Sequence
atgc intronic sequence ATGC exonic sequence...taaggaacatgattttgtatttagtatctattgttgagactgtaactgtctggaaatttccccattctgatgtgtttattctaaagatacccaattgcagAAAATGCCAAAGAGGAAGACTGACAGAGCACATGTACTAGACAAGAAAAAACATCTCTCAAGGCTAAATGTGAAGGAGGCAGGAAAGGTCCTGTTGAAAC
Basic information
species | Oryza sativa |
transcript | LOC_Os07g19470.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g19470.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G099547_T04 (Zea mays), 3'ss of exon 1
taaggaacatgattttgtatttagtatc--tattgttgagactgtaactgtctggaaattt-ccccattctgatgtgtttattctaaagatacccaattgcagAAAATGCCAAAGAGGAAGACTGACAGAGCACATGTACTAGACAAGAAAAAACATCTCTCAAGGCTAAATGTGAAGGAGGCAGGAAAGGTCCTGTTGAAAC
| || || |||| || |||| ||| | | || | | | | |||||||||| ||||| |||| ||||||||||||||||||||||||| ||| | |||||||||||||||||||| |||||||| || ||||| |||||||||||||| |||||||||||||| || |||||||||
--tgctac-tgtttttttaggaagtactagtataaacaattcgagaatgatttttttgtatattccattctgatatgtttgttctgaagatacccaattgcagAAAATGCCCAAGCGAAAGACTGACAGAGCACATGTTTTAGACAAGGCTAAGCATCTTTCAAGGCTAAATGTTAAGGAGGCAGGAAAAGTAATGTTGAAAC
upper sequence: LOC_Os07g19470.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G099547_T05 (Zea mays), 3'ss of exon 1
-------taaggaacatgattttgtatttagtatctattgttg-agactgtaactgtctggaaatttc------cccattctgatgtgtttattctaaagatacccaattgcagAAAATGCCAAAGAGGAAGACTGACAGAGCACATGTACTAGACAAGAAAAAACATCTCTCAAGGCTAAATGTGAAGGAGGCAGGAAAGGTCCTGTTGAAAC
|| | | | | | | ||||| | || | | | || | | || ||| |||||||||| ||||| |||| ||||||||||||||||||||||||| ||| | |||||||||||||||||||| |||||||| || ||||| |||||||||||||| ||||||||||||||
gtgtcactaggaattgctactgtttttttaggaagtactagtataaacaattcgagaatgatttttttgtatattccattctgatatgtttgttctgaagATACCCAATTGCAGAAAATGCCCAAGCGAAAGACTGACAGAGCACATGTTTTAGACAAGGCTAAGCATCTTTCAAGGCTAAATGTTAAGGAGGCAGGAAA--------------
upper sequence: LOC_Os07g19470.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA20G39320.3 (Glycine max), 3'ss of exon 1
taaggaacatgattttgtatttagtatctattgttgagactgtaactgtctggaaatttccccattctgatgtgtttattctaaagatacccaattgcagAAAATGCCAAAGAGGAAGACTGACAGAGCACATGTACTAGACAAGAAAAAACATCTCTCAAGGCTAAATGTGAAGGAGGCAGGAAAGGTCCTGTTGAAAC
| ||| | | | | ||| || || || | || || |||| | || | || | |||||||||||||||||||||||| || ||||| || |||| ||| ||||||| ||||||| |||||||| | || | || ||||||| | || ||
------------gtatgtgtgtgatgtg-attattctgaatgaatgaatccctaa---tccctaatcccct---cttgtctcgcagATACCCAATTGCAGAAAATGCCTAAAAGGAAAACCGACAAAGCTTATGTACTGGACAAGAGCAAACATCTGGCCAGATTGAACATGAAGGAAGGCGGGAA--------------
upper sequence: LOC_Os07g19470.2 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv17s0000g01530.t01 (Vitis vinifera), 3'ss of exon 1
---taaggaacatgattttgtat---ttagt--atctattgttgagactgt----aactgtctgga-aatttccccattctgatgtgtttattcta-aagatacccaattgcagAAAATGCCAAAGAGGAAGACTGACAGAGCACATGTACTAGACAAGAAAAAACATCTCTCAAGGCTAAATGTGAAGGAGGCAGGAAAGGTCCTGTTGAAAC
| || | |||||| ||| | | ||| | | | | || || | | || || ||| || | | ||| || || |||||||||||||||||||| |||| |||||||| ||||||||| | |||| | ||||| | || ||||| ||||||||||| | || || ||||||||
tttttagctattactttttgtgcaaacgagttcaacagttgctaaagcattcctcaatggtgtaaacaaattagtcatactaaaatattttttttataagATACCCAATTGCAGAAAGTGCCTAAGAGGAAAACTGACAGATCTTATGTGTTGGACAAAACGAAGCATCTTGCAAGGCTAAATATCAATGAAGCAGGAAA--------------
upper sequence: LOC_Os07g19470.2 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S121_20V6.1 (Physcomitrella patens), 3'ss of exon 1
----------------taaggaacatgattttgtatttagtatctattgttgagactgtaactgtctggaaatttccccattctgatgtgtttattctaaagatacccaattgcagAAAATGCCAAAGAGGAAGACTGACAGAGCACATGTACTAGACAAGAAAAAACATCTCTCAAGGCTAAATGTGAAGGAGGCAGGAAAGGTCCTGTTGAAAC
| |||| | | ||| || || ||| ||| | || | | | | | | | | | || | | |||||| || ||||||||||||| |||||||| || ||||||||| ||||| | || || || || ||| | || ||||| ||||| || ||
atttgcatataagcgttgtggaatacaaaaatgtcgtt-gtgcgtat-gttctcgttttaggttttagcagacgtgacggtagcgtcaatttggtcttgcagATACTCAGCTGCAGAAAATGCCTAAGAGGAAAACCGACAGAGCATATGTATTGGATCGTAACAAGCACCTCAGCCGACTTAATGTTGTAGAGGCTGGCAA-------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgtctggaaatttccccattctgatgtgtttattctaaagatacccaattgcagAAAATGCCAAAGAGGAAGACTGACAGAGCACATGTACTAGACAAGAAAAAACATCTCTCAAGGCTAAATGTGAAGGAGGCAGGAAAGGTCCTGTTGAAAC
ttctaaa putative branch site (score: 2)
tttattctaaagata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taaggaacatgattttgtatttagtatctattgttgagactgtaactgtctggaaatttccccattctgatgtgtttattctaaagatacccaattgcagAAAATGCCAAAGAGGAAGACTGACAGAGCACATGTACTAGACAAGAAAAAACATCTCTCAAGGCTAAATGTGAAGGAGGCAGGAAAGGTCCTGTTGAAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - acatgat
- - - - - - - - - - - - - - - ttgttga
- - - - - - - - - - - - - - - - - - - - - - - tgtctgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtgttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaagatac