Sequence
atgc intronic sequence ATGC exonic sequencegtaagtagctttcctcaactctacagtacaattcttgtacaaaatgttgcccttgtcatttatttactttctatgcttttagctgctacactgttgtggtttatgtgcagTGATGTCTTCAAATGATGCTATGGGTACAGTTTTTAAGTGTTTGTCAAAGGGCGCTGTTGACTTCTTAGTCAAGCCCATACGTAAGAATGAACTTAAGAA
Basic information
species | Oryza sativa |
transcript | LOC_Os07g49460.3 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g49460.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G033962_T01 (Zea mays), 3'ss of exon 2
gtaagtagctttcctcaactc--tacagtacaattcttgtacaaaatgttgcccttgtcatttatttactttctatgcttttagctgctacactgttgtggtttatgtgcagTGATGTCTTCAAATGATGCTATGGGTACAGTTTTTAAGTGTTTGTCAAAGGGCGCTGTTGACTTCTTAGTCAAGCCCATACGTAAGAATGAACTTAAGAA
||||||| |||||||| | | ||| || || || ||||||||||| | | ||||||||| || | ||||||||||||||||||| | |||||||| ||||||||||||||||| | ||||| |||| ||||||| ||||| ||| ||||||| || ||||||||||| || |||||||| |||||||||||||||||||||||
gtaagtaactttcctctgtacagtgtagttcatatcatgatcaaaatgttgctttcttgatttatttagttccaatgcttttagctgctacaccgatgtggtttttgtgcagTGATGTCTTCGAGTGATGATATGAGTACAGTCTTTAAATGTCTGTCAAAAGGTGCTGTTGACTTTTTGGTCAAGCCTATACGTAAGAATGAACTTAAGAA
upper sequence: LOC_Os07g49460.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G005732_T02 (Zea mays), 3'ss of exon 2
gtaagtagctttc--ctcaactctacagtacaattcttgtacaaaatgttgcccttgtcatttatttactttctatgcttttagctgctacactgttgtggtttatgtgcagTGATGTCTTCAAATGATGCTATGGGTACAGTTTTTAAGTGTTTGTCAAAGGGCGCTGTTGACTTCTTAGTCAAGCCCATACGTAAGAATGAACTTAAGAA
||||||| ||||| ||| || | ||| || || || |||||||||| | ||||||||||| | | ||||||||||||||||||||| ||| |||| ||||||||||||||||| | |||||||||| ||||||| ||||| ||||||||||| || ||||||||||| ||||||||||| |||||||||||||||||||||||
gtaagtaactttcatctctacagtgtagttcatatcatgattaaaatgttgctttcatcatttatttagtcccaatgcttttagctgctacactgatgttgtttgtgtgcagTGATGTCTTCGAGTGATGCTATGAGTACAGTCTTTAAATGTTTGTCAAAAGGTGCTGTTGACTTTTTAGTCAAGCCTATACGTAAGAATGAACTTAAGAA
upper sequence: LOC_Os07g49460.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA11G15580.1 (Glycine max), 3'ss of exon 3
gtaagtagctttcctcaactctacagtacaattcttgtacaaa-atgttgcccttgtcatttatttactttctatgcttttagctgctacactgttgtggtttatgtgcagTGATGTCTTCAAATGATGCTATGGGTACAGTTTTTAAGTGTTTGTCAAAGGGCGCTGTTGACTTCTTAGTCAAGCCCATACGTAAGAATGAACTTAAGAA
|||||| || | || | | ||| | | | | || | || || | || | || | | | | | | || ||| ||| |||| | ||| |||||||||| || ||||| ||||||||| ||| ||||||||||||||||| ||||| ||||| || ||||| || || || || | |||||||||||| ||
gtaagtggcgtaccaaagttatactttttactaaatttaagtatatattttcaatgactattgctcatgtggtgttttgtttattgc-aca-tgttcaaatgcatg--cagTGATGTCATCTCATGATTCTATGGGTATAGTCTTTAAGTGTTTGTCAAAAGGCGCAGTTGATTTTTTAGTGAAACCAATTCGGAGGAATGAACTTAAAAA
upper sequence: LOC_Os07g49460.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA13G19870.1 (Glycine max), 3'ss of exon 2
gtaagtagctttcctcaactctacagtacaattcttgtacaaaatgt----tgcccttgtcatt-tatttactttctatgcttttagctgctacactgttgtggtttatgtgcagTGATGTCTTCAAATGATGCTATGGGTACAGTTTTTAAGTGTTTGTCAAAGGGCGCTGTTGACTTCTTAGTCAAGCCCATACGTAAGAATGAACTTAAGAA
||| ||| | | || || || || | | || | | | | | |||| | | | | ||| ||||| || || || | || | |||||||||||| || ||||| |||||||| ||| |||||||||||||||||||| ||||||||||| |||| || |||||||| |||||||| ||||| ||
----gtaagttttccaagtgcttatatatgtttgttttgaagcatttctttttctcatctcatgatgtaaaatagctactcttttgtatggctt-ctaatgggattggtctgcagTGATGTCATCTCATGATTCTATGGGTTTAGTCTTTAAGTGTTTGTCAAAGGGTGCTGTTGACTTTCTAGTTAAACCCATACGGAAGAATGAGCTTAAAAA
upper sequence: LOC_Os07g49460.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA12G07860.1 (Glycine max), 3'ss of exon 2
gtaagtagctttcctcaactctacagtacaattcttgtacaaaatgttgcccttgtcatttatttactttctatgcttttagctgctacactgttgtggtttatgtgcagTGATGTCTTCAAATGATGCTATGGGTACAGTTTTTAAGTGTTTGTCAAAGGGCGCTGTTGACTTCTTAGTCAAGCCCATACGTAAGAATGAACTTAAGAA
||||| || | || || || | | | | | || | | |||| | | |||| | | ||| | | || |||||||||||| || ||||| ||||||||| ||| ||||||||||||||||| || || ||||| || ||||| || || || || | |||||||||||| ||
gtaagcggcatacc--aaagttatactctgttccaaatttaagtatatattttcaatgactattgctcatgtggtgttttgtttattgcac-atgttcaaatacatgcagTGATGTCATCTCATGATTCTATGGGTATAGTCTTTAAGTGTTTGTCAAAAGGTGCAGTTGATTTTTTAGTGAAACCTATTCGGAGGAATGAACTTAAAAA
upper sequence: LOC_Os07g49460.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA10G05520.1 (Glycine max), 3'ss of exon 2
gtaagtagctttcctcaactctacagtacaattcttgtacaaaatgttgcccttgtcatttatttactttcta-----tgcttttagctgctaca-ctgttgtggtttatgtgcagTGATGTCTTCAAATGATGCTATGGGTACAGTTTTTAAGTGTTTGTCAAAGGGCGCTGTTGACTTCTTAGTCAAGCCCATACGTAAGAATGAACTTAAGAA
||| ||| ||||| | || | | | || || || | || | | || | || || || | || || | || | |||||||||||| || ||||| |||||||| ||| |||||||||||||||||||| ||||||||||| |||| || |||||||| |||||||| ||||| ||
----gtaagtttttccaactgctta-tatatgtttggtttgaagcatttctttttctcatctcatgctgcaagagagctactcttttctatggcttctaatgggattggtctgcagTGATGTCATCTCATGATTCTATGGGTTTAGTCTTTAAGTGTTTGTCAAAGGGTGCTGTTGACTTTCTAGTTAAACCCATACGGAAGAATGAGCTTAAAAA
upper sequence: LOC_Os07g49460.3 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv13s0067g03390.t01 (Vitis vinifera), 3'ss of exon 2
gtaagtagctttcctcaac--tctacagtacaattcttgtacaaaatgttgcccttgtcatttatttactttctatgcttttagctgctacac-tgttgtggtttatgtgcagTGATGTCTTCAAATGATGCTATGGGTACAGTTTTTAAGTGTTTGTCAAAGGGCGCTGTTGACTTCTTAGTCAAGCCCATACGTAAGAATGAACTTAAGAA
|| |||| |||| ||| | |||| | | | | | ||| |||| |||| | | || || |||||| |||| ||| || || | ||| |||||||||||||| || ||||| || |||| | ||| ||||| |||||||||||||| || |||||||| || || ||||| || || || ||||| ||||| ||
gtgagtattattccaaaacgctttacatgcctaagtatttctctttttctgcaattgttatttttatcaaatcaatacttttaattgcttcacctgatgagttttgtgtgcagTGATGTCATCCCATGATTCTGTGGGCATAGTCTTTAAATGTTTGTCAAAGGGTGCAGTTGACTTTTTTGTGAAGCCTATTCGAAAAAATGAGCTTAAAAA
upper sequence: LOC_Os07g49460.3 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv06s0004g03650.t01 (Vitis vinifera), 3'ss of exon 2
gtaagtagctttcctcaactctacagtacaattcttgtacaaaatgt-tgcccttgtcatttatttactttctatgcttttagctgctacactgttgtggtttatgtgcagTGATGTCTTCAAATGATGCTATGGGTACAGTTTTTAAGTGTTTGTCAAAGGGCGCTGTTGACTTCTTAGTCAAGCCCATACGTAAGAATGAACTTAAGAA
||||||| | || | | | || | || | || | | | | ||| | | || |||| || | | | || ||| | ||| | |||||||||||| || ||||| ||||||||| ||| ||||||||| |||| ||||| || ||||| || || || || || || || |||||||||||||| ||
gtaagtatcattt-tagtgttttcattttcatagaaatttaaggcttattttcctatcactcttgctgatttgatgcattgaatttccaccctgacgatctttttatgcagTGATGTCATCCCATGATTCTATGGGTATAGTCTTTAAGTGTCTGTCCAAGGGTGCAGTTGATTTTTTGGTGAAACCTATTCGAAAGAATGAACTTAAAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatttatttactttctatgcttttagctgctacactgttgtggtttatgtgcagTGATGTCTTCAAATGATGCTATGGGTACAGTTTTTAAGTGTTTGTCAAAGGGCGCTGTTGACTTCTTAGTCAAGCCCATACGTAAGAATGAACTTAAGAA
tatttactttctat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtagctttcctcaactctacagtacaattcttgtacaaaatgttgcccttgtcatttatttactttctatgcttttagctgctacactgttgtggtttatgtgcagTGATGTCTTCAAATGATGCTATGGGTACAGTTTTTAAGTGTTTGTCAAAGGGCGCTGTTGACTTCTTAGTCAAGCCCATACGTAAGAATGAACTTAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT