Sequence
atgc intronic sequence ATGC exonic sequencegtaatttactatattgctcagtctttacctagacaaaatctcatcttaattcaggaataccttaggtggactttgacattatctctgtggcagGTTTATACATCATCTGGTGATATGTTTTCCAAAACAAGAATGTTTGATAGCACACCCCGCAGTGGACCCAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os03g20420.3 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g20420.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G120132_T01 (Zea mays), 3'ss of exon 1
--------gtaatttactatattgctcagtctttacctagacaaaatctcatcttaattca-ggaataccttaggtggactttgacattatctctgtggcagGTTTATACATCATCTGGTGATATGTTTTCCAAAACAAGAATGTTTGATAGCACACCCCGCAGTGGACCCAAG----------------------------
| || || | | | || | | | | |||| ||||| | || | | | ||||| || || ||||| ||| | ||||| |||||||||||||||||| | |||||||||||| |||| |||| | || ||||||
ttcgaaggacgaaggaccctaatatttaacaatttctatgttgccttgt--tcttgattcatagcatttgagaacaagtccccaacatttgctatgcttcagGTCTATTCTTCATCAGGTGATATGTTTTCCAAATCTAGAATGTTTGATCACACAGCCCGTACCGGGCCCAAGGTACTTGCTTTGTTATTGCTACCTCAGT
upper sequence: LOC_Os03g20420.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G180889_T01 (Zea mays), 3'ss of exon 1
gtaatttactatattgctcagtctttacctagacaaaatctcatcttaattcaggaataccttaggtggactttgacattatctctgtggcagGTTTATACATCATCTGGTGATATGTTTTCCAAAACAAGAATGTTTGATAGCACACCCCGCAGTGGACCCAAG----------------------------
||||| ||| | |||||| || || | |||| || | | || | | ||| |||||| || || ||||| ||||| ||||| |||||||||||||||||| | ||||||||||||| ||| |||| | |||||||||
gtaatg-actgtcttgctcggttttctcttagataat-ttttttcccagtagagg------------------tgacatctgctatgcttcagGTCTATACTTCATCAGGTGATATGTTTTCCAAATCTAGAATGTTTGATAATACAGCCCGTACCGGACCCAAGGTACTTGCTTTGCTATTGCTACCTCAGT
upper sequence: LOC_Os03g20420.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G131440_T01 (Zea mays), 3'ss of exon 1
----------------------------------------gtaattta-ctatattgctcagtctttacctagacaaaatctcatcttaattc------aggaatacctta---ggtggactttgacattatctctgtggcagGTTTATACATCATCTGGTGATATGTTTTCCAAAACAAGAATGTTTGATAGCACACCCCGCAGTGGACCCAAG
|| | || ||| | | | || | ||| | || |||| || || || | ||||| || || ||||| ||||| ||||| |||||||||||||||||| | ||||||||||||| |||| ||
aaaatcatatcaagttgtgatagatctgctatttcatcacacaacccagctgatttgtatgatgtccatgtaatgactgtcttgcttggttttctcatagATAATATTTTTCCCAGTAGAGGT-GACATCTGCTATGCTTCAGGTCTATACTTCATCAGGTGATATGTTTTCCAAATCTAGAATGTTTGATAACACAGCCT-------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctcatcttaattcaggaataccttaggtggactttgacattatctctgtggcagGTTTATACATCATCTGGTGATATGTTTTCCAAAACAAGAATGTTTGATAGCACACCCCGCAGTGGACCCAAG
ttatctct CT-rich tract
tcttaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatttactatattgctcagtctttacctagacaaaatctcatcttaattcaggaataccttaggtggactttgacattatctctgtggcagGTTTATACATCATCTGGTGATATGTTTTCCAAAACAAGAATGTTTGATAGCACACCCCGCAGTGGACCCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA