Sequence
atgc intronic sequence ATGC exonic sequencegtaattcaagattcacaaactttcgaaaaataggaaagcacaaatttggccattgactatatattcttgccttcatctttcagGGACATTATTCGCGGCAGTCCAGATGTGAAATGGGAAAGCATCAAAGGACTGGAGAATGCCAAACGCCTTCTAAAAGAGGCAGTTGTCATGCCCATAAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g55260.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g55260.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G022777_T01 (Zea mays), 3'ss of exon 4
gtaattcaagattcacaa-actttcgaaaaataggaaagcacaaatttggccattgac-tatatattcttgcc--ttcatctttcagGGACATTATTCGCGGCAGTCCAGATGTGAAATGGGAAAGCATCAAAGGACTGGAGAATGCCAAACGCCTTCTAAAAGAGGCAGTTGTCATGCCCATAAAG
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gtaatctaaacatcattgtggctttaacattcagggacggtgtggtctagctgttgaaacattttatcccatcatttggcctttcagGGATATTATTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAAAGGACTGGAAAATGCAAAACGCCTTCTAAAAGAGGCTGTTGTCATGCCCATAAAG
upper sequence: LOC_Os01g55260.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA08G09050.1 (Glycine max), 3'ss of exon 4
----------------------------------------------------------gtaattcaagattca--caaactttcgaaaaatagg---aaagcacaaatttggccattgactatatattcttgccttcatctttcagGGACATTATTCGCGGCAGTCCAGATGTGAAATGGGAAAGCATCAAAGGACTGGAGAATGCCAAACGCCTTCTAAAAGAGGCAGTTGTCATGCCCATAAAG
|| ||| | | ||| ||| | | | || ||| | ||||| || | | || | | ||||| || ||||| || |||||||||||||| |||||||||||||| || | |||||||||||||| | || |||||||| ||||| ||||| || |||
gtaaattttctctcaatctcttcaacacctctgatagaactgatgactacatggagaagttatttgtgtgttggtcaagattttcatgtgtgaatctattctgtaagtttaattttca--tatatgtttgtcattgcacatcttagGGATATCATTCGTGGAAGTCCAGATGTGAAGTGGGAAAGCATCAAGGGGTTAGAGAATGCCAAACGTTTACTGAAAGAGGCTGTTGTGATGCCGATTAAG
upper sequence: LOC_Os01g55260.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA05G26100.1 (Glycine max), 3'ss of exon 4
-----------------------------------------------------------gtaattcaagattcac--aaactttcgaaaaataggaaagcacaaatttggccattgactatatattcttgccttcatctttcagGGACATTATTCGCGGCAGTCCAGATGTGAAATGGGAAAGCATCAAAGGACTGGAGAATGCCAAACGCCTTCTAAAAGAGGCAGTTGTCATGCCCATAAAG
|| || | || | | |||| || | || || || ||||| || | | || | | ||||| || ||||| || |||||||||||||| |||||||||||||| || | |||||||||||||| | |||||||||| ||||| ||||| || |||
gtaaattttctctcaatctcttcaataccttggatagaaccaatgactacatggagaaattatttgcatgttggtcaagattttcatgtgattctattctgtaagttcaat--tttcttatatgtttgtcattgcacatcttagGGATATCATTCGTGGAAGTCCAGATGTGAAGTGGGAAAGCATCAAGGGGTTAGAGAATGCCAAACGTTTATTAAAAGAGGCTGTTGTGATGCCGATTAAG
upper sequence: LOC_Os01g55260.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv10s0003g03500.t01 (Vitis vinifera), 3'ss of exon 4
----------------------------------------------gtaattcaagattcacaaactttcgaaaa----ataggaaagcacaa-atttggccattg---actatatattcttgcctt--catct-ttcagGGACATTATTCGCGGCAGTCCAGATGTGAAATGGGAAAGCATCAAAGGACTGGAGAATGCCAAACGCCTTCTAAAAGAGGCAGTTGTCATGCCCATAAAG
| ||| | || | | ||| | || || || || |||| || || | || || || || | |||||| || ||||| || |||||||||||||| ||||| |||||||| || | |||||||||||||| || || ||||| |||||||||||||| ||||||
gtaattgaacttcttactttggacctgtaatatatctgttatttttgcaatctgtattgtgcatgtggccaggattttcatattctaacagaagatctgaaaattgtataccatgcttcctcgcgttattgcctgtccagGGATATCATTCGTGGGAGTCCAGATGTGAAGTGGGACAGCATCAAGGGTTTAGAGAATGCCAAACGTCTGCTTAAAGAAGCAGTTGTCATGCCAATAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aataggaaagcacaaatttggccattgactatatattcttgccttcatctttcagGGACATTATTCGCGGCAGTCCAGATGTGAAATGGGAAAGCATCAAAGGACTGGAGAATGCCAAACGCCTTCTAAAAGAGGCAGTTGTCATGCCCATAAAG
cattgac putative branch site (score: 3)
ttcttgccttcatctt putative PPT
attgactatatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattcaagattcacaaactttcgaaaaataggaaagcacaaatttggccattgactatatattcttgccttcatctttcagGGACATTATTCGCGGCAGTCCAGATGTGAAATGGGAAAGCATCAAAGGACTGGAGAATGCCAAACGCCTTCTAAAAGAGGCAGTTGTCATGCCCATAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG