence: GLYMA03G00670.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S124_47V6.1 (Physcomitrella patens), 3'ss of exon 1
-tttgctagttatt-cttgtttgacgaa--ttcataatagttggtttcattttaccatttgactttgaagacacaagtaagtgtttgcttctgttattctgtagATGCTGATATGGAGGACTATGGATTTGAGTACTCAGATGAGGAGCAAGAGGAACAGGATGTTGATATTGAGAATCAATATTACAATTCAAAAG
    |   |  |   | |  |  ||  |  ||||| ||| | |  |  | | ||  |||||  |    |   |   |      ||||||     |  ||   |||||| || ||||| || ||||| || ||||| || || ||||| |  ||||| || |||||||||||||||||||||||||| ||| | ||||
tcccgaaggcaaagacatactccacccagcttcattataatgg--tgaactatat-atttgtttccttatttaatcgatgtcttttgctggacctgatc-acagATGCCGACATGGAAGATTATGGGTTCGAGTATTCGGACGAGGAACCCGAGGAGCAAGATGTTGATATTGAGAATCAATATTATAATACCAAAG

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|298189914|gb|HO038317.1|HO038317
EST:     ACCCTAACTCGGACCTCAAACTCAATCGATTTCATACGACATGGCTTCGG                         ATGCTGATATGGAGGACTATGGATTTGAGTACTCAGATGAGGAGCAAGAGG
genomic: ACCCTAACTCGGACCTCAAACTCAATCGATTTCATACAACATGGCTTCGGgtacctgttc ... tattctgtagATGCTGATATGGAGGACTATGGATTTGAGTACTCAGATGAGGAGCAAGAGG
EST: gi|151398925|gb|EV268796.1|EV268796
EST:     ACCCTAACTCGGACCTCAAACTCAATCGATTTCATACAACATGGCTTCGG                         ATGCTGATATGGAGGACTATGGATTTGAGTACTCAGATGAGGAGCAAGAGG
genomic: ACCCTAACTCGGACCTCAAACTCAATCGATTTCATACAACATGGCTTCGGgtacctgttc ... tattctgtagATGCTGATATGGAGGACTATGGATTTGAGTACTCAGATGAGGAGCAAGAGG
EST: gi|192307527|gb|FK002045.1|FK002045
EST:     ACCCTAACTCGGACCTCAAACTCAATCGATTTCATACAACATGGCTTCGG                         ATGCTGATATGGAGGACTATGGATTTGAGTACTCAGATGAGGAGCAAGAGG
genomic: ACCCTAACTCGGACCTCAAACTCAATCGATTTCATACAACATGGCTTCGGgtacctgttc ... tattctgtagATGCTGATATGGAGGACTATGGATTTGAGTACTCAGATGAGGAGCAAGAGG
EST: gi|208307928|gb|GE105884.1|GE105884
EST:     ACCCTAACTCGGACCTCAAACTCAATCGATTTCATACAACATGGCTTCGG                         ATGCTGATATGGAGGACTATGGATTTGAGTACTCAGATGAGGAGCAAGAGG
genomic: ACCCTAACTCGGACCTCAAACTCAATCGATTTCATACAACATGGCTTCGGgtacctgttc ... tattctgtagATGCTGATATGGAGGACTATGGATTTGAGTACTCAGATGAGGAGCAAGAGG
EST: gi|298189905|gb|HO038308.1|HO038308
EST:     ACCCTAACTCGGACCTCAGACTCAATCGATTTCATACGACATGGCTTCGG                         ATGCTGATATGGAGGACTATGGATATGAGTACTCAGATGAGGAGCAAGAGG
genomic: ACCCTAACTCGGACCTCAAACTCAATCGATTTCATACAACATGGCTTCGGgtacctgttc ... tattctgtagATGCTGATATGGAGGACTATGGATTTGAGTACTCAGATGAGGAGCAAGAGG
EST: gi|151398223|gb|EV268101.1|EV268101
EST:     ACCCTAACTCGGACCTCAAACTCAATCGATTTCATACAACATGGCTTCGG                         ATGCTGATATGGAGGACTATGGATTTGAGTACTCAGATGAGGAGCAAGAGG
genomic: ACCCTAACTCGGACCTCAAACTCAATCGATTTCATACAACATGGCTTCGGgtacctgttc ... tattctgtagATGCTGATATGGAGGACTATGGATTTGAGTACTCAGATGAGGAGCAAGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttaccatttgactttgaagacacaagtaagtgtttgcttctgttattctgtagATGCTGATATGGAGGACTATGGATTTGAGTACTCAGATGAGGAGCAAGAGGAACAGGATGTTGATATTGAGAATCAATATTACAATTCAAAAG
       atttgac  putative branch site (score: 4)
                                      cttctgtt  putative PPT
                                          tgttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgctagttattcttgtttgacgaattcataatagttggtttcattttaccatttgactttgaagacacaagtaagtgtttgcttctgttattctgtagATGCTGATATGGAGGACTATGGATTTGAGTACTCAGATGAGGAGCAAGAGGAACAGGATGTTGATATTGAGAATCAATATTACAATTCAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
-ttgctag
- - - - - - - ttgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - gactttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agacaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcttct