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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttctagctattcttttttgatgtattcataatagttggtttcatttttaccaattgacttacaagacactaagtaagtgtttgcttcttttattttgtagATGCTGATATGGAGGACTATGGATTTGAGTACTCAGATGAGGAGCAAGAGGAGCAAGATGTTGATATTGAGAATCAATATTACAATTCAAAAG

Basic information

species Glycine max
transcript GLYMA19G30100.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G30100.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G132804_T01 (Zea mays), 3'ss of exon 1
ttctagctattcttttttgatgtattcataatagttggtttcattt-ttaccaattgacttaca-agacactaagtaagtgtttgcttcttttattttg--tagATGCTGATATGGAGGACTATGGATTTGAGTACTCAGATGAGGAGCAAGAGGAGCAAGATGTTGATATTGAGAATCAATATTACAATTCAAAAG
   ||          |  ||    |     | | |   | | |||| |  |   ||  ||| |  |||   |   |   || |      | ||||  ||  ||||||| |||||||||||||| || || ||||||||||| |||||||  |||||||| ||||| ||||| ||||| || |||||||| || ||||
--gtaatccgatccctccgactcgtgggctaaattctctattatttgtggcttgttctcttgcggagaattttttttcttgatcatggatgttatggtgattagATGCGGATATGGAGGACTACGGGTTCGAGTACTCAGACGAGGAGCCGGAGGAGCAGGATGTCGATATCGAGAACCAGTATTACAACTCTAAAG

upper sequence: GLYMA19G30100.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G079196_T01 (Zea mays), 3'ss of exon 1
---ttctagctattcttttttgatgta-ttcataatagttggtttcatttttaccaattgacttacaagacactaagtaagtgtttgcttcttttattttgtagATGCTGATATGGAGGACTATGGATTTGAGTACTCAGATGAGGAGCAAGAGGAGCAAGATGTTGATATTGAGAATCAATATTACAATTCAAAAG
    ||  ||         ||  ||   |||    |   |   ||  | |||||   ||   || || || | |      |  | ||  | || |  |   ||||||| || ||||||||||| || || |||||||| || || ||||  |||||||| ||||| || |||||||| || |||||||| || ||||
gtaatcgcgccccctccaattcgtgcgcttcgattttcctatatttctgtttacttgttctattgca-gatatttttcctgattgtggatgttatggtgattagATGCGGACATGGAGGACTACGGGTTCGAGTACTCTGACGAAGAGCCGGAGGAGCAGGATGTCGACATTGAGAACCAGTATTACAACTCCAAAG

upper sequence: GLYMA19G30100.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv08s0040g00430.t01 (Vitis vinifera), 3'ss of exon 1
------ttctagctattcttttttgatgtattcataatagttggtttcatttttaccaattgacttacaagacactaagtaagtgtttgcttcttttattttgtagATGCTGATATGGAGGACTATGGATTTGAGTACTCAGATGAGGAGCAAGAGGAGCAAGATGTTGATATTGAGAATCAATATTACAATTCAAAAG
      ||  |  |     || ||  | |  |    ||  ||  |||  | | ||    ||   | | || |   |  | || | ||||        ||| ||||||||| || |||||||| |||||||||||||||||||| |||||||  |||||||| |||||||||||||||||||||||||||||||| ||||
gtatccttgaaagtgcaaattctttctctcatacagatgcttaatttattctgtaatggtttgttaataaaatgatttggaattctttgg------cattctgtagATGCAGACATGGAGGATTATGGATTTGAGTACTCAGAAGAGGAGCCTGAGGAGCAGGATGTTGATATTGAGAATCAATATTACAATTCTAAAG

upper sequence: GLYMA19G30100.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S105_216V6.1 (Physcomitrella patens), 3'ss of exon 1
ttctagctattcttttttgatgtattcataatagttggtttcatttttaccaattgac-ttacaagacactaagtaagtgtttgcttcttttatt-ttgtagATGCTGATATGGAGGACTATGGATTTGAGTACTCAGATGAGGAGCAAGAGGAGCAAGATGTTGATATTGAGAATCAATATTACAATTCAAAAG
  |||| ||         ||| || |   |   ||  ||  |  || |   | | |   ||  |||   || |     |  ||        | |  ||| |||||| |||||||| || ||||| |||||||| || ||||||||||  || |||||||||||||| || |||||||| || |||||| | ||||
-gctag-tacgtgacaaggatatacttgaatctgtgcgtgacggttattgtactaggtattgtaagtagctcatggttttcttttgatggatgtcattgcagATGCGGATATGGAAGATTATGGCTTTGAGTATTCTGATGAGGAGCCTGAAGAGCAAGATGTTGACATCGAGAATCAGTACTACAATACTAAAG

upper sequence: GLYMA19G30100.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S90_192V6.1 (Physcomitrella patens), 3'ss of exon 1
ttctagctattcttttttgatgtattcataatagttggtttcatttttaccaattgacttacaagacactaagtaagtgtttgcttct--tttattttgt---agATGCTGATATGGAGGACTATGGATTTGAGTACTCAGATGAGGAGCAAGAGGAGCAAGATGTTGATATTGAGAATCAATATTACAATTCAAAAG
|  ||  || |    | ||   | || |  ||          || | |    | ||| |    |  || ||  |||  |||  ||| |   | |  |  |   |||||| || ||||| || ||||| |||||||| || || |||||||  || ||||||||||| |||||||||||||| ||||| ||| | ||||
tatta--tacttgagtctggc-tctttacgatgaggaacgatatatatgtagagtgaatgt--atgcattagttaaccgttatcttttggctgacctgatcacagATGCAGACATGGAAGATTATGGGTTTGAGTATTCTGACGAGGAGCCTGAAGAGCAAGATGTCGATATTGAGAATCAGTATTATAATACCAAAG

upper sequence: GLYMA19G30100.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S124_47V6.1 (Physcomitrella patens), 3'ss of exon 1
--------ttctagctattcttt-tttgatgtattcataatagttggtttcatttttaccaattgacttacaagacactaagtaagtgtttgcttcttttattttgtagATGCTGATATGGAGGACTATGGATTTGAGTACTCAGATGAGGAGCAAGAGGAGCAAGATGTTGATATTGAGAATCAATATTACAATTCAAAAG
            ||  || ||          |  | ||||| ||    |  || |||      | | |||   ||             ||||||     |  |    |||||| || ||||| || ||||| || ||||| || || ||||| |  ||||||||||||||||||||||||||||||||||| ||| | ||||
tcccgaaggcaaagacatactccacccagcttcattataatggtgaactatatatttgtttccttatttaatcgatgtct--------tttgctggacctgatc-acagATGCCGACATGGAAGATTATGGGTTCGAGTATTCGGACGAGGAACCCGAGGAGCAAGATGTTGATATTGAGAATCAATATTATAATACCAAAG

upper sequence: GLYMA19G30100.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ29478 (Selaginella moellendorffii), 3'ss of exon 1
ttctagctattcttttt-tgatgtattcataatagt-tggtttcatttttac-caattgac-ttaca-agacactaagtaagtgtttgcttcttttat--tttgtagATGCTGATATGGAGGACTATGGATTTGAGTACTCAGATGAGGAGCAAGAGGAGCAAGATGTTGATATTGAGAATCAATATTACAATTCAAAAG
    |||| |  |  |   |  |   |||  |  |   | |||| |  |  | |  ||| | || ||  ||  || ||||| | ||   |  |||  |  | | |||| || || ||||| || ||||| ||||||||||| || || || |  |||||||||||||| ||||| |||||||| || ||||| || ||||
-gtaagctctcttcgtagcgcagcgctcactagggcgcgatttcttgctcccgcgcttggcattgcatggatcctcagtaattcttgcttggtttcgtggtgtatagACGCGGACATGGAAGATTATGGCTTTGAGTACTCGGAAGAAGACCCCGAGGAGCAAGATGTCGATATCGAGAATCAGTACTACAACTCTAAAG

upper sequence: GLYMA19G30100.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ28052 (Selaginella moellendorffii), 3'ss of exon 1
ttctagctattcttttt-tgatgtattcataatagt-tggtttcatttttac-caattgac-ttaca-agacactaagtaagtgtttgcttcttttat--tttgtagATGCTGATATGGAGGACTATGGATTTGAGTACTCAGATGAGGAGCAAGAGGAGCAAGATGTTGATATTGAGAATCAATATTACAATTCAAAAG
    |||| |  |  |   |  |   ||   |  |   | |||| |  |  | |  ||| | || ||  ||  || ||||| | ||   |  |||  |  | | |||| || || ||||| || ||||| ||||||||||| || || || |  |||||||||||||| ||||| |||||||| || ||||| || ||||
-gtaagctctcttcgtagcgcagcgctcgctagggcgcgatttcttgctcccgcgcttggcattgcatggatcctcagtaattcttgcttggtttcgtggtgtatagACGCGGACATGGAAGATTATGGCTTTGAGTACTCGGAAGAAGACCCCGAGGAGCAAGATGTCGATATCGAGAATCAGTACTACAACTCTAAAG

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|298187232|gb|HO034381.1|HO034381
EST:     CCCTAACTCGGATCCTCAAACTCAGTTGATTTCATACAACATGGCTTCGG                         ATGCTGATATGGAGGACTATGGATTTGAGTACTCAGATGAGGAGCAAGAGG
genomic: CCCTAACTCGGATCCTCAAACTCAGTTGATTTCATACAACATGGCTTCGGgtacgtgttc ... tattttgtagATGCTGATATGGAGGACTATGGATTTGAGTACTCAGATGAGGAGCAAGAGG
EST: gi|192319385|gb|FK009927.1|FK009927
EST:     CCCTAACTCGGATCCTCAAACTCAGTTGATTTCATACAACATGGCTTCGG                         ATGCTGATATGGAGGACTATGGATTTGAGTACTCAGATGAGGAGCAAGAGG
genomic: CCCTAACTCGGATCCTCAAACTCAGTTGATTTCATACAACATGGCTTCGGgtacgtgttc ... tattttgtagATGCTGATATGGAGGACTATGGATTTGAGTACTCAGATGAGGAGCAAGAGG
EST: gi|4313624|gb|AI460743.1|AI460743
EST:     CCCTAACTCGGATCCTCAAACTCAGTTGATTTCATACAACATGGCTTCGG                         ATGCTGATATGGAGGACTATGGATTTGAGTACTCAGATGAGGAGCAAGAGG
genomic: CCCTAACTCGGATCCTCAAACTCAGTTGATTTCATACAACATGGCTTCGGgtacgtgttc ... tattttgtagATGCTGATATGGAGGACTATGGATTTGAGTACTCAGATGAGGAGCAAGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaccaattgacttacaagacactaagtaagtgtttgcttcttttattttgtagATGCTGATATGGAGGACTATGGATTTGAGTACTCAGATGAGGAGCAAGAGGAGCAAGATGTTGATATTGAGAATCAATATTACAATTCAAAAG
          gacttac  putative branch site (score: 2)
                                  tttgcttcttttattt  putative PPT
                                       ttcttttattttgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttctagctattcttttttgatgtattcataatagttggtttcatttttaccaattgacttacaagacactaagtaagtgtttgcttcttttattttgtagATGCTGATATGGAGGACTATGGATTTGAGTACTCAGATGAGGAGCAAGAGGAGCAAGATGTTGATATTGAGAATCAATATTACAATTCAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - tgtattc
- - - - - - - - - - - - - - - - -gttggtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caagaca