Sequence
atgc intronic sequence ATGC exonic sequencegtatgctagaatattcaaagtttaaatcgttttaaccatgtttatacctaatatagctgtgtgcacactcaaaagaggtattgaagaatttccattatcatgtatataactaatatatatacatgttttcagGTAGAAGAATCACTTTCTGTATATTTGGAATATGTCTCTGGTGGTTCTATCCATAAATTACTTCAGGAGTATGGTCCATTTAAGGAGCCTGTTATTCAAA
Basic information
species | Glycine max |
transcript | GLYMA08G16670.3 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G16670.3 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g35010.1 (Oryza sativa), 3'ss of exon 4
gtatgctagaatattcaaagtttaaatcgttttaaccatgtttatacctaatatagctgtgtgcacactcaaaagaggtattgaagaatttccattatcatgtatataactaatatatatacatgttttcagGTAGAAGAATCACTTTCTGTATATTTGGAATATGTCTCTGGTGGTTCTATCCATAAATTACTTCAGGAGTATGGTCCATTTAAGGAGCCTGTTATTCAAA
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-------------------------------ggagacaccatcagttttactaattttgtgtgattgttcactt-attttctgaaagttctcattaagctttggcttgcctaatttaaacaattttgagcagGCTGATGAAGCTCTGTCCATCTATCTGGAATATGTTTCTGGAGGTTCAATTCATAAATTACTTAGAGAGTACGGTCCATTTAAGGAACCTGTGATTCGTA
upper sequence: GLYMA08G16670.3 (Glycine max), 3'ss of exon 4
lower sequence: Vv04s0044g01290.t01 (Vitis vinifera), 3'ss of exon 4
----------------------------------------------------------gtatgctagaatattcaaagtttaaatcgttttaaccatgtttatacctaatatagctgtgtgcacactcaaaagaggtattgaagaatttccattatcatgtatataac-taatatatatacatgttttcagGTAGAAGAATCACTTTCTGTATATTTGGAATATGTCTCTGGTGGTTCTATCCATAAATTACTTCAGGAGTATGGTCCATTTAAGGAGCCTGTTATTCAAA
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gtatgagctactctcctaatgtttaaaaaagttagggttcatgcatctactcacccatgcatgagtgcacacacatgaatgctatccttttcccgacatgca-atctctttccaatctgttcattc-caagtgagtggacggtgtattt--gaccctgttcttgtaacattctggattgtcatgttgtcagGGTGAAGAAACACTATCAGTTTATTTGGAGTATGTCTCTGGTGGCTCTATCCACAAGTTACTTCAAGAATATGGTCCCTTTAAGGAACCTGTCATTCAAA
upper sequence: GLYMA08G16670.3 (Glycine max), 3'ss of exon 4
lower sequence: EFJ36728 (Selaginella moellendorffii), 3'ss of exon 2
gtatgctagaatattcaaagtttaaatcgttttaaccatgtttatacctaatatagctgtgtgcacactcaaaagaggtattgaagaatttccattatcatgtatataactaatatatatacatgttttcagGTAGAAGAATCACTTTCTGTATATTTGGAATATGTCTCTGGTGGTTCTATCCATAAATTACTTCAGGAGTATGGTCCATTTAAGGAGCCTGTTATTCAAA
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-----------------------------------------------------------------------------gtagtcaag---ctccacttt---gcattcaagca-tgaacgttcg-attttcagATGGAGGATGGCTTATATATTTACCTCGAGTATGTGTCCGGGGGATCGATTCACAAGCTTCTTCAGGAGTATGGTGCATTCAAGGAGCCTGTGATTCGCA
upper sequence: GLYMA08G16670.3 (Glycine max), 3'ss of exon 4
lower sequence: EFJ27940 (Selaginella moellendorffii), 3'ss of exon 2
gtatgctagaatattcaaagtttaaatcgttttaaccatgtttatacctaatatagctgtgtgcacactcaaaagaggtattgaagaatttccattatcatgtatataactaatatatatacatgttttcagGTAGAAGAATCACTTTCTGTATATTTGGAATATGTCTCTGGTGGTTCTATCCATAAATTACTTCAGGAGTATGGTCCATTTAAGGAGCCTGTTATTCAAA
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-----------------------------------------------------------------------------gtagtcaag---ctccacttt---gcattcaagcatta-acgttcg-attttcagATGGAGGATGGCTTATATATTTACCTCGAGTATGTGTCCGGGGGATCGATTCACAAGCTTCTTCAGGAGTATGGTGCATTCAAGGAGCCTGTGATTCGCAMapped 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|254317547|gb|GR826531.1|GR826531EST: TAAATCAGCTTTCACACCCAAATATTGTTCAATACTATGGGAGTGAACTG GTAGAAGAATCACTTTCTGTATATTTGGAATATGTCTCTGGTGGTTCTATC
genomic: TAAATCAGCTTTCACACCCAAATATTGTTCAATACTATGGGAGTGAACTGgtatgctaga ... atgttttcagGTAGAAGAATCACTTTCTGTATATTTGGAATATGTCTCTGGTGGTTCTATC
EST:
gi|26048798|gb|CA785251.1|CA785251EST: TAAATCAGCTTTCACACCCAAATATTGTTCAATACTATGGGAGTGAACTG GTAGAAGAATCACTTTCTGTATATTTGGAATATGTCTCTGGTGGTTCTATC
genomic: TAAATCAGCTTTCACACCCAAATATTGTTCAATACTATGGGAGTGAACTGgtatgctaga ... atgttttcagGTAGAAGAATCACTTTCTGTATATTTGGAATATGTCTCTGGTGGTTCTATC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtattgaagaatttccattatcatgtatataactaatatatatacatgttttcagGTAGAAGAATCACTTTCTGTATATTTGGAATATGTCTCTGGTGGTTCTATCCATAAATTACTTCAGGAGTATGGTCCATTTAAGGAGCCTGTTATTCAAA
aactaat putative branch site (score: 2)
tgttttc putative PPT
attatcatgtatataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgctagaatattcaaagtttaaatcgttttaaccatgtttatacctaatatagctgtgtgcacactcaaaagaggtattgaagaatttccattatcatgtatataactaatatatatacatgttttcagGTAGAAGAATCACTTTCTGTATATTTGGAATATGTCTCTGGTGGTTCTATCCATAAATTACTTCAGGAGTATGGTCCATTTAAGGAGCCTGTTATTCAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG