Sequence
atgc intronic sequence ATGC exonic sequencegtaaggctgagcatttctatggttacatggccatcattttttttttaacctcttaccctctctaataagctgcatgcagGTTGTTGCATCTCAAGACTGGCCAGAAGTTACAAAGTATGCTGGATTGGTGTGTGCTCAGGCTCATCGGCAAGAGCTCATTCAAGATCTTTACAAGACAT
Basic information
species | Oryza sativa |
transcript | LOC_Os06g39640.1 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G079080_T02 (Zea mays), 3'ss of exon 14
--------------------------------gtaaggctgagcatttctatggttacatg-gccatcattttttttttaacctcttaccctctctaataagctgcatgcagGTTGTTGCATCTCAAGACTGGCCAGAAGTTACAAAGTATGCTGGATTGGTGTGTGCTCAGGCTCATCGGCAAGAGCTCATTCAAGATCTTTACAAGACAT
|| |||| | || || | | |||||| || | || | | ||| |||| ||||||||||| |||||||| |||||||||||||||||||||||||||||||| ||||||||||| || |||||||||||||||||||| |||||||| ||||
gtaaggctcgttactactttgccatttcttcatcaatatgtcacattcatcaggatatgcacatccttatttttgttccgaacttat-ctgtctgcctctttctgctcacagGTTGTTGCTTCTCAAGATTGGCCAGAAGTTACAAAGTATGCTGGATTGGTTTGTGCTCAGGCACACCGGCAAGAGCTCATTCAAGACCTTTACAAAACAT
upper sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 14
lower sequence: AC189879.3_FGT003 (Zea mays), 3'ss of exon 13
----------------------------gtaaggctgag-catttctatggttacatggccatcattttttttttaacctcttaccctctctaataagctgcatgcagGTTGTTGCATCTCAAGACTGGCCAGAAGTTACAAAGTATGCTGGATTGGTGTGTGCTCAGGCTCATCGGCAAGAGCTCATTCAAGATCTTTACAAGACAT
| | | ||| | || | ||| |||| || | || | | ||| || ||| ||||| ||||||||||| |||||||| |||||||||||||||||||||||||||||||| ||||||||||| || ||||||||||||||||| || |||||||| ||||
gtaaggctcattactactttccatttctgcatcaacatgtcatattcatcaagatatgcacatctttgtcttggttttggacttatctcactcatatgctgctgacagGTTGTTGCTTCTCAAGATTGGCCAGAAGTTACAAAGTATGCTGGATTGGTTTGTGCTCAGGCACACCGGCAAGAGCTCATTCAGGACCTTTACAAAACAT
upper sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA02G00510.1 (Glycine max), 3'ss of exon 14
---------------gtaaggctgagcatttctatggttacatggccatcattttttttttaacctcttaccctctctaataa-gctgcatgcagGTTGTTGCATCTCAAGACTGGCCAGAAGTTACAAAGTATGCTGGATTGGTGTGTGCTCAGGCTCATCGGCAAGAGCTCATTCAAGATCTTTACAAGACAT
| | || ||| || | |||| | |||| | || || | | | | || | ||||||| ||||||||||||||||| ||||| || || ||||| || || ||||||||||| |||||| | || || ||||| |||||| | ||||| | |
gtacacttatgatccatttgtcttgattttttaatattgcaatggttcacgagggttttggtagctgatatctattgtgcaattgcaatctatagGTTGTAGCATCTCAAGACTGGCCTGAAGTGACGAAATATGCCGGTTTAGTGTGTGCTCAAGCTCATAGACAGGAACTCATACAAGATTTGTACAAAATGT
upper sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA06G23920.1 (Glycine max), 3'ss of exon 14
gtaaggctgagcatttctatggttacatggccatc--attttttttttaacctcttaccctctctaataagctgcatgcagGTTGTTGCATCTCAAGACTGGCCAGAAGTTACAAAGTATGCTGGATTGGTGTGTGCTCAGGCTCATCGGCAAGAGCTCATTCAAGATCTTTACAAGACAT-
| |||||||| | | || || | | | | || || | |||| | | || |||||||| || || || |||||||| ||||| ||||||||||| || ||||| ||||||||| ||||||| |||| || ||||||||||||| | || |
------gtaagcatttccaaactcctatatacagctaagggatgtgctatgcttgatatatactgaatacggta-atccagGTTGTAGCCTCCCAGGACTGGCCTGAAGTAACAAAGTATGCAGGGTTGGTTTGTGCTCAGCCTCATCGAGAAGAACTAATTCAAGATCTTTTCC-GATGTT
upper sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA05G08170.1 (Glycine max), 3'ss of exon 13
gtaaggctgagcatttctatggttacatggccatcattttttttttaacctcttaccctctctaataagctgcatgcagGTTGTTGCATCTCAAGACTGGCCAGAAGTTACAAAGTATGCTGGATTGGTGTGTGCTCAGGCTCATCGGCAAGAGCTCATTCAAGATCTTTACAAGACAT
| || ||||| | || | | | || | | | | | ||| || | || |||||||| || || || |||||||||||||| ||||| ||||| |||||||| ||||||||| ||||||| | || ||||||||||| |||| || |
------gtaagtatttccaaagtcctttaac--ttatagctggccatatatttggtcttct--gattactgttattcagGTTGTAGCCTCCCAGGACTGGCCAGAAGTGACAAAATATGCAGGATTGGTATGTGCTCAGCCTCATCGCGAGGAACTCATTCAAGACCTTTTTAAATGTT
upper sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA17G12850.1 (Glycine max), 3'ss of exon 14
gtaaggctgagcatttctatggttacatggccatcattttttttttaacctcttaccctctctaataagctgcatgcagGTTGTTGCATCTCAAGACTGGCCAGAAGTTACAAAGTATGCTGGATTGGTGTGTGCTCAGGCTCATCGGCAAGAGCTCATTCAAGATCTTTACAAGACAT
| || ||||| | || | | | || | || | | | |||||| | || |||||||| || || || |||||||| ||||| |||||||| || |||||||| || |||||| ||||||| | || |||||||||||||||| || |
------gtaagtatttccaaagtcctttacc--ttatagctggccatacatttgg--ttttctaatcactgttattcagGTTGTAGCCTCCCAGGACTGGCCGGAAGTAACAAAGTACGCAGGATTGGTATGCGCTCAGCCTCATCGTGAGGAACTCATTCAAGATCTTTTTAAATGTT
upper sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA10G00530.1 (Glycine max), 3'ss of exon 6
gtaaggctgagcatttctatggttacatggccatcattttttttttaacctcttaccc--tctctaataagctgcatgcagGTTGTTGCATCTCAAGACTGGCCAGAAGTTACAAAGTATGCTGGATTGGTGTGTGCTCAGGCTCATCGGCAAGAGCTCATTCAAGATCTTTACAAGACAT
||| | | | || | || | || | | |||| | | | | | |||| | | | |||| || ||||||||||||||||| ||| | ||||| |||||||| || ||||||||||| |||||| | || || ||||| |||||| | ||||| | |
gtacgcttatg-atccatttgtcttgat--tttttaattttgcagtggttcttgagctgatatctatcgctcaatacgtagGTAGTAGCATCTCAAGACTGGCCTGAACTGACAAAATATGCTGGTTTAGTGTGTGCTCAAGCTCATAGACAGGAACTCATACAAGATTTGTACAAAATGT
upper sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 14
lower sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 14
gtaaggctga-gcatttctat-ggttacatggccatcattttttttttaacctcttaccctctctaataagctgcatgcagGTTGTTGCATCTCAAGACTGGCCAGAAGTTACAAAGTATGCTGGATTGGTGTGTGCTCAGGCTCATCGGCAAGAGCTCATTCAAGATCTTTACAAGACAT
|||||| | | || || ||| || | |||| || || || | | | | | | | | | |||||||||| |||||||||||||| ||||| ||||| ||||| || || || |||||||| ||||| ||||||| || || |||||| | || || ||||
gtaaggattatacacttttatcaagtagtggagcatcgaaattcattatac---tcagtttttttcttttgttttctttagGTTGTTGCTTCTCAAGACTGGCCTGAAGTGACAAAATATGCGGGTTTAGTTTGTGCTCAAGCTCACAGGCAAGAACTTATACAAGATTTGTATAAAACAT
upper sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 14
lower sequence: Vv05s0020g04190.t01 (Vitis vinifera), 3'ss of exon 12
gtaaggct-----gagcatttctatggttacatggccatcattttttttttaac--ctctt-----accctct--ctaataagctgca--------tgcagGTTGTTGCATCTCAAGACTGGCCAGAAGTTACAAAGTATGCTGGATTGGTGTGTGCTCAGGCTCATCGGCAAGAGCTCATTCAAGATCTTTACAAGACAT
|||| | | | ||| || | | | | ||||| | | | || || | | || ||| || || |||| || || ||||| |||||||| ||||| ||||| ||||| |||||||| |||||||||||||| | || || || || |||||| | ||||||||||
gtaaaatttctttaactgatatcatgcttcctagaaccttgtttttcctaaagtggttattgaggaactttgttgctgatagattgttgtattaattgtagGTAGTAGCTTCTCAGGACTGGCCTGAAGTCACAAAATATGCAGGATTGGTTTGTGCTCAGGCTCACAGACAGGAACTGATACAAGATTTATACAAGACAT
upper sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 14
lower sequence: Vv11s0016g04620.t01 (Vitis vinifera), 3'ss of exon 14
gtaaggctgagcatttctatggttac--atggccatcattttttttttaacctcttaccctctctaataagctgcatgcagGTTGTTGCATCTCAAGACTGGCCAGAAGTTACAAAGTATGCTGGATTGGTGTGTGCTCAGGCTCATCGGCAAGAGCTCATTCAAGATCTTTACAAGACAT
|||||| | | | || | || | | | | || | ||| | | || | ||| || ||||| || || || ||||||||||||||||| || ||||||||||||||||| ||||||||||||||||||||||| || ||||||||| | || || || |
gtaaggatatgaaaacctgtatttcccaaaatctacagttccatgtttgagtccatattgattacaat------tatacagGTAGTAGCCTCCCAAGACTGGCCAGAAGTCACCAAGTATGCTGGATTGGTATGTGCTCAGGCTCATCGGCAAGAACTTATTCAAGATTTGTATAAAACCT
upper sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 14
lower sequence: EFJ24991 (Selaginella moellendorffii), 3'ss of exon 15
gtaaggctgagcatttctatggttacatggccatcattttttttttaacctcttaccctct--ctaataagctgcatgcagGTTGTTGCATCTCAAGACTGGCCAGAAGTTACAAAGTATGCTGGATTGGTGTGTGCTCAGGCTCATCGGCAAGAGCTCATTCAAGATCTTTACAAGACAT
|| | | || || || | || | |||| | ||||||||||||| ||||| ||||| || || || |||||||| ||||| || |||||||| || ||||| ||||| || || |||||||| |||||||| |
---------------------------------gtatgctgctcttccgctgcagccgtgaaactcaattgctgt-tatagGTTGTTGCATCGCAAGATTGGCCCGAGGTGACGAAGTATGCGGGATTAGTTTGTGCTCAAGCACATCGTCAAGAACTGATACAAGATCTCTACAAGACCT
upper sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 14
lower sequence: EFJ15357 (Selaginella moellendorffii), 3'ss of exon 15
gtaaggctgagcatttctatggttacatggccatcattttttttttaacctcttaccctctctaataagctgcatgcagGTTGTTGCATCTCAAGACTGGCCAGAAGTTACAAAGTATGCTGGATTGGTGTGTGCTCAGGCTCATCGGCAAGAGCTCATTCAAGATCTTTACAAGACAT
| |||| || || | ||| | | |||| | ||||||||||||| ||||| ||||| || || || |||||||| ||||| || |||||||| || ||||| ||||| || || |||||||| |||||||| |
----------------------------gtatgctgcttttccgctacagtcgtgaaa-ctcaatt--gctgt-tatagGTTGTTGCATCGCAAGATTGGCCCGAGGTGACGAAGTATGCGGGATTAGTTTGTGCTCAAGCACATCGTCAAGAACTGATACAAGATCTCTACAAGACCTMapped 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|58613128|gb|CK040840.1|CK040840EST: ATGTCACGCATCCTGAAACCGGGGAGGACTCTAGCCCATCCATTGCTGCT GTTGTTGCATCTCAAGACTGGCCAGAAGTTACAAAGTATGCTGGATTGGTG
genomic: ATGTCACGCATCCTGAAACCGGGGAGGACTCTAGCCCATCCATTGCTGCTgtaaggctga ... ctgcatgcagGTTGTTGCATCTCAAGACTGGCCAGAAGTTACAAAGTATGCTGGATTGGTG
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 1 RNA-Seqlibrary.
Block sizes:
59 (upstream exon),
71 (downstream exon)
Score:
8TTGGAGGATTCCTTTGGTCAGTGACATACCAACTATTATATTTGGTGCAGATGTCACGCATCCTGAAACCGGGGAGGACTCTAGCCCATCCATTGCTGCTgtaaggctga ... ctgcatgcagGTTGTTGCATCTCAAGACTGGCCAGAAGTTACAAAGTATGCTGGATTGGTGTGTGCTCAGGCTCATCGGCAAGAGCTCATTCAAGATCTTTACAAGACAT
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acatggccatcattttttttttaacctcttaccctctctaataagctgcatgcagGTTGTTGCATCTCAAGACTGGCCAGAAGTTACAAAGTATGCTGGATTGGTGTGTGCTCAGGCTCATCGGCAAGAGCTCATTCAAGATCTTTACAAGACAT
atcattttttttttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaggctgagcatttctatggttacatggccatcattttttttttaacctcttaccctctctaataagctgcatgcagGTTGTTGCATCTCAAGACTGGCCAGAAGTTACAAAGTATGCTGGATTGGTGTGTGCTCAGGCTCATCGGCAAGAGCTCATTCAAGATCTTTACAAGACAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA