Sequence
atgc intronic sequence ATGC exonic sequencegtgagcgcgccctcgaactcgccttaaccttgtcttatcctccactcgatctggaatggaagctaggttcaatctggggagtataatatctgggggttggttcaattcaactgttaggtccacccctgcagGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATG
Basic information
species | Oryza sativa |
transcript | LOC_Os11g33240.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G064023_T02 (Zea mays), 3'ss of exon 1
-gtgagcgcgccctcgaactcgccttaaccttgtcttatcctccact-cgatctggaatggaagctaggttcaatctggggagtata-atatctgggggttggttcaattcaactgttaggtccacccctgcagGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATG
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catttgcttcccgtagtttcctctgggagtttcggttaaattcggttgtggtgaggacatgatgggatcgtctgtttgtttggttcctgtgtctgtgcagCAGTGCAGGTGCGGTGGTAGCCGAGCGCTC-----CGGCCATGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGGCTGCGATCCCGCATG
upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G064023_T04 (Zea mays), 3'ss of exon 1
gtgagcgcgccctcgaactcgccttaaccttgtcttatcctccactcgatctggaatggaagctaggttcaatctggggagtataatatctgggggttggttcaattcaactgttaggtccacccctgcagGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATG
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gtagtttcctctgggagtttcggttaaattcgg-ttgtggtgaggacatgatgggatcgtctgtttgtttggt--------tcctgtgtctgtgcagcagTGCAGGTGCGGTGGTAGCCGAGCGCTC-----CGGCCATGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGGCTGCGATCCCGCATG
upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 2
gtgagcgcgccctcgaactcgccttaaccttgtctt--atcctccactcgatctgg----aatggaagctaggttcaatc--tggggagtataatatctgggggt-tggttcaattcaactgttaggtccacccctgcagGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATG
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gtaactatccatttg--cttcccgtagtttcctctgggagtttcggttaaattcggttgtggtgaggacatgatgggatcgtctgtttgtttggttcctgtgtctgtgcagCAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGGCTGCGATCCCGCATG
upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G064023_T03 (Zea mays), 3'ss of exon 1
gtgagcgcgccctcgaactcgccttaaccttgtcttatcctccact-cgatctggaatggaagctaggttcaatctggggagtata-atatctgggggttggttcaattcaactgttaggtccacccctgcagGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATG
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--ttgcttcccgtagtttcctctgggagtttcggttaaattcggttgtggtgaggacatgatgggatcgtctgtttgtttggttcctgtgtctgtgcagcagTGCAGGTGCGGTGGTAGCCGAGCGCTC-----CGGCCATGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGGCTGCGATCCCGCATGMapped 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|117245193|gb|CT843395.1|CT843395EST: CTAGGAGCGGCGGCGGGTGCCGTCGTCCTGCTGCTTCCCTTCCGCCTCCGGTCCACCCCTGCAG
genomic: CTAGGAGCGGCGGCGGGTGCCGTCGTCCTGCTGCTTCCCTTCCG---CC--T------C--C-Ggtgagcgcgc .
EST:
gi|88359778|gb|CI622468.1|CI622468EST: CTAGGAGCGGCGGGGGGTGCCGTCGTCCTGCTGCTTCCCTTCCGCCTCCG GCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCC
genomic: CTAGGAGCGGCGGCGGGTGCCGTCGTCCTGCTGCTTCCCTTCCGCCTCCGgtgagcgcgc ... acccctgcagGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gggagtataatatctgggggttggttcaattcaactgttaggtccacccctgcagGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATG
tccacccct CT-rich tract
tataatatct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagcgcgccctcgaactcgccttaaccttgtcttatcctccactcgatctggaatggaagctaggttcaatctggggagtataatatctgggggttggttcaattcaactgttaggtccacccctgcagGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATG
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