Sequence
atgc intronic sequence ATGC exonic sequencegtaggatccgcgtgaccttttctcttcattacacactgaaatgattcattcagaatgcattgatgatgaaattctttgatgttaagGTTGGTTAATCTACTGGAGGATATAATGGATGGCAGCCGGATATTAATATTTATGGACACGAAGAAGGGATGTGATCAAATCACTAGACAGCTTCGGATG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g10050.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g10050.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G143246_T01 (Zea mays), 3'ss of exon 7
gtaggatccgcgtgaccttttctcttcattacacactgaaatgattcattcagaatgcattgatgatgaaattctttgatgttaagGTTGGTTAATCTACTGGAGGATATAATGGATGGCAGCCGGATATTAATATTTATGGACACGAAGAAGGGATGTGATCAAATCACTAGACAGCTTCGGATG
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gtaggatttctacaaaatttcccc---atttcatac--acattattcaaaca--atgtcttagtgatacttttatttgt--acaagGCTGGTTAATCTACTGGAGGATATAATGGATGGTAGCCGAATTTTAATATTTATGGACACCAAGAAGGGATGCGATCAGACTACTAGACAGCTTCGAATG
upper sequence: LOC_Os01g10050.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA08G20670.1 (Glycine max), 3'ss of exon 7
gtaggatccgcgtgaccttttc-tcttcattacacactgaaatgattcattcagaatgcattgatgatgaaattctttgatgtta-agGTTGGTTAATCTACTGGAGGATATAATGGATGGCAGCCGGATATTAATATTTATGGACACGAAGAAGGGATGTGATCAAATCACTAGACAGCTTCGGATG
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gtaggatgtgttctaccttttcattctcgttgcattt---aacaccttatcacatatggccacctgatggagtcttcctatttttcagATTGGTAAAGTTGCTAGAAGACATCATGGATGGCAGCCGAATACTGATATTTATGGATACCAAAAAAGGATGTGATCAGATTACTAGGCAACTCCGCATG
upper sequence: LOC_Os01g10050.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA07G11880.1 (Glycine max), 3'ss of exon 8
gtaggatccgcgtgaccttttctcttcattacacactgaaatgattcattcagaatgcattgatgatgaaattctttgatgttaagGTTGGTTAATCTACTGGAGGATATAATGGATGGCAGCCGGATATTAATATTTATGGACACGAAGAAGGGATGTGATCAAATCACTAGACAGCTTCGGATG
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gtagaatgtgttctaccttattt--tcatt-ctcgttgcatttaacaccttatcacatatggccatggagtcttcctttttgtcagATTGGTAAAATTGCCAGAGGACATCATGGATGGCAGCCGAATACTGATATTTATGGGTACCAAAAAAGGATGTGATCAAATCACTAGACAACTCCGCATG
upper sequence: LOC_Os01g10050.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA07G01260.1 (Glycine max), 3'ss of exon 7
gtaggatccgcgtgacctt-ttctcttcattacacactgaaatgattcattcagaatgcattgatgatgaaattctttgatgt-taagGTTGGTTAATCTACTGGAGGATATAATGGATGGCAGCCGGATATTAATATTTATGGACACGAAGAAGGGATGTGATCAAATCACTAGACAGCTTCGGATG
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gtaggatgtgttctaccttattttcattctcgttgcatttaacaccttatcacatatggccacctaatggagtcttcctatttgtcagATTGGTAAAGTTGCTAGAGGACATCATGGATGGCAGCCGAATACTGATATTTATGGATACCAAAAAAGGATGTGATCAAATCACTAGGCAACTCCGCATGMapped 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|66914774|gb|CX101622.1|CX101622EST: ATTATCCGAGAGTCAGAAGTACAATAA GTTGGTTAATCTACTGGAGGATATAATGGATGGCAGCCGGATATTAATATT
genomic: ATTATCCGAGAGTCAGAAGTACAATAAgtaggatccg ... tgatgttaagGTTGGTTAATCTACTGGAGGATATAATGGATGGCAGCCGGATATTAATATT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cacactgaaatgattcattcagaatgcattgatgatgaaattctttgatgttaagGTTGGTTAATCTACTGGAGGATATAATGGATGGCAGCCGGATATTAATATTTATGGACACGAAGAAGGGATGTGATCAAATCACTAGACAGCTTCGGATG
ttcttt CT-rich tract
aaattcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggatccgcgtgaccttttctcttcattacacactgaaatgattcattcagaatgcattgatgatgaaattctttgatgttaagGTTGGTTAATCTACTGGAGGATATAATGGATGGCAGCCGGATATTAATATTTATGGACACGAAGAAGGGATGTGATCAAATCACTAGACAGCTTCGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG