Sequence
atgc intronic sequence ATGC exonic sequencegtaagagatccatttatctagattatctcttgtaatactttttatctgaattgtttaccctataaactcctttgcatgggtgttcattattctatagACATGCAGAAAGCTCTGTCAGGAATTGTTCCTGCAATTGAAAAGGCACGCCTTTATCGAGGTAAAGGAGGAGAGATAATGCGTTCTGCTGTTTCCCGATT
Basic information
species | Oryza sativa |
transcript | LOC_Os10g36490.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os10g36490.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G303758_T01 (Zea mays), 3'ss of exon 3
gtaagagatccatttatctagatta----tctcttgtaatactttttatctgaattgtttac--------cctataaactcctttgcatgggtgttcattattctatagACATGCAGAAAGCTCTGTCAGGAATTGTTCCTGCAATTGAAAAGGCACGCCTTTATCGAGGTAAAGGAGGAGAGATAATGCGTTCTGCTGTTTCCCGATT
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gtaaatggtggaattgtcatgcatactgttcctttgtgatacttatcattttaactcttaaagctgcttacctgaaagtgacattccatctttatct-ttattttgtagACATGCAGAAAACTTTGTCAGGTATTGTTCCCGCAATCGAAAAGGCGCGTCTTTATCGGGGCAAAGGAGGAGAGATCATGCGCTCCGCTGTTTCTCGATT
upper sequence: LOC_Os10g36490.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA10G42560.1 (Glycine max), 3'ss of exon 10
gtaagagatccatttatctagattatctcttgt--aatactttttatct-gaattgtttaccctataaactcctttgcatgggtgttca--ttattct--atagACATGCAGAAAGCTCTGTCAGGAATTGTTCCTGCAATTGAAAAGGCACGCCTTTATCGAGGTAAAGGAGGAGAGATAATGCGTTCTGCTGTTTCCCGATT
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---actggtc-atatgtttaaatctttctttattgaaggtgattggtttcaaaataattatgatgctagctgaactgtgacatttttgaaattgtcattgacagATAAACAGAAAAGTCTTGCTGGTGTTGTTCCTGCTATTGAGAAAGCACGGCTTTATCGTGGAAAGGGAGGAGAGATAATGCGTGCAGCTGTTTCTCGATT
upper sequence: LOC_Os10g36490.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA20G24470.1 (Glycine max), 3'ss of exon 11
gtaagagatccatttatctagattatctcttgtaatacttttta--tctgaattgtttaccctataaact---cctttgcatgggtgt--tcattattctatagACATGCAGAAAGCTCTGTCAGGAATTGTTCCTGCAATTGAAAAGGCACGCCTTTATCGAGGTAAAGGAGGAGAGATAATGCGTTCTGCTGTTTCCCGATT
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---aatggtcatatggttaaacctttctttactgaaggtgattagtttcaaaatatttatgatgctagctgaactttgacatttttgaaattgccattg-acagATAAACAGAGAAGTCTTGCTGGCGTTGCTCCTGCTATTGAGAAAGCACGGCTTTATCGTGGAAAGGGAGGAGAGATAATGCGTGCAGCTGTTTCTCGATT
upper sequence: LOC_Os10g36490.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv15s0048g00470.t01 (Vitis vinifera), 3'ss of exon 10
-gtaagagatccatttatctagattatctcttgtaatactttttatctgaattgtttaccctataaactcctttgca----tgggtgttcattattctatagACATGCAGA-AAGCTCTGTCAGGAATTGTTCCTGCAATTGAAAAGGCACGCCTTTATCGAGGTAAAGGAGGAGAGATAATGCGTTCTGCTGTTTCCCGATT
|| | | | | | | | ||| || | | | | || | ||||| | || | | ||| | | ||| | ||||| ||| | ||| || || ||| |||| ||||| || |||||||||||||| || || || ||||||||||||||| ||||||||||||| ||
tgtgtctctgcttctaactcaaaagtaattggttgataaattgctttcaagct-tctaatttgcaaactaactcatgatcctgagcatatatt-tcttccagATAAGCAGACAAGGTTTGTT-GGTATAGTTACTGCTATTGAGAAAGCACGCCTTTATCGTGGGAAGGGTGGAGAGATAATGCGTGCTGCTGTTTCCCGGTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatctgaattgtttaccctataaactcctttgcatgggtgttcattattctatagACATGCAGAAAGCTCTGTCAGGAATTGTTCCTGCAATTGAAAAGGCACGCCTTTATCGAGGTAAAGGAGGAGAGATAATGCGTTCTGCTGTTTCCCGATT
ttattct CT-rich tract
ttcattattctata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagagatccatttatctagattatctcttgtaatactttttatctgaattgtttaccctataaactcctttgcatgggtgttcattattctatagACATGCAGAAAGCTCTGTCAGGAATTGTTCCTGCAATTGAAAAGGCACGCCTTTATCGAGGTAAAGGAGGAGAGATAATGCGTTCTGCTGTTTCCCGATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT