Sequence
atgc intronic sequence ATGC exonic sequencegcaagcaagaacgcacgcaattcaaatgagacaccaactgttcgatcgatcgatcgatcgccattgccgatttggcgagcttgattgggctaattttggttttttgggtcgtgcagGGTTGCAGCGATGCGGCAAGAGCTGCAGGCTGCGGTGGATCAACTACCTCAGGCCAGACCTGAAGCGCGGGAGCTTCTCGCAGCAGGAGGAGGACCTCAT
Basic information
species | Oryza sativa |
transcript | LOC_Os05g46610.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g46610.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G175232_T01 (Zea mays), 3'ss of exon 1
gcaagcaagaacgcacgcaattcaaatgagacaccaactgttcgatcgatc---gatcgatcgccattgccgatttggcgagcttgat------------tgggctaattttg--------gttttttgg-gtcgtgcagGGTTGCAGCGATGCGGCAAGAGCTGCAGGCTGCGGTGGATCAACTACCTCAGGCCAGACCTGAAGCGCGGGAGCTTCTCGCAGCAGGAGGAGGACCTCAT
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gcaagcagagctgca---actctcactgttgtatccatcagtctgtcgtctcgtggtcttcctcccacactgacatggggagtgcagcacatatccatcccgcgcctagcttgcctgaattgtcttgtggtggcgtgcagGGCTGCAGCGCTGCGGCAAGAGCTGCCGCCTGCGGTGGATCAACTACCTCCGCCCCGACCTCAAGCGCGGCAGCTTCTCGCAGCAGGAGGAGGACCTCAT
upper sequence: LOC_Os05g46610.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G119693_T01 (Zea mays), 3'ss of exon 1
gcaagcaagaacgcacgcaattcaaatgagacaccaactgttcgatcgatcgatcgatcgccattgccgatttggcgagcttgattgggctaattttggttttttgggtcgtgcagGGTTGCAGCGATGCGGCAAGAGCTGCAGGCTGCGGTGGATCAACTACCTCAGGCCAGACCTGAAGCGCGGGAGCTTCTCGCAGCAGGAGGAGGACCTCAT
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gcaagcaaca-tgcttatattatatacaactcgctcactgcc--attcatcat---atggcgcgcgcc--ttgcctgaattttcgccttcccgttgtggtgccg-gtgccgtgcagGGCTGCAGCGCTGCGGCAAGAGCTGCCGCCTGCGGTGGATCAACTACCTCCGCCCCGACCTCAAGCGCGGCGGCTTCTCGCAGCAGGAGGAGGACCTCAT
upper sequence: LOC_Os05g46610.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S277_14V6.1 (Physcomitrella patens), 3'ss of exon 1
gcaagcaagaacgcacgcaattcaaatgagacaccaactgttcgatcgatcgatcgatcgccattgccgatttggcgagcttgattgggctaattttggttttttgg-gtcgtg-cagGGTTGCAGCGATGCGGCAAGAGCTGCAGGCTGCGGTGGATCAACTACCTCAGGCCAGACCTGAAGCGCGGGAGCTTCTCG-CAGCAGGAGGAGGACCTCAT
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------------taacatatttaaagtgaaa----aaaggttcttttcattgatgtaaggaatctaatcgtgtggagaaattgat--gaatgttcctggacaatgaatgctgcaacagGTCTCCAAAGGTGCGGGAAGAGCTGCAGGTTGCGGTGGATCAACTACCTCCGGCCGGATTTGAAACGAGGCGTATTTTCGGCAGCAG-AGGAGAACTTGAT
upper sequence: LOC_Os05g46610.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S211_139V6.1 (Physcomitrella patens), 3'ss of exon 1
gcaagcaagaacgcacgcaattcaaatgagacaccaactgttcgatcgatcgatc-gatcgccattgccgatttggcgagcttgattgggctaattttggttttttgggtcgt----gcagGGTTGCAGCGATGCGGCAAGAGCTGCAGGCTGCGGTGGATCAACTACCTCAGGCCAGACCTGAAGCGCGGGAGCTTCTC-GCAGCAGGAGGAGGACCTCAT
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------------------aatgaaaatggtttcgcaggaatgaa---gagcgaccaggttagcacactttgttttgtactaatcactaaccaatatttgtgtttgtgaatggatgcaacagGTCTTCAAAGGTGTGGGAAGAGCTGCAGGCTGCGATGGATCAACTACTTGAGACCAGATTTGAAACGAGGGGTATTCTCCGCGACAGAAGAAAG-TTTGATMapped 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|58587092|gb|CF985400.1|CF985400EST: CATCATCCGACATGGCGTCGGCTGCTGGAGCTCCGTCCCCAAGCTCGCAG GGTTGCAGCGATG
genomic: CATCATCCGACATGGCGTCGGCTGCTGGAGCTCCGTCCCCAAGCTCGCAGgcaagcaaga ... ggtcgtgcagGGTTGCAGCGATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cattgccgatttggcgagcttgattgggctaattttggttttttgggtcgtgcagGGTTGCAGCGATGCGGCAAGAGCTGCAGGCTGCGGTGGATCAACTACCTCAGGCCAGACCTGAAGCGCGGGAGCTTCTCGCAGCAGGAGGAGGACCTCAT
ggctaat putative branch site (score: 3)
taattttggtttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcaagcaagaacgcacgcaattcaaatgagacaccaactgttcgatcgatcgatcgatcgccattgccgatttggcgagcttgattgggctaattttggttttttgggtcgtgcagGGTTGCAGCGATGCGGCAAGAGCTGCAGGCTGCGGTGGATCAACTACCTCAGGCCAGACCTGAAGCGCGGGAGCTTCTCGCAGCAGGAGGAGGACCTCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA