Sequence
atgc intronic sequence ATGC exonic sequence...tctagctaaggcgatcatcgttgtaggataagtgcagtgttgttttattgccttacctactgtcaccagtgaatcatcgtctgcttttttttttgggcagGTTTCGAACTTCTTTATTGGCCTCTACTTCTTGAGCGTCGTCAACAAATTCGGAATCAGCACTGTGTATTTGGGATTTGCATCTGTTTGCGCTCTTGCTG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g04190.4 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g04190.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G098011_T01 (Zea mays), 3'ss of exon 13
tctagctaaggcgatcatcgttgtag--gataagtgcagtgttgttttattgccttacctactgtcaccagtgaatcatcgtctgcttttttttttgggcagGTTTCGAACTTCTTTATTGGCCTCTACTTCTTGAGCGTCGTCAACAAATTCGGAATCAGCACTGTGTATTTGGGATTTGCATCTGTTTGCGCTCTTGCTG
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-ctgg-taagacgaacactaccataattaagtaattaaccttggctttacttacatataccattgagtccttcacctggttcctggttttctttttcttcagGTATCCAACTTTTTTATTGGCCTGTACTTCTTGAGTGTTGTCAACAAGTTTGGGATCAGCAATGTATATTTGGGATTTGCATCAGTGTGCGTCCTTGCAG
upper sequence: LOC_Os01g04190.1 (Oryza sativa), 3'ss of exon 13
lower sequence: Vv14s0006g02720.t01 (Vitis vinifera), 3'ss of exon 13
--tctagctaaggcgatcatcgttgtaggataagtgcagtgttgttttattgccttacctactgtcacc-agtgaatcatcgtctgcttttttttttgggcagGTTTCGAACTTCTTTATTGGCCTCTACTTCTTGAGCGTCGTCAACAAATTCGGAATCAGCACTGTGTATTTGGGATTTGCATCTGTTTGCGCTCTTGCTG
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gaagtactttctaaaaacactgtcaaatggaagtttcttcatggtgctaatgcagtag--actttcatctaatggaacttcatg-attttcccattgtatcagATCTCAAACTTTGTGATTGGGCTTTACTTCTTGAGCGTTGTAAACAAGTTCGGGATCAGCACAGTTTACTTGGGATTTTCAGCCGTCTGTCTTCTTGCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tattgccttacctactgtcaccagtgaatcatcgtctgcttttttttttgggcagGTTTCGAACTTCTTTATTGGCCTCTACTTCTTGAGCGTCGTCAACAAATTCGGAATCAGCACTGTGTATTTGGGATTTGCATCTGTTTGCGCTCTTGCTG
gccttac putative branch site (score: 3)
tcatcgtctgcttttt putative PPT
tttttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctagctaaggcgatcatcgttgtaggataagtgcagtgttgttttattgccttacctactgtcaccagtgaatcatcgtctgcttttttttttgggcagGTTTCGAACTTCTTTATTGGCCTCTACTTCTTGAGCGTCGTCAACAAATTCGGAATCAGCACTGTGTATTTGGGATTTGCATCTGTTTGCGCTCTTGCTG
- - - - - - - - - - - - - - - - - - -tgttgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - -cctactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgaatc