Sequence
atgc intronic sequence ATGC exonic sequence...acagaaatttttacattatagctgttagtctgttgaaataattttgctggattctgtaacatgatgaattggtgatgtattaacactttattactctcagGTTGCCATCCCAGTTGTACCCACAATCAGGGTACTTGTGACATTCACAAAGTTTGAAGAGCTACAGCCATTAGAGGAGTTCACCACACCGCCATCCAGCC
Basic information
species | Oryza sativa |
transcript | LOC_Os07g25460.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g25460.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G050885_T01 (Zea mays), 3'ss of exon 1
acagaaatttttacattatagctgttagtctgttgaaataatttt--gctg-gattctgtaacatgatgaattggtgatgtattaac-actttattactctcagGTTGCCATCCCAGTTGTACCCACAATCAGGGTACTTGTGACATTCACAAAGTTTGAAGAGCTACAGCCATTAGAGGAGTTCACCACACCGCCATCCAGCC
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-gggaaatgtttgctgcg-aattggttgctgattttatcaattcttagctccaatattgtaaca--gtgattgtgtaacttagtaatgaattttctcccctcagGTTGCCATCCCAGTCGTGCCTACGATCAGAGTGCTTGTGACATTCACGAAATTCGAGGAGCTACAGCCGCTAGAGGAGTTCGGCACACCACCTTCAAGCC
upper sequence: LOC_Os07g25460.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G140394_T03 (Zea mays), 3'ss of exon 2
acagaaatttttacattatagctgttagtctgttgaa---ataattttgctggattctgtaacatgatgaattggtgatgtattaacactttattactctcagGTTGCCATCCCAGTTGTACCCACAATCAGGGTACTTGTGACATTCACAAAGTTTGAAGAGCTACAGCCATTAGAGGAGTTCACCACACCGCCATCCAGCC
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-ttgctctttgttgattaaacaatttcttccctgcaagttatgatcctttcggtgccattgtaatagtgaattatagctcagtaaagattt--tccctcccagGTCGCTATTCCAGTCGTGCCTACAATCAGAGTGCTTGTGACATTCACAAAATTTGAAGAGCTACAGCCGCTAGATGAGTTCACCACACCACCCTCAAGTC
upper sequence: LOC_Os07g25460.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA20G18890.1 (Glycine max), 3'ss of exon 1
-------acagaaatttttacattatagctgttagtctgttgaaataattttgctggattctgtaacatgatgaattggtgatgtattaacactttattactctcagGTTGCCATCCCAGTTGTACCCACAATCAGGGTACTTGTGACATTCACAAAGTTTGAAGAGCTACAGCCATTAGAGGAGTTCACCACACCGCCATCCAGCC
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attttaaatcacaggattgctatcttggctttttttttcttcttgcatgttttctttctcttgta-tatgatg--tta--aattcatttcccctt--gtatatccagGTTGCCATCCCTGTGGTTCCCACCATCAGAGTATTGGTTACTTTTACAAAGTTTGAAGAACTAGAGCCAGTAGACGAATTTGCAACACCACCATCAAGCC
upper sequence: LOC_Os07g25460.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT3G24210.1 (Arabidopsis thaliana), 3'ss of exon 2
acagaaatttttacattatagctgttagtctgttgaaataattttgctggattctgtaacatgatgaattggtgatgtattaacactttattactctcagGTTGCCATCCCAGTTGTACCCACAATCAGGGTACTTGTGACATTCACAAAGTTTGAAGAGCTACAGCCATTAGAGGAGTTCACCACACCGCCATCCAGCC
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----gtatgttgtcgtttca--tgttaaga-gctaatcttaatgttcttgaagatgagtttttttttctttttcttatagagattgtttgtgaatgt-agGTTGCTATTCCAGTGGTACCTACAATAAAAGTGCTTGTTACATTCACAAAGTTTGAAGAAATTGAGCCTGTAGATGAGTTTAAGACGCCTCTCTCGAGCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctggattctgtaacatgatgaattggtgatgtattaacactttattactctcagGTTGCCATCCCAGTTGTACCCACAATCAGGGTACTTGTGACATTCACAAAGTTTGAAGAGCTACAGCCATTAGAGGAGTTCACCACACCGCCATCCAGCC
tattaac putative branch site (score: 1)
ttactctc putative PPT
tattaacactttatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acagaaatttttacattatagctgttagtctgttgaaataattttgctggattctgtaacatgatgaattggtgatgtattaacactttattactctcagGTTGCCATCCCAGTTGTACCCACAATCAGGGTACTTGTGACATTCACAAAGTTTGAAGAGCTACAGCCATTAGAGGAGTTCACCACACCGCCATCCAGCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
acagaaa
- - - - - - - - - -agctgtt
- - - - - - - - - - - - - - -ctgttga
- - - - - - - - - - - - - - - - - - - - - - - - -gattctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggtgatg