Sequence
atgc intronic sequence ATGC exonic sequencegtacttgtaaaattcccctcatattttatttgccataaaatattttgtcaaacttcacactaacactggatatggattggatttgaagTACACGAAGGTCATGTGGAGGATAAACTTCTCTGTATGGGTTGTAATGCTCGTTTGGGTAACTTCAACTGGGCCGGTATGCAGTGCAGCTGTGGAGCCTG
Basic information
species | Glycine max |
transcript | GLYMA08G46290.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G46290.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G153602_T04 (Zea mays), 3'ss of exon 2
--gtacttgtaaaattcccctcatattttatttgccataaaatattttgtcaaacttc--acactaacactggatatggattggatttgaagTACACGAAGGTCATGTGGAGGATAAACTTCTCTGTATGGGTTGTAATGCTCGTTTGGGTAACTTCAACTGGGCCGGTATGCAGTGCAGCTGTGGAGCCTG
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gtcagtctaccaagcacgatgctttacctcttgtttttagagcgttgccatgagtctccgatgttctcatctgctccatgttctgtttgcagTGGAAGAAGGATATGTTGCGAAAAAGCTCTTTTGCATGGGATGTAAAGCTCGTCTGGGACAGTTCAATTGGGCTGGTATGCAGTGCAGCTGCGGAGCCTG
upper sequence: GLYMA08G46290.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G076665_T01 (Zea mays), 3'ss of exon 3
--gtacttgtaaaattcccctcatattttatttgccataaaatattttgtcaaacttc--acactaacactggatatggattggatttgaagTACACGAAGGTCATGTGGAGGATAAACTTCTCTGTATGGGTTGTAATGCTCGTTTGGGTAACTTCAACTGGGCCGGTATGCAGTGCAGCTGTGGAGCCTG
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gtcagtctgccaagcacgatgctttacctcttgtttttagagcgttgccatgagtctccgatgttctcatctgctccgtgttctgtttgcagTGGAAGAAGGATATGTTGCGAACAAGCTCTTTTGCATGGGATGCAAAGCTCATCTGGGACAGTTCAACTGGGCTGGTATGCAGTGCAGCTGCAGAGCCTG
upper sequence: GLYMA08G46290.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv15s0046g02430.t01 (Vitis vinifera), 3'ss of exon 4
gtacttgta-aaattcccctcatattttatttg-----ccataaaat-attttgtcaaactt-cacactaacactggatatggattggatttgaagTACACGAAGGTCATGTGGAGGATAAACTTCTCTGTATGGGTTGTAATGCTCGTTTGGGTAACTTCAACTGGGCCGGTATGCAGTGCAGCTGTGGAGCCTG
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gtcagcgtctaaacccaagtcatattttatttaaaaacccataaatttgttcttctaaactagcagactaacctttggattgtgaattatatgcagTACATGAAGGTCATGTAGAAGAGAAGCTGCAATGCATGGGCTGCAAAGCTCGATTGGGTTCCTTCAACTGGGCAGGCATGCAGTGCAGCTGTGGAGCTTGMapped 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|51344992|gb|CO985725.1|CO985725EST: AGTTGATTGCACCTCAGTATTTGTTGAGCCCATGAAATGGATGCAAGCAG TACACGAAGGTCATGTGGAGGATAAACTTCTCTGTATGGGTTGTAATGCTC
genomic: AGTTGATTGCACCTCAGTATTTGTTGAGCCCATGAAATGGATGCAAGCAGgtacttgtaa ... ggatttgaagTACACGAAGGTCATGTGGAGGATAAACTTCTCTGTATGGGTTGTAATGCTC
EST:
gi|12688185|gb|BG154521.1|BG154521EST: AGTTGATTGCACCTCAGTATTTGTTGAGCCCATGAAATGGATGCAGGCAG TACACGAAGGTCATGTGGAGGATGAACCTT-TCTGTATGGCTTGTATTGCT
genomic: AGTTGATTGCACCTCAGTATTTGTTGAGCCCATGAAATGGATGCAAGCAGgtacttgtaa ... ggatttgaagTACACGAAGGTCATGTGGAGGATAAAC-TTCTCTGTATGGGTTGTAATGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cataaaatattttgtcaaacttcacactaacactggatatggattggatttgaagTACACGAAGGTCATGTGGAGGATAAACTTCTCTGTATGGGTTGTAATGCTCGTTTGGGTAACTTCAACTGGGCCGGTATGCAGTGCAGCTGTGGAGCCTG
cactaac putative branch site (score: 1)
aatattttgtcaaa 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
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gtacttgtaaaattcccctcatattttatttgccataaaatattttgtcaaacttcacactaacactggatatggattggatttgaagTACACGAAGGTCATGTGGAGGATAAACTTCTCTGTATGGGTTGTAATGCTCGTTTGGGTAACTTCAACTGGGCCGGTATGCAGTGCAGCTGTGGAGCCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG