Sequence
atgc intronic sequence ATGC exonic sequencegtcagatcataactctgtttgcagaattttacagtatttctaattttcatgaattgacaattgtaatcttctatgaaattctttcagGTTAACACCCTCCTAAAAGGTTTAGAAAAAATAGCTGTCAGTGCGGACATTCCAATGCTGGTCTGTGGAGATTTCAATGCAACCCCTGGAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os03g07080.3 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g07080.3 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G124051_T01 (Zea mays), 3'ss of exon 8
-gtcagatcataac---tctgtttgcagaattttacagtatttctaattttcatgaattgacaattgtaatcttctatgaaattctttcagGTTAACACCCTCCTAAAAGGTTTAGAAAAAATAGCTGTCAGTGCGGACATTCCAATGCTGGTCTGTGGAGATTTCAATGCAACCCCTGGAAG
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gttcaaatacttccccctccctctgtataatttcataacattttataatttctttaactgatgaatctcatggcttgc-aaactcttgcagATTCATACCCTCCTAAAAGGGTTGGAAAAAATAGCTGTTAGTGCAGACATTCCAATGTTGGTCTGTGGAGATTTTAATTCAACTCCTGGAAG
upper sequence: LOC_Os03g07080.3 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA09G15980.2 (Glycine max), 3'ss of exon 7
gtcagatcataactctgtttgcagaattttacagtatt--tctaattttcatgaat-tgacaattg-taatcttctatgaaattctttcagGTTAACACCCTCCTAAAAGGTTTAGAAAAAATAGCTGTCAGTGCGGACATTCCAATGCTGGTCTGTGGAGATTTCAATGCAACCCCTGGAAG
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--------gtaaattattttctttagtttgttcgtatgcatcaaattgttctgaacattacagtttctaattttct-----cctattttagGTTCATACTCTCTTAAAAGGTTTGGAAAAAATAGCTGCAAGTGCAGACATTCCGATGTTGGTTTGTGGAGATTTTAATTCAGTTCCGGGAAG
upper sequence: LOC_Os03g07080.3 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA02G26620.1 (Glycine max), 3'ss of exon 7
gtcagatcataactctgtttgcagaattttacagtatttctaattttcatgaat-tgacaattg-taatcttctatgaaattctttcagGTTAACACCCTCCTAAAAGGTTTAGAAAAAATAGCTGTCAGTGCGGACATTCCAATGCTGGTCTGTGGAGATTTCAATGCAACCCCTGGAAG
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-----------------------gtttgttcatatgcatcagattgttttgaacattacaatttctaattttct-----cctattatagGTTCATACTCTCTTAAAAGGGTTGGAAAAAATAGCTGCAAGCGCAGACATTCCGATGTTGGTTTGTGGAGATTTTAATTCAGTTCCAGGAAG
upper sequence: LOC_Os03g07080.3 (Oryza sativa), 3'ss of exon 8
lower sequence: AT3G58560.1 (Arabidopsis thaliana), 3'ss of exon 7
gtcagatcataactctgtttgcagaat--tttacagtatttctaattttcatgaattgacaattgtaatcttctatgaaattctttca----gGTTAACACCCTCCTAAAAGGTTTAGAAAAAATAGCTGTCAGTGCGGACATTCCAATGCTGGTCTGTGGAGATTTCAATGCAACCCCTGGAAG
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gttggtctttatttctcattgtaaaagaactctcag-atttcggattcttaca---tcactattg--atccataatgattcttgcccaaatagGTTCACACATTATTGAAGGGACTGGAGAAAATAGCTGCCAGTGCAGATATTCCAATGCTTGTGTGTGGAGATTTCAACACAGTACCTGCGAG
upper sequence: LOC_Os03g07080.3 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv08s0007g07020.t01 (Vitis vinifera), 3'ss of exon 7
-----------------------------gtcagatcataactctgttt--gcagaattttacagtatttctaattttcatgaattgacaattgtaatcttctatgaaattctttcagGTTAACACCCTCCTAAAAGGTTTAGAAAAAATAGCTGTCAGTGCGGACATTCCAATGCTGGTCTGTGGAGATTTCAATGCAACCCCTGGAAG
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gtaattaattttattttatttttgagtgagcttgagtggggctttttttatgcgtgtgcttatgtctcagttaatcaaactattttattatgtatattcttgtttg---tcatatcagGTTCATACTCTCTTAAAAGGTTTGGAAAAAATAGCTGCCAGTGCAGACATTCCCATGCTGGTTTGTGGCGATTTTAATTCAGTTCCTGGAAGMapped 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|58612497|gb|CK040209.1|CK040209EST: ATACGCATATCAATGTTCACCAAGACCTCAAAGATGTCAAGCTATGGCAG GTTAACACCCTCCTAAAAGGTTTAGAAAAAATAGCTGTCAGTGCGGACATT
genomic: ATACGCATATCAATGTTCACCAAGACCTCAAAGATGTCAAGCTATGGCAGgtcagatcat ... attctttcagGTTAACACCCTCCTAAAAGGTTTAGAAAAAATAGCTGTCAGTGCGGACATT
EST:
gi|29678434|gb|CB674709.1|CB674709EST: ATACGCATATCAATGTTCACCAAGACCTCAAAGATGTCAAGCTATGGCAG GTTAACACCCTCCTAAAAGGTTTAGAAAAAATAGCTGTCAGTGCGGACATT
genomic: ATACGCATATCAATGTTCACCAAGACCTCAAAGATGTCAAGCTATGGCAGgtcagatcat ... attctttcagGTTAACACCCTCCTAAAAGGTTTAGAAAAAATAGCTGTCAGTGCGGACATT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtatttctaattttcatgaattgacaattgtaatcttctatgaaattctttcagGTTAACACCCTCCTAAAAGGTTTAGAAAAAATAGCTGTCAGTGCGGACATTCCAATGCTGGTCTGTGGAGATTTCAATGCAACCCCTGGAAG
ttctttc CT-rich tract
taattttcatgaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagatcataactctgtttgcagaattttacagtatttctaattttcatgaattgacaattgtaatcttctatgaaattctttcagGTTAACACCCTCCTAAAAGGTTTAGAAAAAATAGCTGTCAGTGCGGACATTCCAATGCTGGTCTGTGGAGATTTCAATGCAACCCCTGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG