Sequence
atgc intronic sequence ATGC exonic sequence...tatacatgctcttgacttgaggaagttctgcatggctgcgtgcacctgtttcaaggtctgctaattatattaatttattttttattctttatttatttagGCCACCATCTATCAGCAAAAGGCCTTGGATATAAATGAGAGGGAGCTAGGGCTTGACCACCCTGACACTATGAAAAGCTATGGGGATCTTTCCGTCTTTT
Basic information
species | Glycine max |
transcript | GLYMA07G03250.1 |
intron # | 18 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G03250.1 (Glycine max), 3'ss of exon 18
lower sequence: LOC_Os04g55230.1 (Oryza sativa), 3'ss of exon 17
---tatacatgctcttgacttgaggaagtt------ctgcatggctgcgtgcacctgtttcaaggtctgctaattatatta---atttattttttattctttatttatttagGCCACCATCTATCAGCAAAAGGCCTTGGATATAAATGAGAGGGAGCTAGGGCTTGACCACCCTGACACTATGAAAAGCTATGGGGATCTTTCCGTCTTTT
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gtatttcaatgaatttggtgggctgtattctatctgctgcatagtgatgtgtttttggcacaatgtttggcaactgcatttttcactagacttctgttctttctctgt--agGCAACTATATATCAGCAGAAGGCACTTGATATCAATGAAAGAGAGCTAGGTCTTGACCACCCAGAAACTATGAAGAGTTACGGGGATTTATCTGTCTTCT
upper sequence: GLYMA07G03250.1 (Glycine max), 3'ss of exon 18
lower sequence: AT1G15290.1 (Arabidopsis thaliana), 3'ss of exon 15
---------------------------tatacatgctcttgacttgaggaagttctgcatggctgcgtgcacctgtttcaaggtctgc---taattatattaat-----------ttattttttattctttat------ttatttagGCCACCATCTATCAGCAAAAGGCCTTGGATATAAATGAGAGGGAGCTAGGGCTTGACCACCCTGACACTATGAAAAGCTATGGGGATCTTTCCGTCTTTT
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gtatcatcatcttttatcttcttcccaaatggaaactttgatttcaagtaacaaatagagagtttgatgttctcgttctaggcactgtatataaataaattgatgagaggtaccgtcatctctgattttttatcctctcttgatcagGCAACAATATATCAGCAGAAGGCTCTAGATATAAATGAGAGAGAACTTGGTCTCGACCATCCCGACACTATGAAAAGCTATGGGGATCTTTCTGTATTTT
upper sequence: GLYMA07G03250.1 (Glycine max), 3'ss of exon 18
lower sequence: Vv09s0002g07530.t01 (Vitis vinifera), 3'ss of exon 17
tatacatgctcttga-cttgaggaagttctgcatggc-tgcgtgcacctgtttcaaggtctgctaattatattaatttattttttattct-ttatttatttagGCCACCATCTATCAGCAAAAGGCCTTGGATATAAATGAGAGGGAGCTAGGGCTTGACCACCCTGACACTATGAAAAGCTATGGGGATCTTTCCGTCTTTT
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tttccagctgcttggtctcgttggttttctgtgttgtatgtctgcaagtgact---ggtccagttgctttattctctaaacttaaattttcttccttgtctagGCAACTATATATCAACAGAAGGCTTTGGATATCAATGAGAGGGAACTTGGGCTTGACCATCCTGATACAATGAAAAGCTATGGAGATCTTTCAGTTTTTT
upper sequence: GLYMA07G03250.1 (Glycine max), 3'ss of exon 18
lower sequence: EFJ24726 (Selaginella moellendorffii), 3'ss of exon 17
tatacatgctcttgacttgaggaagttctgcatggctgcgtgcacctgtttcaaggtctgctaattatattaatttattttttatt--ctttatttatttagGCCACCATCTATCAGCAAAAGGCCTTGGATATAAATGAGAGGGAGCTAGGGCTTGACCACCCTGACACTATGAAAAGCTATGGGGATCTTTCCGTCTTTT
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-------------------------------------gtacacaaaagctacatattgtattaatgtaattgatgacttaattgatgactttttgtgatcagGCCATGATATACCAGCAAAAAGCTTTGGACATAAATGAGAGGGAGCTTGGACTTGACCATCCGGATACAATGAAAAGCTATGGTGACTTGGCTGTCTTTTMapped 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|213599768|gb|DB968418.1|DB968418EST: CATATAGTCTTCTAGCTGTGGTTCTCTACCACACTGGAGATTTTAACCAG GCCACCATATACCAGCAAAAGGCCTTGGATATAAATGAGAGGGAGCTAGGG
genomic: CATATAGTCTTCTAGCTGTGGTTCTCTACCACACTGGAGATTTTAACCAGgtaaataata ... atttatttagGCCACCATCTATCAGCAAAAGGCCTTGGATATAAATGAGAGGGAGCTAGGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgtttcaaggtctgctaattatattaatttattttttattctttatttatttagGCCACCATCTATCAGCAAAAGGCCTTGGATATAAATGAGAGGGAGCTAGGGCTTGACCACCCTGACACTATGAAAAGCTATGGGGATCTTTCCGTCTTTT
tattaat putative branch site (score: 2)
tttattttttattctt CT-rich tract
taattatattaattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatacatgctcttgacttgaggaagttctgcatggctgcgtgcacctgtttcaaggtctgctaattatattaatttattttttattctttatttatttagGCCACCATCTATCAGCAAAAGGCCTTGGATATAAATGAGAGGGAGCTAGGGCTTGACCACCCTGACACTATGAAAAGCTATGGGGATCTTTCCGTCTTTT
- - catgctc
- - - - - - tgacttg
- - - - - - - - - - - - - - -gcatggc
- - - - - - - - - - - - - - - - - - - - tgcacct
- - - - - - - - - - - - - - - - - - - - - - - - - - - ggtctgc