Sequence
atgc intronic sequence ATGC exonic sequence...aaatgtctgagtgttgctgattccatcacagattcttcccagcattactgcttcaaacatttctttcaacttttctttatttttgaataattttctgcagGGAAAATGAAAGGTATAGCATTTATTAAAGATCCTGATGGATACTGGATTGAAATCTTTGATCGAAAAACAATAGGAAATGTAACACAAGCTCCCGCTTA
Basic information
species | Glycine max |
transcript | GLYMA12G08470.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G08470.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os05g22970.1 (Oryza sativa), 3'ss of exon 7
aaatgtctgagtgttgctgattccatcacagattcttccc----agcattactgcttcaaacatttctttcaact-tttctttatttttgaataatttt---ctgcagGGAAAATGAAAGGTATAGCATTTATTAAAGATCCTGATGGATACTGGATTGAAATCTTTGATCGAAAAACAATAGGAAATGTAACACAAGCTCCCGCTTA
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--------gcatcttatgaatttccatctgtattttgctctcgtaatgttgaaaatgaagatatttagagcaacaacgtaaatgtattaacacggcttttggctgcagGTAAAATGAAGGGCATTGCATTTATCAAAGACCCTGATGGCTACTGGATTGAAATATTTGACCTGAACAGAATTGGGGCGGTGACTGCGGAAGCATCATG
upper sequence: GLYMA12G08470.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G125310_T01 (Zea mays), 3'ss of exon 7
aaatgtctgagtgttgc--tgattccatcacagattcttcccagcattactgcttcaaacatttctttcaacttttctttatttttgaataattttctgcagGGAAAATGAAAGGTATAGCATTTATTAAAGATCCTGATGGATACTGGATTGAAATCTTTGATCGAAAAACAATAGGAAATGTAACACAAGCTCCCGCTTA---
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tgtcacctccttgttaccttcaatctactcatgataccccttttcattcttatctctgtagcacatagccctgttatttgacatatgatc--tttgctgcagGAAAAATCAAAGGCATCGCTTTCATCAAAGATCCTGATGGTTACTGGATCGAAATATTTGACC---AGACGATTGGGACGGTAACTTCTTCAGCATCATGATG
upper sequence: GLYMA12G08470.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G08110.3 (Arabidopsis thaliana), 3'ss of exon 7
----------aaatgtctgagtgttgctgattccatcacagattcttcccagcattactgcttcaaacatttctttcaacttttctttatt-tttgaataattttctgcagGGAAAATGAAAGGTATAGCATTTATTAAAGATCCTGATGGATACTGGATTGAAATCTTTGATCGAAAAACAATAGGAAATGTAACACAAGCTCCCGCTTA
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gtactactattaccagctgagt-ccaataaacatttgaaattttcttttttcttttgcaactctgtttggggagtctatatttaatcctttatttgatgaaaaccttgcagGAAAGATGAAGAATATAGCCTTCATTAAGGATCCTGATGGCTACTGGATCGAGATCTTTGATCTCAAGACTATCGGAACTACTACCGTAAACGCAGCTTG
upper sequence: GLYMA12G08470.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv06s0061g00460.t01 (Vitis vinifera), 3'ss of exon 7
aaatgtctgagtgttgctgattccatcacagattcttcccagcattactgcttcaaacatttctttcaac--ttttctttatttt-tgaataatttt--ctgcagGGAAAATGAAAGGTATAGCATTTATTAAAGATCCTGATGGATACTGGATTGAAATCTTTGATCGAAAAACAATAGGAAATGTAACACAAGCTCCCGCTTA
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-----tttgggtgctatattgaaaaaaagagaacatcttcttcaactatgatttaaaaaaaaaaaaaaatagttgcttttatattatctgtcatgctggctgcagGTAAAATGAAAGGGTTAGCATTCATTAAGGATCCTGATGGCTATTGGATTGAAATCTTTGACCTTAGAAGAATTGGAACTGTGAGTACCACTGCTGCTTGMapped 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|6724946|gb|AW309345.1|AW309345EST: TGAAAGATTTCAGAATCTGGGAGTTGAGTTTGTTAAGAAGCCAGATGATG GGAAAATGAAAGGTATAGCATTTATTAAAGATCCTGATGGATACTGGATTG
genomic: TGAAAGATTTCAGAATCTGGGAGTTGAGTTTGTTAAGAAGCCAGATGATGgtaacaattt ... ttttctgcagGGAAAATGAAAGGTATAGCATTTATTAAAGATCCTGATGGATACTGGATTG
EST:
gi|12489864|gb|BG043385.1|BG043385EST: TGAAAGATNTCAGAATCTGGGAGTTGAGTNTGTTAAGAAGCCAGATGATG GGAAAATGAAAGGTATAGCATTTATTAAAGATCCTGATGGATACTGGATTG
genomic: TGAAAGATTTCAGAATCTGGGAGTTGAGTTTGTTAAGAAGCCAGATGATGgtaacaattt ... ttttctgcagGGAAAATGAAAGGTATAGCATTTATTAAAGATCCTGATGGATACTGGATTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tactgcttcaaacatttctttcaacttttctttatttttgaataattttctgcagGGAAAATGAAAGGTATAGCATTTATTAAAGATCCTGATGGATACTGGATTGAAATCTTTGATCGAAAAACAATAGGAAATGTAACACAAGCTCCCGCTTA
ttttctgc CT-rich tract
atttctttcaactttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaatgtctgagtgttgctgattccatcacagattcttcccagcattactgcttcaaacatttctttcaacttttctttatttttgaataattttctgcagGGAAAATGAAAGGTATAGCATTTATTAAAGATCCTGATGGATACTGGATTGAAATCTTTGATCGAAAAACAATAGGAAATGTAACACAAGCTCCCGCTTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - -tgagtgt
- - - - - - - tgctgat
- - - - - - - - - - - ccatcac
- - - - - - - - - - - - - - - - - cttccca
- - - - - - - - - - - - - - - - - - - - -gcattac
- - - - - - - - - - - - - - - - - - - - - - - - tgcttca