Sequence
atgc intronic sequence ATGC exonic sequence...gtttaaatgtctgttttgatagcgtcattagcatgaacttagaatttgtttggaatgcagaaagatctagatatgaccagaagtacctgttgtttgacagGTTGCAACTGCTTGTGCTGTCGCCGCATTCAAGCTGCGGCGTCCGGTTCGAATGTACCTCGATCGCAAGACAGACATGATCATGGCGGGAGGGCGGCATC
Basic information
species | Oryza sativa |
transcript | LOC_Os03g57680.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g57680.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM5G899851_T01 (Zea mays), 3'ss of exon 5
--------------------------gtttaaatgtctgtttt-gatagc------gtcattagcatgaacttagaatttgtttggaatgcagaaagatctagatatgaccagaagt--acctgttgtttgacagGTTGCAACTGCTTGTGCTGTCGCCGCATTCAAGCTGCGGCGTCCGGTTCGAATGTACCTCGATCGCAAGACAGACATGATCATGGCGGGAGGGCGGCATC
||| |||| | | |||| ||| | | | | | | ||| || | || || ||| | || | | | | | | | | |||| |||||||| ||| ||||| || || ||||| ||||| | ||||| ||||| ||||||||||||||||||||||||||||| ||||| || ||||||||||
gtaagtactaataaactagagttaatgttgaaatttttatttttgattaccaatccactgccaactaatattcataatgtgatcagattg-agacaaattgtgcaacggataactatcaattttctctttgttagGTTGCATGTGCATGTGCAGTTGCTGCATTGAAGCTACAACGTCCAGTTCGGATGTACCTCGATCGCAAGACAGACATGATAATGGCAGGCGGGCGGCATC
upper sequence: LOC_Os03g57680.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G141535_T01 (Zea mays), 3'ss of exon 5
------------------------------------------------gtttaaatgtc--tgttttgatagc--gtcattagcatgaacttagaatttgtttggaatgcagaaagatctagatatgaccagaagtacctgttgtttgacagGTTGCAACTGCTTGTGCTGTCGCCGCATTCAAGCTGCGGCGTCCGGTTCGAATGTACCTCGATCGCAAGACAGACATGATCATGGCGGGAGGGCGGCATC
|| || || | ||| ||| | | | | || | || ||| ||||| | | |||| |||| || | | | |||| ||| |||| ||| ||||| | || || ||||||||||||||||| ||| | |||||||||||||||||||| |||||||| ||||| |||||| | ||||
gtaagtcctgcctgtaactagagcttcagttcactcaatattttgtgttttcaattgccactgtattgtcaattgaacttcatgatttgaccaaaaaactgttgagatgcaaatggtgttagaaatgatcatggat-tttcctctttgtcagACTGCATGTGCATGTGCCCTTGCTGCCTTCAAGCTGCGGCGTCCAGTTAGGATGTACCTCGATCGCAAGACGGACATGATAATGGCTGGAGGGAGACATC
upper sequence: LOC_Os03g57680.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G141473_T01 (Zea mays), 3'ss of exon 5
----------------------------gtttaaatgt-ctgttttgat-----agcgtcattagcatgaacttaga---atttgtttggaatgcagaaagatctagatatgaccagaagtacctgttgtttgacagGTTGCAACTGCTTGTGCTGTCGCCGCATTCAAGCTGCGGCGTCCGGTTCGAATGTACCTCGATCGCAAGACAGACATGATCATGGCGGGAGGGCGGCATC
| | || | | || |||| | | || | | ||||| | | || || | || || ||| || | | | | | | | | || ||||||||| ||| ||||| || || |||||||||||||||||||| ||||| |||||||| |||||||||||||||||||| ||||| || || |||||||
gtaagtcttaaaaataactagtgcttatgctcaacttttctattttcagttacgaatgtagtgcgtgcgaactgatattcatgtggtcagattgagaaaaaatgtgttattatagatgactggatttcctctgtcagGTTGCATGTGCATGTGCGGTTGCTGCATTCAAGCTGCGGCGTCCAGTTCGGATGTACCTGGATCGCAAGACAGACATGATAATGGCAGGCGGTCGGCATC
upper sequence: LOC_Os03g57680.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G019799_T01 (Zea mays), 3'ss of exon 5
gtttaa-atgtctgttttgatagcgtcattagcatgaacttagaatttgt-ttggaatgcagaaagatctagatatgaccagaagtacctgttgtttgacagGTTGCAACTGCTTGTGCTGTCGCCGCATTCAAGCTGCGGCGTCCGGTTCGAATGTACCTCGATCGCAAGACAGACATGATCATGGCGGGAGGGCGGCATC
|| || || | || || || | | |||||| ||| || || | | | | || ||| | || | ||| ||| ||||| ||| || || || |||||||||||||| | |||||| ||| |||||||| ||||||||||| |||||||| || ||||| ||||| || |
gtaagtcataactaactagagcttttctttgctaaacatcgtctatttgtattgccatccaaagtggatgatgtgagatgccaagaatctcctccttgtcagATTGCATGTGCATGCGCCGTTGCCGCATTCAAGCTACAGCGTCCTGTTAAGATGTACCTTGATCGCAAGACGGACATGATAATAGCGGGTGGGCGACACC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtttggaatgcagaaagatctagatatgaccagaagtacctgttgtttgacagGTTGCAACTGCTTGTGCTGTCGCCGCATTCAAGCTGCGGCGTCCGGTTCGAATGTACCTCGATCGCAAGACAGACATGATCATGGCGGGAGGGCGGCATC
tagatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttaaatgtctgttttgatagcgtcattagcatgaacttagaatttgtttggaatgcagaaagatctagatatgaccagaagtacctgttgtttgacagGTTGCAACTGCTTGTGCTGTCGCCGCATTCAAGCTGCGGCGTCCGGTTCGAATGTACCTCGATCGCAAGACAGACATGATCATGGCGGGAGGGCGGCATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - -tgttttg
- - - - - - - - - - - - - - - gcatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - gaatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -accagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtacctg