Sequence
atgc intronic sequence ATGC exonic sequence...atatttcacaatgattgttcttatgctactttgtctcttgtttttgtcttcagctacaataagctgtataatttcgctaactcttatttttcttaaatagGTAACTTGGATGAAAAGGTACCTGAGAGGGTCTTGTATGAGATTCTTATTCAGGTAGGTCGTGTTGTAGACCTACACATACCACGTGACAAGGAAACTAA
Basic information
species | Oryza sativa |
transcript | LOC_Os05g35274.5 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g35274.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G175676_T06 (Zea mays), 3'ss of exon 1
------atatttcacaatgattgttcttatgctactttgtctcttgttttt-gtcttcagctacaataagctgtataatttcgctaactcttatttttcttaaatagGTAACTTGGATGAAAAGGTACCTGAGAGGGTCTTGTATGAGATTCTTATTCAGGTAGGTCGTGTTGTAGACCTACACATACCACGTGACAAGGAAACTAA
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ctggtacaatttaaccaatgtggtcgttttgttattctacctcttgttttttgttgccagacataata-------tattagtgttgtgtgttatttttcttaaatagGTAACTTGGATGACAAGGTTCCTGAGAGGGTTCTGTATGAAATTCTTATTCAG-----------------------------------------------
upper sequence: LOC_Os05g35274.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G175676_T01 (Zea mays), 3'ss of exon 1
------atatttcacaatgattgttcttatgctactttgtctcttgttttt-gtcttcagctacaataagctgtataatttcgctaactcttatttttcttaaatagGTAACTTGGATGAAAAGGTACCTGAGAGGGTCTTGTATGAGATTCTTATTCAGGTAGGTCGTGTTGTAGACCTACACATACCACGTGACAAGGAAACTAA
|||| || | | || || || || | | ||||||||||| || ||| | |||| || | | | | |||||||||||||||||||||||||||||| ||||| ||||||||||| ||||||| ||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||
ctggtacaatttaaccaatgtggtcgttttgttattctacctcttgttttttgttgccagacataata-------tattagtgttgtgtgttatttttcttaaatagGTAACTTGGATGACAAGGTTCCTGAGAGGGTTCTGTATGAAATTCTTATTCAGGTAGGTCGTGTTGTAGACCTACACATACCTCGTGACAAGGAAACTAG
upper sequence: LOC_Os05g35274.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G175676_T08 (Zea mays), 3'ss of exon 1
atatttcacaatgattgttcttatgctactttgtctcttgtttttgtcttcagctacaataagctgtataatttcgctaactcttatttttcttaaatagGTAACTTGGATGAAAAGGTACCTGAGAGGGTCTTGTATGAGATTCTTATTCAGGTAGGTCGTGTTGTAGACCTACACATACCACGTGACAAGGAAACTAA-----------------------------------------------------
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-----------------------------------------------------ttgccagacataatatattagtgttgtgtgttatttttcttaaataggtaacttggatgacaaggttcctgagagggttctgtatgaaattcttattcagGTAGGTCGTGTTGTAGACCTACACATACCTCGTGACAAGGAAACTAGCCGACCAAAAGGCTATGCTTTTGCTGAGTATGAAACAGAGGAGATTGCCCAAT
upper sequence: LOC_Os05g35274.2 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv02s0109g00370.t01 (Vitis vinifera), 3'ss of exon 1
-atatttcacaatgattgttcttatgctactttgtctcttgtttttgtcttcagctacaataagctgtataatttcgctaactcttatttt--tcttaaatagGTAACTTGGATGAAAAGGTACCTGAGAGGGTCTTGTATGAGATTCTTATTCAGGTAGGTCGTGTTGTAGACCTACACATACCACGTGACAAGGAAACTAA
|| | | | || ||||| | || || | |||| || || | ||| | | | |||| | || |||||||| |||||||| | |||| |||||||| |||||||| ||||| ||||||||||| | || || ||| || |||| || ||||||||||||||| |
agcatgttatt-tatctgcctttatgtt--caagttatttaaataataattcatataaaaaggctaacgtgttttaattggttttaatttcaattgtacatagGTAATTTGGATGAGAGGGTAAGCGAGAGGGTTTTGTATGATATTCTGATTCAGGTAGGGAGGGTGGTGGACTTATACATCCCTCGTGACAAGGAAACTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtcttcagctacaataagctgtataatttcgctaactcttatttttcttaaatagGTAACTTGGATGAAAAGGTACCTGAGAGGGTCTTGTATGAGATTCTTATTCAGGTAGGTCGTGTTGTAGACCTACACATACCACGTGACAAGGAAACTAA
cgctaac putative branch site (score: 2)
ctcttatttttctt CT-rich tract
taactcttatttttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atatttcacaatgattgttcttatgctactttgtctcttgtttttgtcttcagctacaataagctgtataatttcgctaactcttatttttcttaaatagGTAACTTGGATGAAAAGGTACCTGAGAGGGTCTTGTATGAGATTCTTATTCAGGTAGGTCGTGTTGTAGACCTACACATACCACGTGACAAGGAAACTAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA