Sequence
atgc intronic sequence ATGC exonic sequence...gtctctgtagctctaagctgttcagtgttaaatatacatgttaatgtatacaaaattaaggatgcaggtcctaagctaaatatgattttatttggtgcagTCAAGTGGACTTCGATCACATACTCTATCCATCCTTGTCAATGATTGCCCTGGTGTTCTCAACATTGTTACAGGGGTCTTTGCTCGCAGAGGCTACAATA
Basic information
species | Oryza sativa |
transcript | LOC_Os02g39570.5 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g39570.5 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G407044_T02 (Zea mays), 3'ss of exon 8
gtctctgtagctctaagctgtt----cagtgttaaatatacatgttaatgtatacaaaattaaggatgcaggtcctaagctaaatatgattttatttggtgcagTCAAGTGGACTTCGATCACATACTCTATCCATCCTTGTCAATGATTGCCCTGGTGTTCTCAACATTGTTACAGGGGTCTTTGCTCGCAGAGGCTACAATA
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----atatggctttaagaaatggtaataatgcttgacctgcatgtttatgcatactgttgttatcttgcagctgctaatccagtattgattttgtgttgtacagGCGACTGGACTTCGCTCGCATACTCTCTCCATCCTTGTGAATGACTGTCCTGGTGTCCTCAACATTGTAACAGGAGTCTTTGCTCGCAGGGGCTACAATA
upper sequence: LOC_Os02g39570.5 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G007647_T01 (Zea mays), 3'ss of exon 7
gtctctgtagctctaagctgtt--cagtgttaaatatacatgttaatgtatacaaaattaaggatgcaggtcctaagctaaatatgattttatttggtgcagTCAAGTGGACTTCGATCACATACTCTATCCATCCTTGTCAATGATTGCCCTGGTGTTCTCAACATTGTTACAGGGGTCTTTGCTCGCAGAGGCTACAATA
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--acatagatttaaaaaatggtaataatgcttaacctgcatgtttatgaatactgttgttatcttgcagctgctaatccagtattgattttgtgtggtacagGCAACTGGACTTTGCTCGCATACCCTCTCCATCCTTGTGAATGATTGTCCTGGTGTTCTCAACATTGTAACAGGAGTCTTTGCTCGCAGGGGCTACAATA
upper sequence: LOC_Os02g39570.5 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA08G13290.1 (Glycine max), 3'ss of exon 7
gtctctgtagct---ctaagctgttcagtgttaaatatacatgttaatgtata-caaaattaaggatg-caggtcctaagctaaatatgattttatttggtgcagTCAAGTGGACTTCGATCACATACTCTATCCATCCTTGTCAATGATTGCCCTGGTGTTCTCAACATTGTTACAGGGGTCTTTGCTCGCAGAGGCTACAATA
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tctcctgtgccttcactactatgtttattgt-acattagcatgt-aatattcatcaattttctgaatgacatgtcttactgttggtgggataatgcct---tcagACTAGTGGAATTCGATCACACACTTTATCCATGCTTGTGAACGATGCTCCTGGAGTTCTAAACATTGTTACAGGAGTTTTTGCTAGAAGAGGCTATAACA
upper sequence: LOC_Os02g39570.5 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA05G30130.1 (Glycine max), 3'ss of exon 7
----gtctctgtagctctaagctgttcagtgttaaatatacatgttaatgtatacaaaattaaggatgcaggtcctaagctaaatatgattttatttggtgcagTCAAGTGGACTTCGATCACATACTCTATCCATCCTTGTCAATGATTGCCCTGGTGTTCTCAACATTGTTACAGGGGTCTTTGCTCGCAGAGGCTACAATA
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cttcactactatgtttattgtacgtt-agcatgtaatattca--tcaattttatgaatgacatgcttgtgactgtcttactgttggtggaataattcctt-cagACCAGTGGAATTCGATCACACACGTTATCCATGCTTGTGAACGATGCTCCTGGAGTTCTAAACATTGTTACAGGAGTTTTTGCTAGAAGAGGCTATAACAMapped 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|32948361|gb|BP184933.1|BP184933EST: CCATGAACCAAGTACTTGATGCTCACTGGGGCGTCCTTGATGATGAAGAT TCAAGTGGACTTCGATCACATACTCTATCCATCCTTGTCAATGATTGCCCT
genomic: CCATGAACCAAGTACTTGATGCTCACTGGGGCGTCCTTGATGATGAAGATgtaagtttca ... tttggtgcagTCAAGTGGACTTCGATCACATACTCTATCCATCCTTGTCAATGATTGCCCT
EST:
gi|33682200|gb|CF310439.1|CF310439EST: CCATGAACCAAGTACTTGATGCTCACTGGGGCGTCCTTGATGATGAAGAT TCAAGTGGACTTCGATCACATACTCTATCCATCCTTGTCAATGATTGCCCT
genomic: CCATGAACCAAGTACTTGATGCTCACTGGGGCGTCCTTGATGATGAAGATgtaagtttca ... tttggtgcagTCAAGTGGACTTCGATCACATACTCTATCCATCCTTGTCAATGATTGCCCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtatacaaaattaaggatgcaggtcctaagctaaatatgattttatttggtgcagTCAAGTGGACTTCGATCACATACTCTATCCATCCTTGTCAATGATTGCCCTGGTGTTCTCAACATTGTTACAGGGGTCTTTGCTCGCAGAGGCTACAATA
agctaaa putative branch site (score: 3)
ttttattt putative PPT
taagctaaatatgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctctgtagctctaagctgttcagtgttaaatatacatgttaatgtatacaaaattaaggatgcaggtcctaagctaaatatgattttatttggtgcagTCAAGTGGACTTCGATCACATACTCTATCCATCCTTGTCAATGATTGCCCTGGTGTTCTCAACATTGTTACAGGGGTCTTTGCTCGCAGAGGCTACAATA
- - ctgtagc
- - - - - - - -agctgtt
- - - - - - - - - - - - - - - - -atacatg
- - - - - - - - - - - - - - - - - - - - - - - - tacaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agctaaa