Sequence
atgc intronic sequence ATGC exonic sequence...agaaccctacatctgatctgaattgggtcattcggatcttgtcctaattcattctttcttcctaacttttacaacaaactttaacagtttcattttgcagGATGATAAAGATGAGCTTCGTCGATCACCTGGCACTCCTGTTTTCACTGCACCAGAGTGTATTTTAG
Basic information
species | Glycine max |
transcript | GLYMA11G20690.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G20690.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G133854_T01 (Zea mays), 3'ss of exon 7
-agaaccctacatctgatctgaattgggtcattcgg-atcttgtcctaattcattctttcttcctaacttttacaacaaactttaacagtttcattttgcagGATGATAAAGATGAGCTTCGTCGATCACCTGGCACTCCTGTTTTCACTGCACCAGAGTGTATTTTAG
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ttttatggtgaattct-tcgggactatcaaatttgatatattgtcatattggtgttttactgatatattagtactgtgatacttatgcgttt-gcaatgtagGATGATGATGATATGCTTTGGAGATCTCCTGGCACTCCTGTTTTCACTGCCCCGGAGTGCTGTCAAG
upper sequence: GLYMA11G20690.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G057084_T01 (Zea mays), 3'ss of exon 8
--agaaccctacatctgatctgaattgggtcattcggatcttgtcctaattcattctttcttcctaacttttacaacaaactttaacagtttcattttgcagGATGATAAAGATGAGCTTCGTCGATCACCTGGCACTCCTGTTTTCACTGCACCAGAGTGTATTTTAG
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ttacttgagtagatatattcgatcttttcaaaatgtgtttttgtggcaaattgttctggactataaatttttgtatattggtgttttacttgc--tacatagGATGATGATGATATGCTTTGGAGATCTCCTGGCACTCCTGTTTTCACTGCCCCGGAGTGCTGTCAAG
upper sequence: GLYMA11G20690.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv06s0004g02990.t01 (Vitis vinifera), 3'ss of exon 9
agaaccctacatctgatctgaattgggtcattcggatcttgtcctaattcattctttcttcctaacttttacaacaaacttt---aacagtttcattttgcagGATGATAAAGATGAGCTTCGTCGATCACCTGGCACTCCTGTTTTCACTGCACCAGAGTGTATTTTAG
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--ttgtgttcagagtttttaaatttggtagtggaataccttttagttttaaggcgttgaatgcaattcttgtgccaccttgttgaaatggtttc-ttatgcagGATGATAATGATGAGCTCCGCCGTTCTCCTGGCACTCCTGTTTTTACTGCACCAGAGTGCTGTTTAG
upper sequence: GLYMA11G20690.1 (Glycine max), 3'ss of exon 8
lower sequence: EFJ15000 (Selaginella moellendorffii), 3'ss of exon 6
agaaccctacatctgatctgaattgggtcattcggatcttgtcctaattcattctttcttcctaacttttacaacaaactttaacagtttcattttgcagGATGATAAAGATGAGCTT---CGTCGATCACCTGGCACTCCTGTTTTCACTGCACCAGAGTGTATTTTAG---------
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----------------------------------------gtaccacagagtttgtggtgtggtgttgagatga-aagttttgctttctttcttttgccgcagGGCGATGATGATCTTTTACGTCGATCTCCTGGCACTCCTGTCTTCACAGCACCAGAATGCTGTAAAGGTATTTCTCMapped 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|15286203|gb|BI470094.1|BI470094EST: GTCATGGTACAGTAAAGATAGGGGATTTCAGTGTCAGCCAGGCTTTTGAG GATGATAAAGATGAGCTTCGTCGATCACCTGGCACTCCTGTTTTCACTGCA
genomic: GTCATGGTACAGTAAAGATAGGGGATTTCAGTGTCAGCCAGGCTTTTGAGgtaatgtaat ... cattttgcagGATGATAAAGATGAGCTTCGTCGATCACCTGGCACTCCTGTTTTCACTGCA
EST:
gi|208316150|gb|GE117404.1|GE117404EST: GTCATGGTACAGTAAAGATAGGGGATTTCAGTGTCAGCCAGGCTTTTGAG GATGATAAAGATGAGCTTCGTCGATCACCTGGCACTCCTGTTTTCACTGCA
genomic: GTCATGGTACAGTAAAGATAGGGGATTTCAGTGTCAGCCAGGCTTTTGAGgtaatgtaat ... cattttgcagGATGATAAAGATGAGCTTCGTCGATCACCTGGCACTCCTGTTTTCACTGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aattcattctttcttcctaacttttacaacaaactttaacagtttcattttgcagGATGATAAAGATGAGCTTCGTCGATCACCTGGCACTCCTGTTTTCACTGCACCAGAGTGTATTTTAG
tttcatttt CT-rich tract
taactttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agaaccctacatctgatctgaattgggtcattcggatcttgtcctaattcattctttcttcctaacttttacaacaaactttaacagtttcattttgcagGATGATAAAGATGAGCTTCGTCGATCACCTGGCACTCCTGTTTTCACTGCACCAGAGTGTATTTTAG
- - ccctaca
- - - - - - - - - - - - - gtcattc
- - - - - - - - - - - - - - - - - - -cttgtcc