Sequence
atgc intronic sequence ATGC exonic sequenceTGGTCCAACGGTATTAGTGCTTTCTCCAACAAGGGAATTGGCAACACAAATCCAAGATGAAGCGAAAAAGTTTGGGAGATCGTCAAGAATATCGTCTGTTgtacgttcctcctatcttttactcatctgttatgcgtttttgtgtcctataaagttgatgtcatctaattgtacctttttatttgaag
Basic information
species | Oryza sativa |
transcript | LOC_Os01g07740.2 |
intron # | 7 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g07740.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G481227_T01 (Zea mays), 5'ss of exon 3
--------------------------------------------------------------------------------------------------TGGTCCAACGGTATTAGTGCTTTCTCCAACAAGGGAATTGGCAACACAAATCCAAGATGAAGCGAAAAAGTTTGGGAGATCGTCAAGAATATCGTCTGTTgtacgttcctcctatcttttactcatctgttatgcgtttt---tgtgtcctataaagttgatgtcatctaattgtacctttttatttgaag-------------
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GATATAGTAGCTATGGCGAAGACAGGTTCAGGAAAAATACTGGGCTATCTTCTCCCAGGGTTTATTCTTTTGAAGCGCCTGCAGCATAATTCAAGGGAAGgtccaaccgtattagttttgtctccaaccagggaattggcgacacaaattcaagatgaagcaatcaagtttgatagatcttcat--atgtgagcagttgaattcatatgtgagcagatgaacattccatttacatttaatatatgttatatgtcagggatgttaattatttttg--ttgttgtttgaagtgattatatggag
upper sequence: LOC_Os01g07740.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G066440_T01 (Zea mays), 5'ss of exon 6
TGGTCCAACGGTATTAGTGCTTTCTCCAACAAGGGAATTGGCAACACAAATCCAAGATGAAGCGAAAAAGTTTGGGAGATCGTCAAGAATATCGTCTGTTgtacgttcctcctatcttttactcatctgttatg--cgtttttgtgtcc---tataaagttgatgtcatct----aattgtacctttttatttgaag---
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AGGTCCAACAGTATTAGTTTTGTCCCCAACCAGGGAATTGGCAACACAAATTCAAGATGAAGCAATCAAGTTTGGCAGATCTTCAAGAATATCTTCTACTgtatgttgctttatattttcttatatctgttattatcattactctgcctaggtctagaacatttgtcgtgttttaaaatgaattaactacgttgatgcct
upper sequence: LOC_Os01g07740.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G462134_T01 (Zea mays), 5'ss of exon 3
--------------------------------------------------------------------------------------------------TGGTCCAACGGTATTAGTGCTTTCTCCAACAAGGGAATTGGCAACACAAATCCAAGATGAAGCGAAAAAGTTTGGGAGATCGTCAAGAATATCGTCTGTTgtacgttcctcctatcttttactcatctgttatgcgtttt---tgtgtcctataaagttgatgtcatctaattgtacctttttatttgaag-------------
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GATATAGTAGCTATGGCGAAGACAGGTTCAGGAAAAACACTGGGCTATCTTCTCCCAGGGTTTATTCTTTTGAAGCGCCTGCAGCATAATTCAAGGGAAGgtccaacagtattagttttgtctccaaccagggaattggcgacacaaattcaagatgaagcaatcaagtttgacaaatcttcat--atgtgagcagttgaattcatatgtgagcagatgaacattccatttacatttaatatatgttatatgtcagggatgttaattatttttg--ttgttgtttgaagtgattatatggag
upper sequence: LOC_Os01g07740.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA05G08750.1 (Glycine max), 5'ss of exon 9
TGGTCCAACGGTATTAGTGCTTTCTCCAACAAGGGAATTGGCAACACAAATCCAAGATGAAGCGAAAAAGTTTGGGAGATCGTCAAGAATATCGTCTGTTgtacgt---tcctcctatctt-------ttactcatctgttatgcgtttttgtgtcctataaagttgatgtca----tctaattgtacctttttatttgaag--------------------------------------------------------------------------------------------
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GGGCCCCACTGCATTGGTACTTTCACCAACAAGGGAGTTGGCAACACAGATACAAGATGAAGCTGTGAAATTTGGGAAATCATCTAGAATTTCATGTGCTgtaagtaattgttctcattttcatcaaattatttttttgttgggttttcatgcttcagcttgggttcctttgaaattttttgatgaactcacaaatttgagattgttaaatgaatattgcttgtagtatcattcttcattggattgcctggctgggtttgctactatttatttattcattcattatttttatag
upper sequence: LOC_Os01g07740.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA19G00260.1 (Glycine max), 5'ss of exon 5
TGGTCCAACGGTATTAGTGCTTTCTCCAACAAGGGAATTGGCAACACAAATCCAAGATGAAGCGAAAAAGTTTGGGAGATCGTCAAGAATATCGTCTGTTgtacgt---tcctcctatcttt-------tactcatctgttatgcgtttttgtgtcc-tataaagttgatgtcatctaat--tgtacctttttatttgaag---------------------------------------------------------------------------------------
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GGGCCCCACTGCATTGGTACTTTCACCAACAAGGGAGTTGGCAACACAGATACAAGATGAAGCCATGAAGTTTGGGAAATCATCTAGAATTTCATGTGCAgtaagtaattgttcttatttttatcaaattatttttttgttgtgctttcatgcatcagtatggattcatttgaaattattgatgaactcacaaatttgagtttgttaaacaaatattgcttgtagtatcattcttcattggattgcttggctggttttgctactctttatttattcatttttttatagMapped 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|58594039|gb|CF992347.1|CF992347EST: TCCAAGATGAAGCAAAAAAGTTTGGGAGATCATCAAGAATATCGTCTGTT TGTCTATATGGAGGTGCTCCTAAAGGTCCTCAGCTAAGAGATCTAGAGCGC
genomic: TCCAAGATGAAGCGAAAAAGTTTGGGAGATCGTCAAGAATATCGTCTGTTgtacgttcct ... ttatttgaagTGTTTATATGGAGGTGCTCCTAAAGGTCCTCAGCTAAGAGATCTAGAGCGT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TGGTCCAACGGTATTAGTGCTTTCTCCAACAAGGGAATTGGCAACACAAATCCAAGATGAAGCGAAAAAGTTTGGGAGATCGTCAAGAATATCGTCTGTTgtacgttcctcctatcttttactcatctgttatgcgtttttgtgtcctataaagttgatgtcatctaattgtacctttttatttgaag
- - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC