Sequence
atgc intronic sequence ATGC exonic sequence...ttacctacctgctggctgctttttttagtaagttaagctgcatatatatacatacatacagcagtatgctctatgaataatgtttgcatttacgttgcagTGCTCATGGACTGGGAACAGCAGCGCTGTCGGCCAAGGAGCCTGAAGCGCTGCCCTTCTGCGCCATCGCTTACGGCCTGACGGGGATCTTCGGTTCGCTC
Basic information
species | Oryza sativa |
transcript | LOC_Os01g32830.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g32830.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM5G873519_T02 (Zea mays), 3'ss of exon 7
ttacctacctgctggctgctttttttagtaagttaagctgcatatatatacatacatacagcagtatgctctatgaataatgtttgcatttacgttgcagTGCTCATGGACTGGGAACAGCAGCGCTGTCGGCCAAGGAGCCTGAAGCGCTGCCCTTCTGCGCCATCGCTTACGGCCTGACGGGGATCTTCGGTTCGCTC
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--------gtaattcagccattcttcgttttgtgaagcatagcatgattaggccc---tgactgaatgc------aatcttgcct-tgctgatggtgcagCGCTCAAGGACTGGGAACAGCAGCACTGGCGGCCAAGGAACCTGAAGCGCTCCCTTTCTGCGCCATCGCTTATAGTTTCACGGGGATTTTCGGCACGCTG
upper sequence: LOC_Os01g32830.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G478212_T01 (Zea mays), 3'ss of exon 7
-ttacctacctgctg-gctgctttttttagtaagttaagctgcatatatatacatacatacagcagtatgctctatgaataatgtttgcat--ttacgttgcagTGCTCATGGACTGGGAACAGCAGCGCTGTCGGCCAAGGAGCCTGAAGCGCTGCCCTTCTGCGCCATCGCTTACGGCCTGACGGGGATCTTCGGTTCGCTC
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gtaattttctggatacaatgccgttctgcatcgtttggtaatccttcgtttgtgagcatgtgtctgaatgt------aatcttgcttggctgatgatggtgtagTGCTCATGGACTGGGGACAGCAGCACTGTCAGCCAAGGAACCTGAAGCGCTTCCTTTCTGCGCCATCGCTTATGGTCTCACGGGAATTTTTGGCTCCTTG
upper sequence: LOC_Os01g32830.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT1G32080.1 (Arabidopsis thaliana), 3'ss of exon 7
-ttacctacctgctggctgctttttttagtaagttaagctgcatatatatacatacatacagcagtatgctctatgaataatgtttgcatttacgttg--cagTGCTCATGGACTGGGAACAGCAGCGCTGTCGGCCAAGGAGCCTGAAGCGCTGCCCTTCTGCGCCATCGCTTACGGCCTGACGGGGATCTTCGGTTCGCTC
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gtgactccattacaaaagatctttcacatt---ttgaattaaaattatgcattaatgc-cattaggat-caaaagacatgacctttctattttttatggacagTGCTCATGGACTTGGAACAGCAGCTTTGTCGGCTAAGGAGCCAGAGGCTCTTCCCTTTTGTGCAATAGCTTATGCTCTTACCGGAATCTTCGGATCGTTAMapped 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|84117665|gb|CD151432.1|CD151432EST: AAGATTGGCCTCACCGACCCCATCGCGCGAGGAATAGGGACGGCTTCCAG TGCTCATGGACTGGGAACAGCAGCGCTGTCGGCCAAGGAGCCTGAAGCGCT
genomic: AAGCTTGGCCTCAACGACCCCATCGCGCGAGGAATAGGGACGGCTTCCAGgtacatatat ... tacgttgcagTGCTCATGGACTGGGAACAGCAGCGCTGTCGGCCAAGGAGCCTGAAGCGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atatacatacatacagcagtatgctctatgaataatgtttgcatttacgttgcagTGCTCATGGACTGGGAACAGCAGCGCTGTCGGCCAAGGAGCCTGAAGCGCTGCCCTTCTGCGCCATCGCTTACGGCCTGACGGGGATCTTCGGTTCGCTC
tatgaataatgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttacctacctgctggctgctttttttagtaagttaagctgcatatatatacatacatacagcagtatgctctatgaataatgtttgcatttacgttgcagTGCTCATGGACTGGGAACAGCAGCGCTGTCGGCCAAGGAGCCTGAAGCGCTGCCCTTCTGCGCCATCGCTTACGGCCTGACGGGGATCTTCGGTTCGCTC
- - - - -tgctggc
- - - - - - - - tgctttt
- - - - - - - - - - - - - - - - - -agctgca
- - - - - - - - - - - - - - - - - - - - - - - - - catacat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agtatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtttgc