Sequence
atgc intronic sequence ATGC exonic sequencegtgattatttggggttggagttgtttttccttcttgtgtatacagtttattctttctaactaagtatttttgtacagTTGTTGCTTAAAGGAGTTAGCGAGCGAGGTGTTAAAAGAGTCCGTGTCCATATTCTTACAGATGGCCGTGATGTTTTGGATGGTTCAAGTGTGGGGTTTG
Basic information
species | Glycine max |
transcript | GLYMA09G40690.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G40690.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os05g40420.1 (Oryza sativa), 3'ss of exon 4
--------------------------------------gtg-attatttggggttggagttgtttttc--cttcttg-tgtatacagt---ttattctttctaacta--agtatttttgt--acagTTGTTGCTTAAAGGAGTTAGCGAGCGAGGTGTTAAAAGAGTCCGTGTCCATATTCTTACAGATGGCCGTGATGTTTTGGATGGTTCAAGTGTGGGGTTTG
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gtataaaagtactcttttctatagtttgctatcatcttgtatagtatgaggcactaatgtttctttacaacatgttgatctgtccagtatctaattctttttgtcttttgtcattcctgtttatagTTGCTCCTGAATGGTGCAAGTGCGAATGGAGCGAAAAAAATCCGTGTTCACATTCTTACTGATGGACGTGATGTTTTGGATGGCACAAGCGTTGGTTTTG
upper sequence: GLYMA09G40690.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G09780.1 (Arabidopsis thaliana), 3'ss of exon 2
-----------gtg-attatttggggttggagttgtttttccttcttgtgtatacagtttattctttctaacta--agtatttttgtacagTTGTTGCTTAAAGGAGTTAGCGAGCGAGGTGTTAAAAGAGTCCGTGTCCATATTCTTACAGATGGCCGTGATGTTTTGGATGGTTCAAGTGTGGGGTTTG
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gttttgatttgatatgttcttcattattttgttcaaattctggtttaatgtttgttgatgattccttaaacttgttgttgcttttgcgcagTTGTTGATTAAAGGATCTGCTGAACGTGGTGCTAAGAGAATCAGAGTCCATATTCTTACTGATGGTCGTGATGTTTTGGATGGTTCTAGTGTTGGATTTG
upper sequence: GLYMA09G40690.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G08590.2 (Arabidopsis thaliana), 3'ss of exon 2
----gtgattatttggggttggagttgtttttccttcttgtgtatacagtttattctttctaactaagtattttt--gtacagTTGTTGCTTAAAGGAGTTAGCGAGCGAGGTGTTAAAAGAGTCCGTGTCCATATTCTTACAGATGGCCGTGATGTTTTGGATGGTTCAAGTGTGGGGTTTG
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gtacttaattctcatctgttacacatttcttttgaaacgttggcgtttgttaattttctttaatttggttctgtttggtgcagTTGCTGCTTAAGGGTTTTGCAGAACGTGGTGCTAAGAGAATCCGCGTCCATATTCTTACTGATGGTCGTGATGTTTTGGATGGTTCTAGTGTCGGATTTG
upper sequence: GLYMA09G40690.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv08s0056g00200.t01 (Vitis vinifera), 3'ss of exon 3
-------------------gtgattat-ttggggttggagttgtttttccttcttgtgtatacagt--ttattctttctaactaagtatttttgtacagTTGTTGCTTAAAGGAGTTAGCGAGCGAGGTGTTAAAAGAGTCCGTGTCCATATTCTTACAGATGGCCGTGATGTTTTGGATGGTTCAAGTGTGGGGTTTG
|||| ||| | ||||| | |||| | | | | || || | | || | | | | ||||| | | ||||||| ||| ||| |||| |||||| ||||||||||||| ||||| ||||| |||||||||||||||||||| ||||| |||||||
gtatgttttgttgttgaattctattaccttgtgattggatatagttttgtatttcccaggggagatcatgatcctctttggct--ttttctcttggcagTTACTTTTAAAAGGAGCTAGTGAGAATGGTGCAAAAAGAATCCGTGTCCATATCCTTACTGATGGGCGTGATGTTTTGGATGGTTCCAGTGTTGGGTTTGMapped 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|193362271|gb|FK324017.1|FK324017EST: TTCACTCCAGACTTGATCAGTTGCAG TTGTTGCTTAAAGGAGTTAGCGAGCGAGGTGTTAAAAGAGTCCGTGTCCAT
genomic: TTCACTCCAGACTTGATCAGTTGCAGgtgattattt ... ttttgtacagTTGTTGCTTAAAGGAGTTAGCGAGCGAGGTGTTAAAAGAGTCCGTGTCCAT
EST:
gi|208131074|gb|GD927181.1|GD927181EST: TTGGGTTACTGAGTGATGGTGGAGTTCACTCCAGACTTGATCAGTTGCAG TTGTTGCTTAAAGGAGTTAGCGAGCGAGGTGTTAAAAGAGTCCGTGTCCAT
genomic: TTGGGTTACTGAGTGATGGTGGAGTTCACTCCAGACTTGATCAGTTGCAGgtgattattt ... ttttgtacagTTGTTGCTTAAAGGAGTTAGCGAGCGAGGTGTTAAAAGAGTCCGTGTCCAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttttccttcttgtgtatacagtttattctttctaactaagtatttttgtacagTTGTTGCTTAAAGGAGTTAGCGAGCGAGGTGTTAAAAGAGTCCGTGTCCATATTCTTACAGATGGCCGTGATGTTTTGGATGGTTCAAGTGTGGGGTTTG
ttctaac putative branch site (score: 1)
tattttt putative PPT
taactaagtattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgattatttggggttggagttgtttttccttcttgtgtatacagtttattctttctaactaagtatttttgtacagTTGTTGCTTAAAGGAGTTAGCGAGCGAGGTGTTAAAAGAGTCCGTGTCCATATTCTTACAGATGGCCGTGATGTTTTGGATGGTTCAAGTGTGGGGTTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG