Sequence
atgc intronic sequence ATGC exonic sequencegtaagcttgatttattaagtgcttttcctgaatttgctagaatttttgttgtttcattggttttgcctgcggtgtaagcaatggcttaatgttcttttattttgtgatggctatgcattaactgatagtttgagttactcttgtttcatttcttttaatattcctttccttctcagAACTTGAAAGGGATACATTCAGCTAGAGAGTTTGTTTGGTGGTATAATGGGCACCCGGATGGACGAAATCTTGAGCCAGACCTAAAGAGTACTGATACAG
Basic information
species | Glycine max |
transcript | GLYMA05G35620.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G35620.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g17700.1 (Oryza sativa), 3'ss of exon 4
gtaagcttgatttattaagtgcttttcctgaatttgctagaatttttgttgtttcattggttttgcctgcggtgtaagcaatggcttaatgttcttttattttgtgatggctatgcattaactgatagtttgagttactcttgtttcatttcttttaatattcctttccttctcagAACTTGAAAGGGATACATTCAGCTAGAGAGTTTGTTTGGTGGTATAATGGGCACCCGGATGGACGAAATCTTGAGCCAGACCTAAAGAGTACTGATACAG
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-----------------------------------------------------------------------tggcaag--attgtgtagtgctatcaatttatcttatgatttt-cgtt--ttgttttttcatcatgcgtgtgagttgtttattctcagtgtcatctttgttatagGATCTGAGGGGAATACATTCGGCTCGAGAGTTTGTGTGGTGGTATAATGGACATCCAGACATGTGCAACTTGGCACCTGACTTGCAAAGCACAGATTCTG
upper sequence: GLYMA05G35620.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv11s0016g03550.t01 (Vitis vinifera), 3'ss of exon 4
---------gtaagcttgatttattaagtgcttttcctgaatttgctagaatttttgttgtttcattggttttgcctgcggtgt-aagcaatggcttaatgttcttttattttgtgatggctatgcattaactgatagtttgagttactcttgtttcatttcttttaatattcctttccttctcagAACTTGAAAGGGATACATTCAGCTAGAGAGTTTGTTTGGTGGTATAATGGGCACCCGGATGGACGAAATCTTGAGCCAGACCTAAAGAGTACTGATACAG
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gtacgttttataaaaataatgttttgtgc-ctttgtttaaattatccattagtcttgcatattattttctatcacaagggatttcaaatactgaattaatggtttcaggattt-tgataatttaatttcaaaatgttataagcgtagatgtagtttctgttgtttatgtatttcttttc----cagGATTTTGCAGGAATACACTCAGCTAGAGAATTTGTTTGGTGGTATAATGGGCATCCAGACTGCAAAAACCTGGATCCTGATTTGAAGAGCACTGATACAG
upper sequence: GLYMA05G35620.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S302_37V6.1 (Physcomitrella patens), 3'ss of exon 5
gtaagcttgatttattaagtgcttttcctgaatttgctagaatttttgttgtttcattggttttgcctgcggtgtaagcaatggcttaatgttcttttattttgtgatggctatgcattaactgatagtttgagttactcttgtttcatttcttttaatattcctttccttctcagAACTTGAAAGGGATACATTCAGCTAGAGAGTTTGTTTGGTGGTATAATGGGCACCCGGATGGACGAAATCTTGAGCCAGACCTAAAGAGTACTGATACAG
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---------------------------------------------------------------------------atactttatccttgtgagcatttgtttagctcttggaatattcgcatcattagtgcctgtagcacaacttgtgctgatattt-tccgcgttgagtctgcagGAGCTGGTAGGCGTACATGCAGCAAGAGAGTTTGTCTGGTGGTATAATGGTCATCCTGATCAAGTCAACTTGCAACCAGATCTTCAATCTTCAGATACTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgatagtttgagttactcttgtttcatttcttttaatattcctttccttctcagAACTTGAAAGGGATACATTCAGCTAGAGAGTTTGTTTGGTGGTATAATGGGCACCCGGATGGACGAAATCTTGAGCCAGACCTAAAGAGTACTGATACAG
ttttaat putative branch site (score: 3)
ctcttgtttcatttct CT-rich tract
ttgtttcatttctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcttgatttattaagtgcttttcctgaatttgctagaatttttgttgtttcattggttttgcctgcggtgtaagcaatggcttaatgttcttttattttgtgatggctatgcattaactgatagtttgagttactcttgtttcatttcttttaatattcctttccttctcagAACTTGAAAGGGATACATTCAGCTAGAGAGTTTGTTTGGTGGTATAATGGGCACCCGGATGGACGAAATCTTGAGCCAGACCTAAAGAGTACTGATACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA