Sequence
atgc intronic sequence ATGC exonic sequencegtttatgatttgtgcacaacatttcctcctctctacttattacctcctttcactaccttacggaggcttctcctgtagGTCTGAATTTGTGTTCATCAATCCAAATTCCAAAGGGGAGTGCGGCTGTGGTGAATCTTTCATGACTACAAGCAGCAAGGGATCTACATCTTGAATAACG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g01610.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g01610.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G163996_T01 (Zea mays), 3'ss of exon 3
--------gtttatgatttgtgca-caacatttcctcctctctacttattacctcctttcactaccttacggaggcttctcctgtagGTCTGAATTTGTGTTCATCAATCCAAATTCCAAAGGGGAGTGCGGCTGTGGTGAATCTTTCATGACTACAAGCAGCAAGGGATCTACATCTTGAATAACG
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gtatgcctgctactctactacgtagttatttttgttttgccccactgtccatcagtttgaagttacaaactaaacttcctgttgcagGTCCGAGTTTGTGTTCATAAACCCAAATTCCAAAGGGCAGTGTGGCTGCGGTGAGTCTTTCATGACTACAGGCAGCAAAGGGTCGACGTCATGAGGCGTT
upper sequence: LOC_Os01g01610.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA19G37930.1 (Glycine max), 3'ss of exon 2
---------------------gtttatgatttgtgcacaacatttcctcctctctacttattacctcctttcactaccttacggag-gcttctcctgt-agGTCTGAATTTGTGTTCATCAATCCAAATTCCAAAGGGGAGTGCGGCTGTGGTGAATCTTTCATGACTACAAGCAGCAAGGGATCTAC-ATCTTGAATAACG
| | | | || | | || || | | | | | | ||| ||| | || ||||||||||| || || |||||| | ||| ||||||||||||||||||| |||| || |||||||||||||||||||| ||| | || | |||||| | | ||
tcatctgtttactttctttctttcttttcctaatgtgaactacttgctttgttttcagtgct-cttattttaactcctacactttttgcttctcctgtcagATCGGAATTTATTTTCGTCAATCCAAATTCCAAAGGTCAGTGTGGTTGTGGTGAATCTTTCATGACAACAGGAAGTAGTGGATCTTCTAAGCCATGAAAT-
upper sequence: LOC_Os01g01610.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA03G35280.1 (Glycine max), 3'ss of exon 2
---------------gtttatgatttgtgcacaacat---ttcctcctctctacttattacctcc--tttcactacc-ttacggaggcttctcctgt-agGTCTGAATTTGTGTTCATCAATCCAAATTCCAAAGGGGAGTGCGGCTGTGGTGAATCTTTCATGACTACAAGCAGCAAGGGATCTAC-ATCTTGAATAACG
|| | | | | | || | | || || | | | | | | ||| ||| | | ||||||||||| || || |||||| | ||| ||||||||||||| ||||| |||| || |||||||||||||||||||| ||| |||| | |||||| | | ||
ttggttcaaccgtttactttcgttcttttcctaatgtgaactacttctttgttttcagtgctcttattttaacttctactctttttgcttctcctgtcagATCGGAATTTATTTTCGTCAATCCAAATTCTAAAGGTCAGTGTGGTTGTGGTGAATCTTTCATGACAACAGGCAGTAGTGGATCTTCTAAGCCATGAAAT-
upper sequence: LOC_Os01g01610.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv08s0007g03400.t01 (Vitis vinifera), 3'ss of exon 2
------------------gtttatgatttgtgc-acaacatttcctcctctctacttattacctcctttcactaccttacggaggcttctcct---gtagGTCTGAATTTGTGTTCATCAATCCAAATTCCAAAGGGGAGTGCGGCTGTGGTGAATCTTTCATGACTACAAGCAGCAAGGGATCTAC-ATCTTGAATAACG
| ||| | | | || | | || | | |||| || ||| || || ||| || | | |||||||| || | || ||||||||||| || |||||| |||| || |||||||||||||||||||| ||| ||| ||| || | | | | |
tctttctttgttagagataatcatggccagaaccaaaataggcacaccattaacttgattaaaacccttctttaatttgttttcccttgtctttgggcagGTCTGAGTTCATATTTATCAATCCAAACTCTAAAGGGCAGTGTGGTTGTGGTGAATCTTTCATGACAACAGGCAATCCTGGAGCTGCTAAGTAGGTTGGT- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcctcctctctacttattacctcctttcactaccttacggaggcttctcctgtagGTCTGAATTTGTGTTCATCAATCCAAATTCCAAAGGGGAGTGCGGCTGTGGTGAATCTTTCATGACTACAAGCAGCAAGGGATCTACATCTTGAATAACG
accttac putative branch site (score: 3)
cttctcctgt putative PPT
tacttatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttatgatttgtgcacaacatttcctcctctctacttattacctcctttcactaccttacggaggcttctcctgtagGTCTGAATTTGTGTTCATCAATCCAAATTCCAAAGGGGAGTGCGGCTGTGGTGAATCTTTCATGACTACAAGCAGCAAGGGATCTACATCTTGAATAACG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG