Sequence
atgc intronic sequence ATGC exonic sequencegtaaactactcatcctctggagttctgttatgcagtacttctcattctgtcaccaatgtcaaggtttttcccatttattaaattctaataattcctttttctctagGTCTATACTGATTCTAAGACTTTGTTTTCGATGAAGAGTGCATTTGATAGATCATCTCGTAATGGGCCCAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os12g03470.5 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g03470.5 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G077299_T03 (Zea mays), 3'ss of exon 11
gtaaactactcatcctctggagttctgttatgcagtacttctcattctgtcaccaa-tgtcaaggttt--ttcccatttattaaattctaataattcct-ttttctctagGTCTATACTGATTCTAAGACTTTGTTTTCGATGAAGAGTGCATTTGATAGATCATCTCGTAATGGGCCCAAG
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gtaaa--gctcttgctgca-agtttatttatatcagttttctgtctatctgtttaactattcatttccaattgccttctcttaaatttcagtcgtgcttcttttttctagGTCTATAATGATTCTAAGACTTTGTTCAACATGAAGAGCACATTTGACAGAACATCTCGTAGTGGACCCAAG
upper sequence: LOC_Os12g03470.5 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G006130_T01 (Zea mays), 3'ss of exon 12
---------------------gtaaactactcatcctctggagttctgttatgcagtacttctcattctgtcaccaatgtcaaggtt--tttcccatttattaaattctaataattcctttttctct-agGTCTATACTGATTCTAAGACTTTGTTTTCGATGAAGAGTGCATTTGATAGATCATCTCGTAATGGGCCCAAG
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gtaaagtccttactgccaagtctgtttgtttcatttttttctctgccttgattctgtggttctgtctaattattcgatgtcaaggtcagcttgccttctcttaaatttaaccagtgcttctttctcttagGTCTATACTGATTCTAAGACTTTGTTTAACATGAGGAGCACATTTGACAGAACATCTCGTAGTGGACCTAAG
upper sequence: LOC_Os12g03470.5 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G006130_T05 (Zea mays), 3'ss of exon 11
---------------------gtaaactactcatcctctggagttctgttatgcagtacttctcattctgtcaccaatgtcaaggtt--tttcccatttattaaattctaataattcctttttctct-agGTCTATACTGATTCTAAGACTTTGTTTTCGATGAAGAGTGCATTTGATAGATCATCTCGTAATGGGCCCAAG
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gtaaagtccttactgccaagtctgtttgtttcatttttttctctgccttgattctgtggttctgtctaattattcgatgtcaaggtcagcttgccttctcttaaatttaaacagtgcttctttctcttagGTCTATACTGATTCTAAGACTTTGTTTAACATGAGGAGCACATTTGACAGAACATCACGTAGTGGACCTAAGMapped 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|29667817|gb|CB664092.1|CB664092EST: ATGCTTCATCAAGACCACTTGACCATCCTGCTGATTTATATGACTTCCAT GTCTATACTGATTCTAAGACTTTGTTTTCGATGAAGAGTGCATTTGATAGA
genomic: ATGCTTCATCAAGACCACTTGACCATCCTGCTGATTTATATGACTTCCATgtaaactact ... ttttctctagGTCTATACTGATTCTAAGACTTTGTTTTCGATGAAGAGTGCATTTGATAGA
EST:
gi|33381874|gb|CF197217.1|CF197217EST: ATGCTTCATCAAGACCACTTGACCATCCTGCTGATTTATATGACTTCCAT GTCTATACTGATTCTAAGACTTTGTTTTCGATGAAGAGTGCATTTGATAGA
genomic: ATGCTTCATCAAGACCACTTGACCATCCTGCTGATTTATATGACTTCCATgtaaactact ... ttttctctagGTCTATACTGATTCTAAGACTTTGTTTTCGATGAAGAGTGCATTTGATAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.accaatgtcaaggtttttcccatttattaaattctaataattcctttttctctagGTCTATACTGATTCTAAGACTTTGTTTTCGATGAAGAGTGCATTTGATAGATCATCTCGTAATGGGCCCAAG
ttctaat putative branch site (score: 2)
taattcctttttctct CT-rich tract
atttattaaattctaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaactactcatcctctggagttctgttatgcagtacttctcattctgtcaccaatgtcaaggtttttcccatttattaaattctaataattcctttttctctagGTCTATACTGATTCTAAGACTTTGTTTTCGATGAAGAGTGCATTTGATAGATCATCTCGTAATGGGCCCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA