Sequence
atgc intronic sequence ATGC exonic sequencegtcagttacgctcagcttcttttacctttgaaatttgcatatatccttcatcctctgctctgtattaatttattaatgctctctatatatattttgataatacctctgacttttacatatccagGCCTTTCGCGCACAGAACATTGAAAGTGCAAAGTCAAGGCTCAGTATGTGTGCACAAGACATCAGGGAAGAATTGAAATCTAAACAAGACAACCAAGAAC
Basic information
species | Oryza sativa |
transcript | LOC_Os01g01420.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g01420.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G049672_T01 (Zea mays), 3'ss of exon 3
-------------------------gtcagttacgct----cagcttcttttacctttgaaatttgcatatatccttcatcctctgctctgtattaatttattaatgctctctatat-atattttgataatacctctgacttttacatatccagGCCTTTCGCGCACAGAACATTGAAAGTGCAAAGTCAAGGCTCAGTATGTGTGCACAAGACATCAGGGAAGAATTGAAATCTAAACAAGACAACCAAGAAC
| | ||| | | || ||||| |||| |||||| ||| | |||| ||| | | || ||||||| | | | | | | | || | | || | | | || |||| ||||| || | |||||||||||||||||||||||||||| |||||||||| | ||||||||||| || || |||||| | |||| ||| ||| |
gtcagtaattaagttaactgctttagcctcttatgttgaaatagattcttgaacctgataaattttaata-actaatcattgtctattattcatggatttatttacaatattggtgttacaacttacaacaaggccttaactgtttggctctagGCTTTTCGTGCCCGAAACATTGAAAGTGCAAAGTCAAGGCTCACTATGTGTGCAGACGACATCAGGGAGGAGTTAAAATCTTCAGAAGATAACTTAGACC
upper sequence: LOC_Os01g01420.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G101662_T01 (Zea mays), 3'ss of exon 3
-------------------------gtcagttacgct----cagcttcttttacctttgaaatttgcatatatccttcatcctctgctctgtattaatttattaatgctctctatatatattttgataatacctctgacttttacatatccagGCCTTTCGCGCACAGAACATTGAAAGTGCAAAGTCAAGGCTCAGTATGTGTGCACAAGACATCAGGGAAGAATTGAAATCTAAACAAGACA-ACCAAGAAC--
| | ||| | | || ||||| || | | |||||| | | | |||| | | | | ||| ||||||| | | | | |||| | | | | | | ||| || || || |||| ||| | | | ||||||| |||||||||||||||||||| |||||||| | | || |||| ||| || |||| | | |||| | ||| |
gtcaataactaagtaaattggtttcgcctcttatgttgaaatagattcttgaacttgtaaaatttcaaca-actaatcattatatattattcattgatttatttacgatattgatat---tacaacttacaacaataactgttg-atctctagGCTTTTTGTGTCTAAAACATTGGAAGTGCAAAGTCAAGGCTCACTATGTGTGTAGACGATATCAAGGAG---TTAAAATGTTCAGAAGATAGACCTATGTTCA
upper sequence: LOC_Os01g01420.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G070276_T01 (Zea mays), 3'ss of exon 2
-------------------------gtcagttacgctca----gcttcttttacctttgaaatttgcatatatccttcatcctctgctctgtattaattt-attaatgctctctatatatattttgataatacctctgacttttacatatccagGCCTTTCGCGCACAGAACATTGAAAGTGCAAAGTCAAGGCTCAGTATGTGTGCACAAGACATCAGGGAAGAATTGAAATCTAAACAAGACA-ACCAAGAAC----
| | ||| | | | | ||||| || | | |||||| | | | |||| | | | | ||| |||| ||| | | | | |||| | | | | | | ||| || || || |||| ||| | | | |||||| |||||||||||||||||||| ||||||| || || |||| ||| || |||| | | |||| | ||| |
gtcaataactaagtaaattggtttagcctcttatgttgaaaaagattcttgaacttgtaaaatttcaaca-actaatcattatatattattcattgattttatttacgatattgatat---tacaacttacaacaataactgttg-atctctagGCTTTTTGTGTCTAAGACATTGGAAGTGCAAAGTCAAGGCTCACTATGTGTAGAC--GATATCAAGGAG---TTAAAATGTTCAGAAGATAGACCTATGTTCATA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttattaatgctctctatatatattttgataatacctctgacttttacatatccagGCCTTTCGCGCACAGAACATTGAAAGTGCAAAGTCAAGGCTCAGTATGTGTGCACAAGACATCAGGGAAGAATTGAAATCTAAACAAGACAACCAAGAAC
cttttac CT-rich tract
tctctatatatatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagttacgctcagcttcttttacctttgaaatttgcatatatccttcatcctctgctctgtattaatttattaatgctctctatatatattttgataatacctctgacttttacatatccagGCCTTTCGCGCACAGAACATTGAAAGTGCAAAGTCAAGGCTCAGTATGTGTGCACAAGACATCAGGGAAGAATTGAAATCTAAACAAGACAACCAAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC