Sequence
atgc intronic sequence ATGC exonic sequenceTGAGGTTGCCTCAAAGTATCCTGGTATTCAGTATAATGAGATCATTGTCGACAACTGCTGTATGCAACTTGTTGCAAAGCCTGAGCAATTTGATGTCATGgtatgctctttacttcatacattctatctggagcatcactgtctgttcagtactttggagctgccttgtttgaactgcactgagtttctttgcgtgtgct...
Basic information
species | Oryza sativa |
transcript | LOC_Os04g40310.2 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g40310.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G025366_T02 (Zea mays), 5'ss of exon 2
TGAGGTTGCCTCAAAGTATCCTGGTATTCAGTATAATGAGATCATTGTCGACAACTGCTGTATGCAACTTGTTGCAAAGCCTGAGCAATTTGATGTCATGgtatgctctttacttcatacattctatctggagcatcactgtctg-ttcagtactttggagctgccttgtttgaactg-cactgagtttc-tttgcgtgtgct-
||| ||||| ||||| ||||||||||||||||| ||||| || ||||| |||||||||| ||||||||||||| |||||||||| |||||||||||||||||||| | | || | | | | | || ||| | | || | ||||| || ||||| ||| | || || | ||| ||| ||
TGAAGTTGCTTCAAAATATCCTGGTATTCAGTACAATGAAATGATTGTTGACAACTGCTCTATGCAACTTGTTTCAAAGCCTGAACAATTTGATGTCATGgtatgtatctaaatttctgggcatttttctgtgtat-actatttaatttggaacttt---acttttttgttcaaacaaaccttggattacatttctctgttcta
upper sequence: LOC_Os04g40310.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA11G08920.1 (Glycine max), 5'ss of exon 2
TGAGGTTGCCTCAAAGTATCCTGGTATTCAGTATAATGAGATCATTGTCGACAACTGCTGTATGCAACTTGTTGCAAAGCCTGAGCAATTTGATGTCATGgtatgctctttacttcatacattctatctggagcatcactgtctgttcagtactttggagctgccttgtttgaactgcactgagtttctttgcgtgtgct---
||||||||| ||| ||||||||| || |||| ||||| || ||||| ||||||||||| ||||| |||||| |||| || ||||| ||||||||||||||||| || | | || || | | | |||| | | || | | || | || | | | | || ||||
AGAGGTTGCCACAAGGTATCCTGGAATCAAGTACAATGAAATTATTGTAGACAACTGCTGCATGCAGCTTGTTTCAAAACCGGAGCAGTTTGATGTCATGgtatgtaaatttactatttgatcctgattctcaattatttatctgctttg---attaatacattcatggtgtaattatgggggatcaatgcttgtttgcttcc
upper sequence: LOC_Os04g40310.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA16G22640.1 (Glycine max), 5'ss of exon 2
TGAGGTTGCCTCAAAGTATCCTGGTATTCAGTATAATGAGATCATTGTCGACAACTGCTGTATGCAACTTGTTGCAAAGCCTGAGCAATTTGATGTCATGgtatgctctttacttcatacattctat-ctggagcatcactgtctgttcagtactttggagctgccttgtttgaac-tgcactgagtttctttgcgtgtgct----
|||||||| ||||||| ||||| || ||||||| || || ||||| || |||||||||||||| |||||| |||||||||| || ||||||||||||||||| || |||||||||| |||| |||| | | || | | | || || | | |||| | || | ||
AGAGGTTGCTACAAAGTACCCTGGAATAAAGTATAACGAAATTATTGTGGATAACTGCTGTATGCAGCTTGTTTCAAAGCCTGAACAGTTTGATGTCATGgtatgtgtatt------tacattctattctggtttgctgctgtttatgcacttatgtaattttgtctaatgtatttatgcagtaagcacacacacccttgagttaa
upper sequence: LOC_Os04g40310.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA02G04780.1 (Glycine max), 5'ss of exon 2
TGAGGTTGCCTCAAAGTATCCTGGTATTCAGTATAATGAGATCATTGTCGACAACTGCTGTATGCAACTTGTTGCAAAGCCTGAGCAATTTGATGTCATGgtatgc-tctttacttcatacattctatctggagcatcactgtctgttca-gtactttggagctgccttgtttgaactgcactgagtttctttgcgtgtgct----
|||||||| ||||||| ||||| || ||||||| || || ||||| || |||||||||||||| |||||| |||||||||| || ||||||||||||||||| | ||||| | | || || || | | | | | | ||| |||| || | |||| |||| | | | | ||
AGAGGTTGCTACAAAGTACCCTGGAATCAAGTATAACGAAATTATTGTGGATAACTGCTGTATGCAGCTTGTTTCAAAGCCTGAACAGTTTGATGTCATGgtatgtgtatttacatttca-atcctggcttgcagctatttatgcacttatgtaatttg--tctaatgtatttg---tgcagtaacccccccgccccccgcccccc
upper sequence: LOC_Os04g40310.2 (Oryza sativa), 5'ss of exon 2
lower sequence: AT4G35260.1 (Arabidopsis thaliana), 5'ss of exon 2
TGAGGTTGCCTCAAAGTATCCTGGTATTCAGTATAATGAGATCATTGTCGACAACTGCTGTATGCAACTTGTTGCAAAGCCTGAGCAATTTGATGTCATGgtatgctctttacttcatacattctatctggagcatcactgt-ctgttcagtactttggagct--gccttgtttgaactgcactgagtttctttgcgtgtgct-
|||||||| ||||||||| | || || ||||| |||||||| || |||||||||||||||||||| || || || |||||||| |||||||||||||| | | || ||| | || || | ||| | || | ||| | | | | ||| || || ||| | | | |
CGAGGTTGCGAAAAAGTATCCCAGCATCACCTACAATGAAATCATTGTTGATAACTGCTGTATGCAACTTGTAGCCAAACCAGAGCAATTCGATGTCATGgtatgtttcagagtt-atatac---atatgaattttcatgacgttctttaagtcttcgatgttttactttgagaaaaagataccagtcatctctccctagtttg
upper sequence: LOC_Os04g40310.2 (Oryza sativa), 5'ss of exon 2
lower sequence: AT2G17130.2 (Arabidopsis thaliana), 5'ss of exon 2
TGAGGTTGCCTCAAAGTATCCTGGTATTCAGTATAATGAGATCATTGTCGACAACTGCTGTATGCAACTTGTTGCAAAGCCTGAGCAATTTGATGTCATGgtatgctctttacttcatacattctatctggagcatcactgtctgttcagtactttggagctgccttgtttgaactgcactgagtttctttgcgtgtgct
|||||||| |||||||| | ||| || ||||| |||||||| || || || |||||||||||||| || | || |||||||| |||||||||||| ||| | || || || | || | || || ||||| | | || | |||| ||
AGAGGTTGCTAAGAAGTATCCAAGCATTGCTTACAATGAAATCATTGTTGATAATTGTTGTATGCAACTTGTGGCTAGACCAGAGCAATTCGATGTCATGgtaaatgtttttcagcacttgttgatgcttgggc-----tagcttccttctattttggt-ttatttacttgtatctgctttgcag---------------
upper sequence: LOC_Os04g40310.2 (Oryza sativa), 5'ss of exon 2
lower sequence: AT4G35650.1 (Arabidopsis thaliana), 5'ss of exon 2
TGAGGTTGCCTCAAAGTATCCTGGTATTCAGTATAATGAGATCATTGTCGACAACTGCTGTATGCAACTTGTTGCAAAGCCTGAGCAATTTGATGTCATGgta-tgctctttacttcatacat-----tctatctggagcatcactgtctgttcagtactttggagctgccttgtttgaactgcactgagtttctttgcgtgtgct-------------------
|||||||| | | ||| | || ||| || ||||| || || || ||||| ||||||||||| ||||| || ||||||||||||||||||||||||||| ||||||| ||| || | || | || ||| ||| || || | | | || || ||| | | | | |
AGAGGTTGCTAAACATTATTCGGGGATTACTTACAATGAAATAATCGTAGACAATTGCTGTATGCAGCTTGTCGCCAAGCCTGAGCAATTTGATGTCATGgtaatgctcttcttttcctagttacaaatcaaaatgagtcattttgaaatgtgacagacgatgaaaccatc--attgatgttgttttgatgtctctcatggatattttttgttggtttgtttcag
upper sequence: LOC_Os04g40310.2 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv03s0038g03120.t01 (Vitis vinifera), 5'ss of exon 2
TGAGGTTGCCTCAAAGTATCCTGGTATTCAGTATAATGAGATCATTGTCGACAACTGCTGTATGCAACTTGTTGCAAAGCCTGAGCAATTTGATGTCATGgtatgctctttacttcatacattctatc--tggagcatcactgtctgttcagtactttggagctgccttgtttgaactgcactgagtttctttgcgtgtgct-
|| ||||| ||| || || ||||| || | || || ||||| || |||||||| |||||||| ||| ||||||| ||||||||||||||||||||||| || || ||| | ||| | | | | | || || || |||| | | | | || | |||| | | | ||
GGAAGTTGCGAAAAATTACCCCAGTATTGCATACAGCGAAATTATTGTGGATAACTGCTGCATGCAACTGGTTTCAAAGCCGGAGCAATTTGATGTCATGgtatgtggctttgcaaatggatttatttcatgggaaacctttctatagccactaattct--gctgatat-tattacttgatatatgtttgtatctataaactg
upper sequence: LOC_Os04g40310.2 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv04s0210g00180.t01 (Vitis vinifera), 5'ss of exon 2
TGAGGTTGCCTCAAAGTATCCTGGTATTCAGTATAATGAGATCATTGTCGACAACTGCTGTATGCAACTTGTTGCAAAGCCTGAGCAATTTGATGTCATGgtatgctctt----tacttcata-cattctatctggagcatca-ctgtctgttcagtactttggagctgccttgtttgaactgcactgagtttctttgcgtgtgct
|||||||| |||| |||||||| || |||| | ||| || ||||| ||||| ||||| ||||| |||||| ||||||||||||| ||||||||||||||||| | || | ||| || | || || | || || ||| | || | || | | | | || || || |
AGAGGTTGCAACAAAATATCCTGGAATCAAGTACAGTGAAATTATTGTGGACAATTGCTGCATGCAGCTTGTTTCAAAGCCTGAGCAGTTTGATGTCATGgtatgtgaatatactattgtatagcactttaattgagatgcaaattgcttggtcaatgttt----gtcatgttctgtaattattcttaagatttcctgatagca--
upper sequence: LOC_Os04g40310.2 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S152_81V6.1 (Physcomitrella patens), 5'ss of exon 2
TGAGGTTGCCTCAAAGTATCCTGGTATTCAGTATAATGAGATCATTGTCGACAACTGCTGTATGCAACTTGTTGCAAAGCCTGAGCAATTTGATGTCATGgtatgctctt-tacttcatac---attctatctgg---------agcatcactgtctgttc-agtactttggagctgccttg-------tttgaactgc-actgagtttctttgcgt--gtgct----------------------
|||||| ||| ||||||||| | || ||||||| ||| ||||||| || || ||||||||||| ||||| | |||||| | |||||||||||||||||| | ||| || ||| | ||| | || | | || ||| | | | | | ||| | | | || | ||||| | | | || ||||| | |||||
TGAGGTGGCCAAAAAGTATCCCGCCATCAAGTATAACGAGGTCATTGTGGATAATTGCTGTATGCAGCTTGTGTCGAAGCCTCAACAATTTGATGTCATGgtaagttctcgtatgtcaggctcaattttctccgacttttagttattggcagtgtttatgctaatgacttgatgttactgtgacatcagctggaactctgattcaagttgtttgccttggtgctattgtgtgtatttttcccccag
upper sequence: LOC_Os04g40310.2 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ29002 (Selaginella moellendorffii), 5'ss of exon 2
TGAGGTTGCCTCAAAGTATCCTGGTATTCAGTATAATGAGATCATTGTCGACAACTGCTGTATGCAACTTGTTGCAAAGCCTGAGCAATTTGATGTCATGgtatgctctttacttcatacattctatctggagcatcactgtctgttcagtactttggagctgccttgtttgaactgcactgagtttctttgcgtgtgct
||||| ||| |||||||| || || |||| || |||||||| |||||||||||||||||||| || || | || |||||||| |||||||||||| | || || | | |||| || || || | | | || || ||
CGAGGTGGCCAAGAAGTATCCCGGGATCAAGTACAACGAGATCATCGTCGACAACTGCTGTATGCAGCTCGTGTCTCGCCCCGAGCAATTCGATGTCATGgta-accagttgctccttccatttcat-tgcagtgttttatcatccacgaacctgtgcag----------------------------------------
upper sequence: LOC_Os04g40310.2 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ13705 (Selaginella moellendorffii), 5'ss of exon 2
TGAGGTTGCCTCAAAGTATCCTGGTATTCAGTATAATGAGATCATTGTCGACAACTGCTGTATGCAACTTGTTGCAAAGCCTGAGCAATTTGATGTCATGgtatgctctttacttcatacattctatctggagcatcactgtctgttcagtactttggagctgccttgtttgaactgcactgagtttctttgcgtgtgct
||||| ||| ||||| || || || |||| || |||||||| |||||||||||||||||||| || || | || |||||||| || ||||||||| | || || | | |||| || || || | | | || || ||
CGAGGTGGCCAAGAAGTACCCCGGGATCAAGTACAACGAGATCATCGTCGACAACTGCTGTATGCAGCTCGTGTCTCGCCCCGAGCAATTCGACGTCATGgta-accagttgctccttccatttcat-tgcagtgttttatcatccacgaacctgtgcag----------------------------------------Mapped 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|29687051|gb|CB683326.1|CB683326EST: ACAACTGCTGTATGCAACTTGTTGCAAAGCCTGAGCAATTTGATGTCATG GTTACACCAAACCTTTATGGCAATTTGGTTGCTAACACGGCTGCAGGTATT
genomic: ACAACTGCTGTATGCAACTTGTTGCAAAGCCTGAGCAATTTGATGTCATGgtatgctctt ... cgttttgtagGTTACACCAAACCTTTATGGCAATTTGGTTGCTAACACGGCTGCAGGTATT
EST:
gi|29662276|gb|CB658551.1|CB658551EST: ACAACTGCTGTATGCAACTTGTTGCAAAGCCTGAGCAATTTGATGTCATG GTTACACCAAACCTTTATGGCAATTTGGTTGCTAACACGGCTGCAGGTATT
genomic: ACAACTGCTGTATGCAACTTGTTGCAAAGCCTGAGCAATTTGATGTCATGgtatgctctt ... cgttttgtagGTTACACCAAACCTTTATGGCAATTTGGTTGCTAACACGGCTGCAGGTATT
EST:
gi|87018960|gb|CI256845.1|CI256845EST: ACAACTGCTGTATGCAACTTGTTGCAAAGCCTGAGCAATTTGATGTCATG GTTACACCAAACCTTTATGGCAATTTGGTTGCTAACACGGCTGCAGGTATT
genomic: ACAACTGCTGTATGCAACTTGTTGCAAAGCCTGAGCAATTTGATGTCATGgtatgctctt ... cgttttgtagGTTACACCAAACCTTTATGGCAATTTGGTTGCTAACACGGCTGCAGGTATT
EST:
gi|29662277|gb|CB658552.1|CB658552EST: ACAACTGCTGTATGCAACTTGTTGCAAAGCCTGAGCAATTTGATGTCATG GTTACACCAAACCTTTATGGCAATTTGGTTGCTAACACGGCTGCAGGTATT
genomic: ACAACTGCTGTATGCAACTTGTTGCAAAGCCTGAGCAATTTGATGTCATGgtatgctctt ... cgttttgtagGTTACACCAAACCTTTATGGCAATTTGGTTGCTAACACGGCTGCAGGTATT
EST:
gi|29687448|gb|CB683723.1|CB683723EST: ACAACTGCTGTATGCAACTTGTTGCAAAGCCTGAGCAATTTGATGTCATG GTTACACCAAACCTTTATGGCAATTTGGTTGCTAACACGGCTGCAGGTATT
genomic: ACAACTGCTGTATGCAACTTGTTGCAAAGCCTGAGCAATTTGATGTCATGgtatgctctt ... cgttttgtagGTTACACCAAACCTTTATGGCAATTTGGTTGCTAACACGGCTGCAGGTATT
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:
60 (upstream exon),
71 (downstream exon)
Score:
18TGAGGTTGCCTCAAAGTATCCTGGTATTCAGTATAATGAGATCATTGTCGACAACTGCTGTATGCAACTTGTTGCAAAGCCTGAGCAATTTGATGTCATGgtatgctctt ... cgttttgtagGTTACACCAAACCTTTATGGCAATTTGGTTGCTAACACGGCTGCAGGTATTGCTGGAGGGACAGGTGTTATGCCTGGAG
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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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TGAGGTTGCCTCAAAGTATCCTGGTATTCAGTATAATGAGATCATTGTCGACAACTGCTGTATGCAACTTGTTGCAAAGCCTGAGCAATTTGATGTCATGgtatgctctttacttcatacattctatctggagcatcactgtctgttcagtactttggagctgccttgtttgaactgcactgagtttctttgcgtgtgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG