Sequence
atgc intronic sequence ATGC exonic sequencegtatgaagatgcagtagaatattctctctctttttaggcttcttgaggctaatagtgtgttttactacaacagGTTATACCAGCTTGCTTCCATGGGATTTGCAGCATTTGGTGTCTTTCTTCTTGCAAAGCGTGCACTACAGCATTTTCTCGAAAGAAAACGACGACATGAA
Basic information
species | Oryza sativa |
transcript | LOC_Os07g45350.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g45350.3 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G020574_T01 (Zea mays), 3'ss of exon 6
--------------------gtatgaagatgcagtagaatattctctctctttttaggcttc--ttgaggctaatagtgt--gttttac---tacaacagGTTATACCAGCTTGCTTCCATGGGATTTGCAGCATTTGGTGTCTTTCTTCTTGCAAAGCGTGCACTACAGCATTTTCTCGAAAGAAAACGACGACATGAA
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aatcttgggaaatgggccaagtaggaaaatttgttagaacatatttttggttgttacttcttagttagggcatcttatgctagtatcatgtttgtggcagGTTATACCGAATTGCTTCCATGGGTTTTGCAACATTTGGTGTCTTCCTTCTTGCAAAGCGTGCACTACAGCATTTTCTAGAAAGAAGACGGCGGCATGAA
upper sequence: LOC_Os07g45350.3 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM5G871572_T01 (Zea mays), 3'ss of exon 7
----------gtatgaagatgcagtagaatattctctctcttt--ttaggcttcttgaggctaatagtgtgttttactacaacagGTTATACCAGCTTGCTTCCATGGGATTTGCAGCATTTGGTGTCTTTCTTCTTGCAAAGCGTGCACTACAGCATTTTCTCGAAAGAAAACGACGACATGAA
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gtaggaaaaattgttagaacttagaacattttcttttgttcttagttagggtatcttatgctagtagcatgttt----gtgacagGTTATACCGCCTTGCTTCAATGGGCTTTGCAACATTTGGTGCCTTCCTTCTTGCAAAGCGTGCAATACAACATTTTCTAGAAAGAAAGCGCCGGCATGAA
upper sequence: LOC_Os07g45350.3 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G020574_T07 (Zea mays), 3'ss of exon 7
gtatgaagatgcagtagaatattctctctctttttaggcttc--ttgaggctaatagtgt--gttttac---tacaacagGTTATACCAGCTTGCTTCCATGGGATTTGCAGCATTTGGTGTCTTTCTTCTTGCAAAGCGTGCACTACAGCATTTTCTCGAAAGAAAACGACGACATGAA
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gtaggaaaatttgttagaacatatttttggttgttacttcttagttagggcatcttatgctagtatcatgtttgtggcagGTTATACCGAATTGCTTCCATGGGTTTTGCAACATTTGGTGTCTTCCTTCTTGCAAAGCGTGCACTACAGCATTTTCTAGAAAGAAGACGGCGGCATGAAMapped 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|33683627|gb|CF311866.1|CF311866EST: TCCCCGAAAAGCATCGATCAACTTATCATGAATCTTGGGAAATGGGCCAA GTTATACCAGCTTGCTTCCATGGGATTTGCAGCATTTGGTGTCTTTCTTCT
genomic: TCCCCGAAAAGCATCGATCAACTTATCATGAATCTTGGGAAATGGGCCAAgtatgaagat ... actacaacagGTTATACCAGCTTGCTTCCATGGGATTTGCAGCATTTGGTGTCTTTCTTCT
EST:
gi|86905521|gb|CI285484.1|CI285484EST: TCCCCGAAAAGCATCGATCAACTTATCATGAATCTTGGGAAATGGGCCAA GTTATACCAGCTTGCTTCCATGGGATTTGCAGCATTTGGTGTCTTTCTTCT
genomic: TCCCCGAAAAGCATCGATCAACTTATCATGAATCTTGGGAAATGGGCCAAgtatgaagat ... actacaacagGTTATACCAGCTTGCTTCCATGGGATTTGCAGCATTTGGTGTCTTTCTTCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atattctctctctttttaggcttcttgaggctaatagtgtgttttactacaacagGTTATACCAGCTTGCTTCCATGGGATTTGCAGCATTTGGTGTCTTTCTTCTTGCAAAGCGTGCACTACAGCATTTTCTCGAAAGAAAACGACGACATGAA
ggctaat putative branch site (score: 3)
ttttact putative PPT
tcttttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgaagatgcagtagaatattctctctctttttaggcttcttgaggctaatagtgtgttttactacaacagGTTATACCAGCTTGCTTCCATGGGATTTGCAGCATTTGGTGTCTTTCTTCTTGCAAAGCGTGCACTACAGCATTTTCTCGAAAGAAAACGACGACATGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA