Sequence
atgc intronic sequence ATGC exonic sequenceTGCAGTCATATAAGAAGATCATTGGTTTTGTGCCACAAGATGACATTGTCCATGGGAACTTGACGGTTGAGGAAAACTTGTGGTTTAGTGCGTGCTGCAGgtattaaatacaggcatatggtgcatagcttggttactttcattattgattatttttccttccattaaatatgcttatatcaaaacttatgacatagcac...
Basic information
species | Oryza sativa |
transcript | LOC_Os10g30610.1 |
intron # | 7 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os10g30610.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G430675_T01 (Zea mays), 5'ss of exon 8
TGCAGTCATATAAGAAGATCATTGGTTTTGTGCCACAAGATGACATTGTCCATGGGAACTTGACGGTTGAGGAAAACTTGTGGTTTAGTGCGTGCTGCAGgtattaaatacaggcatatggtgcatagcttggttactttcattattgattatttttcc-ttccattaaatatgcttatatcaaaacttatgacatagcac-----
||||||||||||||||||| |||||||||||||| |||||||| ||||||||||||||| |||| || |||||||| ||||||||||| | || |||||||||| ||| | | || || || || ||||| | ||| ||||| ||||| || ||| ||| | |||| ||| |
TGCAGTCATATAAGAAGATAATTGGTTTTGTGCCTCAAGATGATATTGTCCATGGGAACCTGACCGTCGAGGAAAATCTGTGGTTTAGTTCATGTTGCAGgtatttgatagaaa------atacaaagtttaattgctttccgagtctattccttttctgttccactattctgttttagtacaacatttatcgaataacttattac
upper sequence: LOC_Os10g30610.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA02G21570.1 (Glycine max), 5'ss of exon 7
TGCAGTCATATAAGAAGATCATTGGTTTTGTGCCACAAGATGACATTGTCCATGGGAACTTGACGGTTGAGGAAAACTTGTGGTTTAGTGCGTGCTGCAGgtattaaatacaggcatatggtgcatagcttggttactttcattattgattatttttccttccattaaatatgcttatatcaaaacttatgacatagcac--
| || || |||||||| || ||||| ||||||||||||||||| || || ||||| ||| ||||||| || ||||| || |||| ||||| |||||||| | | | | | || | || || | || || || || | | |||| || || | | | | |||| || || |
TCCACTCCTATAAGAAAATTATTGGCTTTGTGCCACAAGATGATATAGTTCATGGAAACCTGACGGTGGAAGAAAATTTCCGGTTCAGTGCACTGTGCAGgtaaatcacatggtttgaaattccagatgctgtatattctctttttttttttcaagtttatgcatttaacattggcgt-cctagatttat-acttaatagat
upper sequence: LOC_Os10g30610.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA13G20750.1 (Glycine max), 5'ss of exon 7
TGCAGTCATATAAGAAGATCATTGGTTTTGTGCCACAAGATGACATTGTCCATGGGAACTTGACGGTTGAGGAAAACTTGTGGTTTAGTGCGTGCTGCAGgtattaaatacaggcatatggtgcatagcttggttactttcattattgattatttttccttccattaaatatgcttatatcaaaacttatgacatagcac--
| || | ||| |||| || ||||||| ||||||||||||||| ||||| |||||||||||||| || |||||||| | | || || || | ||||||||| || || | | | ||| || || | || | || || | | || | || || | | || ||| |||
TTCATTGTTATCAGAAAATTATTGGTTATGTGCCACAAGATGATATTGTGCATGGGAACTTGACAGTGGAGGAAAATCTTCGTTTCAGCGCAAGATGCAGgtatctgattt--gccttcgagaacttactttgtgcctctttttttccatatgcttgaaatgtgtgaactttgtttgttattacctctaattcattgcaatt
upper sequence: LOC_Os10g30610.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA11G20220.1 (Glycine max), 5'ss of exon 6
TGCAGTCATATAAGAAGATCATTGGTTTTGTGCCACAAGATGACATTGTCCATGGGAACTTGACGGTTGAGGAAAACTTGTGGTTTAGTGCGTGCTGCAGgtattaaatac---aggcatat------ggtgcatagcttggttactttcattattgat-tatttt----tccttccattaaatat------gcttatat---caaaacttatgacatagcac-------------------------------------------------------------------------
| ||||| ||||| ||||| |||||||||||||||||||| ||||| ||||| || ||||| || |||||||| | ||||||||||| | ||||||||| ||| | |||| | | | || ||| | ||| | | | | | |||| ||||| ||| ||| ||| ||| ||| ||| | | ||| |
TCAGATCATACAAGAAAATCATAGGTTTTGTGCCACAAGATGATATTGTGCATGGCAATTTGACAGTGGAGGAAAATCTATGGTTTAGTGCTAGATGCAGgtatactatatgttaagcattttattctgttacacgactttttatgtttaacaagtactatgttttaacatccttaggttagctatttagctacttttattcacaagtcttgtaa-ataaaaaggtttgtgagtttattgaatacattttcttactatcaattttctctcttcactatatttgtttgtcattgtag
upper sequence: LOC_Os10g30610.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA12G08290.1 (Glycine max), 5'ss of exon 5
TGCAGTCATATAAGAAGATCATTGGTTTTGTGCCACAAGATGACATTGTCCATGGGAACTTGACGGTTGAGGAAAACTTGTGGTTTAGTGCGTGCTGCAGgtattaaatacaggcatatggtgcatagcttggttactttcattattgattatttttccttcca-ttaaatatgcttatatcaaaacttatgacatagcac---
| |||||| ||||| |||||||| ||||||||||||||||| ||||| ||||| || ||||| || |||||||| | ||||||||||| | ||||||||| ||| | | | | |||| || ||| || | | | ||| ||| | || || | | | |
TCAGGTCATACAAGAAAATCATTGGGTTTGTGCCACAAGATGATATTGTGCATGGCAATTTGACAGTGGAGGAAAATCTATGGTTTAGTGCTAGATGCAGgtatactatatg----ttaagcattttattctcttacacgactttagaattgcggttgcggtgagccagataacctttagcgggcaattgcgagaaaacgcagt
upper sequence: LOC_Os10g30610.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA10G06550.1 (Glycine max), 5'ss of exon 7
TGCAGTCATATAAGAAGATCATTGGTTTTGTGCCACAAGATGACATTGTCCATGGGAACTTGACGGTTGAGGAAAACTTGTGGTTTAGTGCGTGCTGCAGgtat-taaat-acaggcatatggtgcatagcttggttactttcattattgattatttttcct-tccattaaatatgcttatatcaaaacttatgacatagcac
| || | ||| |||| || ||||||| ||||||||||||||| ||||| ||||| |||||||| || |||||||| | | || ||||| | ||||||||| || | | || | | | || || || || || || ||| || | | || | || || | | || ||| |
TTCATTGTTATCAGAAAATTATTGGTTATGTGCCACAAGATGATATTGTGCATGGAAACTTGACAGTGGAGGAAAATCTTCGTTTCAGTGCAAGATGCAGgtatctatgtgatttgcctcggagaacttactctgtgcctgtctttttttcatatgcttgaaatgtgtgaactttgtttgttattacctctagttcattg---
upper sequence: LOC_Os10g30610.2 (Oryza sativa), 5'ss of exon 7
lower sequence: AT2G37010.1 (Arabidopsis thaliana), 5'ss of exon 8
TGCAGTCATATAAGAAGATCATTGGTTTTGTGCCACAAGATGACATTGTCCATGGGAACTTGACGGTTGAGGAAAACTTGTGGTTTAGTGCGTGCTGCAGgtattaaatacaggcatatggtgcatagcttggttactttcattattgattatttttccttccattaaata-tgcttatatc---aaaacttatgacatagcac----------------------------
| | || ||||||||||||| ||| ||||||||||||||||| |||| ||||| || | || || || || ||| | | ||||| || | |||||||| | || ||||| | | | | | | ||| || | | | || |||| ||| || |||| |||| | | |||| ||
TAAACTCGTATAAGAAGATCACTGGATTTGTGCCACAAGATGATGTTGTGCATGGCAATCTTACCGTCGAAGAGAACCTTCGATTTAGCGCAAGATGCAGgtaa-atttattctcatatcatagaggagattgagagtccaattcttaaaaaaatacatttttattacatagtgtttatgcttcaaaaaaatgttgcatatcatttatttatatatgtttctttacatgcag
upper sequence: LOC_Os10g30610.2 (Oryza sativa), 5'ss of exon 7
lower sequence: AT5G60740.1 (Arabidopsis thaliana), 5'ss of exon 8
TGCAGTCATATAAGAAGATCATTGGTTTTGTGCCACAAGATGACATTGTCCATGGGAACTTGACGGTTGAGGAAAACTTGTGGTTTAGTGCGTGCTGCAGgtattaaatacaggcatatggtgcatagcttggttactttcattattgattatttttccttccattaaatatgcttatatcaaaacttatgacatagcac
| || || || |||||||| || |||||||| || ||||||||||| |||||||| ||||| || || |||||||| | ||||| || || | ||||||| | | || | | ||| | | | ||| || || | || | |||
TTCAATCCTACAAGAAGATTATAGGTTTTGTACCTCAAGATGACATAGTCCATGGAAACTTAACAGTGGAGGAAAATCTTTGGTTCAGCGCAAGATGCAGgttagctacttttttgcttaatgaaaatcttattcaactg---tatgcataatctcattggtcactgcatacag--------------------------
upper sequence: LOC_Os10g30610.2 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv08s0040g01620.t01 (Vitis vinifera), 5'ss of exon 9
TGCAGTCATATAAGAAGATCATTGGTTTTGTGCCACAAGATGACATTGTCCATGGGAACTTGACGGTTGAGGAAAACTTGTGGTTTAGTGCGTGCTGCAGgtat-taaatacaggcatatggtgcatagcttggttactttcattattgattatttttccttccattaaatatgcttatatcaaaacttatgacatagcac--
| || ||||||||||| || ||||||||||| ||||||||||| || || |||||||| ||||| || ||||| || | |||| ||||| | ||||||||| | | | | | ||||| | ||| | | | || || | ||| || ||| | ||||||| | |
TCCACTCATATAAGAAAATTATTGGTTTTGTACCACAAGATGATATAGTGCATGGGAATTTGACAGTAGAGGAGAATCTCCGGTTCAGTGCACGGTGCAGgtatgtgactttttgtcctttatgcatgctaaatgcattttaagctattaacgttattaaatgttttatattcatccataac---tcttatgattcaagatca
upper sequence: LOC_Os10g30610.2 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv13s0019g04600.t01 (Vitis vinifera), 5'ss of exon 8
TGCAGTCATATAAGAAGATCATTGGTTTTGTGCCACAAGATGACATTGTCCATGGGAACTTGACGGTTGAGGAAAACTTGTGGTTTAGTGCGTGCTGCAGgtat--taaat---acaggcatatggtgcatagcttggttactttca--ttattgattatttttccttccattaaatatgcttatatcaaaacttatgacatagcac
| || ||||| ||||| ||||| || ||||||||||||||||||||||| ||||| || ||||| || || ||||| | ||||| ||||| | ||||||||| ||| | ||| || ||| || || ||| |||| || |||||||| | | | || ||| | || | | ||
TCCACTCATACAAGAAAATCATGGGATTTGTGCCACAAGATGACATTGTGCATGGAAATTTGACAGTGGAAGAAAATCTCTGGTTCAGTGCAAGATGCAGgtatgctaagttccacatccaaatgcaatttaattta-ttatcttcaacttcttgattatcaaaatattt-tgactcataattaattatcaatcttttactg-----
upper sequence: LOC_Os10g30610.2 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv06s0004g02490.t01 (Vitis vinifera), 5'ss of exon 8
TGCAGTCATATAAGAAGATCATTGGTTTTGTGCCACAAGATGACATTGTCCATGGGAACTTGACGGTTGAGGAAAACTTGTGGTTTAGTGCGTGCTGCAGgtattaaatacaggcatatggtgcatagcttggttactttcattattgattatttttccttccattaaatatgcttatatcaaaacttatgacatagcac--------
|||| || || ||||| || ||||||||||||||||||||||| ||||| ||||| |||||||| ||| |||| || | ||||| ||||| | ||||||||| | | | || ||| ||||| | ||||||| || | | |||| || | | |||| | ||||| || |
TGCACTCGTACAAGAAAATTATTGGTTTTGTGCCACAAGATGATATTGTGCATGGAAACTTGACAGTTCAGGAGAATCTATGGTTCAGTGCAAGGTGCAGgtatgtcacatttaattccattgggtagacca---actttag--actgattatcttacttcaaattacat---cattcccaaaaaataatgacctaagaatttattaa
upper sequence: LOC_Os10g30610.2 (Oryza sativa), 5'ss of exon 7
lower sequence: PP1S167_121V6.1 (Physcomitrella patens), 5'ss of exon 9
TGCAGTCATATAAGAAGATCATTGGTTTTGTGCCACAAGATGACATTGTCCATGGGAACTTGACGGTTGAGGAAAACTTGTGGTTTAGTGCGTGCTGCAGgtattaaatacaggcatatggtgcatagcttggttactttcattattgat-tatttttccttccattaaatatgcttatatcaaaacttatgaca-tagcac--
|||| ||||| || |||||||| || ||||| || ||||||||||||||||| | ||||| |||||||||||||||||||| || || | |||||||| |||| | | || | | | || | | | ||||| || | | || | || | || | || | |||| | | |
TGCATTCATACAAACGCATCATTGGATTCGTGCCTCAGGATGACATTGTCCATGGCAGTTTGACTGTTGAGGAAAACTTGTGGTTCAGCGCAAATTACAGgtatttc-tacatggctttgctttctgg--tgatgccacttattatcgagatctggtttataaaatgtagggcatttgttcatgaattcatgattctggtgcag
upper sequence: LOC_Os10g30610.2 (Oryza sativa), 5'ss of exon 7
lower sequence: PP1S77_119V6.1 (Physcomitrella patens), 5'ss of exon 8
TGCAGTCATATAAGAAGATCATTGGTTTTGTGCCACAAGATGACATTGTCCATGGGAACTTGACGGTTGAGGAAAACTTGTGGTTTAGTGCGTGCTGCAGgt----attaaatacaggcatatggtgcatag---cttggttactttcattattgatt-----------atttttccttccattaaatatgcttatatcaaaacttatgacatagcac---------------------------------------------------------
| || || || || | |||||||| |||||||| || |||||||| |||||||| ||| | || ||||||||||| | | ||| ||||| | | ||| | | | |||| | ||| ||| || || | || | || | || | | | | || ||| | || |||| | | || |
TTCAATCCTACAAAAGCATCATTGGGTTTGTGCCGCAGGATGACATCGTCCATGGCAACCTTACTGTTGAGGAAAATCTTTTGTTCAGTGCCAATTACCGgttcgtaccgaccataggctccacattcatgtgtcctttgtcacctccacttctggtcctgcattgtgaatctctttgtataccaagtataatgatg--aaaatgtgtaacgatgattgaggtaagaatagatcaatcatgttaagttttctttcactggattgcgtcattgcagMapped 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|29678525|gb|CB674800.1|CB674800EST: CATGGGAACTTGACGGTTGAGGAAAACTTGTGGTTTAGTGCGTGCTGCAG GTCAAGCAAAGGCATGTCAAAATCTGATAAGATTATAGTTCTTGAACGGGT
genomic: CATGGGAACTTGACGGTTGAGGAAAACTTGTGGTTTAGTGCGTGCTGCAGgtattaaata ... tctggagtagGTCAAGCAAAGGCATGTCAAAATCTGATAAGATTATAGTTCTTGAACGGGT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TGCAGTCATATAAGAAGATCATTGGTTTTGTGCCACAAGATGACATTGTCCATGGGAACTTGACGGTTGAGGAAAACTTGTGGTTTAGTGCGTGCTGCAGgtattaaatacaggcatatggtgcatagcttggttactttcattattgattatttttccttccattaaatatgcttatatcaaaacttatgacatagcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG