Sequence
atgc intronic sequence ATGC exonic sequencegtgagtttacctatgcttaacttctcttggcatcttgtcctgttccctgtcgtatcctcaatcgaaaatttgtaatatttgattgagattaatgttttatacatagGAAATGAAGCAGCAAGGAGTGGTGGATGATAGGCTCCAATTGTTACGTGACGTTACTGGATCATTTAGGCCTGCAGTGCTGACAGCACTCATGGGAGTCA
Basic information
species | Oryza sativa |
transcript | LOC_Os06g36090.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g36090.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G366146_T01 (Zea mays), 3'ss of exon 10
gtgagtttacctatgcttaacttctcttggcatcttgtcctgttccctgtcgtatcctcaatcgaaaatttgtaatatttgatt--gagattaatgt---------tttatacatagGAAATGAAGCAGCAAGGAGTGGTGGATGATAGGCTCCAATTGTTACGTGACGTTACTGGATCATTTAGGCCTGCAGTGCTGACAGCACTCATGGGAGTCA
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gtgagttcacct----tcaattattctcagcaatttttcctgtcccatttgttaccttcctcaatgtgcttgtatcgtcaaatatggaaactgatggaaaactccgttgtttcccagGAAATGAAACAGCAAGGAGTGCAGGATGACCGACTCCAATTGTTGCGTGAGGTTACGGGATCATTCAGGCCTGGAGTGCTGACAGCACTTATGGGTGTCA
upper sequence: LOC_Os06g36090.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G029506_T01 (Zea mays), 3'ss of exon 14
gtgagtttacctatgcttaacttctcttggcat-cttgtcctgttccctgtc-------gtatcctcaatcgaaaatttgtaatatttgattgagattaatgttttatacatagGAAATGAAGCAGCAAGGAGTGGTGGATGATAGGCTCCAATTGTTACGTGACGTTACTGGATCATTTAGGCCTGCAGTGCTGACAGCACTCATGGGAGTCA
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gtgagttgaccttcgagtattctcagcagttgttcctgtcccatttcttaccttcttcaatgtgcttgtacggtaaaatatggaaactgatggggaattctattgtttgcccagGAAATGAAACATCAAGGAGTGCAGGATGACAGACTCCAATTGTTGCGTGAGGTTACAGGATCATTCAGGCCTGGAGTGCTGACAGCACTTATGGGTGTCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtatcctcaatcgaaaatttgtaatatttgattgagattaatgttttatacatagGAAATGAAGCAGCAAGGAGTGGTGGATGATAGGCTCCAATTGTTACGTGACGTTACTGGATCATTTAGGCCTGCAGTGCTGACAGCACTCATGGGAGTCA
gattaat putative branch site (score: 3)
aaaatttgtaatattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtttacctatgcttaacttctcttggcatcttgtcctgttccctgtcgtatcctcaatcgaaaatttgtaatatttgattgagattaatgttttatacatagGAAATGAAGCAGCAAGGAGTGGTGGATGATAGGCTCCAATTGTTACGTGACGTTACTGGATCATTTAGGCCTGCAGTGCTGACAGCACTCATGGGAGTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG