Sequence
atgc intronic sequence ATGC exonic sequence...ggctacaacatttcttttctttctactaggtaatgttagttgtttgtcatatcttgaatagtattcaatcttactatgtgtcatctttttgtttggtcagAGCTTAAAGCATAACCCCAATGGAAGATTTGTCGTAGTTTGTGGAGATGGTGAATTCATAATTTATACTGCATTGGCTTGGAGGAATAGGTCATTTGGAT
Basic information
species | Oryza sativa |
transcript | LOC_Os06g05180.1 |
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
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtcatatcttgaatagtattcaatcttactatgtgtcatctttttgtttggtcagAGCTTAAAGCATAACCCCAATGGAAGATTTGTCGTAGTTTGTGGAGATGGTGAATTCATAATTTATACTGCATTGGCTTGGAGGAATAGGTCATTTGGAT
atcttac putative branch site (score: 3)
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