Sequence
atgc intronic sequence ATGC exonic sequencegtatttactgtattaaaatatgttcataacatagccctcagcagccttactgtaagttccacgggctagactgaatgtctgattcattattgttttccctttgtttccagGTTTTCTTTGCTACGCTGCTATAGTAGTTGCCGCAGCACTGGTGCTTATATATTTTGTTGTCCCTCAACATGGACAAACAAACATCATGGTGTACATCGG
Basic information
species | Oryza sativa |
transcript | LOC_Os11g09140.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os11g09140.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G104147_T03 (Zea mays), 3'ss of exon 4
--------------------gtatttactgtattaaaatatgttcataac--atagccctca--gcagccttactgtaagttccacgggctagactgaatgtctgattcattattgttttccctttgtttccagGTTTTCTTTGCTACGCTGCTATAGTAGTTGCCGCAGCACTGGTGCTTATATATTTTGTTGTCCCTCAACATGGACAAACAAACATCATGGTGTACATCGG
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gtatttttttttggaaacaggtatctagtatactgaa-tattaccaagattggttaacatcattacgactttgttacaattccaaagaaccagatttattaattatttaactatt-----ccttgtatttgcagCTTTCCTTTGCTATGCGGCTATAGTAGTTGCGTCAGCCTTAGTGCTTATATATTTTGTTGTCCCTCATCATGGACAAACAAACATAATGGTGTACATTGG
upper sequence: LOC_Os11g09140.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G129268_T01 (Zea mays), 3'ss of exon 4
-------------------------------------gtatttactg-tattaaaatatgttcataacatagccctcagcagccttactgtaagttccacgggctagactgaatgtctgattcattattgttttccctttgtttccagGTTTTCTTTGCTACGCTGCTATAGTAGTTGCCGCAGCACTGGTGCTTATATATTTTGTTGTCCCTCAACATGGACAAACAAACATCATGGTGTACATCGG
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gtatttactattgttttttttgaagcaggtatttagtatactgagtactaccgagactgattaacatcattattcattatgactttgttacaattccaataagctagatt--attcttaattacttatcagtt-ccttgtattttcagCTTTCCTTTGCTATGCGGCTATAGTAGTTGCAGCAGCCTTAGTGCTTATATATTTTGTTGTCCCTCATCATGGACAAACAAACATAATGGTGTACATTGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttccacgggctagactgaatgtctgattcattattgttttccctttgtttccagGTTTTCTTTGCTACGCTGCTATAGTAGTTGCCGCAGCACTGGTGCTTATATATTTTGTTGTCCCTCAACATGGACAAACAAACATCATGGTGTACATCGG
gtctgat putative branch site (score: 4)
ttattgttttcccttt putative PPT
attcattattgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatttactgtattaaaatatgttcataacatagccctcagcagccttactgtaagttccacgggctagactgaatgtctgattcattattgttttccctttgtttccagGTTTTCTTTGCTACGCTGCTATAGTAGTTGCCGCAGCACTGGTGCTTATATATTTTGTTGTCCCTCAACATGGACAAACAAACATCATGGTGTACATCGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA