Sequence
atgc intronic sequence ATGC exonic sequencegtcagttacaatagttgcacagattgcctgagcggtgtctgcacttttgctattgtaatttgaggtggttatcagagtactgtgaaatcttgacatactttgctttttgcagTAACTTCTCAGAGATCTTTGATGTTGATTGGTTTATATCATTTCTGTCAAAAGATGTCAAAATTATCAAGCAACTTCCTACTAAGGGTAGTAGGAAAGCA
Basic information
species | Glycine max |
transcript | GLYMA06G02110.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G02110.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G20550.1 (Arabidopsis thaliana), 3'ss of exon 5
gtcagttacaatagttgcacagattgcctgagcggtgtctgcacttttgcta-ttgtaatttgaggtggttatcagagtactgtgaaatcttgacatactttgctttttgcagTAACTTCTCAGAGATCTTTGATGTTGATTGGTTTATATCATTTCTGTCAAAAGATGTCAAAATTATCAAGCAACTTCCTACTAAGGGTAGTAGGAAAGCA-
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------------------------------gttcgtactagctctcgtaaaaatcaaaacattatgcatcttatttagtattaacatacttttgtgctttttatatatgccagTGACTTCTCGAACATTTTCGATGTTGATTGGTTTATGTCATTTCTCTCAAAAGATGTCAAAATCATTGAGAAACTTCC-ACAGAAAGGAGGGCAAACATGG
upper sequence: GLYMA06G02110.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G76270.1 (Arabidopsis thaliana), 3'ss of exon 4
gtcagttacaatagttgcacagattgcctgag-cggtgtctgcacttttgctattgtaatttgaggtggttatcagagtactgtgaaatcttgacatactttgctttttgcagTAACTTCTCAGAGATCTTTGATGTTGATTGGTTTATATCATTTCTGTCAAAAGATGTCAAAATTATCAAGCAACTTCCTACTAAGGGTAGTAGGAAAGCA-
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-------------------------gtctgagacagattaagcatacttagctttttcttatgaga--aacgttatgcatctttgtaactttgtgaatttttg-----tgcagTGACTTCTCGCATATTTTCGATGTTGATTGGTTTATCTCATTTCTGTCTGGAGACGTCAGAATTATAAAGCAACTTCC-ACTGAAAGGAGGGCGTACATGG
upper sequence: GLYMA06G02110.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0001g00100.t01 (Vitis vinifera), 3'ss of exon 5
gtcagttacaatagttgcacagattgcctgagcggtgtctgcacttt------tgctattg-----taat-ttgaggtggttatcagagta-----ctgtgaaatc--ttgaca-------tactttgctttttgcagTAACTTCTCAGAGATCTTTGATGTTGATTGGTTTATATCATTTCTGTCAAAAGATGTCAAAATTATCAAGCAACTTCCTACTAAGGGTAGTAGGAAAGCA
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gttagtcattgaatgagcatatgcgttctgctacctttttgcaatttatattttgttgttggttcttagtattcaaatcttaaaaagagcatcttgctgtgatatcagttaacaaatttgttactctgtcttctgcagTAATTTCTCAGAGATCTTTGATGTTGATTGGTTTATTAAGTATCTATCAAAGGATGTTAAAATCATAAAACAGCTTCCTGAAAAGAAAGGGAAAACTGGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttgaggtggttatcagagtactgtgaaatcttgacatactttgctttttgcagTAACTTCTCAGAGATCTTTGATGTTGATTGGTTTATATCATTTCTGTCAAAAGATGTCAAAATTATCAAGCAACTTCCTACTAAGGGTAGTAGGAAAGCA
tcttgac putative branch site (score: 3)
ctttgcttttt putative PPT
aaatctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagttacaatagttgcacagattgcctgagcggtgtctgcacttttgctattgtaatttgaggtggttatcagagtactgtgaaatcttgacatactttgctttttgcagTAACTTCTCAGAGATCTTTGATGTTGATTGGTTTATATCATTTCTGTCAAAAGATGTCAAAATTATCAAGCAACTTCCTACTAAGGGTAGTAGGAAAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA