Sequence
atgc intronic sequence ATGC exonic sequence...gactccattttgctgtcattttttttgacatataatctagcaaatacatgcctgttcaatataatgattctcttgttataacatttgactttgtatgcagGAAAAGTATGAGGAAGCTATGGCTTCACTAGCACAAATGGAGAACAGAGCAGTCATGGCAGAAACTATGCTGGAAGCAACACTGCAGTATCAATCAAGCC
Basic information
species | Oryza sativa |
transcript | LOC_Os01g61860.2 |
intron # | 15 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g61860.2 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G096470_T01 (Zea mays), 3'ss of exon 15
gactccattttgctgtcattttttt-tgacatataatctagcaaatacat----gcctgttcaatataatgattctcttgttataacatttgactttgtatgcagGAAAAGTATGAGGAAGCTATGGCTTCACTAGCACAAATGGAGAACAGAGCAGTCATGGCAGAAACTATGCTGGAAGCAACACTGCAGTATCAATCAAGCC
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-ttaatgtttgggcatgaatatgtcgcagcatgtaatgaagcaagtaaatttttgcttgttcagttttatgatccgctgcttgtg-tactta---ctctattcagGAGAAGTACGAGGGAGCTATGGCTTCACTTGCTCAAATGGAGAACAGAGCAGTTATGGCAGAAACTATGTTAGAGGCAACCATTCAGTACCAATCTAGTC
upper sequence: LOC_Os01g61860.2 (Oryza sativa), 3'ss of exon 15
lower sequence: GLYMA20G38810.1 (Glycine max), 3'ss of exon 15
gactccattttgctgtcattttttttgacatataatctagcaaataca-tgcctgttcaatataatg-attctcttgttataacatttgactttgtatgcagGAAAAGTATGAGGAAGCTATGGCTTCACTAGCACAAATGGAGAACAGAGCAGTCATGGCAGAAACTATGCTGGAAGCAACACTGCAGTATCAATCAAGCC
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catgtcaatgcctttttatactgctatat-tatatttcgactggtacaatggtgaatttttctattgcaatatcttacaatcatacat-attatattggcagGAAAAGTATGAAGAAGCAACTGCTGCACTTGCTGAAATGGAGAAGAGGGCAGTTATGGCAGAATCTATGCTGGAGGCTACATTGCAGTACCAATCTGGCC
upper sequence: LOC_Os01g61860.2 (Oryza sativa), 3'ss of exon 15
lower sequence: GLYMA10G44110.1 (Glycine max), 3'ss of exon 15
---gactccattttgctgtcattttttttgacatataatctagcaaatacatgcctgttcaatataatgattctcttgttataacatttgactttgtatgcagGAAAAGTATGAGGAAGCTATGGCTTCACTAGCACAAATGGAGAACAGAGCAGTCATGGCAGAAACTATGCTGGAAGCAACACTGCAGTATCAATCAAGCC
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catgtcaatgcctttttatactgctatattatatttcgactagcacaatgatgaat-ttttgtactgcaaca-tcttacaatcatacat-attatattgacagGAAAAGTATGAAGAAGCAACTGCTGCACTTGCTGAAATGGAGAAGAGAGCAGTTATGGCAGAATCTATGCTGGAGGCTACATTGCAGTACCAATGTGGCC
upper sequence: LOC_Os01g61860.2 (Oryza sativa), 3'ss of exon 15
lower sequence: AT3G55020.1 (Arabidopsis thaliana), 3'ss of exon 15
---gactccattttgctgtcattttttttgacatataatctagcaaatacatgcctgttcaatataatgattctcttgttataacatttgactttgtatgcagGAAAAGTATGAGGAAGCTATGGCTTCACTAGCACAAATGGAGAACAGAGCAGTCATGGCAGAAACTATGCTGGAAGCAACACTGCAGTATCAATCAAGCC
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agctgcgtgatttgaatgcaactttatat--ccttttcctttttttgtattctcctgttctatcttagatcgtttctgtaacga-atatgataactggtctagGAAAAATACGAGGAAGCTGTTGCTGCACTGGCTGAAATGGAGAAGAGAGCAGTGATGGCAGAGTCCATGCTCGAGGCAACTTTGCAGTATCAATCTGGCCMapped 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|163927799|gb|EG710555.1|EG710555EST: TCGCTGAGCAAGATGCTGCTGCTCAGAAATATGCTGCACATGTGCTCCAG GAAAAGTATGAGGAAGCTATGGCTTCACTAGCACAAATGGAGAACAGAGCA
genomic: TCGCTGAGCAAGATGCTGCTGCTCAGAAATATGCTGCACATGTGCTCCAGgttagtttaa ... ttgtatgcagGAAAAGTATGAGGAAGCTATGGCTTCACTAGCACAAATGGAGAACAGAGCA
EST:
gi|58663408|gb|CK052094.1|CK052094EST: TCGCTGAGCAAGATGCTGCTGCTCAGAAATATGCTGCACATGTGCTCCAG GAAAAGTATGAGGAAGCTATGGCTTCACTAGCACAAATGGAGAACAGAGCA
genomic: TCGCTGAGCAAGATGCTGCTGCTCAGAAATATGCTGCACATGTGCTCCAGgttagtttaa ... ttgtatgcagGAAAAGTATGAGGAAGCTATGGCTTCACTAGCACAAATGGAGAACAGAGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acatgcctgttcaatataatgattctcttgttataacatttgactttgtatgcagGAAAAGTATGAGGAAGCTATGGCTTCACTAGCACAAATGGAGAACAGAGCAGTCATGGCAGAAACTATGCTGGAAGCAACACTGCAGTATCAATCAAGCC
ttcaatataatgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gactccattttgctgtcattttttttgacatataatctagcaaatacatgcctgttcaatataatgattctcttgttataacatttgactttgtatgcagGAAAAGTATGAGGAAGCTATGGCTTCACTAGCACAAATGGAGAACAGAGCAGTCATGGCAGAAACTATGCTGGAAGCAACACTGCAGTATCAATCAAGCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG