Sequence
atgc intronic sequence ATGC exonic sequencegtgaatttctttattcccatggatttcttgatgcattactgtttcccctcaatgaggtttacaagaaatttctttattaaagaagtggttttctttattctcatgcttacagGGAATCCTCCAATCACAAGGAAGGTTATTAAGGAAAATGAGGTTTATGCCATCTTCCTTGTCATCAAATTCTCATCGGCTGCTGACTGCCCTTGTTGACT
Basic information
species | Glycine max |
transcript | GLYMA04G32540.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G32540.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os12g38970.1 (Oryza sativa), 3'ss of exon 6
gtgaatttctttattcccatggatttcttgatgcat--tactgtttcccctcaatgaggtttacaagaaatttct-ttattaaagaagtggttttctttattctcatgcttacagGGAATCCTCCAATCACAAGGAAGGTTATTAAGGAAAATGAGGTTTATGCCATCTTCCTTGTCATCAAATTCTCATCGGCTGCTGACTGCCCTTGTTGACT
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gtaaagtacttcttatctgca-attcaacaatgtttgctaccacctctgttcattcatgctcttactgcataggtgtcactaacctgatataattttgaattataatgc----agGGAGTCCTTCAATCACAAGGAAGGCTCTTACGGAAAATGAGATTCATGCCATCTTCCTTGTCTTCGAAATCACATCGTTTATTAACTGCTCTTGTTGATT
upper sequence: GLYMA04G32540.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os07g01880.1 (Oryza sativa), 3'ss of exon 6
gtgaatttctttattcccatggatttcttgatg--cattactgtttcccctcaatgaggtttacaagaaatttcttt-attaaagaagtggttttctttattctcatgcttacagGGAATCCTCCAATCACAAGGAAGGTTATTAAGGAAAATGAGGTTTATGCCATCTTCCTTGTCATCAAATTCTCATCGGCTGCTGACTGCCCTTGTTGACT
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gtaaagtacttcttatctgca-attcaacaatgttcgctaccacctctgttcattcatgctcttaccgcataggtctcactaacctgatataattttgaattgtaatgc----agGGAGTCCTTCAATCACAAGGAAGGCTCTTACGGAAAATGAGATTCATGCCATCTTCCTTGTCTTCGAAATCACATCGTTTATTAACTGCTCTTGTTGATT
upper sequence: GLYMA04G32540.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv17s0000g07160.t01 (Vitis vinifera), 3'ss of exon 6
gtgaatttctttattcccatggatttcttgatgcattactgtttcccctcaatgaggtttacaagaaatttctttattaaagaagtggttttctttattctcatgcttacagGGAATCCTCCAATCACAAGGAAGGTTATTAAGGAAAATGAGGTTTATGCCATCTTCCTTGTCATCAAATTCTCATCGGCTGCTGACTGCCCTTGTTGACT
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-ttattgttagtagaacaatgcagaactttctatat-gtccttttgctagagtgacattcatggagaatttgtcctt---------gatgtcctttatgccaat-catgcagGGAATTCTCCAATCACAAGGGAGAATTTTGAGAAAGATGAGATTTATGCCCTCGTCTTTGTCATCGAATTCTCACAGGTTGTTAACAGCTCTTGTTGATTMapped 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|193617255|gb|FK567473.1|FK567473EST: TACAAGATGCACAGCATGATCAAGCACATCTTTTCCT-AGACATGGAAAG GGAATCCTCCAATCACAAGGAAGGTTA
genomic: TACAAGATGCACAGCATGATCAAGCACATCTTTTCCTTAGACATGGAAAGgtgaatttct ... atgcttacagGGAATCCTCCAATCACAAGGAAGGTTA
EST:
gi|41146012|gb|CK606223.1|CK606223EST: TACAAGATGCACAGCATGATCAAGCACATCTTTTCCTTAGACATGGAAAG GGAATCCTCCAATCACAAGGAAGGTTATTAAGGAAAATGAGGTTTATGCCA
genomic: TACAAGATGCACAGCATGATCAAGCACATCTTTTCCTTAGACATGGAAAGgtgaatttct ... atgcttacagGGAATCCTCCAATCACAAGGAAGGTTATTAAGGAAAATGAGGTTTATGCCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttacaagaaatttctttattaaagaagtggttttctttattctcatgcttacagGGAATCCTCCAATCACAAGGAAGGTTATTAAGGAAAATGAGGTTTATGCCATCTTCCTTGTCATCAAATTCTCATCGGCTGCTGACTGCCCTTGTTGACT
ttttctttattctcat CT-rich tract
aagaaatttctttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaatttctttattcccatggatttcttgatgcattactgtttcccctcaatgaggtttacaagaaatttctttattaaagaagtggttttctttattctcatgcttacagGGAATCCTCCAATCACAAGGAAGGTTATTAAGGAAAATGAGGTTTATGCCATCTTCCTTGTCATCAAATTCTCATCGGCTGCTGACTGCCCTTGTTGACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT