Sequence
atgc intronic sequence ATGC exonic sequencegtttgagttgatttatacatttggtcccgtgtattctatttccatccaatgatctgtaaggtttaatgatgcacctaacttgtttgtgatgaattttgataaacagATTAGGTCAGCAATTGAAAACAGTACCTCAGATTATGACAAGGAAAAGTTACAGGAAAGATTAGCCAAGCTTTCTGGTGGTGTTGCAGTGCTTAAG
Basic information
species | Glycine max |
transcript | GLYMA20G19980.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G19980.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G416120_T01 (Zea mays), 3'ss of exon 11
gtttgagttgatttatacatttggtcccgtgtattctatttccatccaatgatctgtaaggtttaatgatgcacctaacttgtttgtgatgaattttgataaacagATTAGGTCAGCAATTGAAAACAGTACCTCAGATTATGACAAGGAAAAGTTACAGGAAAGATTAGCCAAGCTTTCTGGTGGTGTTGCAGTGCTTAAG
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gttcgtgc--aatattacttttgttgtgctgtcttaaattgct-tctaactttctg---gttctgataattta--tggattatggattatggatgttg-----cagATTAGATCAGCAGTTGAGAACAGCACTTCAGATTATGACAAGGAAAAGCTCCAGGAACGGTTGGCAAAGCTCTCTGGAGGTGTTGCTGTTCTGAAG
upper sequence: GLYMA20G19980.1 (Glycine max), 3'ss of exon 12
lower sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 11
gtttgagttgatttatacatttggtcccgt-gtattctatttccatccaa--tgatctgtaaggtttaatgatgcacctaacttgtttgtgatgaattttga--taaacagATTAGGTCAGCAATTGAAAACAGTACCTCAGATTATGACAAGGAAAAGTTACAGGAAAGATTAGCCAAGCTTTCTGGTGGTGTTGCAGTGCTTAAG
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gttagcgtgtttttcgcttttttatcatttagtggttcagtgtcatatacctttgcccttttttccaactggtagttttaatatgttttgaatttttattaaaccacgcagATACGATCCATGGTTGAAGCAAGCACTTCTGATTATGACAAGGAGAAGTTGCAAGAAAGGTTGGCTAAGCTTTCGGGTGGTGTTGCTGTACTAAAG
upper sequence: GLYMA20G19980.1 (Glycine max), 3'ss of exon 12
lower sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 10
-----gtttgagttgatttatacatttggtcccgtgtattcta-tttccatccaatgatctgtaaggtttaatgatgcacctaact-tgtttgtgatgaattttgataaacagATTAGGTCAGCAATTGAAAACAGTACCTCAGATTATGACAAGGAAAAGTTACAGGAAAGATTAGCCAAGCTTTCTGGTGGTGTTGCAGTGCTTAAG
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gtaatttttaaccttataccctgataaattggttagtaataaaatttgtatgcaagaaattatgaagtgtatgaaagtagttcgttctaattgcttggtattgcaactaacagATTAGGTCAGCAATTGAACTGAGCACCTCAGATTATGACAAGGAAAAACTGCAAGAAAGGTTGGCTAAGCTCTCTGGAGGTGTTGCAGTGTTGAAGMapped 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|208238924|gb|GE037128.1|GE037128EST: TTCTTGATGGAGCGGGTGACAAGAAAGCACTTGAGGAAAGATGCGAGCAG ATTAGGTCAGCAATTGAAAACAGTACCTCA
genomic: TTCTTGATGGAGCGGGTGACAAGAAAGCACTTGAGGAAAGATGCGAGCAGgtttgagttg ... tgataaacagATTAGGTCAGCAATTGAAAACAGTACCTCA
EST:
gi|19268755|gb|BM885011.1|BM885011EST: TTCTTGATGGAGCGGGTGACAAGAAAGCACTTGAGGAAAGATGCGAGCAG ATTAGGTCAGCAATTGAAAACAGTACCTCAGATTATGACAAGGAAAAGTTA
genomic: TTCTTGATGGAGCGGGTGACAAGAAAGCACTTGAGGAAAGATGCGAGCAGgtttgagttg ... tgataaacagATTAGGTCAGCAATTGAAAACAGTACCTCAGATTATGACAAGGAAAAGTTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atctgtaaggtttaatgatgcacctaacttgtttgtgatgaattttgataaacagATTAGGTCAGCAATTGAAAACAGTACCTCAGATTATGACAAGGAAAAGTTACAGGAAAGATTAGCCAAGCTTTCTGGTGGTGTTGCAGTGCTTAAG
atgaattttgataaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgagttgatttatacatttggtcccgtgtattctatttccatccaatgatctgtaaggtttaatgatgcacctaacttgtttgtgatgaattttgataaacagATTAGGTCAGCAATTGAAAACAGTACCTCAGATTATGACAAGGAAAAGTTACAGGAAAGATTAGCCAAGCTTTCTGGTGGTGTTGCAGTGCTTAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG