Sequence
atgc intronic sequence ATGC exonic sequence...agcatatgacactaatattctcaacaaaatattgtattccttattttcttatctacaaatagatattccttatttactcctaattttcccaccatgttagGTTCCTGGAGCAGATGGACTTGTGGTCAGAGTTGTTTCATCAGTGGACAAGAAACTGGAAGTTAAACCACATTTTTTCAAGATTTTGCAAGAGGACAATT
Basic information
species | Oryza sativa |
transcript | LOC_Os06g49130.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g49130.2 (Oryza sativa), 3'ss of exon 7
lower sequence: AT1G16710.1 (Arabidopsis thaliana), 3'ss of exon 8
----------------------------------------------------------agcatatgacactaatattctcaacaaaatattgtattccttattttcttatctacaaatagat-attccttatttactcctaattttcccacca-tgttagGTTCCTGGAGCAGATGGACTTGTGGTCAGAGTTGTTTCATCAGTGGACAAGAAACTGGAAGTTAAACCACATTTTTTCAAGATTTTGCAAGAGGACAATT
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gtaatctggcggtggaatacagggttttaaagtctcatgtgattttgcattgagtcctatcttctattgtttgttgaagtgctacttcactggaaacaatagattgaagcttactggttggtcactgattgtttaatttttcttttactggcactaacagATTCCAACTGTTGAATCCCTTGTGGTTAGAGTTGTTTCATCTGTTGACAAGAAGCTAGAAGTTAAATCTCGATTTCTTGAAATTTTTCGGGAGGATAATT
upper sequence: LOC_Os06g49130.2 (Oryza sativa), 3'ss of exon 7
lower sequence: AT1G79000.2 (Arabidopsis thaliana), 3'ss of exon 9
----------------------------------------------------------agcatatgacactaatattctcaacaaaatattgtattccttattttctt--atctacaaatagatatt--ccttatttactcctaattttcccaccatgttagGTTCCTGGAGCAGATGGACTTGTGGTCAGAGTTGTTTCATCAGTGGACAAGAAACTGGAAGTTAAACCACATTTTTTCAAGATTTTGCAAGAGGACAATT
||| | | | || || | | | || | || ||| | | | | || || | | || ||| || | || || | || |||| || || |||||| | |||||||||||||| || |||||||| |||||||| ||||| | ||| | | ||||| | ||||| | ||
gtaatttaatggtggagtttgttaacgtttatttctttcatttattttcacatctgcaagctctttatttttatttttctatttgtttgatctagtgattctttgttagaaacagtatattgaagctgactttgttttttctttgacttgatacga--acagATTCCCACTGCCGAGTCCCTTGTGATTAGAGTTGTTTCATCTGTTGACAAGAAGCTGGAAGTCAAACCTCGATTTCTTGAAATTTTTCGGGAGGATAGTT
upper sequence: LOC_Os06g49130.2 (Oryza sativa), 3'ss of exon 7
lower sequence: PP1S193_70V6.1 (Physcomitrella patens), 3'ss of exon 9
--------------------------------------------------------------------------------agcatatgacactaatatt---ctcaacaaaatattgtattccttattttcttatctacaaatagatattccttatttactcctaattttcc------caccatg---ttagGTTCCTGGAGCAGATGGACTTGTGGTCAGAGTTGTTTCATCAGTGGACAAGAAACTGGAAGTTAAACCACATTTTTTCAAGATTTTGCAAGAGGACAATT
| ||| || | || || ||| ||| | | | | ||| | | || ||| ||| ||| | || | || | || ||| ||||||| | | ||||| | | |||||||||||||| || || ||||||||||| |||||||| || | || ||||| | ||||| ||||| || | |
gtacttgcacgtgcttttatttagttactgtagttattcttggatttgatctttcgagctgtcatgtttcaatcctatgtctttcacgaccttagttttaatttcgacagaattgcaaaagcaatgctgtctc-ttgctacatctccattgcttgattagtgctgacttgctgtatgatactatgagtttagGTTGCCAGTGCAGAGGCCTTAGTGGTCAGAGTTGTGTCCTCTGTGGACAAGAAGCTGGAAGTCAAGCAACGGTTTTTGGAAATTTTTCAAGAAGAAGACT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcttatctacaaatagatattccttatttactcctaattttcccaccatgttagGTTCCTGGAGCAGATGGACTTGTGGTCAGAGTTGTTTCATCAGTGGACAAGAAACTGGAAGTTAAACCACATTTTTTCAAGATTTTGCAAGAGGACAATT
tcctaat putative branch site (score: 2)
ttttcccacc CT-rich tract
tacaaatagatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agcatatgacactaatattctcaacaaaatattgtattccttattttcttatctacaaatagatattccttatttactcctaattttcccaccatgttagGTTCCTGGAGCAGATGGACTTGTGGTCAGAGTTGTTTCATCAGTGGACAAGAAACTGGAAGTTAAACCACATTTTTTCAAGATTTTGCAAGAGGACAATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA