Sequence
atgc intronic sequence ATGC exonic sequencegtttgttactataacccccccccccccccccccctctctttatatttaatgcgtcatgttatttcattacatcagcttttttcattgaaattgcttcacatgcagcaaaacattggcttgcagtgtgttaatattctccttttgcagGCTGCCCATGATGCTTTTGTTGAAACTAGTGGAGCCCTTAACACTATTGCGGCTTCTTTGATGAAGATTGCTAATGACATACGGTTGTTAGGAAG
Basic information
species | Glycine max |
transcript | GLYMA02G01920.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G01920.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os03g21950.1 (Oryza sativa), 3'ss of exon 9
gtttgttactataacccccccccccccccccccctctctttatatttaatgcgtcatgttatttcatt-acatcagcttttttcattgaaattgcttcacatgcagcaaaacattggcttgcagtgtgttaatattctccttttgcagGCTGCCCATGATGCTTTTGTTGAAACTAGTGGAGCCCTTAACACTATTGCGGCTTCTTTGATGAAGATTGCTAATGACATACGGTTGTTAGGAAG
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-----------------------------------cacaacattattaactttggaaatgtttttattgatgctagttgttggggtttg--ttctttctaatac--taagacaatccttttct---------tctttcaattgagtagGCAGCGCATGATGCTTTTGTTGAGAGCAGTGGTGCTGTAAACACAATTTCTGCATCTCTTATGAAGATAGCAAATGACATACGCTTGTTAGGAAG
upper sequence: GLYMA02G01920.1 (Glycine max), 3'ss of exon 9
lower sequence: AT5G50950.3 (Arabidopsis thaliana), 3'ss of exon 8
gtttgttacta--taacccccccccccccccccccctctctttatatttaatgcgtcatgttatttcattacatcagcttttttcattgaaattgcttcacatgcagcaaaacattggcttgcagtgtgttaatattctccttttgcagGCTGCCCATGATGCTTTTGTTGAAACTAGTGGAGCCCTTAACACTATTGCGGCTTCTTTGATGAAGATTGCTAATGACATACGGTTGTTAGGAAG
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gttagcctctaaataactttcatcatcatcaatgtccaaatttagtcttagcgtcttccactgggtt-ctaaatcaaacaagatgcttctgaatggttgatgtatatgaaa----taagttgttgagt-----tattacgcctttgtagGCTGCACACGATGCTTGTGTTGAAACAAGTGGATCTCTTAACACAATCGCCACATCATTGATGAAGATTGCCAATGATATACGTTTTCTTGGAAG
upper sequence: GLYMA02G01920.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv07s0005g00880.t01 (Vitis vinifera), 3'ss of exon 10
gtttgttactataacccccccccccccccccccctctctttatatttaatgcgtcatgttatttcattacatcagcttttttcattgaaattgcttcacatgcagcaaaacattggcttgcagtgtgttaatattctccttttg---cagGCTGCCCATGATGCTTTTGTTGAAACTAGTGGAGCCCTTAACACTATTGCGGCTTCTTTGATGAAGATTGCTAATGACATACGGTTGTTAGGAAG
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--------------------------------------ttgttaggtagtgaaggaatatattccatt-tattgcctcatatcttgtaaa-------atttactacaaaatatt---ttgcattct-taaatgtttttcttttctgccagGCTGCACATGATGCATTTGTTGAAACTAGTGGTTCAGTTAACACTGTTGCTACTTCCCTGATGAAGATTGCTAATGATATACGCTTATTAGGAAGMapped 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|16279870|gb|BI943659.1|BI943659EST: AGGAAACCAATCTGCCTTTTGTTACGGCAGAAAATAAGTTTGAGGCCTTG GCTGCCCATGATGCTTTTGTTGAAACTAGTGGAGCCCTTAACACTATTGCT
genomic: AGGAAACCAATCTGCCTTTTGTTACGGCAGAAAATAAGTTTGAGGCCTTGgtttgttact ... ccttttgcagGCTGCCCATGATGCTTTTGTTGAAACTAGTGGAGCCCTTAACACTATTGCG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcttcacatgcagcaaaacattggcttgcagtgtgttaatattctccttttgcagGCTGCCCATGATGCTTTTGTTGAAACTAGTGGAGCCCTTAACACTATTGCGGCTTCTTTGATGAAGATTGCTAATGACATACGGTTGTTAGGAAG
tgttaat putative branch site (score: 3)
tattctccttttgc CT-rich tract
tgttaatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgttactataacccccccccccccccccccctctctttatatttaatgcgtcatgttatttcattacatcagcttttttcattgaaattgcttcacatgcagcaaaacattggcttgcagtgtgttaatattctccttttgcagGCTGCCCATGATGCTTTTGTTGAAACTAGTGGAGCCCTTAACACTATTGCGGCTTCTTTGATGAAGATTGCTAATGACATACGGTTGTTAGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA