Sequence
atgc intronic sequence ATGC exonic sequencegtaaacatttttagtctgctgatcaatttgaaccaatgttgattttcatttaagcagggacactgaacatgttaatgatttattgaccagGTCCTAGGTAACAAATACCAGAGCAAGTTGCTTGAAATCATTGATGCCAG
Basic information
species | Glycine max |
transcript | GLYMA06G01270.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G01270.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os02g04030.3 (Oryza sativa), 3'ss of exon 4
------------------------------gtaaacatt--tttagtc--tgctgatcaatttgaaccaatgttgattttcatttaagcag-ggacactgaacatgttaatga----tttattgaccagGTCCTAGGTAACAAATACCAGAGCAAGTTGCTTGAAATCATTGATGCCAG
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gtaatccaatccatccacaatcttttcgatgtcaatgtcacatcgatcattcgtaattaagctacatttg-atcaatttgcaactaaacattacataatgtttgcatttatgtgccctgttttaaccagGTCCTAGGCAACAAGTACCAGAGCAAGCTGCTGGAAGTGATTGATCCCAG
upper sequence: GLYMA06G01270.1 (Glycine max), 3'ss of exon 6
lower sequence: AT2G18180.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaaacatttttagtctgctgatcaatttgaaccaatgttgattttcatttaagcagggacactgaacatgttaatgatttattgaccagGTCCTAGGTAACAAATACCAGAGCAAGTTGCTTGAAATCATTGATGCCAG
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gcaagtatacaaaccctttttatcactcttgactgatataaat---------gagagatattcttactacttagctaatttgatattcagGTTCTTGGCAACAAGTACCAAAGCAAGTTGCTTGAAATAATTGATGCTAG
upper sequence: GLYMA06G01270.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv03s0038g04480.t01 (Vitis vinifera), 3'ss of exon 6
gtaaacatttttagtctgctgatcaatttgaaccaatgttgattttcatttaagcagggacactgaacatgttaatgattt-attg-accagGTCCTAGGTAACAAATACCAGAGCAAGTTGCTTGAAATCATTGATGCCAG
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gtgaccattt---gtcttctgtttaccttaaactattacttgttttgatcaaacaaaatccacttaaccatctaacggttttattgtaccagGTGTTGGGTAATAAATACCAGAGCAAGTTGCTTGAAGTAATCGATGCTAGMapped 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|41145355|gb|CK605566.1|CK605566EST: GGAGCACCATTAAGTCATTCCTAGATCCCAAGACCACCTCAAAAATCCAT GTCCTAGGTAACAAATACCAGAGCAAGTTGCTTGAAATCATTGATGCCAG
genomic: GGAACACCATTAAGTCATTCCTAGATCCCAAGACCACCTCAAAAATCCATgtaaacattt ... tattgaccagGTCCTAGGTAACAAATACCAGAGCAAGTTGCTTGAAATCATTGATGCCAG
EST:
gi|41145747|gb|CK605958.1|CK605958EST: GGAACACCATTAAGTCATTCCTAGATCCCAAGACCACCTCAAAAATCCAT GTCCTAGGTAACAAATACCAGAGCAAGTTGCTTGAAATCATTGATGCCAG
genomic: GGAACACCATTAAGTCATTCCTAGATCCCAAGACCACCTCAAAAATCCATgtaaacattt ... tattgaccagGTCCTAGGTAACAAATACCAGAGCAAGTTGCTTGAAATCATTGATGCCAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgttgattttcatttaagcagggacactgaacatgttaatgatttattgaccagGTCCTAGGTAACAAATACCAGAGCAAGTTGCTTGAAATCATTGATGCCAG
tgttaat putative branch site (score: 3)
atgttaatgatttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaacatttttagtctgctgatcaatttgaaccaatgttgattttcatttaagcagggacactgaacatgttaatgatttattgaccagGTCCTAGGTAACAAATACCAGAGCAAGTTGCTTGAAATCATTGATGCCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG