Sequence
atgc intronic sequence ATGC exonic sequencegtaactctgtcaaactcgctatgcttgtagtctgtattgtatttattttttcttagaatcatgtttattttgtatcagcttcatagtttctgattcaacacaaatatacaaattacatgtgctcattacactgacgaaacatccaaaaacaccactaaaataaataacggatattgtatcagGTTAGCTGTAGTGTCAATGGCAGGGCTCGCTGCTGAAGGTCTAGAATATGACAAAGTTGTCGGTCAATCGGCAGATCTTTTCACCCTTCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os04g54640.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g54640.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G004352_T01 (Zea mays), 3'ss of exon 7
gtaactctgtcaaactcgctatgcttgtagtctgtattgt---atttattttttcttagaatcatgtttattttgtatcagcttcatagtttctgattcaacacaaatatacaaattacatgtgctcattacactgacgaaacatccaaaaacaccactaaaataaataacggatattgtatcagGTTAGCTGTAGTGTCAATGGCAGGGCTCGCTGCTGAAGGTCTAGAATATGACAAAGTTGTCGGTCAATCGGCAGATCTTTTCACCCTTCAG
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gtaaccctctt---ttttccatgcatgtaatctacagtttttaacctgtccatgcctgtaatatacagtgggtagcttggtgttcatagtgtaaagttgaactttgcactgcacacc-tgcaaaaaagtcactaggatcaaacaagtatgaaagctactgacacctacaatttttgttc--tcagGTTAGCTGTAGTTTCAATGGCAGGACTGGCTGCTGAAGGTCTAGAATATGACAAAGTTGTAGGTCAATCAGCAGATCTTTTCACCCTTCAG
upper sequence: LOC_Os04g54640.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA08G14970.1 (Glycine max), 3'ss of exon 7
gtaac-tctgtcaaactcgctatgcttgtagtctgtattgtatttattttttcttagaatcatgtttattttgtatcagcttcatagtttctgattcaacacaaatata--caaattacatgtgctcattacactgacgaaacatccaaaaacaccactaa-aataaataacggatattgtatcagGTTAGCTGTAGTGTCAATGGCAGGGCTCGCTGCTGAAGGTCTAGAATATGACAAAGTTGTCGGTCAATCGGCAGATCTTTTCACCCTTCAG
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gtactatttatttaccatacacctcttattgctcttatccaatgtgagagaaaa-aaagccatgacaact---tataacttttcaagaaccaagtaccaaccaaaccaagccttattaatcacaaaacttgcctttaagaaatacgaagagttgtaattagtaatttaaaaaaaat-tcatatcagATTGGCTGTTGTGTCAATGGCTGGACTGGCAGCAGAAGGTTTAACATATGACAAGGTGGTTGGTCAATCTGCTGATCTTTTCAGTCTCCAG
upper sequence: LOC_Os04g54640.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA05G31720.1 (Glycine max), 3'ss of exon 7
gtaactctgtcaaactcgc-tatgcttgtagtctgtattgtat-ttattttttcttagaatcatgtttattttgtatcagcttcatagtttctgattcaacacaaatatacaaattacatgtgctcattacact-gacgaaacatccaaaaacaccactaaaataaataacggatattgtatcagGTTAGCTGTAGTGTCAATGGCAGGGCTCGCTGCTGAAGGTCTAGAATATGACAAAGTTGTCGGTCAATCGGCAGATCTTTTCACCCTTCAG
||| | | | || | | || | | | || | | | | | |||| | | ||| | || || | | | | ||| ||| | | ||| | ||| | | || | || | | | | | | | | | |||||| || ||||| ||||||||||| || || || || |||||| || ||||||||| || || |||||||| || |||||||||| || |||
------gtgtttatttaccatacacctctaatttctcttattcactgtggaagaaaaaagccatgccaact---tataacttttcaagaaccaagtactaaccaagc---caagcctta-ataatcacaaaacttggcttaatagg-aagagttttaattagtaatttcatttttttcatatcagATTGGCTGTTGTGTCAATGGCTGGACTGGCAGCAGAAGGTTTAACATATGACAAGGTGGTTGGTCAATCTGCTGATCTTTTCAGTCTCCAG
upper sequence: LOC_Os04g54640.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv07s0031g01560.t01 (Vitis vinifera), 3'ss of exon 7
gtaactctgtcaaactcgctatgcttgtagtctgtattgtatttattttttcttagaatcatgtttattttgtatcagcttcatagtttctgattcaacacaaata-tacaaattacatgt--gctcattacactgacgaaacatccaaaaacaccactaaaata--aataacggatattgtatcagGTTAGCTGTAGTGTCAATGGCAGGGCTCGCTGCTGAAGGTCTAGAATATGACAAAGTTGTCGGTCAATCGGCAGATCTTTTCACCCTTCAG
| || | || | ||| | | |||| | | | ||| | | | | | | | | || || | || | | || | |||||| || || || ||||||| || || || || ||||| || ||||||||||||| || |||||||| || ||||||||||| ||||||
---------------------------------------------------------------------------------------acataatcctccatagatagttcggattatggattagttaatttaaattaagggaattgccggtagacagctgacattccacctttaactgttattccagGTTGGCGGTTGTAGCAATGGCTGGACTTGCAGCAGAAGGCCTGCAATATGACAAAGTGGTTGGTCAATCTGCCGATCTTTTCACTCTTCAG
upper sequence: LOC_Os04g54640.1 (Oryza sativa), 3'ss of exon 7
lower sequence: EFJ34800 (Selaginella moellendorffii), 3'ss of exon 6
gtaactctgtcaaactcgctatgcttgtagtctgtattgtatttattttttcttagaatcatgtttattttgtatcagcttcatagtttctgattcaacacaaatatacaaattacatgtgctcattacactgacgaaacatccaaaaacaccactaaaataaataacggatattgtatcagGTTAGCTGTAGTGTCAATGGCAGGGCTCGCTGCTGAAGGTCTAGAATATGACAAAGTTGTCGGTCAATCGGCAGATCTTTTCACCCTTCAG
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-----------------------------------------------------------------------------------------------------------------------------gtatctgaactcgaactcctttctttcttttgaagtttctttc---tattgtatcagGCTGGCTGTCGTTTCAATGGCTGGGCTTGCTGCCGAGGCTCTAAAATATGACAAAGTTATTGGCCAGTCTGCCGATTTATTCTCCCTTCAG
upper sequence: LOC_Os04g54640.1 (Oryza sativa), 3'ss of exon 7
lower sequence: EFJ23530 (Selaginella moellendorffii), 3'ss of exon 6
gtaactctgtcaaactcgctatgcttgtagtctgtattgtatttattttttcttagaatcatgtttattttgtatcagcttcatagtttctgattcaacacaaatatacaaattacatgtgctcattacactgacgaaacatccaaaaacaccactaaaataaataacggatattgtatcagGTTAGCTGTAGTGTCAATGGCAGGGCTCGCTGCTGAAGGTCTAGAATATGACAAAGTTGTCGGTCAATCGGCAGATCTTTTCACCCTTCAG
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-----------------------------------------------------------------------------------------------------------------------------gtatctgaactcgaactcctttctttcttttgaagtttctttc---tattgtatcagGCTGGCTGTCGTTTCAATGGCTGGGCTTGCTGCCGAGGCTCTAAAATATGACAAAGTTATTGGCCAGTCTGCCGATTTATTCTCTCTTCAGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|38476935|gb|CF961068.1|CF961068EST: TTGCAAAAGCTAATATACAGTGGCCAGCTTGATCAAAAGGAAATAGACAG GTTAGCTGTAGTGTCAATGGCAGGGCTCGCTGCTGAAGGTCTAGAATATGA
genomic: TTGCAAAAGCTAATATACAGTGGCCAGCTTGATCAAAAGGAAATAGACAGgtaactctgt ... attgtatcagGTTAGCTGTAGTGTCAATGGCAGGGCTCGCTGCTGAAGGTCTAGAATATGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acactgacgaaacatccaaaaacaccactaaaataaataacggatattgtatcagGTTAGCTGTAGTGTCAATGGCAGGGCTCGCTGCTGAAGGTCTAGAATATGACAAAGTTGTCGGTCAATCGGCAGATCTTTTCACCCTTCAG
aaataac putative branch site (score: 2)
actaaaataaataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaactctgtcaaactcgctatgcttgtagtctgtattgtatttattttttcttagaatcatgtttattttgtatcagcttcatagtttctgattcaacacaaatatacaaattacatgtgctcattacactgacgaaacatccaaaaacaccactaaaataaataacggatattgtatcagGTTAGCTGTAGTGTCAATGGCAGGGCTCGCTGCTGAAGGTCTAGAATATGACAAAGTTGTCGGTCAATCGGCAGATCTTTTCACCCTTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT