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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttatgaaggaaattagatgctataaaagcctataaagttgttaaagattactcttttcttgaaaatcaattaatatgttggttgtcttatgttggcagGCTGTTTGCAGTCGTGGATGACATTTTCTGTTTGTTTCAAGGTCATCTTGAGAATGTTGCTAACCTTAAGCAACAATATGGATTGAACAAAACAGCAACT

Basic information

species Glycine max
transcript GLYMA10G38840.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G38840.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv14s0036g00050.t01 (Vitis vinifera), 3'ss of exon 2
ttttatgaaggaaattagatgctataaaagcctataaagttgttaaagattactcttttc---ttgaaaatcaattaatatgttggttgtcttatgttggcagGCTGTTTGCAGTCGTGGATGACATTTTCTGTTTGTTTCAAGGTCATCTTGAGAATGTTGCTAACCTTAAGCAACAATATGGATTGAACAAAACAGCAACT
|||  ||  |    ||   | | |    | |   | |  || |      || | |||  |   | |       |||   || |   || |||| | ||| |||  |||||||||| |||||||| || ||||| ||||||||||| ||| ||||||||||||||   ||||||||||| ||||| || ||||||||| ||| |
tttcttgttgc---tttcttcccaacttaccacttgactttatccctcttttcacttggcatatcggttgctgattgtgatctatcttctctttttttgtcagATTGTTTGCAGTTGTGGATGATATATTCTGCTTGTTTCAAGGACATATTGAGAATGTTGCTCTTCTTAAGCAACAGTATGGGTTAAACAAAACAACAAAT

upper sequence: GLYMA10G38840.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv05s0020g04160.t01 (Vitis vinifera), 3'ss of exon 1
ttttatgaaggaaattagatgctataaaagcctataaagttgttaaagattactcttttc---ttgaaaatcaattaatatgttggttgtcttatgttggcagGCTGTTTGCAGTCGTGGATGACATTTTCTGTTTGTTTCAAGGTCATCTTGAGAATGTTGCTAACCTTAAGCAACAATATGGATTGAACAAAACAGCAACT
|||  ||  |    ||   | | |    | |   | |  || |      || | |||  |   | |       |||   || |   |  |||| | ||| |||  |||||||||| |||||||| || ||||| ||||||||||| ||| ||||||||||||||   ||||||||||| ||||| || ||||||||||||| |
tttcttgttgc---tttcttcccaacttaccacttgactttatccctcttttcacttggcatatcggttgctgattgtgatctatctcctctttttttgtcagATTGTTTGCAGTTGTGGATGATATATTCTGCTTGTTTCAAGGACATATTGAGAATGTTGCTCTTCTTAAGCAACAGTATGGGTTAAACAAAACAGCAAAT
















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|10237547|gb|BE806435.1|BE806435
EST:     TCCGGTCTCTTGGCCTATTCTCTTCACAAACAGAACCCCCTCCTCCCAAG                         GCTGTTTGCAGTCGTGGATGACATTTTCTGTTTGTTTCAAGGTCATCTTGA
genomic: TCCGGTCTCTTGGCCTATTCTCTTCACAAACAGAACCCCCTCCTCCCAAGgtccttcact ... atgttggcagGCTGTTTGCAGTCGTGGATGACATTTTCTGTTTGTTTCAAGGTCATCTTGA
EST: gi|213618026|gb|DB963659.1|DB963659
EST:     TCCGGTCTCTTGGCCTATTCTCTTCACAAACAGAACCCCCTCCTCCCAAG                         GCTGTTTGCAGTCGTGGATGACATTTTCTGTTTGTTTCAAGGTCATCTTGA
genomic: TCCGGTCTCTTGGCCTATTCTCTTCACAAACAGAACCCCCTCCTCCCAAGgtccttcact ... atgttggcagGCTGTTTGCAGTCGTGGATGACATTTTCTGTTTGTTTCAAGGTCATCTTGA
EST: gi|192333018|gb|FK024667.1|FK024667
EST:     TCCGGTCTCTTGGCCTATTCTCTTCACAAACAGAACCCCCTCCTCCCAAG                         GCTGTTTGCAGTCGTGGATGACATTTTCTGTTTGTTTCAAGGTCATCTTGA
genomic: TCCGGTCTCTTGGCCTATTCTCTTCACAAACAGAACCCCCTCCTCCCAAGgtccttcact ... atgttggcagGCTGTTTGCAGTCGTGGATGACATTTTCTGTTTGTTTCAAGGTCATCTTGA
EST: gi|192295822|gb|FG990874.1|FG990874
EST:     TCCGGTCTCATGGCCTATTCTCTTCACAAACAGAACCCCCTCCTCCCAAG                         GCTGTTTGCAGTCGTGGATGACATTTTCTGTTTGTTTCAAGGTCATCTTGA
genomic: TCCGGTCTCTTGGCCTATTCTCTTCACAAACAGAACCCCCTCCTCCCAAGgtccttcact ... atgttggcagGCTGTTTGCAGTCGTGGATGACATTTTCTGTTTGTTTCAAGGTCATCTTGA
EST: gi|7283825|gb|AW596427.1|AW596427
EST:     TCCGGTCTCTTGGCCTATTCTCTTCACAAACAGAACCCCCTCCTCCCAAG                         GCTGTTTGCAGTCGTGGATGACATTTTCTGTTTGTTTCAAGGTCATCTTGA
genomic: TCCGGTCTCTTGGCCTATTCTCTTCACAAACAGAACCCCCTCCTCCCAAGgtccttcact ... atgttggcagGCTGTTTGCAGTCGTGGATGACATTTTCTGTTTGTTTCAAGGTCATCTTGA
EST: gi|4293386|gb|AI442040.1|AI442040
EST:     TCCGGTCTCTTGGCCTATTCTCTTCACAAACAGAACCCCCTCCTCCCAAG                         GCTGTTTGCAGTCGTGGATGACATTTTCTGTTTGTTTCAAGGTCATCTTGA
genomic: TCCGGTCTCTTGGCCTATTCTCTTCACAAACAGAACCCCCTCCTCCCAAGgtccttcact ... atgttggcagGCTGTTTGCAGTCGTGGATGACATTTTCTGTTTGTTTCAAGGTCATCTTGA
EST: gi|15814188|gb|BI786463.1|BI786463
EST:     TCCGGTCTCTTGGCCTATTCTCTTCACAAACAGAACCCCCTCCTCCCAAG                         GCTGTTTGCAGTCGTGGATGACATTTTCTGTTTGTTTCAAGGTCATCTTGA
genomic: TCCGGTCTCTTGGCCTATTCTCTTCACAAACAGAACCCCCTCCTCCCAAGgtccttcact ... atgttggcagGCTGTTTGCAGTCGTGGATGACATTTTCTGTTTGTTTCAAGGTCATCTTGA
EST: gi|7283802|gb|AW596404.1|AW596404
EST:     TCCGGTCTCTTGGCCTATTCTCTTCACAAACAGAACCCCCTCCTCCCAAG                         GCTGTTTGCAGTCGTGGATGACATTTTCTGTTTGTTTCAAGGTCATCTTGA
genomic: TCCGGTCTCTTGGCCTATTCTCTTCACAAACAGAACCCCCTCCTCCCAAGgtccttcact ... atgttggcagGCTGTTTGCAGTCGTGGATGACATTTTCTGTTTGTTTCAAGGTCATCTTGA
EST: gi|254326313|gb|GR840905.1|GR840905
EST:     TCCGGTCTCTTGGCCTATTCTCTTCACAAACAGAACCCCCTCCTCCCAAG                         GCTGTTTGCAGTCGTGGATGACATTTTCTGTTTGTTTCAAGGTCATCTTGA
genomic: TCCGGTCTCTTGGCCTATTCTCTTCACAAACAGAACCCCCTCCTCCCAAGgtccttcact ... atgttggcagGCTGTTTGCAGTCGTGGATGACATTTTCTGTTTGTTTCAAGGTCATCTTGA
EST: gi|5606908|gb|AI901006.1|AI901006
EST:     TCCGGTCTCTTGGCCTATTCTCTTCACAAACAGAACCCCCTCCTCCCAAG                         GCTGTTTGCAGTCGTGGATGACATTTTCTGTTTGTTTCAAGGTCATCTTGA
genomic: TCCGGTCTCTTGGCCTATTCTCTTCACAAACAGAACCCCCTCCTCCCAAGgtccttcact ... atgttggcagGCTGTTTGCAGTCGTGGATGACATTTTCTGTTTGTTTCAAGGTCATCTTGA
EST: gi|254320536|gb|GR826985.1|GR826985
EST:     TCCGGTCTCTTGGCCTATTCTCTTCACAAACAGAACCCCCTCCTCCCAAG                         GCTGTTTGCAGTCGTGGATGACATTTTCTGTTTGTTTCAAGGTCATCTTGA
genomic: TCCGGTCTCTTGGCCTATTCTCTTCACAAACAGAACCCCCTCCTCCCAAGgtccttcact ... atgttggcagGCTGTTTGCAGTCGTGGATGACATTTTCTGTTTGTTTCAAGGTCATCTTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagattactcttttcttgaaaatcaattaatatgttggttgtcttatgttggcagGCTGTTTGCAGTCGTGGATGACATTTTCTGTTTGTTTCAAGGTCATCTTGAGAATGTTGCTAACCTTAAGCAACAATATGGATTGAACAAAACAGCAACT
                        aattaat  putative branch site (score: 3)
          ttttcttgaaaatcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttatgaaggaaattagatgctataaaagcctataaagttgttaaagattactcttttcttgaaaatcaattaatatgttggttgtcttatgttggcagGCTGTTTGCAGTCGTGGATGACATTTTCTGTTTGTTTCAAGGTCATCTTGAGAATGTTGCTAACCTTAAGCAACAATATGGATTGAACAAAACAGCAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- -tatgaag
- - - - - - - - -gatgcta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaaatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gttggtt