Sequence
atgc intronic sequence ATGC exonic sequencegtaacttcctgttgatgtgcatttcagtactcgctgccaaaagaactttttagattagcatcgtcaaatggtgaattgcttttctacagGTTTTCCTTATATCTACACGGGCAGGAAATTTAGGTGTCAACCTGGTCAGTGCTAATCGTGTGGTGATTTTTGACCCAAGTTGGAACCCTGCGCAAGACT
Basic information
species | Oryza sativa |
transcript | LOC_Os05g15890.3 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g15890.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G146041_T03 (Zea mays), 3'ss of exon 4
gtaacttcctgttgatgtgcatttcagtactcgctgccaaaagaactttttagattagcatcg--tcaaatggtgaattgcttttctacagGTTTTCCTTATATCTACACGGGCAGGAAATTTAGGTGTCAACCTGGTCAGTGCTAATCGTGTGGTGATTTTTGACCCAAGTTGGAACCCTGCGCAAGACT
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gtcaattttggtggatgtggatttttttgt--acttctaacaaaattttgaaggccatagttgagttaagtggttaaattcttttatgcagGTTTTCCTTATATCTACTCGAGCAGGTAATTTAGGTGTAAACCTTGTTAGTGCTAACCGCGTGGTGATATTTGATCCAAGTTGGAACCCTGCCCAAGACT
upper sequence: LOC_Os05g15890.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G146041_T02 (Zea mays), 3'ss of exon 5
gtaacttcctgttgatgtgcatttcagtactcgctgccaaaagaactttttagattagcatcg--tcaaatggtgaattgcttttctacagGTTTTCCTTATATCTACACGGGCAGGAAATTTAGGTGTCAACCTGGTCAGTGCTAATCGTGTGGTGATTTTTGACCCAAGTTGGAACCCTGCGCAAGACT--------------------------------------------------------------------------------
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gtcaattttggtggatgtggatttttttgt--acttctaacaaaattttgaaggccatagttgagttaagtggttaaattcttttatgcaggttttccttatatctactcgagcaggtaatttaggtgtaaaccttgttagtgctaaccgcgtggtgatatttgatccaagTTGGAACCCTGCCCAAGACTTGCAAGCACAAGACAGATCATTTCGGTATGGACAGAGACGGCATGTTACAGTATTTCGCCTACTTGGTGCCGGTTCACTTMapped 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|27548508|gb|CA766438.2|CA766438EST: ATGCACGCCAATTACTAATTGATGAGTTCAATAGATGCCCAAGCAAACAG GTTTTCCTTATATCTACACGGGCAGGAAATTTAGGTGTCAACCTGGTCAGT
genomic: ATGCACGCCAATTACTAATTGATGAGTTCAATAGATGCCCAAGCAAACAGgtaacttcct ... ttttctacagGTTTTCCTTATATCTACACGGGCAGGAAATTTAGGTGTCAACCTGGTCAGT
EST:
gi|33794394|gb|CF323081.1|CF323081EST: ATGCACGCCAATTACTAATTGATGAGTTCAATAGATGCCCAAGCAAACAG GTTTTCCTTATATCTACACGGGCAGGAAATTTAGGTGTCAACCTGGTCAGT
genomic: ATGCACGCCAATTACTAATTGATGAGTTCAATAGATGCCCAAGCAAACAGgtaacttcct ... ttttctacagGTTTTCCTTATATCTACACGGGCAGGAAATTTAGGTGTCAACCTGGTCAGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgccaaaagaactttttagattagcatcgtcaaatggtgaattgcttttctacagGTTTTCCTTATATCTACACGGGCAGGAAATTTAGGTGTCAACCTGGTCAGTGCTAATCGTGTGGTGATTTTTGACCCAAGTTGGAACCCTGCGCAAGACT
ttgcttttct CT-rich tract
aactttttagatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaacttcctgttgatgtgcatttcagtactcgctgccaaaagaactttttagattagcatcgtcaaatggtgaattgcttttctacagGTTTTCCTTATATCTACACGGGCAGGAAATTTAGGTGTCAACCTGGTCAGTGCTAATCGTGTGGTGATTTTTGACCCAAGTTGGAACCCTGCGCAAGACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA