Sequence
atgc intronic sequence ATGC exonic sequence...agtaggataaggcttttgatgctattgttgtttgtacctagttgatttctatatcaacatattgggtgtcatatgcttatgaatttcattgattggccagATTCCTCTAGCTCGATATTTACCTACTTGGAGAGGGAACGTTATAGATGCACAAATCGAAATGAATCCATCCCGTGTTTTAGGCATGTCTCTATCTGTCA
Basic information
species | Glycine max |
transcript | GLYMA16G01410.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G01410.2 (Glycine max), 3'ss of exon 5
lower sequence: AT1G17350.1 (Arabidopsis thaliana), 3'ss of exon 7
agtaggataaggcttttgatgctattgttgtttgtacctagttgatttctatatca-acatattgggtgtcatatgcttatgaattt-cattgattg-gccagATTCCTCTAGCTCGATATTTACCTACTTGGAGAGGGAACGTTATAGATGCACAAATCGAAATGAATCCATCCCGTGTTTTAGGCATGTCTCTATCTGTCA
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---atgaaaacataaccaaaaagacagatctccattatgaatcaacttgaatatttcacttgtcgtctaaggcctattaataacctgatgttgaatatatcagATTCCTCTAGCTCGATACTTGCCAACATGGAGAGGAAATGTTATAGATGTGGAAATGGAGATGAATCCAGGTCGTGTTCTAGGTATGTCACTGTCCGTAA
upper sequence: GLYMA16G01410.2 (Glycine max), 3'ss of exon 5
lower sequence: AT1G17350.2 (Arabidopsis thaliana), 3'ss of exon 7
-----------------------------------------------------------------------------agtaggataaggcttttgatgctattgttgtttgtacctagttgatttctatatca-acatattgggtgtcatatgcttatgaattt-cattgattg-gccagATTCCTCTAGCTCGATATTTACCTACTTGGAGAGGGAACGTTATAGATGCACAAATCGAAATGAATCCATCCCGTGTTTTAGGCATGTCTCTATCTGTCA
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gttaccaacaaaaagcttagagcattatacacatccttttttgttttttaactctctttagacaaaaccttcggctttagatgaaaacataaccaaaaagacagatctccattatgaatcaacttgaatatttcacttgtcgtctaaggcctattaataacctgatgttgaatatatcagATTCCTCTAGCTCGATACTTGCCAACATGGAGAGGAAATGTTATAGATGTGGAAATGGAGATGAATCCAGGTCGTGTTCTAGGTATGTCACTGTCCGTAA
upper sequence: GLYMA16G01410.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv09s0002g00680.t01 (Vitis vinifera), 3'ss of exon 6
agtaggataaggcttttgatgctattgttgtttgtacctagttgatttctatatcaacatattgggtgtcatatgcttatgaattt---cattgat---tggccagATTCCTCTAGCTCGATATTTACCTACTTGGAGAGGGAACGTTATAGATGCACAAATCGAAATGAATCCATCCCGTGTTTTAGGCATGTCTCTATCTGTCA
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-ttgagagttattctgcgttgccatgatc--tagaacttgtttttttggtgaatgaatatatc---ttttctgtgtttgaaaacctgaacagtggtgtcttttcagATTCCTCTTGCTCATTACCTACCAACATGGAGAGGAAATGTTATAGATGCAGAGATAGAAATGAATCCATCGCGTATCGTCGGTATGTCTCTGTCTGTCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttctatatcaacatattgggtgtcatatgcttatgaatttcattgattggccagATTCCTCTAGCTCGATATTTACCTACTTGGAGAGGGAACGTTATAGATGCACAAATCGAAATGAATCCATCCCGTGTTTTAGGCATGTCTCTATCTGTCA
cattgat putative branch site (score: 4)
ttatgaatttcatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agtaggataaggcttttgatgctattgttgtttgtacctagttgatttctatatcaacatattgggtgtcatatgcttatgaatttcattgattggccagATTCCTCTAGCTCGATATTTACCTACTTGGAGAGGGAACGTTATAGATGCACAAATCGAAATGAATCCATCCCGTGTTTTAGGCATGTCTCTATCTGTCA
- - - - - - - - tgatgct
- - - - - - - - - - - - - - tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - atcaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcttatg