Sequence
atgc intronic sequence ATGC exonic sequence...ttgctttggtcatttggactgctatatgtattttatggaccttaagttcatcaccaatgatctcattgtaaacaaaatcttatatgactttgccccccagGAATTACGATAGCTGAGTATTACCGTGACATGGGTTACAATGTCAGCATGATGGCTGATTCCACCTCACGATGGGCTGAGGCATTGCGTGAAATTTCTGG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g07870.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g07870.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G421857_T02 (Zea mays), 3'ss of exon 11
----ttgctttggtcatttggactgctatatgtattttatggaccttaagttcatcaccaatgatctcattgtaaacaaaatcttatatgactttgccccccagGAATTACGATAGCTGAGTATTACCGTGACATGGGTTACAATGTCAGCATGATGGCTGATTCCACCTCACGATGGGCTGAGGCATTGCGTGAAATTTCTGG
|| | || || | || | ||||||| | | | | ||| || | | ||| | || || || ||| | |||||||||| || |||||||||| |||||| ||||| ||||| ||||| ||||||||||| |||||||| || |||||||||||||||||||| || || ||
tgatatgggtgcctctttcagtttgtcagctgtatttc---tgcttgtcgcttttcagtgcagagtttctgttaacaatcatgttgtacc-ttttttaactcagGAATTACAATTGCTGAGTATTTCCGTGATATGGGCTACAACGTCAGTATGATGGCTGACTCCACCTCCCGGTGGGCTGAGGCATTGCGTGAGATCTCAGG
upper sequence: LOC_Os02g07870.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G128877_T03 (Zea mays), 3'ss of exon 8
-ttgctttggt-catttggactgctatatgtattttatggaccttaagttcatcaccaatgatctcattgtaaacaaaatcttatatgactttgccccccagGAATTACGATAGCTGAGTATTACCGTGACATGGGTTACAATGTCAGCATGATGGCTGATTCCACCTCACGATGGGCTGAGGCATTGCGTGAAATTTCTGG
| | ||| | | || | || | || | | | | | | | || || | | ||| | || || || |||| ||| |||||||||| || || ||||||| ||||| ||||| ||||| || || ||||||||||| ||||||||||||||||||||||| |||||||| || || ||
atgatatgggtgcctctgtccatctgtcagttgtatctctgcttgtcgctgttcggtgtggagtttctgttaacaatcatattgtac--ctttttcccgcagGAATTACAATTGCCGAGTATTTTCGTGATATGGGCTACAACGTTAGTATGATGGCTGACTCCACCTCACGATGGGCTGAGGCTTTGCGTGAGATCTCAGG
upper sequence: LOC_Os02g07870.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA07G00430.1 (Glycine max), 3'ss of exon 12
ttgctttggtcatttggactgctatatgtattttatggaccttaagttcatcaccaatgatctcattgtaaacaa-aatcttatatgactttgccccccagGAATTACGATAGCTGAGTATTACCGTGACATGGGTTACAATGTCAGCATGATGGCTGATTCCACCTCACGATGGGCTGAGGCATTGCGTGAAATTTCTGG
| | | || || | || | || |||| | | ||| | ||| | | | | || || | ||| | || |||| ||||||| || |||||||||||| | || |||||||| |||||||| |||||||| ||||| || || ||||||| || |||||||||||||| |||||
atcatattttcccttataatgattaataaatttgtttggcctgtgctgcatgag-agttttaacactgattttgataatgtaattcttttttgaattgcagGAATCACATTAGCTGAGTATTTTAGAGATATGGGTTATAATGTCAGTATGATGGCAGATTCTACATCTAGATGGGCAGAAGCATTGCGTGAAATCTCTGG
upper sequence: LOC_Os02g07870.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA08G23990.1 (Glycine max), 3'ss of exon 12
ttgctttggtcatttggactgctatatgtattttatggaccttaagttcatcaccaatgatctcattg---taaacaaaatcttatatgactttgccccccagGAATTACGATAGCTGAGTATTACCGTGACATGGGTTACAATGTCAGCATGATGGCTGATTCCACCTCACGATGGGCTGAGGCATTGCGTGAAATTTCTGG
| || | | || | || | ||| ||| | || ||| | | | | | | | || || | | || || || | ||| ||||||| || |||||||||||| | | || |||||||| |||||||| |||||||| ||||| || || ||||||| || |||||||||||||| |||||
-tatatttgcc-cttaaaatgattaatgaattgtttg-accgtgtgctgcttgagagttttaacactgattttgataatatatttcttttttttcaattgcagGAATCACATTAGCTGAGTATTTCAGAGATATGGGTTATAATGTCAGTATGATGGCAGATTCTACATCTAGATGGGCAGAAGCATTGCGTGAAATCTCTGG
upper sequence: LOC_Os02g07870.1 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv04s0008g02580.t01 (Vitis vinifera), 3'ss of exon 12
-ttgctttggtca-tttggactgctatat--gtattttatggaccttaagttcatcaccaatgatctcattgtaaacaaaatcttatatgactttgccccccagGAATTACGATAGCTGAGTATTACCGTGACATGGGTTACAATGTCAGCATGATGGCTGATTCCACCTCACGATGGGCTGAGGCATTGCGTGAAATTTCTGG
|| | ||||| ||| || | | ||||| | || | | | | || || ||||| || ||| |||| || || || || || || | | |||||||||||||||||||| |||||||| ||||| || || || ||||||||||| |||||||| || |||||
tttccattggtagcttttttttggtgaagcaacatttttccaagttttgtatatttattcaaaattattttctaaaccaatgtgatcatgg----aatgttcagGTATCACAATTGCCGAATACTTTAGAGACATGGGTTACAATGTCAGTATGATGGCAGATTCAACATCTCGTTGGGCTGAGGCTTTGCGTGAGATATCTGG
upper sequence: LOC_Os02g07870.1 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 12
ttgctttggtcatttggactgctatatgtattttatggaccttaagttcatcaccaatgatctcattgtaaacaaaatcttatatgactttg--ccccccagGAATTACGATAGCTGAGTATTACCGTGACATGGGTTACAATGTCAGCATGATGGCTGATTCCACCTCACGATGGGCTGAGGCATTGCGTGAAATTTCTGG
|| | || | | | | | | | || | || || | || | | | || |||||| | || |||| || || |||||||| || | | | || ||||| |||||||| || |||||||| ||||| || || |||||||| ||||||||||| ||||| || ||
--cctgaagcttttagtggtcttgtctatcacctttgtgttaccttgttatggaaggtgctgagatgatgttctccaactaatatgattgtgggtttttcagGTATCACTATAGCTGAATACTTCAGAGATATGGGCTACAATGTTAGTATGATGGCAGATTCAACATCTCGATGGGCAGAGGCATTGCGAGAAATATCAGG
upper sequence: LOC_Os02g07870.1 (Oryza sativa), 3'ss of exon 11
lower sequence: PP1S8_312V6.1 (Physcomitrella patens), 3'ss of exon 12
----------------------------ttgctttg-gtcatttgga-ctgctatatgtattttatggaccttaagttc-atcaccaatgatctcat-tgtaaacaaaatctt----atatgactttgccccccagGAATTACGATAGCTGAGTATTACCGTGACATGGGTTACAATGTCAGCATGATGGCTGATTCCACCTCACGATGGGCTGAGGCATTGCGTGAAATTTCTGG
|| || | | | || | | | || ||| | || | | ||| |||||| ||| | || || | || || |||| || || | || || || | | | || ||||||||||||||||| |||||||| || || || || || ||||||||||| | ||||| ||||||||
gttattttcttttcttctgagactctactttctaggtgctgtatgaaaccatttcatcctctttggatgtttgaaatgctatcctgtatgatcgcatacttccgcatcattatgcaaatgctgtttcctgttgcagGTATCACTTTGGCAGAATACTTCAGGGATATGGGTTACAATGTCAGTATGATGGCAGACTCTACATCTCGCTGGGCTGAGGCGCTTCGTGAGATTTCTGG
upper sequence: LOC_Os02g07870.1 (Oryza sativa), 3'ss of exon 11
lower sequence: EFJ33015 (Selaginella moellendorffii), 3'ss of exon 11
ttgctttggtcatttggactgctatatgtattttatggaccttaagttcatcaccaatgatctcattgtaaacaaaatcttatatgactttgccccccagGAATTACGATAGCTGAGTATTACCGTGACATGGGTTACAATGTCAGCATGATGGCTGATTCCACCTCACGATGGGCTGAGGCATTGCGTGAAATTTCTGG
|||| | | | |||| || | || ||| || | ||| || |||| ||||| | |||||||||| |||||||||||| || |||||||| ||||||||||| || || || ||||||| || || ||||||||||| || ||
--------------------------------gtatgtccttccaattcaggctcagcg--ctgatttta----------tcgatggttt-------cagGCATTACTCTGGCTGAGTATTTCCGTGACATGGGCTATAATGTCAGTATGATGGCTGACTCGACGTCGAGATGGGCCGAAGCCTTGCGTGAAATATCCGG
upper sequence: LOC_Os02g07870.1 (Oryza sativa), 3'ss of exon 11
lower sequence: EFJ30330 (Selaginella moellendorffii), 3'ss of exon 12
ttgctttggtcatttggactgctatatgtattttatggaccttaagttcatcaccaatgatctcattgtaaacaaaatcttatatgactttgccccccagGAATTACGATAGCTGAGTATTACCGTGACATGGGTTACAATGTCAGCATGATGGCTGATTCCACCTCACGATGGGCTGAGGCATTGCGTGAAATTTCTGG
|||| | | | |||| ||| | || ||| || | ||| || |||| ||||| | |||||||||| |||||||||||| || |||||||| ||||||||||| || || || ||||||| || || ||||||||||| || ||
--------------------------------gtatgtccttccaattcaggctcaacg--ctgatttta----------tcgatggttt-------cagGCATTACTCTGGCTGAGTATTTCCGTGACATGGGCTATAATGTCAGTATGATGGCTGACTCGACGTCGAGATGGGCCGAAGCCTTGCGTGAAATATCCGGMapped 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|58660984|gb|CK049664.1|CK049664EST: TAACACATCCAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTATACAG GAATTACGATAGCTGAGTATTACCGTGACATGGGTTACAATGTCAGCATGA
genomic: TAACACATCCAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTATACAGgtaatggtgt ... tgccccccagGAATTACGATAGCTGAGTATTACCGTGACATGGGTTACAATGTCAGCATGA
EST:
gi|58653094|gb|CK041774.1|CK041774EST: TAACACATCCAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTATACAG GAATTACGATAGCTGAGTATTACCGTGACATGGGTTACAATGTCAGCATGA
genomic: TAACACATCCAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTATACAGgtaatggtgt ... tgccccccagGAATTACGATAGCTGAGTATTACCGTGACATGGGTTACAATGTCAGCATGA
EST:
gi|58674416|gb|CK063102.1|CK063102EST: TAACACATCCAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTATACAG GAATTACGATAGCTGAGTATTACCGTGACATGGGTTACAATGTCAGCATGA
genomic: TAACACATCCAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTATACAGgtaatggtgt ... tgccccccagGAATTACGATAGCTGAGTATTACCGTGACATGGGTTACAATGTCAGCATGA
EST:
gi|27547953|gb|CA765929.2|CA765929EST: AACGCATCCAACATGCCTGTCGCTGCTCGNGAAAGCTTNCATTTTT-CAG GNATTACGATAGCTGNGT-TTANCGGGACATGGGT
genomic: AACACATCCAACATGCCTGTCGCTGCTCGTGAA-GCTTCCATTTATACAGgtaatggtgt ... tgccccccagGAATTACGATAGCTGAGTATTACCGTGACATGGGT
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:
72 (upstream exon),
71 (downstream exon)
Score:
15ACAGAGGATGGACGTGAAGAGTCTGTGATGAAGAGAACAACACTGGTGGCTAACACATCCAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTATACAGgtaatggtgt ... tgccccccagGAATTACGATAGCTGAGTATTACCGTGACATGGGTTACAATGTCAGCATGATGGCTGATTCCACCTCACGATGGGCTGAGGCATTGCGTGAAATTTCTGG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttcatcaccaatgatctcattgtaaacaaaatcttatatgactttgccccccagGAATTACGATAGCTGAGTATTACCGTGACATGGGTTACAATGTCAGCATGATGGCTGATTCCACCTCACGATGGGCTGAGGCATTGCGTGAAATTTCTGG
ctttgcccccc CT-rich tract
attgtaaacaaaatct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgctttggtcatttggactgctatatgtattttatggaccttaagttcatcaccaatgatctcattgtaaacaaaatcttatatgactttgccccccagGAATTACGATAGCTGAGTATTACCGTGACATGGGTTACAATGTCAGCATGATGGCTGATTCCACCTCACGATGGGCTGAGGCATTGCGTGAAATTTCTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
-tgctttg
- - - - -tcatttg
- - - - - - - - gactgct
- - - - - - - - - - - - tatgtat
- - - - - - - - - - - - - - - - - - - - - - -gttcatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaacaaa