Sequence
atgc intronic sequence ATGC exonic sequencegttcggccctcatacttcaaatccaactatcctgcaatccttgtatgaacaatgctttgggttcttgcctgggctttctactttctacaagcaatcatgtgcctgctacttctgtagGTAGTGAAAGAGACAATTGACCCAAGTGCTCGTGTTGAGTTCAAACCCAATACTGCAGATGATCCACACATGAGAAAACCAGACATCTCGAAGGCCAAAT
Basic information
species | Oryza sativa |
transcript | LOC_Os03g17230.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g17230.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G347717_T01 (Zea mays), 3'ss of exon 6
gttcggccctcatacttcaaatccaactatcctgcaatccttgtatgaacaatgctttgggttcttgcctgggctttctactttctacaagcaatcatg-tgcctgctacttctgtagGTAGTGAAAGAGACAATTGACCCAAGTGCTCGTGTTGAGTTCAAACCCAATACTGCAGATGATCCACACATGAGAAAACCAGACATCTCGAAGGCCAAAT
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------gtctgaaatttggtatccattcttctttcgaaataccacggcttcatgtctccaatatgcctaccagcctaccaggaatcatgagtcatgacactgcacttttttgccgcagGTGGTAAAAGAAACAATCGACCCAGGTGCATCTGTCGAGTTCAAACCCAATACTGCGGATGATCCGCACATGAGAAAACCTGACATTTCGAAGGCTAAAT
upper sequence: LOC_Os03g17230.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA13G19640.1 (Glycine max), 3'ss of exon 6
gttcggccctcatacttcaaatccaactatcctgcaatccttgtatgaacaatgctttgggttcttgcctgggctttctactttctacaagcaatcatgtgcctgctacttctgtagGTAGTGAAAGAGACAATTGACCCAAGTGCTCGTGTTGAGTTCAAACCCAATACTGCAGATGATCCACACATGAGAAAACCAGACATCTCGAAGGCCAAAT
| | | || || ||| | | | | || | | | | ||| | | | ||| | || |||| | || | |||| || ||||| |||||||| |||||||| | || | |||||| |||||||| ||||||||||||||||| || ||||| || || || ||
-----ccttttacacagtaagggcaaacttttggtagtg-------gagtgagattgaagttactttattatggatcctatcattgtcatcttttcatata-----taaacacgcagGTTGTAAAAGAAACAATTGATTCAAGTGCTACAATAGAATACAAACCAAATACTGCTGATGATCCACACATGAGGAAGCCAGATATTAGCAAAGCGAAGG
upper sequence: LOC_Os03g17230.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA10G05260.1 (Glycine max), 3'ss of exon 6
gttcggccctcatacttcaaatccaactatcctgcaatccttgtatgaacaatgctttgggttcttgcctgggctttctactttctacaagcaatcatgtgcctgctacttctgtagGTAGTGAAAGAGACAATTGACCCAAGTGCTCGTGTTGAGTTCAAACCCAATACTGCAGATGATCCACACATGAGAAAACCAGACATCTCGAAGGCCAAAT
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-----tgccttttacagtaagggcacacttttggcgagtggagtgagattgaagtt---actttcattatggatatcctatcattgtcatcttttcataaacacac---------agGTTGTCAAAGAAACAATTGATTCAAGTGCTACAATAGAATACAAACCAAATACTGCTGATGATCCACACATGAGGAAGCCAGATATTAGCAAAGCCAAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttgcctgggctttctactttctacaagcaatcatgtgcctgctacttctgtagGTAGTGAAAGAGACAATTGACCCAAGTGCTCGTGTTGAGTTCAAACCCAATACTGCAGATGATCCACACATGAGAAAACCAGACATCTCGAAGGCCAAAT
ctacttct CT-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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcggccctcatacttcaaatccaactatcctgcaatccttgtatgaacaatgctttgggttcttgcctgggctttctactttctacaagcaatcatgtgcctgctacttctgtagGTAGTGAAAGAGACAATTGACCCAAGTGCTCGTGTTGAGTTCAAACCCAATACTGCAGATGATCCACACATGAGAAAACCAGACATCTCGAAGGCCAAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG