Sequence
atgc intronic sequence ATGC exonic sequence...aagtaccaatatagatgcaaaaatggaaatttttcgttttctacacatcagttatgtaaattatgtactagtctgatatggtctctttattttggcaagaTGGTTAGGAATTTTAAACAACCACTTCTGAAGCTACTGGAGTCTGGGAATATAGACCTTTGCTTTGCCAATGAGGATGAGGCAACAGAGCTTCTAAGG
Basic information
species | Glycine max |
transcript | GLYMA17G37040.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G37040.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g01620.1 (Oryza sativa), 3'ss of exon 5
aagtaccaatatagatgcaaaaatggaaatttttcgttttctacacatcagttatgtaaattatgtactagtctgatatggtctctttattttggcaagaTGGTTAGGAATTTTAAACAACCACTTCTGAAGCTACTGGAGTCTGGGAATATAGACCTTTGCTTTGCCAATGAGGATGAGGCAACAGAGCTTCTAAGG
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----------------gtctgaccgcagctcattggtaccgta-aggtctttttt-tggtacaggcaccagtctgattttgtttatttattacac--agATGGTTCGTGACTATAGGACACAACTCATTGACCTTTTGGAAACTGGCAACATTGACCTTTGCTTTGCCAATGAGGATGAAGCTAGAGAGCTTCTAGG-
upper sequence: GLYMA17G37040.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G19600.1 (Arabidopsis thaliana), 3'ss of exon 5
aagtaccaatatagatgcaaaaatggaaatttttcgttttctacacatcagttatgtaaattatgtactagtctg-atatggtctctttattttggcaagaTGGTTAGGAATTTTAAACAACCACTTCTGAAGCTACTGGAGTCTGGGAATATAGACCTTTGCTTTGCCAATGAGGATGAGGCAACAGAGCTTCTAAGG
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--gtatatctttgattggaaaaacgaaactctt---gtttcagttcctccttttaaaatatgatctgtggctttacaaatgatcaagcatttgtgactagATGGTCAGGAATTCTAAATCAGAGCTTCGACAGCTTCTGGAGTCTGGTAACATAGATCTTTGCTTTGCTAACGAGGACGAAGCAGCAGAGCTCCTTAG-
upper sequence: GLYMA17G37040.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv18s0001g12750.t01 (Vitis vinifera), 3'ss of exon 5
--aagtaccaatatag-atgcaaaaatggaaatttttcgttttctacacatcagttatgtaaattatgtactagtctgatatggtctctttattttggcaagaTGGTTAGGAATTTTAAACAACCACTTCTGAAGCTACTGGAGTCTGGGAATATAGACCTTTGCTTTGCCAATGAGGATGAGGCAACAGAGCTTCTAAGG
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tttgactgcagtatcctactcatgcactggaacagacttgttctgaattgctgggtaaggattgtctcttttaacc--attgcttttttttaccttggccagATGGTTCGGAACTTTAGAGGACCTCTTCTAGAGTTACTGCAATCAGGGGATATAGATCTTTGCTTTGCCAATGAGGATGAAGCAAGAGAGCTGTTAAG-
upper sequence: GLYMA17G37040.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv06s0004g07610.t01 (Vitis vinifera), 3'ss of exon 4
aagtaccaatatagatgcaaaaatggaaatttttcg--ttttctacacatcagttatgtaaattatgtactagtctgatatggtctctttattttggcaagaTGGTTAGGAATTTTAAACAACCACTTCTGAAGCTACTGGAGTCTGGGAATATAGACCTTTGCTTTGCCAATGAGGATGAGGCAACAGAGCTTCTAAGG
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aatatcctactcatgcactggaacagacttgttctgaattactgggtcaggaattgtcttttttaaccatt-gtttttttttttattattaccatggccagTTGGTTCGGAACTTTAGAGGACCTCTTCTAAAGTTACTGCAATCAGGGGATATAGATCTTTGCTTTGCCAATGAGGATGAAACAAGAGAGCTGTTAAG-Mapped 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|58016921|gb|CX703663.1|CX703663EST: AGCAAAACAGGAAGGTCTTCTTGTTTCCTTAGACTTGGCCAGCTTTGAGA TGGTTAGGAATTTTAAACAACCACTTCTGAAGCTACTGGAGTCTGGGAATA
genomic: AGCAAAACAGGAAGGTCTTCTTGTTTCCTTAGACTTGGCCAGCTTTGAGGtattctacac ... tttggcaagaTGGTTAGGAATTTTAAACAACCACTTCTGAAGCTACTGGAGTCTGGGAATA
EST:
gi|57574958|gb|CX547933.1|CX547933EST: AGCAAAACAGGAAGGTCTTCTTGTTTCCTTAGACTTGGCCAGCTTTGAGA TGGTTAGGAATTTTAAACAACCACTTCTGAAGCTACTGGAGTCTGGGAATA
genomic: AGCAAAACAGGAAGGTCTTCTTGTTTCCTTAGACTTGGCCAGCTTTGAGGtattctacac ... tttggcaagaTGGTTAGGAATTTTAAACAACCACTTCTGAAGCTACTGGAGTCTGGGAATA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catcagttatgtaaattatgtactagtctgatatggtctctttattttggcaagaTGGTTAGGAATTTTAAACAACCACTTCTGAAGCTACTGGAGTCTGGGAATATAGACCTTTGCTTTGCCAATGAGGATGAGGCAACAGAGCTTCTAAGG
gtctgat putative branch site (score: 4)
tctctttatttt putative PPT
ttatgtaaattatgta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aagtaccaatatagatgcaaaaatggaaatttttcgttttctacacatcagttatgtaaattatgtactagtctgatatggtctctttattttggcaagaTGGTTAGGAATTTTAAACAACCACTTCTGAAGCTACTGGAGTCTGGGAATATAGACCTTTGCTTTGCCAATGAGGATGAGGCAACAGAGCTTCTAAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - -gatgcaa
- - - - - - - - - - - - - - - - - - - - ctacaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatgtac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatatg