Sequence
atgc intronic sequence ATGC exonic sequencegtaagtttttctgcattttgttggctctgtagttcaatgatgtaacatctacttgatgtaactataacacaacaattataccttccagAGGGATGTAGTTTCTTCTCATTTGGATGGAGGGGGTTCAGTTGGCGAGGAAGGTGTGGAAGATGCCTTTGAACTACTTCATGAGATCAATGAACGCATCC
Basic information
species | Oryza sativa |
transcript | LOC_Os02g11840.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g11840.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 14
-----------------------------------------------gtaagtttttctgcattttgttggctctgtagttcaatgatgtaacatctactt----gatgtaacta--------taacacaacaatta-----taccttccagAGGGATGTAGTTTCTTCTCATTTGGATGGAGGGGGTTCAGTTGGCGAGGAAGGTGTGGAAGATGCCTTTGAACTACTTCATGAGATCAATGAACGCATCC
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gtgagttctgtcactgtcttaattgcctatgttcagttgacctttcagttacatccactattttttgtcctttttaatgtcaaattaagaagaaattatttttctggtcaaattgaaatgtattaatacaaaagtttccttttatcttgtagAGGGATGTAGTTTCATCTCATTTAGACGGAGGGGGTTCAGCTGCTGAGGAAGGTGTGGAAGATGCCTTTGAACTGCTTCATGAGATCAATGAACGTGTCC
upper sequence: LOC_Os02g11840.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G141587_T02 (Zea mays), 3'ss of exon 14
--------------------------------------------------gtaagtttttctgcattttgttggctctgtagttcaatgatgtaa-catctacttgatgtaacta---------taacacaacaatta-----taccttccagAGGGATGTAGTTTCTTCTCATTTGGATGGAGGGGGTTCAGTTGGCGAGGAAGGTGTGGAAGATGCCTTTGAACTACTTCATGAGATCAATGAACGCATCC
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gtgagttctgtcattaccttattaattgcctatgttcagtcgacctttctgttacatccactgatttgtgtcttttatgtcaaattaagaagcaatcattttttctggtcaaatggacatgtactaacacaaaagtttccttttatcttgtagAGGGATGTAGTTTCATCTCATTTGGATAGAGGGGGTTCAGCTGGTGAGGAAGGTGTGGAAGATGCCTTTGAACTGCTTCATGAGATCAACGAACGTGTCC
upper sequence: LOC_Os02g11840.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 14
------------------------------------------------------------gtaagtttttctgc-attttgttggctctgtagttcaatgatgtaacatctacttgatgtaactataacacaacaa-ttatacc-ttccagAGGGATGTAGTTTCTTCTCATTTGGATGGAGGGGGTTCAGTTGGCGAGGAAGGTGTGGAAGATGCCTTTGAACTACTTCATGAGATCAATGAACGCATCC
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gtgaggattctaaatacttgacccttttattttacacttgttgactttttatgaaaaagcatcgttttcccccctatgtttttggttaaatgaatatctgatggcacttactagtgaagcacagtaaacattttaacttccattgttgcagCGTGATGTCGTTGCATCATATTTAGATAGTGGAAGCCCTGTAGATGAGCAAGGTGTTGAAGATGCCTTTGAGCTCCTTCATGAAATGAATGAACGTGTCA
upper sequence: LOC_Os02g11840.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 3
--------------gtaagtttttctgcattttgttggctctgtagttcaatgat------gtaacatctact--tgatgtaactataacacaacaa-ttatacc-ttccagAGGGATGTAGTTTCTTCTCATTTGGATGGAGGGGGTTCAGTTGGCGAGGAAGGTGTGGAAGATGCCTTTGAACTACTTCATGAGATCAATGAACGCATCC
| | | | | || | | | ||| ||||| | || |||| ||| | | |||| || || || || ||| ||||| ||| | || |||| ||| | || || | || | ||| ||||||| |||||||||||||| || |||||||| || |||||||| ||
gtgaggattctaaattgtcccccccccccctctcttatgtttttggttaaatgaatatctgatggcacttactagtgaagcactgtaaacattttaacttccactgttgcagCATGATGTTGTTGCATCATATTTAGATAGTGGAGGGCCTGTAGATGAGCAAGGTGTTGAAGATGCCTTTGAGCTCCTTCATGAAATGAATGAACGTGTCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcaatgatgtaacatctacttgatgtaactataacacaacaattataccttccagAGGGATGTAGTTTCTTCTCATTTGGATGGAGGGGGTTCAGTTGGCGAGGAAGGTGTGGAAGATGCCTTTGAACTACTTCATGAGATCAATGAACGCATCC
ctataac putative branch site (score: 3)
taccttcc putative PPT
aacaattata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtttttctgcattttgttggctctgtagttcaatgatgtaacatctacttgatgtaactataacacaacaattataccttccagAGGGATGTAGTTTCTTCTCATTTGGATGGAGGGGGTTCAGTTGGCGAGGAAGGTGTGGAAGATGCCTTTGAACTACTTCATGAGATCAATGAACGCATCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA