Sequence
atgc intronic sequence ATGC exonic sequencegtactcctagtggaatattatatcttttttttacacaaaaaaaacaatttattttacttttaagttttaaccctgaccattctgatattcagGAATCACACGGGATACATTGTTGCTGAGAATGAAGAAATCTCAGTGGCAAGATGTAGTTGATCTTAATCTTACGGGCGTATTCCTTTGCACACAG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g30060.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g30060.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G043602_T03 (Zea mays), 3'ss of exon 4
gtactcctagtggaatattatatcttttttttacacaaaaaaaacaatttattttacttttaagttttaaccctgaccattctgatattcagGAATCACACGGGATACATTGTTGCTGAGAATGAAGAAATCTCAGTGGCAAGATGTAGTTGATCTTAATCTTACGGGCGTATTCCTTTGCACACAG
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------gtaatgcca-attat-tattattattttgcaactactacaatttgtttcacttccaacaattggagcaaa--aaactgataat-agGAATCACACGGGACACATTGTTGATGAGAATGAAGAAATCACAGTGGCAAGATGTGATTGATTTGAATCTTACAGGCGTTTTCCTTTGCACGCAG
upper sequence: LOC_Os02g30060.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA11G37320.1 (Glycine max), 3'ss of exon 5
gtactcctagtggaatattatatcttttttttacacaaaaaaaacaatttattttacttttaagttttaaccctgaccattctgatattcagGAATCACACGGGATACATTGTTGCTGAGAATGAAGAAATCTCAGTGGCAAGATGTAGTTGATCTTAATCTTACGGGCGTATTCCTTTGCACACAG
| | || | | | | | | | | | ||| || | | | | || ||| |||| ||||||||| || | ||| || || ||||||||||||||||||| ||||| ||||| ||||||| ||||| || || || || |||||||| |||
------------gtaagttggaaagctcctgtgcttgagctct-ctctctctttctctaatcattctcaagtagtcatattatgat-ttcagGAATAACTAGAGATGGTTTATTAATGAGAATGAAGAAATCTCAATGGCAGGATGTTATTGATCTAAATCTCACTGGTGTTTTTCTTTGCACCCAG
upper sequence: LOC_Os02g30060.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA18G01280.1 (Glycine max), 3'ss of exon 5
----------gtactcctagtggaatattatatcttttttttacacaaaaaaaacaatttattttacttttaagttttaaccctgaccattctgatattcagGAATCACACGGGATACATTGTTGCTGAGAATGAAGAAATCTCAGTGGCAAGATGTAGTTGATCTTAATCTTACGGGCGTATTCCTTTGCACACAG
||||| |||| | | || | | | | | | | ||| || | | | || ||| |||| ||||||||| ||| | ||| || || ||||||||||||||||||| ||||| ||||| ||||||| ||||| || || || || ||||||||||||
gtaagttggaaagctcct-gtggttgagctaacctctctccctctcc-------ccctctttttctctaggcattctcaaataatcatattatgat-ttcagGAATAACAAGAGATGGTTTATTAATGAGAATGAAGAAATCTCAATGGCAGGATGTTATTGATCTAAATCTCACTGGTGTTTTTCTTTGCACACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaaaaacaatttattttacttttaagttttaaccctgaccattctgatattcagGAATCACACGGGATACATTGTTGCTGAGAATGAAGAAATCTCAGTGGCAAGATGTAGTTGATCTTAATCTTACGGGCGTATTCCTTTGCACACAG
ccattct CT-rich tract
aacaatttattttact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactcctagtggaatattatatcttttttttacacaaaaaaaacaatttattttacttttaagttttaaccctgaccattctgatattcagGAATCACACGGGATACATTGTTGCTGAGAATGAAGAAATCTCAGTGGCAAGATGTAGTTGATCTTAATCTTACGGGCGTATTCCTTTGCACACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG