Sequence
atgc intronic sequence ATGC exonic sequencegtaagttgattacttacttttttacattgtctcagaatgcatcctttgaatttccattgaaactgatgccagttgtctgataaatatcagtgtgtcatttacccatatttcatcatgcatgtcattattttgactgttcacttgcttaatttgcagTATGAGCCAGAGCTCTTCCCTGGGCTGATTTACCGGATGAAGCAGCCAAAGATTGTGCTTCTCATTTTTGTCTCTGGCAAGATTGTTCTCACTGGAGCTA
Basic information
species | Oryza sativa |
transcript | LOC_Os10g29660.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os10g29660.2 (Oryza sativa), 3'ss of exon 4
lower sequence: AT3G13445.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaagttgattacttacttttttacattgtctcagaatgcatcctttgaatttccattgaaactgatgccagttgtctgataaatatcagtgtgtcatttacccatatttcatcatgcatgtcattattttgactgttcacttgcttaatttgcagTATGAGCCAGAGCTCTTCCCTGGGCTGATTTACCGGATGAAGCAGCCAAAGATTGTGCTTCTCATTTTTGTCTCTGGCAAGATTGTTCTCACTGGAGCTA
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---------------------------------------------gtgagtg---atcttaacttatac-atttagtagtcaaggaccgac-ttttagagataaaaacgttgtgctgatggccattacctctctctcatattggcgtgtggt-tagTATGAGCCCGAGCTCTTCCCAGGGCTGATTTATAGGATGAAAGTCCCAAAAATCGTCCTTCTAATCTTTGTCTCTGGGAAGATCGTAATAACAGGAGCCA
upper sequence: LOC_Os10g29660.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 7
gtaagttgattacttacttttttacattgtctcagaatgcatcctttgaatttccattgaaactgatgccagttgtctgataaatatcagtgtgtcatttacccatatttcatcatgcatgtcattattttgactgttcacttgcttaatttg--cagTATGAGCCAGAGCTCTTCCCTGGGCTGATTTACCGGATGAAGCAGCCAAAGATTGTGCTTCTCATTTTTGTCTCTGGCAAGATTGTTCTCACTGGAGCTA
|| | | | | | | | ||| | ||| || | | || | || | ||| | |||| | | | | || ||| |||||||| ||||| | |||||||| |||| || || ||||| || |||||||||||||| || || ||||| || || || |||||||||||||||||||
----------------------------------------------------------aaatttaaattgaatcattttaaaaaaaatcatgtaaatgttgtctgtgttctctactgtgccttattgtattgaatatagtttggattttgttgggcagTATGAACCAGAATTGTTCCCTGGCTTGATCTATCGAATGAAACAACCAAAGATTGTGCTGCTTATCTTTGTGTCAGGGAAAATTGTTCTCACTGGAGCTA
upper sequence: LOC_Os10g29660.2 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S13_321V6.1 (Physcomitrella patens), 3'ss of exon 6
gtaagttgattacttacttttttacattgtctcagaatgcatcctttgaatttccattgaaactgatgccagttgtctgataaatatcagtgtgtcattta--cccatatttcatcat-gcatgtcattattttgactgttcacttgcttaatttgcagTATGAGCCAGAGCTCTTCCCTGGGCTGATTTACCGGATGAAGCAGCCAAAGATTGTGCTTCTCATTTTTGTCTCTGGCAAGATTGTTCTCACTGGAGCTA
||| || | |||| || || | | || | ||| | | | | || | | | |||| || || || |||||||||||||||||| | ||||| || |||| ||| |||||||||||||||| |||||| | || || || || || || |||||||| || || || || |
---------------------------------------------------------tgataccgggcaaagttaaggcgagaaaatgacttctgcagcaaatcccttgtctagttattggagatttaccgaagaactggtcgtttact--gtttgcagTATGAGCCAGAATTGTTCCCAGGATTGATATACAGGATGAAGCAGCCAAAAATTGTGTTACTGATCTTCGTGTCCGGAAAGATTGTCCTTACCGGTGCCA
upper sequence: LOC_Os10g29660.2 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ17606 (Selaginella moellendorffii), 3'ss of exon 6
gtaagttgattacttacttttttacattgtctcagaatgcatcctttgaatttccattgaaactgatgccagttgtctgataaatatcagtgtgtcatttacccatatttcatcatgcatgtcattattttgactgttcacttgcttaatttgcagTATGAGCCAGAGCTCTTCCCTGGGCTGATTTACCGGATGAAGCAGCCAAAGATTGTGCTTCTCATTTTTGTCTCTGGCAAGATTGTTCTCACTGGAGCTA
|| | | || | ||||| || || | | || || | ||| | | || |||||| ||||| ||| ||||||| || || |||||| | ||||||||||| ||||| || | ||||| || ||||||||||| || || ||||| ||||| |
-------------------------------------------------------------------------------------------gt-taagctatgctcatttc-tcctgt-tcttcttcttctcttggttaagacattcgtttcgcagTACGAGCCGGAGATCTTCCCAGGACTCATTTACAGAATGAAGCAGCCTAAGATCGTCTTGCTCATCTTCGTCTCTGGCAAAATCGTGCTCACGGGAGCAA
upper sequence: LOC_Os10g29660.2 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ36040 (Selaginella moellendorffii), 3'ss of exon 6
gtaagttgattacttacttttttacattgtctcagaatgcatcctttgaatttccattgaaactgatgccagttgtctgataaatatcagtgtgtcatttacccatatttcatcatgcatgtcattattttgactgttcacttgcttaatttgcagTATGAGCCAGAGCTCTTCCCTGGGCTGATTTACCGGATGAAGCAGCCAAAGATTGTGCTTCTCATTTTTGTCTCTGGCAAGATTGTTCTCACTGGAGCTA
||| | ||| || ||| | | | || | | || || | || ||||| | | ||||||| || |||||||| ||||| || |||| ||||| ||||||||||| ||||| ||||| || || || |||||||| |||||||| || ||||| || |
-------------------------------------------------------------------------------gtaagt---cgtgcttcctttgtc-acacttacactcttttctcttttgcgggtcttatcactaaagttttgtgcagTACGAACCAGAGCTGTTCCCCGGATTGATCTACCGAATGAAGCAGCCTAAGATCGTGCTCCTGATCTTCGTCTCTGGAAAGATTGTGCTTACTGGTGCAA
upper sequence: LOC_Os10g29660.2 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ04980 (Selaginella moellendorffii), 3'ss of exon 6
gtaagttgattacttacttttttacattgtctcagaatgcatcctttgaatttccattgaaactgatgccagttgtctgataaatatcagtgtgtcatttacccatatttcatcatgcatgtcattattttgactgttcacttgcttaatttgcagTATGAGCCAGAGCTCTTCCCTGGGCTGATTTACCGGATGAAGCAGCCAAAGATTGTGCTTCTCATTTTTGTCTCTGGCAAGATTGTTCTCACTGGAGCTA
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-------------------------------------------------------------------------------gtaagt---cgtgcttcctttgtc-acacttatactcttttctcttttgcgggtcttatcactaaagttttgtgcagTACGAACCAGAGCTGTTCCCCGGATTGATCTACCGAATGAAGCAGCCTAAGATCGTGCTCCTGATCTTCGTCTCTGGAAAGATTGTGCTTACTGGTGCAA
upper sequence: LOC_Os10g29660.2 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ29072 (Selaginella moellendorffii), 3'ss of exon 6
gtaagttgattacttacttttttacattgtctcagaatgcatcctttgaatttccattgaaactgatgccagttgtctgataaatatcagtgtgtcatttacccatatttcatcatgcatgtcattattttgactgttcacttgcttaatttgcagTATGAGCCAGAGCTCTTCCCTGGGCTGATTTACCGGATGAAGCAGCCAAAGATTGTGCTTCTCATTTTTGTCTCTGGCAAGATTGTTCTCACTGGAGCTA
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-------------------------------------------------------------------------------------------gt-taagctatgctcatttc-tcctgt-tcttcttcttctcttggttaagacatttgtttcgcagTACGAGCCGGAGATCTTCCCAGGACTCATTTACAGAATGAAGCAGCCTAAGATCGTCCTGCTCATCTTCGTCTCTGGCAAAATCGTGCTCACGGGAGCAAMapped 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|8324452|gb|AU091604.1|AU091604EST: TTCCTATTCGCCTGGAGGGCCTTGCTTATTCTCATGGCGCATTCTCTAGT TATGAGCCAGAGCTCTTCCCTGGGCTGATTTACCGGATGAAGCAGCCAAAG
genomic: TTCCTATTCGCCTGGAGGGCCTTGCTTATTCTCATGGCGCATTCTCTAGTgtaagttgat ... taatttgcagTATGAGCCAGAGCTCTTCCCTGGGCTGATTTACCGGATGAAGCAGCCAAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cccatatttcatcatgcatgtcattattttgactgttcacttgcttaatttgcagTATGAGCCAGAGCTCTTCCCTGGGCTGATTTACCGGATGAAGCAGCCAAAGATTGTGCTTCTCATTTTTGTCTCTGGCAAGATTGTTCTCACTGGAGCTA
cttgctt CT-rich tract
tcattatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttgattacttacttttttacattgtctcagaatgcatcctttgaatttccattgaaactgatgccagttgtctgataaatatcagtgtgtcatttacccatatttcatcatgcatgtcattattttgactgttcacttgcttaatttgcagTATGAGCCAGAGCTCTTCCCTGGGCTGATTTACCGGATGAAGCAGCCAAAGATTGTGCTTCTCATTTTTGTCTCTGGCAAGATTGTTCTCACTGGAGCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT