Sequence
atgc intronic sequence ATGC exonic sequencegtacatagcataccactaatattgtattgtactacactctgttttcctcaatctgatcagaaataaagtggatttgtttacgaggatatcttctttccaaagttgtatgactgcacttgtactgttgttcaacctctttatgtcctcatttcagATACACAGAAGACATGGAGCTTGATGATGCCATCCATACTGCCATTTTGACTCTGAAAGAAGG
Basic information
| species | Oryza sativa |
| transcript | LOC_Os02g42320.4 |
| intron # | 7 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g42320.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G085243_T01 (Zea mays), 3'ss of exon 9
gtacatagcataccactaatattgtattgtactacactctgttttcctcaatctgatcagaaataaagtggatttgtttacgaggatatcttctttccaaagttgtatgactgcacttgtactgttgttcaacctctttatgtcctcatttcagATACACAGAAGACATGGAGCTTGATGATGCCATCCATACTGCCATTTTGACTCTGAAAGAAGG
| | | || | | | | ||| | | ||| || || | | ||| | ||| | | | || | | ||||| ||||| ||||||||||| || ||||||||||||||||||||||| ||||| ||||||||| ||||||||||
------------------------------------------gtgtaagatttagagcccattaccaccccctgtgtgccataacagatcatcctttc-----cttctgatttcacatcttatatttataa-------tatgttttcattgtagATACACAGAGGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGACTTTGAAAGAAGG
upper sequence: LOC_Os02g42320.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM5G824831_T03 (Zea mays), 3'ss of exon 9
gtacatagcataccactaatattgtattgtactacactctgttttcctcaatc-tgatcagaaataaagtggatttgt-ttacgaggatatcttctttccaaagttgtatgactgcacttgtactgttgttcaacctctttatgtcctcatttcagATACACAGAAGACATGGAGCTTGATGATGCCATCCATACTGCCATTTTGACTCTGAAAGAAGG
| | | ||||| |||| | | ||| | || ||| || | | | |||||| | ||| | ||| ||| | || | |||| ||||| |||||||||||||| ||||||||||||||||||||||| ||||| ||||||||| ||||||||||
---------------------------------------tatctacctcatcagtgatta-atgtaagcagcatgtgtgctataattgttcatcctttccc------tctgatttcacatgttatatt----------tgtatggtttcattgtagATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGACTTTGAAAGAAGG
upper sequence: LOC_Os02g42320.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G115948_T01 (Zea mays), 3'ss of exon 5
gtacatagcataccactaatattgtattgtactacactctgttttcctcaatc-tgatcagaaataaagtggatttgt-ttacgaggatatcttctttccaaagttgtatgactgcacttgtactgttgttcaacctctttatgtcctcatttcagATACACAGAAGACATGGAGCTTGATGATGCCATCCATACTGCCATTTTGACTCTGAAAGAAGG
| | | ||||| |||| | | ||| | | || ||| || | | | |||||| | ||| | ||| ||| | || | |||| ||||| |||||||||||||| ||||||||||||||||||||||| ||||| ||||||||| ||||||||||
---------------------------------------tatctacctcatcagtgatta-atgtaaggagcatgtgtgctataattgttcatcctttccc------tctgatttcacatgttatatt----------tgtatggtttcattgtagATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGACTTTGAAAGAAGG
upper sequence: LOC_Os02g42320.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM5G850355_T08 (Zea mays), 3'ss of exon 8
gtacatagcataccactaatattgtattgtactacactctgttttcctcaatctgatcagaaataaagtggatttgtttacgaggatatcttctttccaaagttgtatgactgcacttgtactgttgttcaacctctttatgtcctcatttcagATACACAGAAGACATGGAGCTTGATGATGCCATCCATACTGCCATTTTGACTCTGAAAGAAGG
| ||| || || ||| | | | | | | || | | | || || | | | ||||| ||||| ||||||||||| || ||||||||||||||||||||||| ||||| ||||||||| ||||||||||
----------------------------------------------------agtgtaagatttagagcccattaccacccctgtgtgccataacag-atcattctttccttctgatttcac-atcttatatttataatatgttttcattgtagATACACAGAGGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGACTTTGAAAGAAGG
upper sequence: LOC_Os02g42320.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM5G850355_T06 (Zea mays), 3'ss of exon 2
gtacatagcataccactaatattgtattgtactacactctgttttcctcaatctgatcagaaataaagtggatttgtttacgaggatatcttctttccaaagttgtatgactgcacttgtactgttgttcaacctctttatgtcctcatttcagATACACAGAAGACATGGAGCTTGATGATGCCATCCATACTGCCATTTTGACTCTGAAAGAAGG
| || | |||| || ||| | || ||| | | | | | | || | ||| | ||| | | | || || ||||| ||||| ||||||||||| || ||||| ||||||||||||||||| ||||| ||||||||| ||||||||||
-------------------------------ccactccttgttggagacagtcttaccac------------cctgtgtgccataacagatcattctt---tccttctgatttcac--atcttatattttaa------tatgttttcattgtagATACACAGAGGATATGGAACTTGATGATGCCATCCACACTGCAATTTTGACTTTGAAAGAAGG
upper sequence: LOC_Os02g42320.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA08G17810.3 (Glycine max), 3'ss of exon 9
gtacatagcataccactaatattgtattgtactacactctgttttcctcaatctgatcagaaataaagtggatttgtttacgaggatatcttctttccaaagttgtatgactgcacttgtactgttgttcaacctctttatgtcctcatttcagATACACAGAAGACATGGAGCTTGATGATGCCATCCATACTGCCATTTTGACTCTGAAAGAAGG
||| | ||| | | | || | || || ||| ||| | || | || | ||| || || || |||| || | || | || | ||| |||||||| || ||||||||||||||||| |||| || || || ||||||||||| |||||
-----------------------------------actttctttctttggagataattgtgattatgttgagtttcattagttacacctcattttcct-------tat-----catttctatggttg----acttgattgtccactta---cagGTACACAGATGATATGGAGCTTGATGATGCAGTCCACACAGCAATATTGACTCTGAAGGAAGG
upper sequence: LOC_Os02g42320.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA15G41330.1 (Glycine max), 3'ss of exon 9
gtacatagcataccactaatattgtattgtactacactctgttttcctcaatctgatcagaaataaagtggatttgtttacgaggatatcttctttccaaagttgtatgactgcacttgtactgttgttcaacctctttatgtcctcatttcagATACACAGAAGACATGGAGCTTGATGATGCCATCCATACTGCCATTTTGACTCTGAAAGAAGG
|| | || | || | || || | || || || | | | | | || | || | ||| | ||| || | || ||| |||||||| || ||||||||||||||||| |||| || || || ||||||||||| |||||
-------------------------------------------------aagataatt-gtgattatgtttccctgagtgatttgagattcatttgttatacctcattttccccatcatttctatggttga----cttgattgtccacttacagGTACACAGATGATATGGAGCTTGATGATGCAGTCCACACAGCAATGTTGACTCTGAAGGAAGG
upper sequence: LOC_Os02g42320.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT1G79210.3 (Arabidopsis thaliana), 3'ss of exon 9
gtacatagcataccactaatattgtattgtactacactctgttttcctcaatctgatcagaaataaagtggatttgtttacgaggatatcttctttccaaagttgtatgactgcacttgtactgttgttcaacctctttatgtcctcatttcagATACACAGAAGACATGGAGCTTGATGATGCCATCCATACTGCCATTTTGACTCTGAAAGAAGG
| | | || | ||| | || | || |||| | ||| | || | | || |||| ||||||||||| ||||| |||||||||||||| || || || || ||||| |||| |||||
----------------------------------------------------------------------------gtgataataatttaccatttgtggtgatgagtttatgatcttggaagcatgtc--atttcatcttagtctttgatcagGTACACAGAAGATATGGAACTTGATGATGCCATTCACACGGCAATATTGACATTGAAGGAAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagttgtatgactgcacttgtactgttgttcaacctctttatgtcctcatttcagATACACAGAAGACATGGAGCTTGATGATGCCATCCATACTGCCATTTTGACTCTGAAAGAAGG
cctctttatgtcctc CT-rich tract
tctttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacatagcataccactaatattgtattgtactacactctgttttcctcaatctgatcagaaataaagtggatttgtttacgaggatatcttctttccaaagttgtatgactgcacttgtactgttgttcaacctctttatgtcctcatttcagATACACAGAAGACATGGAGCTTGATGATGCCATCCATACTGCCATTTTGACTCTGAAAGAAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
