Sequence
atgc intronic sequence ATGC exonic sequence...ttaaccccaaataagtctaggtttcatcttcaactaaaatattgtttttttttgcgtgctatcacactctcataatgtaaatcctgttgccatttttcagAGATTAAGCTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATCAACCATATCCTCGTGGAGAAATTTGTGTTAGGGGAACTACGATATTTTTTGG
Basic information
species | Oryza sativa |
transcript | LOC_Os11g04980.1 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os11g04980.2 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G176546_T01 (Zea mays), 3'ss of exon 7
ttaaccccaaataagtctaggtttcatct--tcaactaaaatattgtttttttttgcgtgctatcacactctcataatgtaaatcct---gttgccatttttcagAGATTAAGCTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATCAACCATATCCTCGTGGAGAAATTTGTGTTAGGGGAACTACGATATTTTTTGG
| | || | || | | | | | | |||| |||| | | | ||||| | || |||||| ||| | ||| ||||||| ||||| | || || ||||||||||||||||||||||| || ||||| |||||||| |||||||||||||||||||||||||| ||| ||| ||||| ||
---aatcaaatgacatccatatccaaaataattgggtgtgcctttgtgcttttgtat-tattgtcacagtttcgtaatgtggatctttgtgtttccatttt-cagAGGTGAAACTTGTGGATGTCCCAGAAATGAATTATACATCTGATGATCAACCTTATCCTCGTGGAGAAATTTGTGTTAGAGGACCTATAATATTCCAGGG
upper sequence: LOC_Os11g04980.2 (Oryza sativa), 3'ss of exon 16
lower sequence: GLYMA20G28200.1 (Glycine max), 3'ss of exon 16
---ttaaccccaaataagtctaggtttcatcttcaactaaaatattgtttttttttgcgtgctatcacactctcataatgtaaatcctgttgccatttttcagAGATTAAGCTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATCAACCATATCCTCGTGGAGAAATTTGTGTTAGGGGAACTACGATATTTTTTGG
| ||| || | | | | || | || | ||| | | || | | | | | || | | | |||| | |||||||||| || ||||||||||| ||||||||||| || || ||||| ||||| || |||| ||||| ||||||||||| ||||| | | ||| ||
ctccttttatgaaagaatttaaaagatgaaattatgtttaatttatgtcagctgtagctt--tgttatgc-ctagtgccaacagttttgttcttttgtttcagAGATAAAACTAGTGGATGTTCCAGAAATGAACTATACATCTGATGATCAGCCCAATCCCCGTGGTGAAATTTGTGTCAGGGGTCCCCTTGTTTTTCGAGG
upper sequence: LOC_Os11g04980.2 (Oryza sativa), 3'ss of exon 16
lower sequence: GLYMA10G39540.1 (Glycine max), 3'ss of exon 16
---ttaaccccaaataagtctaggtttcatcttcaactaaaatattgtttttttttgcgtgctatcacactctcataatgtaaatcctgttgccatttttcagAGATTAAGCTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATCAACCATATCCTCGTGGAGAAATTTGTGTTAGGGGAACTACGATATTTTTTGG
|| || || | | | | || | | || | ||| | | | || | || | || | | | |||| | |||||||||| || || |||||||| ||||||||||| || || ||||| ||||| || |||| ||||| ||||||||||| ||||| | | | ||| ||
cactttttatggaagaatttaaaagatgaagttatatttaatttatgtcatctgtagctttcttatgc---ctagtgccaagagttttgttcttttgtttcagAGATAAAACTTGTGGATGTTCCAGAAATGAACTATACATCTGATGATCAGCCCAATCCCCGTGGTGAAATTTGTGTCAGGGGTCCCATTGTTTTTCGGGG
upper sequence: LOC_Os11g04980.2 (Oryza sativa), 3'ss of exon 16
lower sequence: AT5G27600.1 (Arabidopsis thaliana), 3'ss of exon 16
-ttaaccccaaataagtctaggtttcatcttca-actaaaatattgtttttt---tttgcgtgctatcac--actctcataatgtaaatcctgttgccatttttcagAGATTAAGCTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATCAACCATATCCTCGTGGAGAAATTTGTGTTAGGGGAACTACGATATTTTTTGG
| | | | | | || | | | | | ||| |||| | | ||| || | | | | | || || ||| | |||| | || || |||||||| || |||||||||||||| || || ||||||||||| || ||||| ||||| ||||| || ||| | | || || ||
gtaagcaatgtgttattttaaagacagtgtatatatcagaatccaaacttttgtatccaaattgtatgactggtttttgtgttttgaaaatgttttttctttcttagAGGTAAAACTTGTGGATGTTCCCGAAATGAATTACACATCAGACGATCAACCATACCCACGTGGTGAAATCTGTGTAAGAGGACCAATCATCTTCAAAGG
upper sequence: LOC_Os11g04980.2 (Oryza sativa), 3'ss of exon 16
lower sequence: AT3G05970.1 (Arabidopsis thaliana), 3'ss of exon 16
-ttaaccccaaa-taagtcta-ggtttcatcttcaactaaaatattgtttttttttgcgtgctatcacactctcataatgtaaatcctgttgccatttttcagAGATTAAGCTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATCAACCATATCCTCGTGGAGAAATTTGTGTTAGGGGAACTACGATATTTTTTGG
| | | | | | ||| | | | || | || | | | | | | || || | || ||| || | || ||||||| | ||||| |||||||||||||||||||| || || || | |||||| || |||| ||||| ||||| ||||||||||| ||| || ||| ||
gtgagctttttactgactctgcgatatgataagtagagtaatttggaactaaatatccattttaaattgct-ttgggatttaatatgcatttctatatttcagAAGTAAAGCTTGTGGATGTCCCAGAAATGAACTATACATCAGCGGATCAGCCCCATCCCCGTGGCGAAATATGTGTTAGGGGTCCTATCATTTTTACAGG
upper sequence: LOC_Os11g04980.2 (Oryza sativa), 3'ss of exon 16
lower sequence: Vv14s0128g00720.t01 (Vitis vinifera), 3'ss of exon 16
ttaaccccaaataagtctagg----tttcatcttcaactaaaatattgtttttttttgcgtgctatcacactctcataatgtaaatcctgttgccatttttcagAGATTAAGCTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATCAACCATATCCTCGTGGAGAAATTTGTGTTAGGGGAACTACGATATTTTTTGG
| | || || | || | | || ||||||| | | || | | || | | | ||| | | | | || | | ||||||| || ||||| |||||||| || |||||||||||||||||||||||||| || |||||||| || ||||| ||||| ||||| | | || ||
taattgccggatgtctttaagaaaatggtattcacaactaatgaactaattcact--gagttgtgt-ggattctggttgc-tccctgcccttttcctctttcagAAATAAAGCTTGTGGATGTTCCTGAAATGAATTACACCTCTGAGGATCAGCCCTATCCTCGCGGTGAAATATGTGTCAGGGGTCCCGTTCTCTTCCAAGG
upper sequence: LOC_Os11g04980.2 (Oryza sativa), 3'ss of exon 16
lower sequence: Vv05s0020g03080.t01 (Vitis vinifera), 3'ss of exon 16
ttaaccccaaataagtctaggtttcatcttcaactaaaatattgtttttttt-tgcgtgctatcacactctcata---atgtaaatcctgttgccatttttcagAGATTAAGCTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATCAACCATATCCTCGTGGAGAAATTTGTGTTAGGGGAACTACGATATTTTTTGG
| | | || | | | | | |||| | | || || | | ||||| | | | | || || | ||| | | ||||||| | ||||| |||||||| || |||||||| ||||| ||||||||||| || ||||||||||| ||||| |||||| |||| | | | ||| | ||
----aacaagaaaaatgtggctcctgagtacaacaattttctttccattgtggtctgtgctgctctattttgggataaatttatgttaatttgtcctctttcagAAGTGAAGCTTGTGGATGTTCCGGAAATGAACTACACATCTGAGGATCAGCCCTATCCTCGTGGTGAAATCTGTGTTCGGGGTCCCATTCTTTTTCTAGGMapped 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|29679209|gb|CB675484.1|CB675484EST: TTGTGATGATAGGTTAATTGGTCATGTTGGACCTCCAAATCCATCTTGTG AGATTAAGCTAGTGGATGTCCCAGAAATGAAT-ACACCTCT
genomic: TTGTGATGATAGGTTAATTGGTCATGTTGGACCTCCAAATCCATCTTGTGgtaagatctg ... catttttcagAGATTAAGCTAGTGGATGTCCCAGAAATGAATTACACCTCT
EST:
gi|66919239|gb|CX106087.1|CX106087EST: TTGTGATGATAGGTTAA-TGGTCATGTTGGACCTCCAAATCCATCTTGTG AGATTAAGCTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATCAAC
genomic: TTGTGATGATAGGTTAATTGGTCATGTTGGACCTCCAAATCCATCTTGTGgtaagatctg ... catttttcagAGATTAAGCTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATCAAC
EST:
gi|29679207|gb|CB675482.1|CB675482EST: TTGTGATGATAGGTTAATTGGTCATGTTGGACCTCCAAATCCATCTTGTG AGATTAAGCTAGTGGATGTCCCAGAAATGAATTACACCTCTG
genomic: TTGTGATGATAGGTTAATTGGTCATGTTGGACCTCCAAATCCATCTTGTGgtaagatctg ... catttttcagAGATTAAGCTAGTGGATGTCCCAGAAATGAATTACACCTCTG
EST:
gi|58590451|gb|CF988759.1|CF988759EST: TTGTGATGATAGGTTAATTGGTCATGTTGGACCTCCAAATCCATCTTGTG AGATTAAGCTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATCAAC
genomic: TTGTGATGATAGGTTAATTGGTCATGTTGGACCTCCAAATCCATCTTGTGgtaagatctg ... catttttcagAGATTAAGCTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATCAAC
EST:
gi|58595336|gb|CF993644.1|CF993644EST: TTGTGATGATGGGTTAATTGGTCATGTTGGACCTCCAAATCCATCTTGTG AGATTAAGCTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATCAAC
genomic: TTGTGATGATAGGTTAATTGGTCATGTTGGACCTCCAAATCCATCTTGTGgtaagatctg ... catttttcagAGATTAAGCTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATCAAC
EST:
gi|109974356|gb|DT806865.1|DT806865EST: TTGTGATGATAGGTTAATTGGTCATGTTGGACCTCCAAATCCATCTTGTG AGATTAAACTAGTGGATGTCCCAAAAATGAATTACACCTCTGAGGATCAAC
genomic: TTGTGATGATAGGTTAATTGGTCATGTTGGACCTCCAAATCCATCTTGTGgtaagatctg ... catttttcagAGATTAAGCTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATCAAC
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:
45 (upstream exon),
44 (downstream exon)
Score:
12ATTGAAGGATATGGAATGACAGAGACATCCTGTGTCATCGCTACAATGGATTGTGATGATAGGTTAATTGGTCATGTTGGACCTCCAAATCCATCTTGTGgtaagatctg ... catttttcagAGATTAAGCTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATCAACCATATCCTCGTGGAGAAATTTGTGTTAGGGGAACTACGATATTTTTTGG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttttttgcgtgctatcacactctcataatgtaaatcctgttgccatttttcagAGATTAAGCTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATCAACCATATCCTCGTGGAGAAATTTGTGTTAGGGGAACTACGATATTTTTTGG
ccatttttc CT-rich tract
ataatgtaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttaaccccaaataagtctaggtttcatcttcaactaaaatattgtttttttttgcgtgctatcacactctcataatgtaaatcctgttgccatttttcagAGATTAAGCTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATCAACCATATCCTCGTGGAGAAATTTGTGTTAGGGGAACTACGATATTTTTTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - -caaataag
- - - - - - - - - - - - - - - caactaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgttgc