Sequence
atgc intronic sequence ATGC exonic sequence...attcttttttgggatttcaagcctcatgagtagctgcatacagaacaaatctagtaattcatttattgaattctttactgtgctgagtacatctctgcagTTCCCAGAAACTTTAGACTGCTTGAAGAGCTTGAGCGAGGTGAGAAGGGCATTGGTGATGGGACAGTGAGCTATGGAATGGATGATGCTGATGACATATA
Basic information
species | Oryza sativa |
transcript | LOC_Os03g50440.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g50440.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G090172_T02 (Zea mays), 3'ss of exon 1
-attcttttttgggatttcaagcctcatgagtagctgcatacagaacaaatctagtaattcatttattgaattctttactgtgctgagtacatctctgcagTTCCCAGAAACTTTAGACTGCTTGAAGAGCTTGAGCGAGGTGAGAAGGGCATTGGTGATGGGACAGTGAGCTATGGAATGGATGATGCTGATGACATATA
|| || | | | | | | | | || | || || || || || | ||| || | ||||||||||||||||||||||| ||||| ||||| || || || ||||||||||||||||||||||| || ||||||||||| |||||||||||||||||||||||
ttttgttcacaagaacaatggatttgaattctgaatacctgttatgcatgttgtgtgata-ataatttagatcataccttgttctatggtgtcttctgcagTTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCATTGGTGATGGAACTGTGAGCTATGGGATGGATGATGCTGATGACATATA
upper sequence: LOC_Os03g50440.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G022859_T01 (Zea mays), 3'ss of exon 1
-attcttttttgggatttcaagcctca----tgagtagctgcatacagaacaaatctagtaattcatttattgaattctttactgtgctgagtacatctctgcagTTCCCAGAAACTTTAGACTGCTTGAAGAGCTTGAGCGAGGTGAGAAGGGCATTGGTGATGGGACAGTGAGCTATGGAATGGATGATGCTGATGACATATA
|| || | | | | | ||| || |||| || | | |||| ||||| || |||| | | | || | ||||||||||||||||||||||| ||||| ||||| || || || ||||||||||||||||||||||| || ||||||||||| ||||| ||||||||||||||||
ttttgttcacaagcacaatgaatttgaactctgaatatctgc-tattcatgttgcttgataata-atttagatcatactttgttctatggcgt---tttctgcagTTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCATTGGTGATGGAACTGTGAGCTATGGGATGGACGATGCTGATGACATATT
upper sequence: LOC_Os03g50440.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA09G22600.1 (Glycine max), 3'ss of exon 1
---attcttttttgggatttcaagcctcatgagtagctgcatacagaacaaatctagtaattcatttattgaattctttactgtgctgagtacatctctgcagTTCCCAGAAACTTTAGACTGCTTGAAGAGCTTGAGCGAGGTGAGAAGGGCATTGGTGATGGGACAGTGAGCTATGGAATGGATGATGCTGATGACATATA
||| | | ||| ||| | | || || | || || || | | ||| | |||||| | || | | || |||||||||| || || || ||| | | ||||||||||| ||||||||||||| ||||| ||||| || || ||||||||||||||||| ||||| ||||||||
tgccttcatcagtcatattgcaactatttcaattaa--acagctttgaaggatttaatagaacttagatttgaaa-tttactcttcttaattggtccctgcagTTCCTAGGAATTTCAGATTATTGCAAGAGCTTGAGAGAGGTGAGAAGGGAATTGGGGATGGAACTGTTAGCTATGGAATGGATGACGCTGACGACATATA
upper sequence: LOC_Os03g50440.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA05G35000.1 (Glycine max), 3'ss of exon 1
--attcttttttgggatttcaagcctcatga-gtagctgcatacagaacaaatctagtaatt--catttattgaattctttactgtgctgagtacatctctgcagTTCCCAGAAACTTTAGACTGCTTGAAGAGCTTGAGCGAGGTGAGAAGGGCATTGGTGATGGGACAGTGAGCTATGGAATGGATGATGCTGATGACATATA
| | | ||| | || || ||| || | |||| | |||||| || ||| || | | | | || || | || |||||| || ||||| ||| | | |||||||||||| ||||||||||||| ||||| ||||| || || |||||||||||||||||||||||||| || ||
taacttatcattgattgtgttcatcttttgttgtaactttttttttt-taaattt-gtaattggcacctatc---ttgtcaaactttttttgtctatgtatgtagTTCCTAGGAACTTCAGATTATTGGAAGAGCTTGAGAGAGGTGAGAAGGGAATTGGAGATGGAACTGTTAGCTATGGAATGGATGATGCTGATGATATCTA
upper sequence: LOC_Os03g50440.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA08G04710.1 (Glycine max), 3'ss of exon 1
---attcttttttgggatttcaagcctcatg--agtagctgcatacagaacaaatctagtaattcatttattgaattctttactgtgctgagtacatctctgcagTTCCCAGAAACTTTAGACTGCTTGAAGAGCTTGAGCGAGGTGAGAAGGGCATTGGTGATGGGACAGTGAGCTATGGAATGGATGATGCTGATGACATATA
|| | ||| | |||| | || | || | |||| | |||||| | | | ||| | | || || | |||||||| || || || ||| | | |||||||||||| ||||||||||||| ||||| ||||| || || ||||| |||||||||||||||||||| || ||
cttatcactgattgtg--ttcatcttttattgtaacttcttttttttttgtaaattt-gtaatttgc--acctatcttgttaaaatttttggtctatgttcgcagTTCCTAGGAATTTCAGATTATTGGAAGAGCTTGAGAGAGGTGAGAAGGGAATTGGAGATGGAACTGTTAGCTACGGAATGGATGATGCTGATGATATCTA
upper sequence: LOC_Os03g50440.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA07G24950.1 (Glycine max), 3'ss of exon 1
---attcttttttgggatttcaagcctcatgagtagctgcatacagaacaaatctagtaattcatttattgaattctttactgtgctgagtacatctctgcagTTCCCAGAAACTTTAGACTGCTTGAAGAGCTTGAGCGAGGTGAGAAGGGCATTGGTGATGGGACAGTGAGCTATGGAATGGATGATGCTGATGACATATA
| | | ||| ||| | | || || | || || || | | ||| | |||||| | || | | || |||||||||| || || || ||| | | |||||||||||| ||||||||||||| ||||| ||||| || || ||||||||||||||||||||||||||||||||
attgccttcatcagtcattgtaagtatttcaattaa--acagctttgaaggatttaatagaacttagatttgaaa-tttactcttcttaattggtccctgcagTTCCTAGGAATTTCAGATTATTGGAAGAGCTTGAGAGAGGTGAGAAGGGAATTGGGGATGGAACTGTTAGCTATGGAATGGATGATGCTGATGACATATA
upper sequence: LOC_Os03g50440.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT1G70660.2 (Arabidopsis thaliana), 3'ss of exon 1
---------------------------------------------------------------------attcttttttgggatttcaagcctcatgagtagctgcatacagaacaaatctagta-attcatttattga--attctttactgtg-ctgagtacatct---ctgcagTTCCCAGAAACTTTAGACTGCTTGAAGAGCTTGAGCGAGGTGAGAAGGGCATTGGTGATGGGACAGTGAGCTATGGAATGGATGATGCTGATGACATATA
||| || | | ||| ||| | | | || | | | || | | || || |||| ||| | || || ||| | | | |||||||||||||||||||||| | | |||||||| || |||||||||| || ||||| |||||||||||||| ||||||||||||||||||||||| || |
gtaagtctaatccaatttttttttttgattcgattagtctctttgatttggaatctagggttttactttattgcttccttaggtttaaagtaacgattttgattacacagattgcgaagtcactctatatcgttgttgatcatttgtatctttgattgattttgtgtggtttgcagTTCCCAGAAACTTTAGATTATTGGAAGAGCTAGAAAGAGGTGAGAAAGGAATTGGAGATGGGACAGTGAGTTATGGAATGGATGATGCTGATGATATTTT
upper sequence: LOC_Os03g50440.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT1G23260.1 (Arabidopsis thaliana), 3'ss of exon 1
attcttttttgggatttcaagcctcatgagtagctgcatacagaacaaatctagtaattcatttattgaat--tctttact-gtgctgagtacatctctgcagTTCCCAGAAACTTTAGACTGCTTGAAGAGCTTGAGCGAGGTGAGAAGGGCATTGGTGATGGGACAGTGAGCTATGGAATGGATGATGCTGATGACATATA
| | | |||| | ||| || ||| | ||| | | | | ||| || | | |||| | ||| | || |||||| || ||||||||| || | ||||||||||| |||||||||| || ||||| ||||| || || |||||||||||||||||||||||||| || ||
-gaatgtgatcggatccatggtctc--gattaggtatatatctgatctgtaaaatgatttgatttgggggcgatatttataagagcttgattttgtgatgtagTTCCGAGGAACTTTAGATTGTTGGAAGAGCTTGAAAGAGGTGAGAAAGGTATTGGAGATGGTACTGTTAGCTATGGAATGGATGATGCTGATGATATTTA
upper sequence: LOC_Os03g50440.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv01s0011g05630.t01 (Vitis vinifera), 3'ss of exon 1
---------attcttttttgggatttcaagcctcatgagtagctgcatacagaacaaatctagtaattcatttattgaattctttactgtgctgagtacatctctgcagTTCCCAGAAACTTTAGACTGCTTGAAGAGCTTGAGCGAGGTGAGAAGGGCATTGGTGATGGGACAGTGAGCTATGGAATGGATGATGCTGATGACATATA
| |||| ||| || || |||| || | | || ||| | || ||| |||| | || | ||| | |||||||| || || || ||| | || |||||||||||| |||| || ||||| ||||| ||||| || || || ||||||||||||||||||||||| |||||
ttatcttggaaaattttctggttgttgttgctacatggtcttttgagtgcttg-catgcatagcaggagatatat------ctttgtgattttgtggtcatat--gcagTTCCAAGGAATTTCAGATTACTGGAAGAGCTTGAGAGAGGGGAAAAGGGAATTGGCGATGGAACTGTCAGTTATGGAATGGATGATGCTGATGATATATA
upper sequence: LOC_Os03g50440.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S60_129V6.1 (Physcomitrella patens), 3'ss of exon 2
attcttttttgggatttcaagcctcatgagtagctgcatacagaacaaatctagtaattcatttattgaattctttactgtgctgag---tacatctctgcagTTCCCAGAAACTTTAGACTGCTTGAAGAGCTTGAGCGAGGTGAGAAGGGCATTGGTGATGGGACAGTGAGCTATGGAATGGATGATGCTGATGACATATA
||||| | || | | || | | ||| | | | ||| || |||||| | || || | || |||||| || |||||| | || || || ||||||||| | |||||||| || || || ||||| |||||||||||||| |||||||| | || || |||
---ttttttcaaatgctgaaacttaatttttgtttttatatctgatccttagtaccttcttttttttcttttcttttaaatatggaactttatacaactatagTTCCTAGGAACTTTCGTCTTCTCGAGGAGCTTGAGAGGGGTGAGAAAGGTATCGGCGATGGCACAGTGAGCTATGGCATGGATGACGGCGACGATGTATTMapped 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|27545659|gb|CA763865.2|CA763865EST: GTCCGAGGGATCCGCCGGGGTCGTCGTCG TTCCCAGAAACTTTAGACTGCTTGAAGAGCTTGAGCGAGGTGAGAAGGGCA
genomic: GTCCGAGGGATCCGCCGGGGTCGTCGTCGgtgagtagcc ... atctctgcagTTCCCAGAAACTTTAGACTGCTTGAAGAGCTTGAGCGAGGTGAGAAGGGCA
EST:
gi|88415272|gb|CI586478.1|CI586478EST: GGAGGAGGTGCTCGCGATGGGGTCCGAGGGATCCGCCGGGGTCGTCGTCG TTCCCAGAAACTTTAGACTGCTTGAAGAGCTTGAGCGAGGTGAGAAGGGCA
genomic: GGAGGAGGTGCTCGCGATGGGGTCCGAGGGATCCGCCGGGGTCGTCGTCGgtgagtagcc ... atctctgcagTTCCCAGAAACTTTAGACTGCTTGAAGAGCTTGAGCGAGGTGAGAAGGGCA
EST:
gi|58592031|gb|CF990339.1|CF990339EST: GGGTCCGAGGGATCCG-CGGGGTCGTCGTCG TTCCCAGAAACTTTAGACTGCTTGAAGAGCTTGAGCGAGGTGAGAAGGGCA
genomic: GGGTCCGAGGGATCCGCCGGGGTCGTCGTCGgtgagtagcc ... atctctgcagTTCCCAGAAACTTTAGACTGCTTGAAGAGCTTGAGCGAGGTGAGAAGGGCA
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:
69 (upstream exon),
75 (downstream exon)
Score:
47AGGAAGGAAGGAAGGAAGGAATCGCAAGGCGAAGAGTCGGAGCTGGCGGAGGAGGAGGTGCTCGCGATGGGGTCCGAGGGATCCGCCGGGGTCGTCGTCGgtgagtagcc ... atctctgcagTTCCCAGAAACTTTAGACTGCTTGAAGAGCTTGAGCGAGGTGAGAAGGGCATTGGTGATGGGACAGTGAGCTATGGAATGGATGATGCTGATGACATATA
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caaatctagtaattcatttattgaattctttactgtgctgagtacatctctgcagTTCCCAGAAACTTTAGACTGCTTGAAGAGCTTGAGCGAGGTGAGAAGGGCATTGGTGATGGGACAGTGAGCTATGGAATGGATGATGCTGATGACATATA
catctct CT-rich tract
taattcatttattgaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attcttttttgggatttcaagcctcatgagtagctgcatacagaacaaatctagtaattcatttattgaattctttactgtgctgagtacatctctgcagTTCCCAGAAACTTTAGACTGCTTGAAGAGCTTGAGCGAGGTGAGAAGGGCATTGGTGATGGGACAGTGAGCTATGGAATGGATGATGCTGATGACATATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - -caagcct
- - - - - - - - - - - - - - - - - tgcatac
- - - - - - - - - - - - - - - - - - - - - gaacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgctga