Sequence
atgc intronic sequence ATGC exonic sequencegtaccgtattaatatttctccctttctatttttgtgatttttgtgaatatatcgaattataattatatgtttatcttggcagGGCAAGCATTGAACCAAAATTTCATGACTTGTATTTGAAGTTCTTTGTCAAAGTGAACTCAAGATTCTTAAACAAAGAAGTACTGAAGGCTACATATGAG
Basic information
species | Oryza sativa |
transcript | LOC_Os03g01240.1 |
intron # | 17 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g01240.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G082573_T01 (Zea mays), 3'ss of exon 4
gtaccgtattaatatttctccctttctatttttgtgatttttgtgaatatatcgaattataattata--tgtttatcttggcagGGCAAGCATTGAACCAAAATTTCATGACTTGTATTTGAAGTTCTTTGTCAAAGTGAACTCAAGATTCTTAAACAAAGAAGTACTGAAGGCTACATATGAG
|||| | ||| | || | | | | ||||| | ||| || || |||| || || | ||||| |||||||||||||||| |||| || ||||| ||||| |||||||||||| ||||| ||||||| || ||| ||||| ||| ||||||| || |||||||||
-----gtatcattatcaattactgattttgtata-gatttgtctgacaatgctgaggtatacaaatcactgctcatcttaacagGGCAAGCATTGAATCAAATTTCCATGATCTGTATCTGAAGTTCTTTGATAAAGTAAACTCAAAATCCTTGAACAAGGAAATACTGAAAGCCACATATGAG
upper sequence: LOC_Os03g01240.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G414487_T01 (Zea mays), 3'ss of exon 3
gtaccgtattaatatttctccctttctatttttgt---gatttttgtgaatatatcgaattataattata--tgtttatcttggcagGGCAAGCATTGAACCAAAATTTCATGACTTGTATTTGAAGTTCTTTGTCAAAGTGAACTCAAGATTCTTAAACAAAGAAGTACTGAAGGCTACATATGAG
|||| | ||||| || || |||||| ||||| | ||| || || |||| || || | ||||| ||||||||||||||||||||| || ||||| ||||| |||| ||||||| ||||| ||||||| || ||| ||||| ||| || |||| || |||||||||
-----gtatca----ttctcaattactgattttgtatagatttgtctgacaatgctgaggtatacaaatcactgctaatcttaacagGGCAAGCATTGAACCAAATTTCCATGATCTGTATATGAATTTCTTTGATAAAGTAAACTCAAAATCCTTGAACAAGGAAATATTGAAAGCCACATATGAG
upper sequence: LOC_Os03g01240.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G467385_T01 (Zea mays), 3'ss of exon 3
gtaccgtattaatatttctccctttctatttttgt---gatttttgtgaatatatcgaattataattata--tgtttatcttggcagGGCAAGCATTGAACCAAAATTTCATGACTTGTATTTGAAGTTCTTTGTCAAAGTGAACTCAAGATTCTTAAACAAAGAAGTACTGAAGGCTACATATGAG
|||| | ||||| || || |||||| ||||| | ||| || || |||| || || | ||||| ||||||||||||||||||||| || ||||| ||||| |||||||||||| ||||| ||||||| || | | ||||| ||| ||||||| || |||||||||
-----gtatca----ttctcaattactgattttgtatagatttgtctgacaatgctgaggtatacaaatcactgctcatcttaacagGGCAAGCATTGAACCAAATTTCCATGATCTGTATCTGAAGTTCTTTGATAAAGTAAACTCAAAATCCATGAACAAGGAAATACTGAAAGCCACATATGAG
upper sequence: LOC_Os03g01240.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G424289_T01 (Zea mays), 3'ss of exon 4
gtaccgtattaatatttctccctttctatttttgt---gatttttgtgaatatatcgaattataattata--tgtttatcttggcagGGCAAGCATTGAACCAAAATTTCATGACTTGTATTTGAAGTTCTTTGTCAAAGTGAACTCAAGATTCTTAAACAAAGAAGTACTGAAGGCTACATATGAG
|||| | ||||| || || |||||| ||||| | ||| || || |||| || || | ||||| ||||||||||||||||||||| || ||||| ||||| |||||||||||| ||||| ||||||| || ||| ||||| ||| ||||||| || |||||||||
-----gtatca----ttctcaattactgattttgtatagatttgtctgacaatgctgaggtatacaaatcactgctcatcttaacagGGCAAGCATTGAACCAAATTTCCATGATCTGTATCTGAAGTTCTTTGATAAAGTAAACTCAAAATCCTTGAACAAGGAAATACTGAAAGCCACATATGAG
upper sequence: LOC_Os03g01240.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G457909_T01 (Zea mays), 3'ss of exon 2
gtaccgtattaatatttctccctttctatttttgtgatttttgtgaatatatcgaattataattata--tgtttatcttggcagGGCAAGCATTGAACCAAAATTTCATGACTTGTATTTGAAGTTCTTTGTCAAAGTGAACTCAAGATTCTTAAACAAAGAAGTACTGAAGGCTACATATGAG---------
| || | ||||| | ||| || || |||| || || | ||||| ||||||||||||||||||||| || ||||| |||||| |||||||||||| ||||| ||||||| || ||| ||||| ||| ||||||| || |||||||||
------------------------gattttgtatagatttgtctgacaatgctgaggtatacaaatcactgctcatcttaacagggcaagcattgaaccaaatttccatgatttgtatctgaagTTCTTTGATAAAGTAAACTCAAAATCCTTGAACAAGGAAATACTGAAAGCCACATATGAGAACTGCAAG
upper sequence: LOC_Os03g01240.1 (Oryza sativa), 3'ss of exon 17
lower sequence: AC196144.3_FGT002 (Zea mays), 3'ss of exon 1
gtaccgtattaatattt--ctccctttctatttttgt---gatttttgtgaatatatcgaattataattata--tgtttatcttggcagGGCAAGCATTGAACCAAAATTTCATGACTTGTATTTGAAGTTCTTTGTCAAAGTGAACTCAAGATTCTTAAACAAAGAAGTACTGAAGGCTACATATGAG
|| | | | | | || || || |||||| ||||| | ||| || || |||| || || | ||||| ||||||||||||||||||||| || ||||| ||||| |||||||||||| ||||| ||||||| || ||| ||||| ||| ||||||| || |||||||||
gt-tcatctccctgctcagcttaattactgattttgtatagatttgtctgacaatgctgaggtatacaaatcactgctcatcttaacagGGCAAGCATTGAACCAAATTTCCATGATCTGTATCTGAAGTTCTTTGATAAAGTAAACTCAAAATCCTTGAACAAGGAAATACTGAAAGCCACATATGAG
upper sequence: LOC_Os03g01240.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G419699_T01 (Zea mays), 3'ss of exon 1
---------------------------------------gtaccgtattaatat--ttctccctttctatttttgt---gatttttgtgaatatatcgaattataattata--tgtttatcttggcagGGCAAGCATTGAACCAAAATTTCATGACTTGTATTTGAAGTTCTTTGTCAAAGTGAACTCAAGATTCTTAAACAAAGAAGTACTGAAGGCTACATATGAG
|| | | ||| ||||| || || |||||| ||||| | ||| || || |||| || || | ||||| |||||||||||||||||||| || ||||| ||||| |||||||||||| ||||| ||||||| || ||| ||
atacaggaacaatattatccttggtttgcacaatacatggtcatgaaaaggtatcattctcaattactgattttgtatagatttgtctgacaatgctgagGTATACAAATCACTGCTCATCTTAATAGGGCAAGCATTGAACCAAATTTCCATGATCTGTATCTGAAGTTCTTTGATAAAGTAAACTCAAAATCCTTGAA---------------------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttttgtgatttttgtgaatatatcgaattataattatatgtttatcttggcagGGCAAGCATTGAACCAAAATTTCATGACTTGTATTTGAAGTTCTTTGTCAAAGTGAACTCAAGATTCTTAAACAAAGAAGTACTGAAGGCTACATATGAG
tttatctt CT-rich tract
atttttgtgaatatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaccgtattaatatttctccctttctatttttgtgatttttgtgaatatatcgaattataattatatgtttatcttggcagGGCAAGCATTGAACCAAAATTTCATGACTTGTATTTGAAGTTCTTTGTCAAAGTGAACTCAAGATTCTTAAACAAAGAAGTACTGAAGGCTACATATGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG