Sequence
atgc intronic sequence ATGC exonic sequencegtacggtttccttcttgcctcttgcttttgcaattgatgagattccactatatgaattgtaccttgaagttctagttttgccatgaagttctataaatttatttttatttctttaagtaggcattgccctcaatagctcaactgttgtagttatcccgcagAGTAAAGCAGGAGTTCAGGAGCTTTATATGGGCAGGAATTCACCACTGTTTACTTCAATGAGAGTTTTACCTGAGACATCAGATGATGACCATTTG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g14050.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g14050.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G144403_T02 (Zea mays), 3'ss of exon 2
gtacggtttccttcttgcctcttgcttttgcaattgatgagattccactatatgaattgtaccttgaagttctagttttgccatgaagttctataaatttatttttatttctttaagtaggcattgccctcaatagctcaactgttgtagttatcccgcagAGTAAAGCAGGAGTTCAGGAGCTTTATATGGGCAGGAATTCACCACTGTTTACTTCAATGAGAGTTTTACCTGAGACATCAGATGATGACCATTTG
| || | || | | ||| || ||| ||||| || || | ||| || | || | ||| ||||| | ||| ||| ||||| | |||||| |||||| | ||||||| ||||| |||||||||||| ||||| | ||||| || ||||||||| |||| ||||||||||||||||||||||||
---------------------------------------------ctttaacaaagtttttctatgacagtcacattt--------agttccattaa---gtaggcattcctatcggtcgat-----tctctgtagcttacctgatgttgttattctgcagAGCAAAGCAAGTATTCAGGAACTTTACATGGGCAGGAATCCACCAATCTTTACCTCCATGAGAGTTCTACCAGAGACATCAGATGATGACCATTTG
upper sequence: LOC_Os01g14050.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G144403_T01 (Zea mays), 3'ss of exon 4
gtacggtttccttcttgcctcttgcttttgcaattgatgagattccactatatga-attgtaccttgaagttctagttttgccatgaagttctataa-atttatttttatttct-ttaagtaggcattgcc-----------ctcaatagctcaactgttgtagttatcccgcagAGTAAAGCAGGAGTTCAGGAGCTTTATATGGGCAGGAATTCACCACTGTTTACTTCAATGAGAGTTTTACCTGAGACATCAGATGATGACCATTTG
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gtatggtttccttctttttccttggttttatgattcat-attctctattttgtggcattttacctcgaactgctactttaacaaagtttttctatgacagtcacatttagttccattaagtaggcattcctatcggtcgattctctgtagcttacctgatgttgttattctgcagAGCAAAGCAAGTATTCAGGAACTTTACATGGGCAGGAATCCACCAATCTTTACCTCCATGAGAGTTCTACCAGAGACATCAGATGATGACCATTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttctttaagtaggcattgccctcaatagctcaactgttgtagttatcccgcagAGTAAAGCAGGAGTTCAGGAGCTTTATATGGGCAGGAATTCACCACTGTTTACTTCAATGAGAGTTTTACCTGAGACATCAGATGATGACCATTTG
ttatccc CT-rich tract
tttaagta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacggtttccttcttgcctcttgcttttgcaattgatgagattccactatatgaattgtaccttgaagttctagttttgccatgaagttctataaatttatttttatttctttaagtaggcattgccctcaatagctcaactgttgtagttatcccgcagAGTAAAGCAGGAGTTCAGGAGCTTTATATGGGCAGGAATTCACCACTGTTTACTTCAATGAGAGTTTTACCTGAGACATCAGATGATGACCATTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG