Sequence
atgc intronic sequence ATGC exonic sequencegtatgggtattattaggattcattgcttagactatgacctgttgtgtctcaactgaaattgtttgttgtgcgttgataatcagGATGCTTGTGTATGAGTATGTCAACAATGGGAATCTCGAAAGTTGGTTACATGGAGAGTTATCCCAATATAGTTCTCTCACTTGGCTAGCGCGCATGAAA
Basic information
species | Oryza sativa |
transcript | LOC_Os11g01740.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os11g01740.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G162702_T01 (Zea mays), 3'ss of exon 2
--------------------------------------gtatgg-gtattat-taggattcattgcttagactatgacctgttgtgtc-tcaactgaaattgtttgttgtgcgttgataatcagGATGCTTGTGTATGAGTATGTCAACAATGGGAATCTCGAAAGTTGGTTACATGGAGAGTTATCCCAATATAGTTCTCTCACTTGGCTAGCGCGCATGAAA
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gtaagaacacaaagacacctttttaatttttctctaaaatatgatgtcctatgcattattcttttggtacttaagagaaagggaagtcattaacaggaatcacttgacatgtatatgcaaccagGATGCTTGTGTATGAGTATGTGAATAATGGAAATCTTGAAAGTTGGCTCCATGGGGAATTGTCCCAGTACAGTTCTCTCACTTGGTTGGCTCGCATGAAA
upper sequence: LOC_Os11g01740.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT5G18500.1 (Arabidopsis thaliana), 3'ss of exon 3
gtatgggtattattaggattcattgcttagactatgacctgttgtgtctcaactgaaattgtttgttgtgcgttgataatcagGATGCTTGTGTATGAGTATGTCAACAATGGGAATCTCGAAAGTTGGTTACATGGAGAGTTATCCCAAT-ATAGTTCTCTCACTTGGCTAGCGCGCATGAAA
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gtatgtatgttctgttgttgaatgatctgcagtttttcttctgaattttcactaaacatcaaatgcggta-acacttaattagGATGCTGGTGTATGAGTATGTTAACAATGGAAATTTGGAGCAATGGCTCCGTGGAGA-CAATCAAAATCATGAGTATCTTACATGGGAGGCACGAGTGAAAMapped 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|58607362|gb|CK035395.1|CK035395EST: CACAAGAATTTGGTTCGCCTTTTGGGGTACTGTGTTGAAGGCACTCAAAG GATGCTTGTGTATGAGTATGTCAACAATGGGAATCTCGAAAGTTGGTTACA
genomic: CACAAGAATTTGGTTCGCCTTTTGGGGTACTGTGTTGAAGGCACTCAAAGgtatgggtat ... tgataatcagGATGCTTGTGTATGAGTATGTCAACAATGGGAATCTCGAAAGTTGGTTACA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agactatgacctgttgtgtctcaactgaaattgtttgttgtgcgttgataatcagGATGCTTGTGTATGAGTATGTCAACAATGGGAATCTCGAAAGTTGGTTACATGGAGAGTTATCCCAATATAGTTCTCTCACTTGGCTAGCGCGCATGAAA
cgttgat putative branch site (score: 5)
aaattgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgggtattattaggattcattgcttagactatgacctgttgtgtctcaactgaaattgtttgttgtgcgttgataatcagGATGCTTGTGTATGAGTATGTCAACAATGGGAATCTCGAAAGTTGGTTACATGGAGAGTTATCCCAATATAGTTCTCTCACTTGGCTAGCGCGCATGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA