Sequence
atgc intronic sequence ATGC exonic sequencegtggagcctcttttttcctatctcattatgggggtgaaatttgaagtattacatgaatgccatccatatgcatcggtttatctagattagtttctggtttcacgccaggtgcttcaagtgtcgtaggaggtttcatttcatgcatatctgatatctcaattatgtcggtactgacatgttatttacattgttgccagTGTAACAATGAAAAACTGCTGGAGAACCCATACCTTCAAATGCGTGGGATACTGCAGTTGTCAAACGATCTAGGAGTTCAATAATCACTCGAATGTGCTA
Basic information
species | Oryza sativa |
transcript | LOC_Os01g74310.5 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g74310.5 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G459642_T04 (Zea mays), 3'ss of exon 4
gtggagcctcttttttcctatctcattatgggggtgaaatttgaagtattacatgaatgccatccatatgcatcggtttatctagattagtttctggtttcacgccaggt-gcttcaagtgtcgtaggaggtttcatttcatgcatatctgatatctcaattatgtcggtactgacatgttatttacattgttgccagTGTAACAATGAAAAACTGCTGGAGAACCCATACCTTCAAATGCGTGGGATACTGCAGTTGTCAAACGATCTAGGAGTTCAATAATCACTCGAATGTGCTA
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-----------gttattcttcctcatctt-------atatt---attattac-cgaggaacaatgctttgcattt-tatacctagaatagctcttactgacatgttgaaccacttgaagcctcctagtaggcttaattccatgtgtatcctatcacctcattaagttggtgctgac---ttgtttgtgttattgccagTGTAACAATGAGAAACTTCTGGAGAACCCATACCTTCAGATGCGTGGGATATTGCAGTTATCAAATGACCTAGGAGTTCAATGATAAGATCGTGATGACA
upper sequence: LOC_Os01g74310.5 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA20G23240.1 (Glycine max), 3'ss of exon 19
gtggagcctcttttttcctatctcattatgggggtgaaatttgaagtattacatgaatgccatccatatgcatcggtttatctagattagtttctggtttcacgccaggtgcttcaagtgtcgtaggaggtttcatttcatgcatatctgatatctcaattatgtcggtactgacatgttatttacattgttgccagTGTAACAATGAAAAACTGCTGGAGAACCCATACCTTCAAATGCGTGGGATACTGCAGTTGTCAAACGATCTAGGAGTTCAATAATCACTCGAATGTGCTA
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--------------------------------------------------------------------------ccttattttaaatt--tctttgtttgtttgcttaataattta-gtatttttggtgatt-------aattataaatgttac-------atgtttgtgct----ttgtatttgcactgca--cagAGCAACAATGAAAAACTGTTAGAGAATCCTTACCTTCAAATGTGTGGCATACTTCAATTGGAAAATGATCTTGGATTTGACTTGTGA-------------
upper sequence: LOC_Os01g74310.5 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA18G52540.1 (Glycine max), 3'ss of exon 15
gtggagcctcttttttcctatctcattatgggggtgaaatttgaagtattacatgaatgccatccatatgcatcggtttatctagattagtttctggtttcacgccaggtgcttcaagtgtcgtaggaggtttcatttcatgcatatctgatatctcaattatgtcggtactgacatgttatttacattgttgccagTGTAACAATGAAAAACTGCTGGAGAACCCATACCTTCAAATGCGTGGGATACTGCAGTTGTCAAACGATCTAGGAGTTCAATAATCACTCGAATGTGCTA
|||| | ||| || | | | ||| | ||| | | |||| | ||| | |||| | || ||| ||||| | ||| || ||||||||||||||||| | |||||||| || ||||||||| |||| ||||| || || |||| ||||| || || | | |
-----------------------------------------------------------------------------------------gtttttttttttttttgcagttttcttaatagtgtactatttttggtgaatttaatatttactattac--ttatatgattat--gcattgtatttgccatgt----agAGTAACAATGAAAAACTGTTAGAGAACCCGTATCTTCAAATGTGTGGCATACTTCAACTGGCAAATGATCTGGGGATTGACCTGTGA-------------
upper sequence: LOC_Os01g74310.5 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA10G43560.2 (Glycine max), 3'ss of exon 16
gtggagcctcttttttcctatctcattatgggggtgaaatttgaagtattacatgaatgccatccatatgcatcggtttatctagattagtttctggtttcacgccaggtgcttcaagtgtcgtaggaggtttcatttcatgcatatctgatatctcaattatgtcggtactgacatgttatttacattgttgccagTGTAACAATGAAAAACTGCTGGAGAACCCATACCTTCAAATGCGTGGGATACTGCAGTTGTCAAACGATCTAGGAGTTCAATAATCACTCGAATGTGCTA
|| | || ||| | | || || || | || | |||| | || | || | || || | | |||| || || | ||||| || || ||| ||||||||||||||| | ||||| || |||||||||||| |||| ||||| || ||| |||| ||||| ||| || | | | | || | |
----------------------------------------------------------------------------ttattttaaatttctctttgtttgtttgcttaataattta-gtgttcttggtgattaa---ttataaatgttt-----------catgtttgtgct----ttttattggcactgca--cagACCAACAATGAAAAACTGTTAGAGAATCCTTACCTTCAAATGTGTGGCATACTTCAATTGGCAAATGATCTTGGATTTGACTTGTGATGTTAAACTCTTG
upper sequence: LOC_Os01g74310.5 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv13s0019g00680.t01 (Vitis vinifera), 3'ss of exon 16
gtggagcctcttttttcctatctcattatgggggtgaaatttgaagtattacatgaatgccatccatatgcatcggtttatctagattagtttctggtttcacgccaggtgcttcaagtgtcgtaggaggtttcatt-tcatgcatatctgatatctcaattatgtcggtactgacatgttatttacattgttgccagTGTAACAATGAAAAACTGCTGGAGAACCCATACCTTCAAATGCGTGGGATACTGCAGTTGTCAAACGATCTAGGAGTTCAATAATCACTCGAATGTGCTA-
| | || | | | || || | || || ||| | || ||| ||| || || | || | ||||| | |||| | ||||| ||| | ||||||||||| ||| | ||||| ||||||||||| |||||||| ||| | ||| ||||||| ||||| || | | || | || |||| |
------------------------------------------------------------------------------tttttaaa---gatcctaacttt-tgtcataattcattagccctttagtacgtggcataatcacatgtaactaaaatttt--ctatgttg---------tgttgct---attgtg--cagAGCAACAATGAAAAGCTGTTAGAGAATCCATACCTTCAGATGCGTGGCATAATTCAGCTGTCAAATGATCTTGGGACTGGGTTATAA-TCTGATGTTTTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catatctgatatctcaattatgtcggtactgacatgttatttacattgttgccagTGTAACAATGAAAAACTGCTGGAGAACCCATACCTTCAAATGCGTGGGATACTGCAGTTGTCAAACGATCTAGGAGTTCAATAATCACTCGAATGTGCTA
tactgac putative branch site (score: 1)
atgttatttacatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtggagcctcttttttcctatctcattatgggggtgaaatttgaagtattacatgaatgccatccatatgcatcggtttatctagattagtttctggtttcacgccaggtgcttcaagtgtcgtaggaggtttcatttcatgcatatctgatatctcaattatgtcggtactgacatgttatttacattgttgccagTGTAACAATGAAAAACTGCTGGAGAACCCATACCTTCAAATGCGTGGGATACTGCAGTTGTCAAACGATCTAGGAGTTCAATAATCACTCGAATGTGCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG