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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catttatttatctctttttctccgactataaaaagtaactaagtattttgcaaacaattagattgacaatggaactattgaccccttctggatcctgtagGTATCTGCTGCCCGAGAAGAAGTACCTGGTAGACGTGGGTACCCCGGTTACATGTATACAGATCTTGCAACAATATACGAACGTGCTGGAAGAATTGAGG

Basic information

species Glycine max
transcript GLYMA09G38110.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 3'ss of exon 9
catttatttatctctttttctccgactataaaaagtaactaagtatt----ttgcaaacaattagattgacaatggaactattgaccccttctggat-cctgtagGTATCTGCTGCCCGAGAAGAAGTACCTGGTAGACGTGGGTACCCCGGTTACATGTATACAGATCTTGCAACAATATACGAACGTGCTGGAAGAATTGAGG
     |  | ||  ||| | | |||||  || || | |  || |  |    ||  |   | |  ||||| || |   || |        || ||  |   |||||||||| || |||||||||||||| || ||||| |||||||| || || || |||||||| ||||| ||||| ||||| || || |||||  | ||||| |
-----acatctccttttatgttcgactgcaataaatgataaattgctgaaattttatttattgtgattggcactaatacaacacggtaattgtgcttatatgtagGTATCAGCAGCCCGAGAAGAAGTGCCAGGTAGGCGTGGGTATCCTGGATATATGTATACTGATCTGGCAACCATATATGAGCGAGCTGGGCGTATTGAAG

upper sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G181151_T02 (Zea mays), 3'ss of exon 9
--catttat--ttatctctttttctccgactataaaa-agtaactaagtattttgcaaacaattagattgacaatggaactattgaccccttctggatcctgtagGTATCTGCTGCCCGAGAAGAAGTACCTGGTAGACGTGGGTACCCCGGTTACATGTATACAGATCTTGCAACAATATACGAACGTGCTGGAAGAATTGAGG
   |||||   | | |  || |  |  |   || |||  |||| |   | |  ||       | |  ||   |||    |||      | || ||  |  ||||||| ||||| ||||||||||| || || ||||| ||||| || || || || |||||||| ||||| ||||||||||| || ||||||||  | ||||| |
agtatttaagatcaacctttgtatttaggtaatcaaatggtaaattgatttcatgtt-----tgatgtttctaataatgctacatgggcattgtgctttttgtagGTTTCTGCAGCCCGAGAAGAGGTGCCAGGTAGGCGTGGTTATCCTGGATATATGTATACTGATCTGGCAACAATATATGAGCGTGCTGGGCGTATTGAAG

upper sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G094497_T01 (Zea mays), 3'ss of exon 9
catttatttatctctttttctccgactataaaaagtaactaagtattttgcaaacaattagattgacaatggaactat-tgaccccttctggatcctgtagGTATCTGCTGCCCGAGAAGAAGTACCTGGTAGACGTGGGTACCCCGGTTACATGTATACAGATCTTGCAACAATATACGAACGTGCTGGAAGAATTGAGG
  ||||| ||| |    ||  ||   | ||  |  ||| ||| |         |        ||   |||    |||  ||  |  |      |  ||||||| ||||| ||||||||||| || || ||||| ||||| || || || || |||||||| ||| | ||||||||||| || ||||||||  | ||||| |
-ttttatatatttaagattaaccttttctattagctaattaaatgacaaattgatgtcgttgtttctaataatgctacatgggcattgtgcttttttgtagGTTTCTGCAGCCCGAGAAGAGGTGCCAGGTAGGCGTGGTTATCCTGGATATATGTATACTGATTTGGCAACAATATATGAGCGTGCTGGGCGTATTGAAG

upper sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 9
lower sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 10
catttatttatctctttttctccga-ctataaaaagtaactaagtattttgcaaacaattagattgacaatggaactattgaccccttctggatcctgtagGTATCTGCTGCCCGAGAAGAAGTACCTGGTAGACGTGGGTACCCCGGTTACATGTATACAGATCTTGCAACAATATACGAACGTGCTGGAAGAATTGAGG
    |  | | |  | |||    |  || |  | | |   | |   ||  |   | |   ||  ||| ||| |   |  | ||     ||    ||  ||||| ||||||||||| |||||||| ||||| || ||||| ||||| ||||||||||| || ||  | || || ||||||||  | || ||  ||||||| |
---gtgataaccgatatttgcatgctctgttcacaattcttgaactttgagatgataggaagcctga-aatagtgtt--taacgttgactaatacccttagGTCTCTGCTGCCCGTGAAGAAGTGCCTGGAAGGCGTGGTTACCCAGGTTACATGTACACCGACTTGGCTACCATATACGAGAGAGCAGGGCGAATTGAAG

upper sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 9
lower sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 9
catttatttatctctttttctccgactataaaaagtaactaagt--attttgcaaacaattagattgacaatggaactattgaccccttctggatcctgtagGTATCTGCTGCCCGAGAAGAAGTACCTGGTAGACGTGGGTACCCCGGTTACATGTATACAGATCTTGCAACAATATACGAACGTGCTGGAAGAATTGAGG
| | || || | |  ||   |     || |  ||||| |  | |  ||| | |||||   |  | |||   | |   |    ||  ||| | |   ||| ||||||||||||||||||||||||| || || || |||||||| || || || |||||||| ||||| || || || || |||||||||||| | ||||| |
cttctaattttgttcttgagtattttta-atcaagtaccccattgaattcttcaaactcatc-actgatgcttgtgatgcaaactacttattgcaactgcagGTATCTGCTGCCCGAGAAGAAGTTCCCGGGAGGCGTGGGTATCCTGGGTATATGTATACTGATCTGGCGACGATTTATGAACGTGCTGGACGTATTGAAG

upper sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 9
lower sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 9
catttatttatctctttttctccgactataaaaagtaactaagt----attttgcaaacaattagattgacaatggaactattgaccccttctggatcctg--tagGTATCTGCTGCCCGAGAAGAAGTACCTGGTAGACGTGGGTACCCCGGTTACATGTATACAGATCTTGCAACAATATACGAACGTGCTGGAAGAATTGAGG
       |   |||  || ||  |   || ||   |    ||      || | |        |  | |||| ||  |  | ||| |   |||     | |    |||| |||||||| || ||||||||||| ||| | ||||||||||| ||||| ||||| || |||||||| || || || |||||||||||| | |||||||
-----gctgcactcggttacttagttaatcaagtattttgaaacctcgatatcgagggtctatgtaatgacgatata-tttttgtcgttttcaattacttaaacagGTGTCTGCTGCTCGTGAAGAAGTACCCGGTCGTCGTGGGTACCCTGGTTATATGTACACCGATCTTGCCACCATTTATGAACGTGCTGGACGTATTGAGG

upper sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 9
lower sequence: PP1S85_75V6.1 (Physcomitrella patens), 3'ss of exon 8
----------------------------------------------------catttatttatctctttt----tctccg-actataaaaagtaactaagtattttgcaaacaattagattg---------------acaatggaa----ctattgaccccttctggatcctgtagGTATCTGCTGCCCGAGAAGAAGTACCTGGTAGACGTGGGTACCCCGGTTACATGTATACAGATCTTGCAACAATATACGAACGTGCTGGAAGAATTGAGG
                                                      | | ||| |   ||||    | |  |   | |||||| |  |    |||||||       | ||  ||               | ||||  |    ||  ||| || |       |    |||| ||||| || || ||||||||||||||  | ||||| || || ||||||||||| || |||||||| || || ||||||||||||||  |||||||||
gtaccagtctttaccttaaagatctgcttgcccttgtggtatggtacttctgactctgtttttggtttttgaaatgttagtgttctaaaaaatgcccctctattttgttggttctaagtctgcacctttagtatgccagaatgacatattcttatgatccttaactatgcgaacagGTTTCTGCAGCTCGTGAAGAAGTACCTGGGCGTCGTGGATATCCTGGTTACATGTACACGGATCTTGCCACTATTTACGAACGTGCTGGGCGAATTGAGG

upper sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 9
lower sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 8
---------------------------------------------------------------------------------------catttatttatctctttttctccgactataaaaagtaactaagtattttgcaaacaattagattgacaatggaacta--ttgaccccttctggatcct----gtagGTATCTGCTGCCCGAGAAGAAGTACCTGGTAGACGTGGGTACCCCGGTTACATGTATACAGATCTTGCAACAATATACGAACGTGCTGGAAGAATTGAGG
                                                                                         | | |  |    |||||   | | | |  ||  ||   |  |  |||  ||  ||  |  || |   ||  || |  ||   ||  |||  || ||     ||||| |||||||| || |||||||| |||||  | ||||| || || |||||||||||||| ||||| || || || || |||||||||||| |||| || |
gtacaagtgtttctcttaaagacttttcgcttggactcctttttcagaagttagctcctgtgaaattctacatgctactccgcagttggtatctgaaatagtttttaagcaaatttgtaatctattcagttggtttttaattaag-accttcagtgtgctacaaattttttccactctcaattcttcaaatagGTTTCTGCTGCTCGTGAAGAAGTGCCTGGGCGTCGTGGATATCCTGGTTACATGTATACTGATCTGGCCACCATTTATGAACGTGCTGGACGAATCGAAG

upper sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 9
lower sequence: EFJ11911 (Selaginella moellendorffii), 3'ss of exon 8
catttatttatctctttttctccgactataaaaagtaactaagtattttgcaaacaattagattgacaatggaactattgaccccttctggatcctgtagGTATCTGCTGCCCGAGAAGAAGTACCTGGTAGACGTGGGTACCCCGGTTACATGTATACAGATCTTGCAACAATATACGAACGTGCTGGAAGAATTGAGG
                                             | | | |       || ||| ||   || |||| ||   |    |  |  ||||||| ||||| || || || || || |||||| | ||||| || || ||||| |||||||||||| | |||||||| ||||| ||||||||| ||||||| |
--------------------------------------------gtatggtatgtttcaagtttgtcatgagagctat-gataaccagggctttgtgtagGTGTCTGCCGCTCGTGAGGAGGTGCCTGGTCGTCGTGGATATCCTGGTTATATGTATACAGATTTGGCAACAATTTACGAGCGTGCTGGACGAATTGAAG

upper sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 9
lower sequence: EFJ13375 (Selaginella moellendorffii), 3'ss of exon 8
catttatttatctctttttctccgactataaaaagtaactaagtattttgcaaacaattagattgacaatggaactattgaccccttctggatcctgtagGTATCTGCTGCCCGAGAAGAAGTACCTGGTAGACGTGGGTACCCCGGTTACATGTATACAGATCTTGCAACAATATACGAACGTGCTGGAAGAATTGAGG
                                          ||||  |   |    | |  ||    |||  | |  |||   |    |  |  ||||||| ||||| || || || || || |||||| | ||||| || || ||||| |||||||||||| | |||||||| ||||| ||||||||| ||||||| |
------------------------------------------gtatgatcgtatgtttcaagtttttcatgagagttatgataaccatggctttgtgtagGTGTCTGCCGCTCGTGAGGAGGTGCCTGGTCGTCGTGGATATCCTGGTTATATGTATACAGATTTGGCAACAATTTACGAGCGTGCTGGACGAATTGAAG

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|18734533|gb|BM528238.1|BM528238
EST:     TTCTTGTGATACTCACAGATATGAGTTCTTATGCTGATGCTCTTCGTGAG                         GTATCTGCTGCCCGAGAAGAAGTACCTGGTAGACGTGGGTACCCCGGTTAC
genomic: TTCTTGTGATACTCACAGATATGAGTTCTTATGCTGATGCTCTTCGTGAGgtaatgcacc ... gatcctgtagGTATCTGCTGCCCGAGAAGAAGTACCTGGTAGACGTGGGTACCCCGGTTAC
EST: gi|27426098|gb|CA937618.1|CA937618
EST:     CTTGTGATACTCACAGATATGAGTTCTTATGCTGATGCTCTTCGTGAG                         GTATCTGCTGCCCGAGAAGAAGTACCTGGTAGACGTGGGTACCCCGGTTAC
genomic: CTTGTGATACTCACAGATATGAGTTCTTATGCTGATGCTCTTCGTGAGgtaatgcacc ... gatcctgtagGTATCTGCTGCCCGAGAAGAAGTACCTGGTAGACGTGGGTACCCCGGTTAC
EST: gi|16279376|gb|BI943404.1|BI943404
EST:     TTCTTGTGATACTCACAGATATGAGTTCTTATGCTGATGCTCTTCGTGAG                         GTATCTGCTGCCCGAGAAGAAGTACCTGGTAGACGTGGGTACCCCGGTTAC
genomic: TTCTTGTGATACTCACAGATATGAGTTCTTATGCTGATGCTCTTCGTGAGgtaatgcacc ... gatcctgtagGTATCTGCTGCCCGAGAAGAAGTACCTGGTAGACGTGGGTACCCCGGTTAC
EST: gi|16283538|gb|BI945603.1|BI945603
EST:     TTCTTGTGATACTCACAGATATGAGTTCTTATGCTGATGCTCTTCGTGAG                         GTATCTGCTGACCGAGAAGAAGTACCTGTTAGACGTGGGTACCCCGGTTAC
genomic: TTCTTGTGATACTCACAGATATGAGTTCTTATGCTGATGCTCTTCGTGAGgtaatgcacc ... gatcctgtagGTATCTGCTGCCCGAGAAGAAGTACCTGGTAGACGTGGGTACCCCGGTTAC
EST: gi|16277730|gb|BI942533.1|BI942533
EST:     TTCTTGTGATACTCACAGATATGAGTTCTTATGCTGATGCTCTTCGTGAG                         GTATCTGCTGCCCGAGAAGAAGTACCTGGTAGACGTGGGTACCCCGGTTAC
genomic: TTCTTGTGATACTCACAGATATGAGTTCTTATGCTGATGCTCTTCGTGAGgtaatgcacc ... gatcctgtagGTATCTGCTGCCCGAGAAGAAGTACCTGGTAGACGTGGGTACCCCGGTTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgcaaacaattagattgacaatggaactattgaccccttctggatcctgtagGTATCTGCTGCCCGAGAAGAAGTACCTGGTAGACGTGGGTACCCCGGTTACATGTATACAGATCTTGCAACAATATACGAACGTGCTGGAAGAATTGAGG
                              tattgac  putative branch site (score: 2)
      aaacaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catttatttatctctttttctccgactataaaaagtaactaagtattttgcaaacaattagattgacaatggaactattgaccccttctggatcctgtagGTATCTGCTGCCCGAGAAGAAGTACCTGGTAGACGTGGGTACCCCGGTTACATGTATACAGATCTTGCAACAATATACGAACGTGCTGGAAGAATTGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA