Sequence
atgc intronic sequence ATGC exonic sequencegtatataatattgaaatagtggtctctcaaatgaaaaataaacttcgaaaaatattgaggcatgttatttgtcgatgtcatctgttggtcttgttatgtgaatcctaagactagttattatcttgtttctcagTATCTTAACACAGCTGAATTTGCAATGCGCGAAGAGCTGTCCCTGAAGGCAGCTATCCTTGCTGAGAAATTCGCTCCAGATCTTTCATG
Basic information
species | Oryza sativa |
transcript | LOC_Os03g02150.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g02150.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G700148_T01 (Zea mays), 3'ss of exon 11
gtatataatattgaaatagtggtctctcaaatgaaaaataaacttcgaaaaatattgaggcatgttatttgtcgatgtcatctgttggtcttgttatgtgaatcctaagactagttattatcttgtttctcagTATCTTAACACAGCTGAATTTGCAATGCGCGAAGAGCTGTCCCTGAAGGCAGCTATCCTTGCTGAGAAATTCGCTCCAGATCTTTCATG-----------
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gtaattaatctttgtgt----gtgtgtgtggggggggggggtctt--aaccgcactata--ctattgtttattcatgtcattcctgctttctaatat-tgaatcctc----------ttttcttac--ctcagTACCTTGATACAGCTGAATTTGCAATGCGTGAAGAGTTGTCTCTGAAGGCAGCTATTCTTGCAGAAAAATTTGCTCCACAACTATTGTGGTAAGATTTTG
upper sequence: LOC_Os03g02150.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G137236_T01 (Zea mays), 3'ss of exon 12
gtatataatattgaaatagtggtctctcaaatgaaaaataaacttcgaaaaatattgaggcatgttatttgtcgatgtcatctgttggtcttgttatgtgaatcctaagactagttattatcttgtttctcagTATCTTAACACAGCTGAATTTGCAATGCGCGAAGAGCTGTCCCTGAAGGCAGCTATCCTTGCTGAGAAATTCGCTCCAGATCTTTCATG
|| | | | | || | | || | || ||| | ||||||| |||| | | | | | || || || |||| || ||||| ||| | ||||| |||||||||||||| |||||| |||| |||||||||||||| ||||| || ||||| |
---------------gtaactactcttttgaggggggggggggtcttaaccacactgta--ctattttttattcatgtcat-------tcttactttctaagGCTGAATCCTC----TTCTCTTACCTCACAGTACCTTGATACAGCAGAATTTGCAATGCGTGAAGAGTTGTCTCTGAAGGCAGCTATTCTTGCAGAAAAATTTG----------------
upper sequence: LOC_Os03g02150.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 11
-----------------------------------gtatataatattgaaatag-tggtctctcaaatgaaaaataaacttcgaaaaatattgaggcatgttatttgtcgatgtcatctgttggtcttgttatgtgaatcctaagactagttattatcttgtttct-cagTATCTTAACACAGCTGAATTTGCAATGCGCGAAGAGCTGTCCCTGAAGGCAGCTATCCTTGCTGAGAAATTCGCTCCAGATCTTTCATG
| | || ||| || || | | | || | ||| || || | | | | | | || || || || | || || | | ||| ||| | ||||||| | |||||| || ||||||||||| || || |||| || || |||||||| ||||||||||| || || ||||| ||||||||
gtatagagctaggtccgaactaattcatgcaatttgaaaatctcattaaagtaaaccctacccccttcccaacagcaacctcatggaacaataaacaaaataaagaaaatgaaccagctatta-cctggatacacaaaatgattagtttgcaattccaacttttttgtagTATCTCAGCACAGCGGAGTTTGCAATGCGTGAGGAATTGTCACTTAAAGCAGCTATTCTTGCTGAGAAGTTTGCACCAGACCTTTCATG
upper sequence: LOC_Os03g02150.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 11
-----------------------------------gtatataatattgaaatag-tggtctctcaaatgaaaaataaacttcgaaaaatattgaggcatgttatttgtcgatgtcatctgttggtcttgttatgtgaatcctaagactagttattatcttgtttct-cagTATCTTAACACAGCTGAATTTGCAATGCGCGAAGAGCTGTCCCTGAAGGCAGCTATCCTTGCTGAGAAATTCGCTCCAGATCTTTCATG
| | || ||| || || || |||| || | |||| || || | | | | | || || || || | || ||| | || | | | ||||| | ||||||| | |||||| || ||||||||||| || || |||| || || |||||||| ||||||||||| || || ||||||||||||||
gtatggagctaggtccaaactaattcatgaaatttgaaaatctcattaaagtaaaccgtatctccttcccaacagaaacctcatggaacaataaacaaaagaaagaaaatgaaccagctatta-cctggatacac-aatgattagtttgctattccaactgtttttgtagTATCTCAGCACAGCGGAGTTTGCAATGCGTGAGGAATTGTCACTTAAAGCAGCTATTCTTGCTGAGAAGTTTGCACCAGATCTTTCATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catctgttggtcttgttatgtgaatcctaagactagttattatcttgtttctcagTATCTTAACACAGCTGAATTTGCAATGCGCGAAGAGCTGTCCCTGAAGGCAGCTATCCTTGCTGAGAAATTCGCTCCAGATCTTTCATG
ttatcttgtttctc CT-rich tract
ttattatcttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatataatattgaaatagtggtctctcaaatgaaaaataaacttcgaaaaatattgaggcatgttatttgtcgatgtcatctgttggtcttgttatgtgaatcctaagactagttattatcttgtttctcagTATCTTAACACAGCTGAATTTGCAATGCGCGAAGAGCTGTCCCTGAAGGCAGCTATCCTTGCTGAGAAATTCGCTCCAGATCTTTCATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT