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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccatagtctgtaaatattatttatggaagtagattgctaagcattacactttctaattgttgtgtggcaatctctatccagATATCCTTCTCCTGGATGTGGCTCCCCTCACTCTCGGAATTGAAACTGTTGGTGGAGTCATGACAAAGTTGATTCCCAGAAACACTGTTATCCCGACCAA

Basic information

species Glycine max
transcript GLYMA08G02940.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G02940.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g02410.1 (Oryza sativa), 3'ss of exon 5
---gtaccatagtc-tgtaaatattatttatggaagtagattgctaag--cattacactt---tctaattgttgtgtggcaatctc--tatccagATATCCTTCTCCTGGATGTGGCTCCCCTCACTCTCGGAATTGAAACTGTTGGTGGAGTCATGACAAAGTTGATTCCCAGAAACACTGTTATCCCGACCAA
     ||| |  ||   || ||| |  ||  ||  |   |   ||  |  |||    |||   | || || | |||     || |   ||  ||||||||||||||||||||||||| ||||| || ||||| || || ||||| |||||||||||||| |||||||| ||||| ||||| || ||||| |||||
gttcgaccttgatcacatacatagtcctttgggttggtaacaactgcgatcatctgtcttgcatatacttatcgtgctttgattttggtacgcagATATCCTTCTCCTGGATGTGGCACCCCTTACCCTCGGTATCGAGACTGTCGGTGGAGTCATGACCAAGTTGATCCCCAGGAACACCGTCATCCCCACCAA

upper sequence: GLYMA08G02940.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G415007_T01 (Zea mays), 3'ss of exon 5
gtaccatagtctgta---aatattatttatggaagtagattgc-----taagca-ttacactttcta-attgttgtgtggcaatctctatccagATATCCTTCTCCTGGATGTGGCTCCCCTCACTCTCGGAATTGAAACTGTTGGTGGAGTCATGACAAAGTTGATTCCCAGAAACACTGTTATCCCGACCAA
|| |  |  ||| |    | |  |||   |||  ||   ||       ||||   | |  ||   || ||   ||||       ||  || |||||||||| ||||| ||||||||||| ||||| || || ||||| || || |||||||||||||| |||||||| || || |||||||| |||||||||||
gttcggtgctctttcactagtgctatagctgggtgtttttttttcttgtaagtggtcatcctgcttacataagtgtgattttgccttgatgcagATATCCTCCTCCTTGATGTGGCTCCTCTCACCCTGGGTATTGAGACCGTCGGTGGAGTCATGACCAAGTTGATCCCGAGGAACACTGTCATCCCGACCAA

upper sequence: GLYMA08G02940.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G114793_T01 (Zea mays), 3'ss of exon 5
----------------gtaccatagtctgtaaatattatttatggaagtagattgctaagcattacactttc-taattgttgtgtggcaatctctatccagATATCCTTCTCCTGGATGTGGCTCCCCTCACTCTCGGAATTGAAACTGTTGGTGGAGTCATGACAAAGTTGATTCCCAGAAACACTGTTATCCCGACCAA
                 |    |  | ||  | |  ||  | |     | | |   | | ||||   ||| | ||| |||  | |      ||  || |||||||||| ||||| ||||||||||||||||| || || || || || || |||||||||||||| |||||||| || || |||||||| |||||||||||
gttcggctcatgttttttgtgctcttttgccactggtaggtgttttttttggtaagtgatcattctgcttacataagtgtgattt--ttgccttgatgcagATATCCTCCTCCTTGATGTGGCTCCCCTCACCCTGGGTATCGAGACCGTCGGTGGAGTCATGACCAAGTTGATCCCGAGGAACACTGTCATCCCGACCAA

upper sequence: GLYMA08G02940.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv16s0098g01580.t01 (Vitis vinifera), 3'ss of exon 5
gtaccatagtctgtaaatattatttatggaag----tagattgctaagcattacactttctaattgttgtgtggcaatctc-tat-ccagATATCCTTCTCCTGGATGTGGCTCCCCTCACTCTCGGAATTGAAACTGTTGGTGGAGTCATGACAAAGTTGATTCCCAGAAACACTGTTATCCCGACCAA
|||  ||  ||  |    |  || |  | |      |  || ||   |    |   || |||| | ||||   |   | || | |  |||||||||||||| ||||||||||||| |||||||| || |||||||| ||||| || || ||||| || ||||||||||||||||| |||||||| |||||
gtattatt-tccatcctcaccatcttcgcagaaccttcaatggcatggttgaaagtttgctaactcttgttctgttgtttcatgtatcagATATCCTTCTCTTGGATGTGGCTCCACTCACTCTTGGTATTGAAACGGTTGGCGGGGTGATGACCAAATTGATTCCCAGAAACACCGTTATCCCAACCAA

upper sequence: GLYMA08G02940.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv02s0025g02140.t01 (Vitis vinifera), 3'ss of exon 5
------gtaccatagtctgtaaatatt--atttatggaagtagattgctaagcattacactttctaattgttgtgtggcaatc--tctatccagATATCCTTCTCCTGGATGTGGCTCCCCTCACTCTCGGAATTGAAACTGTTGGTGGAGTCATGACAAAGTTGATTCCCAGAAACACTGTTATCCCGACCAA
       | ||||  ||| | |||     ||  ||||  ||  || |        |  |   |  |  | |  | ||  | |   || || ||||||| |||||| ||||||||||||| |||||||| ||||||||||| |||||||| || ||||| ||||||||||| || ||||||||||||||||||||
gtatcatttccattctctatcaatgaccgatagatggttgtgcatcgagtgttgatgaatggtagacatttgatatgatatttgttccatgcagATATTCTTCTCTTGGATGTGGCTCCGCTCACTCTTGGAATTGAAACCGTTGGTGGGGTGATGACCAAGTTGATTCCTAGGAACACTGTTATCCCGACCAA

upper sequence: GLYMA08G02940.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ29073 (Selaginella moellendorffii), 3'ss of exon 5
gtaccatagtctgtaaatattatttatggaagtagattgctaagcattacactttctaattgttgtgtggcaatc----tctatc--cagATATCCTTCTCCTGGATGTGGCTCCCCTCACTCTCGGAATTGAAACTGTTGGTGGAGTCATGACAAAGTTGATTCCCAGAAACACTGTTATCCCGACCAA
                               |||       |    |     ||| ||||   | ||||  ||      || |||  |||  || |||||| |||| || || ||||| ||||| || || || || ||||||||||| ||||| ||| |||| ||||| |||||||| || ||||||||
-------------------------------gtaagcaaagacttgtcttcttttgtaatccatctgtgctaacgcgcgtccatcgacagGCATTCTTCTCTTGGACGTTGCGCCCCTTACTCTGGGTATCGAGACCGTTGGTGGAGTGATGACCAAGCTGATCCCCAGGAACACTGTCATTCCGACCAA

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|17518873|gb|BM187915.1|BM187915
EST:     TGCAGTGCAAGGAAGCATTTTGAGTGGAGAGGGTGGTGAAGAAACCAAAG                         ATATCCTTCTCCTGGATGTGGCTCCCCTCACTCTCGGAATTGAAACTGTTG
genomic: TGCAGTGCAAGGAAGCATTTTGAGTGGAGAGGGTGGTGAAGAAACCAAAGgtaccatagt ... ctctatccagATATCCTTCTCCTGGATGTGGCTCCCCTCACTCTCGGAATTGAAACTGTTG
EST: gi|18730292|gb|BM525797.1|BM525797
EST:     TGCAGTGCAAGGAAGCATTTTGAGTGGAGAGGGTGGTGAAGAAACCAAAG                         ATATCCTTCTCCTGGATGTGGCTCCCCTCACTCTCGGAATTGAAACTGTTG
genomic: TGCAGTGCAAGGAAGCATTTTGAGTGGAGAGGGTGGTGAAGAAACCAAAGgtaccatagt ... ctctatccagATATCCTTCTCCTGGATGTGGCTCCCCTCACTCTCGGAATTGAAACTGTTG
EST: gi|7924822|gb|AW830848.1|AW830848
EST:     GCAGTGCAAGGAAGCATTTTGAGTGGAGAGNGGTGGTGAAGAAACCAAAG                         ATATCCTTCTC-TGGGATGTGGCTCCCCTCACTCTCGGAAT
genomic: GCAGTGCAAGGAAGCATTTTGAGTGGAGAG-GGTGGTGAAGAAACCAAAGgtaccatagt ... ctctatccagATATCCTTCTCCTGG-ATGTGGCTCCCCTCACTCTCGGAAT
EST: gi|254328819|gb|GR833191.1|GR833191
EST:     GAAGAAACCAAAG                         ATATCCTTCTCCTGGATGTGGCTCCCCTCACTCTCGGAATTGAAACTGTTG
genomic: GAAGAAACCAAAGgtaccatagt ... ctctatccagATATCCTTCTCCTGGATGTGGCTCCCCTCACTCTCGGAATTGAAACTGTTG
EST: gi|15285743|gb|BI469634.1|BI469634
EST:     TGCAGTGCAAGGAAGCATTTTGAGTGGAGAGGGTGGTGAAGAAACCAAAG                         ATATCCTTCTCCTGGATGTGGCTCCCCTCACTCTCTTTATTGAAACTGTTG
genomic: TGCAGTGCAAGGAAGCATTTTGAGTGGAGAGGGTGGTGAAGAAACCAAAGgtaccatagt ... ctctatccagATATCCTTCTCCTGGATGTGGCTCCCCTCACTCTCGGAATTGAAACTGTTG
EST: gi|18734607|gb|BM528280.1|BM528280
EST:     TGCAGTGCAAGGAAGCATTTTGAGTGGAGAGGGTGGTGAAGAAACCAAAG                         ATATCCTTCTCCTGGATGTGGCTCCCCTCACTCTCGGAATTGAAACTGTTG
genomic: TGCAGTGCAAGGAAGCATTTTGAGTGGAGAGGGTGGTGAAGAAACCAAAGgtaccatagt ... ctctatccagATATCCTTCTCCTGGATGTGGCTCCCCTCACTCTCGGAATTGAAACTGTTG
EST: gi|9258803|gb|BE346950.1|BE346950
EST:     TGCAGTGCAAGGAAGCATTTTGAGTGGAGAGGGTGGTGAAGAAACCAAAG                         ATATCCTTCTCCTGGATGTGGCTCCCCTCACTCTCGGAATTGAAACTGTTG
genomic: TGCAGTGCAAGGAAGCATTTTGAGTGGAGAGGGTGGTGAAGAAACCAAAGgtaccatagt ... ctctatccagATATCCTTCTCCTGGATGTGGCTCCCCTCACTCTCGGAATTGAAACTGTTG
EST: gi|192328286|gb|FK022920.1|FK022920
EST:     TGCAGTGCAAGGAAGCATTTTGAGTGGAGAGGGTGGTGAAGAAACCAAAG                         ATATCCTTCTCCTGGATGTGGCTCCCCTCACTCTCGGAATTGAAACTGTTG
genomic: TGCAGTGCAAGGAAGCATTTTGAGTGGAGAGGGTGGTGAAGAAACCAAAGgtaccatagt ... ctctatccagATATCCTTCTCCTGGATGTGGCTCCCCTCACTCTCGGAATTGAAACTGTTG
EST: gi|13180745|gb|BG352085.1|BG352085
EST:     GGAGAGGGTGGTGAAGAAACCAAAG                         ATATCCTTCTCCTGGATGTGGCTCCCCTCACTCTCGGAATTGAAACTGTTG
genomic: GGAGAGGGTGGTGAAGAAACCAAAGgtaccatagt ... ctctatccagATATCCTTCTCCTGGATGTGGCTCCCCTCACTCTCGGAATTGAAACTGTTG
EST: gi|193337800|gb|FK302111.1|FK302111
EST:     TGAAGAAACCAAAG                         ATTATCCTTCTCCTGGATGTGGCTCCCCTCACTCTCGGAATTGAAACTGTT
genomic: TGAAGAAACCAAAGgtaccatagt ... ctctatccagA-TATCCTTCTCCTGGATGTGGCTCCCCTCACTCTCGGAATTGAAACTGTT
EST: gi|298166661|gb|HO010100.1|HO010100
EST:     TGCAGTGCAAGGAAGCGTTTTGAGTGGAGAGGGTGGTGAAGAAACCAAAG                         ATATCCTTCTCCTGGATGTGGCCCCCCTCACTCTCGGA
genomic: TGCAGTGCAAGGAAGCATTTTGAGTGGAGAGGGTGGTGAAGAAACCAAAGgtaccatagt ... ctctatccagATATCCTTCTCCTGGATGTGGCTCCCCTCACTCTCGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagtagattgctaagcattacactttctaattgttgtgtggcaatctctatccagATATCCTTCTCCTGGATGTGGCTCCCCTCACTCTCGGAATTGAAACTGTTGGTGGAGTCATGACAAAGTTGATTCCCAGAAACACTGTTATCCCGACCAA
                        ttctaat  putative branch site (score: 2)
                                            tctctatcc  putative PPT
                       tttctaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaccatagtctgtaaatattatttatggaagtagattgctaagcattacactttctaattgttgtgtggcaatctctatccagATATCCTTCTCCTGGATGTGGCTCCCCTCACTCTCGGAATTGAAACTGTTGGTGGAGTCATGACAAAGTTGATTCCCAGAAACACTGTTATCCCGACCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG