Sequence
atgc intronic sequence ATGC exonic sequence...ggctacaacatttcttttctttctactaggtaatgttagttgtttgtcatatcttgaatagtattcaatcttactatgtgtcatctttttgtttggtcagAGCTTAAAGCATAACCCCAATGGAAGATTTGTCGTAGTTTGTGGAGATGGTGAATTCATAATTTATACTGCATTGGCTTGGAGGAATAGGTCATTTGGAT
Basic information
species | Oryza sativa |
transcript | LOC_Os06g05180.2 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 10
------------------------------------------------------ggctacaacatttcttttctttctac-----taggtaatgttagttgtttgt-catatcttgaatagtattcaatcttactatgtgtcatc-tttttgtttggtcagAGCTTAAAGCATAACCCCAATGGAAGATTTGTCGTAGTTTGTGGAGATGGTGAATTCATAATTTATACTGCATTGGCTTGGAGGAATAGGTCATTTGGAT
| || | | |||| | || | || | ||| ||| | || | || ||| | | | ||||| | | || | || |||||| ||||||||||||| |||||||| || |||||| | || || || || |||||||||||||| | ||||||||||||||| |||| ||||||||||||||||||||||
gtacttttggatgctgatgtgttctttgtattttaaaacttgttactattgtaggtttatagtgtggtttttaagtggacatcttttcgttttattatttggtggtgctcattttgtgtggcgtataatctgattgtgattaattatttttggttggtcagAGCTTGAAGCATAATCCTAATGGACGGTTCGTTGTTGTATGTGGAGATGGTGAGTACATAATTTATACTGCCCTGGCCTGGAGGAATAGGTCATTTGGAT
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 11
ggctacaacatttcttttctttctactaggtaatgttagttg-tttgtcatatcttgaatagtattcaatcttactatgtgtcatctttttgtttggtcagAGCTTAAAGCATAACCCCAATGGAAGATTTGTCGTAGTTTGTGGAGATGGTGAATTCATAATTTATACTGCATTGGCTTGGAGGAATAGGTCATTTGGAT
|| | | | | | || || | | | || | | | || | || | | ||||| | | || || ||| ||||| ||||||||||||| ||||||||||| |||||| | || || || || ||||||||||| || | ||||||||||||||| |||| ||||||||||| |||||||| |
-ccttccctagaccccacccatgcggaagcctctggcaccgggtctgcccttttttcagtaatgtataatctgattgtgagtaatcattttggttggtcagAGCTTGAAGCATAACCCTAATGGACGGTTCGTTGTTGTATGTGGAGATGGCGAGTACATAATTTATACTGCCCTGGCCTGGAGGAATAGATCATTTGGGT
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 11
-------ggctacaacatttcttttctttctactaggtaatgttagttgtttgtcatatcttgaatagtattcaatcttactatgtgtc-atctttttgtttggtcagAGCTTAAAGCATAACCCCAATGGAAGATTTGTCGTAGTTTGTGGAGATGGTGAATTCATAATTTATACTGCATTGGCTTGGAGGAATAGGTCATTTGGAT
| | || || | ||| | | ||| | | || | | |||| | | ||| | || ||| || | || ||| |||| |||||||| || || ||||| || ||||| || || |||||||||||||| | ||| || || ||||||||||| ||||| |||||||||||||| |
agaagtgagttttaaaataatagtccttattgc-gggt----tcaattatcagcaatattt---gttttatgggtggtggctgattgttgatttcatttattgtgcagAATTTAAAGCACAATCCAAATGGGAGGTTTGTTGTTGTATGTGGAGATGGTGAGTACATTATATACACTGCATTGGCATGGAGAAATAGGTCATTTGGTT
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 11
-------ggctacaacatttcttttctttctactaggt-aatgttagttgtttgtcatatcttgaatagtattcaatcttactatgtgtcatctttttgtttggtcagAGCTTAAAGCATAACCCCAATGGAAGATTTGTCGTAGTTTGTGGAGATGGTGAATTCATAATTTATACTGCATTGGCTTGGAGGAATAGGTCATTTGGAT
| | || | | ||| | || | | ||| | | | | || || | || |||| | | | || | || ||| |||| |||||||| || || ||||| || ||||| || || |||||||||||||| | ||| || || ||||||||||| ||||| |||||||||||||| |
agaagtgagttttaaaacaatagtccttattgctggttcaattatcaacaatatttgtttcatgggtggtg-----acttattgt---tgatttaatttgttgtgcagAATTTAAAGCACAATCCAAATGGGAGGTTTGTTGTTGTGTGTGGAGATGGTGAGTACATTATATACACTGCATTGGCATGGAGAAATAGGTCATTTGGTT
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 11
lower sequence: AT3G15980.5 (Arabidopsis thaliana), 3'ss of exon 11
---------------------ggctacaacatttcttttctttctactaggtaatgttagttgtttgtcatatcttgaatagtattcaatcttactatgtgtcatctttttgtttggtcagAGCTTAAAGCATAACCCCAATGGAAGATTTGTCGTAGTTTGTGGAGATGGTGAATTCATAATTTATACTGCATTGGCTTGGAGGAATAGGTCATTTGGAT
| | || | | ||| | | || | | | | || || || ||||| | | | | | | || | | ||||||||| ||||| ||||| ||||| || ||||||||||| || || ||||| || | |||||| || ||||| ||||| |||||
atttgaaatgaagcgttaatagatgataaaaatgaaactctgtttcatatgaagtcccaagagtgtg----gtccagaataattatgtcttgcctcacatatagCTATTCTAACTC-TCAGAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGCGGTGATGGAGAGTACATAATCTACACTGCTTTGGCGTGGAGA----------------
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 11
lower sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 11
---ggctacaacatttcttttctttctactaggtaatgttagt-tgtttgtcatatcttgaatagtattcaatcttactatgtgtcatctttttgtttggtcagAGCTTAAAGCATAACCCCAATGGAAGATTTGTCGTAGTTTGTGGAGATGGTGAATTCATAATTTATACTGCATTGGCTTGGAGGAATAGGTCATTTGGAT
|| ||| || | | ||| | | || | | | || | | | | | | | ||| | |||||| || || | ||||||||| ||||| ||||| ||||| || ||||||||||| ||||| || || |||| ||||| || || || ||||||||||| |||||||||||||| |
aagtgcctcaaagttatgggtatcgctaagccgcgtcttcagaatatatatc-tgttctcacttgatctgtgtctca-tatgtgggtactcttgaatc--tcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGTGGTGACGGAGAATATATAATCTACACGGCTTTGGCTTGGAGAAATAGGTCATTTGGTT
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 11
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 15
ggctac-aacatttcttttctttct-actaggtaatgttagttgtttgtcatatcttgaatagtattcaatcttactatgtgtcatctttttgtttggtcagAGCTTAAAGCATAACCCCAATGGAAGATTTGTCGTAGTTTGTGGAGATGGTGAATTCATAATTTATACTGCATTGGCTTGGAGGAATAGGTCATTTGGAT
||| ||| | | | || | || || || | | | || | || || |||| | | |||||| || ||||||||| ||||| ||||| ||||| || ||||| |||||||||||||||||||| | || || || ||||| ||||| ||| | |||||||||||||| |
--ttactggtattagtaagaaatatgaccttaaatcatttattaattttgtgactacccactgtcatttatgtttctattatttaattttttgctttttcagAGCTTGAAGCACAACCCTAATGGTAGGTTTGTGGTAGTTTGTGGAGATGGTGAGTATATTATCTACACTGCCTTGGCGTGGCGAAATAGGTCATTTGGCT
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 11
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 11
-----ggctacaacatttcttttctttctactaggtaatgttagttgtttgtcatatcttgaatagtattcaatcttactatgtgtcatctttttgtttggtcagAGCTTAAAGCATAACCCCAATGGAAGATTTGTCGTAGTTTGTGGAGATGGTGAATTCATAATTTATACTGCATTGGCTTGGAGGAATAGGTCATTTGGAT
| | || | | ||| | | || | | | | || || || ||||| | | | | | | || | | ||||||||| ||||| ||||| ||||| || ||||||||||| || || ||||| || | |||||| || ||||| ||||| ||||| ||||| || ||||| |
taatagatgataaaaatgaaactctgtttcatatgaagtcccaagagtgtg----gtccagaataattatgtcttgcctcacatatagctattctaactc-tcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGCGGTGATGGAGAGTACATAATCTACACTGCTTTGGCGTGGAGAAATAGATCTTTTGGGT
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 11
------ggctacaacatttcttttctttctactaggtaatgttagttgtttgtcatatcttgaatagtattcaatcttactatgtgtcatctttttgtttggtcagAGCTTAAAGCATAACCCCAATGGAAGATTTGTCGTAGTTTGTGGAGATGGTGAATTCATAATTTATACTGCATTGGCTTGGAGGAATAGGTCATTTGGAT
|||| | | || |||| || | || ||| || |||| || | || || || |||| || | | | | ||||||| | ||||||| |||| |||||||| ||||| || ||||| || ||||||||||||||||| | ||| || ||||| || ||||| |||||||||||||| ||||| |
gcattaagctaggatgaatgattg-tttccacca---tattttaatttattgttat-ttatgtttacatttatttcttccttttttttttttttttgtgtt-tcagAGCCTAAAACATAACCCAAATGGGAGGTTTGTTGTTGTTTGTGGAGATGGTGAGTACATTATATATACAGCTTTGGCATGGAGGAATAGGTCTTTTGGTT
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 11
lower sequence: EFJ36319 (Selaginella moellendorffii), 3'ss of exon 6
ggctacaacatttcttttctttctactaggtaatgttagttgtttgtcatatcttgaatagtattcaatcttactatgtgtcatctttttgtttggtcagAGCTTAAAGCATAACCCCAATGGAAGATTTGTCGTAGTTTGTGGAGATGGTGAATTCATAATTTATACTGCATTGGCTTGGAGGAATAGGTCATTTGGAT
|| ||| ||| | | ||| | | | | || | | | | | | | || |||||| | || |||||||| |||||||||||||| || |||||||| ||||| |||| | |||||| || | | || ||||| || | |||||||||||
----------------------------------gtaagtagttc-tttcgttttgctttctgtgta----taggacattttctgatataatgtgtgcagAGCCTGAAACATAACCCAAATGGAAGATTTGTGGTGGTTTGTGGTGATGGCGAATATACAATTTACACCCCTGTTGCCTGGAGAAACAAGTCATTTGGAT
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 11
lower sequence: EFJ09529 (Selaginella moellendorffii), 3'ss of exon 6
ggctacaacatttcttttctttctactaggtaatgttagttgtttgtcatatcttgaatagtattcaatcttactatgtgtcatctttttgtttggtcagAGCTTAAAGCATAACCCCAATGGAAGATTTGTCGTAGTTTGTGGAGATGGTGAATTCATAATTTATACTGCATTGGCTTGGAGGAATAGGTCATTTGGAT
|||| ||||| | | || | | || |||| | || | | || | | |||||| | || |||||||| |||||||||||||| || |||||||| ||||| |||| | |||||| || | | || ||||| || | |||||||||||
-----------------------------gtaag--tagttctctctcttttttttctgggtatcggacattttctgatataatatgtg--------cagAGCCTGAAACATAACCCAAATGGAAGATTTGTGGTGGTTTGTGGTGATGGGGAATATACAATTTACACCCCTGTTGCCTGGAGAAACAAGTCATTTGGATMapped 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|58609972|gb|CK038005.1|CK038005EST: GATTGCCATTGGCTGTTAAAGAATTAGGAAGTTGTGATCTTTACCCACAG AGCTTAAAGCATAACCCCAATGGAAGATTTGTCGTAGTTTGTGGAGATGGT
genomic: GATTGCCATTGGCTGTTAAAGAATTAGGAAGTTGTGATCTTTACCCACAGgtatttttga ... gtttggtcagAGCTTAAAGCATAACCCCAATGGAAGATTTGTCGTAGTTTGTGGAGATGGT
EST:
gi|29630380|gb|CB635389.1|CB635389EST: GATTGCCATTGGCTGTTAAAGAATTAGGAAGTTGTGATCTTTACCCACAG AGCTTAAAGCATAACCCCAATGGAAGATTTGTCGTAGTTTGTGGAGATGGT
genomic: GATTGCCATTGGCTGTTAAAGAATTAGGAAGTTGTGATCTTTACCCACAGgtatttttga ... gtttggtcagAGCTTAAAGCATAACCCCAATGGAAGATTTGTCGTAGTTTGTGGAGATGGT
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:
75 (upstream exon),
72 (downstream exon)
Score:
51GTTACAGATGGGGAAAGATTGCCATTGGCTGTTAAAGAATTAGGAAGTTGTGATCTTTACCCACAGgtatttttga ... gtttggtcagAGCTTAAAGCATAACCCCAATGGAAGATTTGTCGTAGTTTGTGGAGATGGTGAATTCATAATTTATACTGCATTGGCTTGGAGGAATAGGTCATTTGGAT
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtcatatcttgaatagtattcaatcttactatgtgtcatctttttgtttggtcagAGCTTAAAGCATAACCCCAATGGAAGATTTGTCGTAGTTTGTGGAGATGGTGAATTCATAATTTATACTGCATTGGCTTGGAGGAATAGGTCATTTGGAT
atcttac putative branch site (score: 51)
tcatctttttgttt putative PPT
aatagtatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggctacaacatttcttttctttctactaggtaatgttagttgtttgtcatatcttgaatagtattcaatcttactatgtgtcatctttttgtttggtcagAGCTTAAAGCATAACCCCAATGGAAGATTTGTCGTAGTTTGTGGAGATGGTGAATTCATAATTTATACTGCATTGGCTTGGAGGAATAGGTCATTTGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- -tacaaca
- - - - - - - - - - - - - - - - - - - - tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - -tcttgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctatgtg