Sequence
atgc intronic sequence ATGC exonic sequencegtacttgcttttgaaagcatttactgtattttcatccttacggagatgaatatttcttttctacaatgcatactgaatcgctattcaaaaatgtatttaatgcagTGAAGGTGGCCAAATGTGTGCAATTAAAGAGGTCAAGGTTATTTCTGATGATTCTAACTCGAAAGAGTGTCTCAGGCAGCTACATCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os11g10100.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os11g10100.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA05G32510.1 (Glycine max), 3'ss of exon 2
gtacttgcttttgaaagcatttactgtattttcatccttacggagatgaatatttcttttctacaatgcatactgaatcgctattcaaaaatgtatttaatgcagTGAAGGTGGCCAAATGTGTGCAATTAAAGAGGTCAAGGTTATTTCTGATGATTCTAACTCGAAAGAGTGTCTCAGGCAGCTACATCAG
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-----ttatttcatcattattctttcagattgtgtattcgcctcaatgtctatattctggacagattactgaaaccatttcttttccgcttcctatgtttgacagTGAAAATGGACAAATGTGTGCAATAAAAGAGGTCAAGGTTGTCTCTGATGATCAAACATCAAAAGAGTGCCTCAAACAACTTAACCAG
upper sequence: LOC_Os11g10100.2 (Oryza sativa), 3'ss of exon 2
lower sequence: AT1G53570.3 (Arabidopsis thaliana), 3'ss of exon 2
gtacttgcttttgaaagcatttactgtattttcatccttacggagatgaatatttcttttctacaatgcatactgaatcgctattcaaaaatgtatttaa--tgcagTGAAGGTGGCCAAATGTGTGCAATTAAAGAGGTCAAGGTTATTTCTGATGATTCTAACTCGAAAGAGTGTCTCAGGCAGCTACATCAG
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ataaaggcaatagaaagaa-----aaagtttctattatgctagctctttacattgtaactctaaactgcttgttt--ccatcgtataatgttttcgccaacttacagTGAGAAAGGGAAAATGTGTGCTATTAAAGAGGTCAAGGTCATTTCTGACGATCAAACATCAAAAGAATGTCTGAAGCAACTAAATCAGMapped 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|29680776|gb|CB677051.1|CB677051EST: AAGTTGTTAGGCAGTGGTACATTTGGGCAAGTATACCAAGGATTTAACAG TGAAGGTGGCCAAATGTGTGCAATTAAAGAGGTCAAGGTTATTTCTGATGA
genomic: AAGTTGTTAGGCAGTGGTACATTTGGGCAAGTATACCAAGGATTTAACAGgtacttgctt ... tttaatgcagTGAAGGTGGCCAAATGTGTGCAATTAAAGAGGTCAAGGTTATTTCTGATGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatttcttttctacaatgcatactgaatcgctattcaaaaatgtatttaatgcagTGAAGGTGGCCAAATGTGTGCAATTAAAGAGGTCAAGGTTATTTCTGATGATTCTAACTCGAAAGAGTGTCTCAGGCAGCTACATCAG
atttaat putative branch site (score: 4)
tattcaaaaatgtatt 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
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gtacttgcttttgaaagcatttactgtattttcatccttacggagatgaatatttcttttctacaatgcatactgaatcgctattcaaaaatgtatttaatgcagTGAAGGTGGCCAAATGTGTGCAATTAAAGAGGTCAAGGTTATTTCTGATGATTCTAACTCGAAAGAGTGTCTCAGGCAGCTACATCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT