Sequence
atgc intronic sequence ATGC exonic sequence...aatttggggagcttttcctgcttttcatttattgccttaatttgctcagccaattatatagtgttagcaattgatggtagttcttataaatgtcttgcagCTTCCACGGTTGTACAATGTGTACAAAGAAATGGGAATTGTGACATCATTCCAGAACATGCTCGACAATATTTTCATTCCACTTTTTGAGGTCACTGTCA
Basic information
species | Glycine max |
transcript | GLYMA01G29470.2 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G29470.2 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os05g28180.3 (Oryza sativa), 3'ss of exon 3
aatttggggagcttttcctgcttttcatttattgccttaatttgctcagccaattatatagtgttagcaattgatggtagttcttataaatgtctt-gcagCTTCCACGGTTGTACAATGTGTACAAAGAAATGGGAATTGTGACATCATTCCAGAACATGCTCGACAATATTTTCATTCCACTTTTTGAGGTCACTGTCA
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tattcaaagtggtatacacctcgttatgttactgatatatttatgatatttgat-attcggagttgcattcagataattgtttttctacattcctttgcagATCCCACGCTTATATAATGTGTACAAGGAAATGGGTATTGTTACATCATTCCAAACTCTTCTGGACAACATTTTCCTTCCTCTGTTTGAGGTCACCATTG
upper sequence: GLYMA01G29470.2 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G416667_T01 (Zea mays), 3'ss of exon 11
aatttggggagcttttcctgcttttcatttattgccttaatttgctcagc-caattatatagtgttagcaattgatggtagttcttataaatgt---cttgcagCTTCCACGGTTGTACAATGTGTACAAAGAAATGGGAATTGTGACATCATTCCAGAACATGCTCGACAATATTTTCATTCCACTTTTTGAGGTCACTGTCA
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----tcttaaccatgacaatgttacctttttccccagtgaaatatttagtgcaaaaacattacattattcttttctgatatattttgtggacattcttttgcagATTCCACGCTTATATAATGTGTACAAGGAAATGGGTATCGTTACATCATTCCAAAATCTTCTTGACAACATTTTCGTTCCTCTTTTTGAGGTTACTATTG
upper sequence: GLYMA01G29470.2 (Glycine max), 3'ss of exon 12
lower sequence: AT2G38280.1 (Arabidopsis thaliana), 3'ss of exon 11
--------------------------------aatttggggagcttttcctgcttttcatttattgccttaatttgctcagccaattat--atagtgttagcaattgatggtagttcttataaatgtcttgcagCTTCCACGGTTGTACAATGTGTACAAAGAAATGGGAATTGTGACATCATTCCAGAACATGCTCGACAATATTTTCATTCCACTTTTTGAGGTCACTGTCA
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gttagccatctctttgatacttgtgtgctccatgtccttccatgagtgtatgtgttttttttgtctccgtgtgtttgtaacatgactgctaactgagctatattttccttgttttctgtttgtctgctcactagCTCCCACGCTTGTACAACATTTACAAGGACATGGGTATTGTGACATCGTTCCAGAATATCCTGGACAATATATTCATTCCTCTGTTTGAAGCCACGGTAG
upper sequence: GLYMA01G29470.2 (Glycine max), 3'ss of exon 12
lower sequence: Vv08s0105g00570.t01 (Vitis vinifera), 3'ss of exon 11
aatttggggagcttttcctgcttttcatttattgccttaatttgctcagccaa----ttatatagtgttagcaat-tgatggtagttcttataaatgtcttgc-agCTTCCACGGTTGTACAATGTGTACAAAGAAATGGGAATTGTGACATCATTCCAGAACATGCTCGACAATATTTTCATTCCACTTTTTGAGGTCACTGTCA
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-----ctggaatgtatctaacctgacattc-tggggtttgttagcaaaagcaaaatgttggattttgttattgttcttatggtataatatccttctgtttttccagCTTCCCCGGCTGTATAATGTGTACAAGGATATGGGAATTGTTACATCATTTCAGAACATGCTGGACAATATCTTTCTTCCCCTGTTTGAGGTTACTGTGAMapped 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|7925052|gb|AW831078.1|AW831078EST: GGATAGTGAATAATGATTTGTACAGCGAGAATGTCGTTTGGTTGATTCAG CTTCCACGGTTGTACAATGTGTACAAAGAAATGGGAATTGTGACATCATTC
genomic: GGATAGTGAATAATGATTTGTACAGCGAGAATGTCGTTTGGTTGATTCAGgtattcttta ... tgtcttgcagCTTCCACGGTTGTACAATGTGTACAAAGAAATGGGAATTGTGACATCATTC
EST:
gi|254332340|gb|GR846385.1|GR846385EST: GGATAGTGAATAATGATTTGTACAGCGAGAATGTCGTTTGGTTGATTCAG CTTCCACGGTTGTACAATGTGTACAAAGAAATGGGAATTGTGACATCATTC
genomic: GGATAGTGAATAATGATTTGTACAGCGAGAATGTCGTTTGGTTGATTCAGgtattcttta ... tgtcttgcagCTTCCACGGTTGTACAATGTGTACAAAGAAATGGGAATTGTGACATCATTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcagccaattatatagtgttagcaattgatggtagttcttataaatgtcttgcagCTTCCACGGTTGTACAATGTGTACAAAGAAATGGGAATTGTGACATCATTCCAGAACATGCTCGACAATATTTTCATTCCACTTTTTGAGGTCACTGTCA
aattgat putative branch site (score: 4)
aattatatagtgtta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatttggggagcttttcctgcttttcatttattgccttaatttgctcagccaattatatagtgttagcaattgatggtagttcttataaatgtcttgcagCTTCCACGGTTGTACAATGTGTACAAAGAAATGGGAATTGTGACATCATTCCAGAACATGCTCGACAATATTTTCATTCCACTTTTTGAGGTCACTGTCA
- - tggggag
- - - - - - - -tcctgct
- - - - - - - - - - - - - - -tattgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatggta