Sequence
atgc intronic sequence ATGC exonic sequencegtgcgttcttgctagtgcaattttccgttcagttattacaagctcggtttggttgtctgtcgagtaggtggccgcctgacataattagcatcgctgatagaggtggttcatgtctacctggcaaaatctgcagGGCTTTGATCCGGAGGCTTTCATCGGTTGACCTGACGGGGCTCTCCCATCAGCAGAAGCTGGCATTCTGGATCAACATCTACAATTCGTGCATGATGAAT
Basic information
species | Oryza sativa |
transcript | LOC_Os09g28850.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os09g28850.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G066516_T01 (Zea mays), 3'ss of exon 4
gtgcgttcttgctagtgcaattttccgttca-gttattacaagctcgg---tttggttgtctgtcgagtaggtggccgcctgacataatta-gcatcgctgatagaggtggttcatgtctacctggcaaaatctgcagGGCTTTGATCCGGAGGCTTTCATCGGTTGACCTGACGGGGCTCTCCCATCAGCAGAAGCTGGCATTCTGGATCAACATCTACAATTCGTGCATGATGAAT
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----------gtgagtgagttgtccgattcgtattgccgcgcgctggtaatttgggctgcctggcgagtgggtggcggtttggcttgaacacgcgtcgcggacgttgatcggggctgtcaac------aaatctgcagGGCCTTGCTGCGGAGGCTGTCGTCGGTTGACCTGGCGGGGCTCTCCCATCAGCAGAAGCTGGCCTTCTGGATCAACGTCTACAATTCCTGCATGATGAAC
upper sequence: LOC_Os09g28850.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA06G04060.1 (Glycine max), 3'ss of exon 6
gtgcgttcttgctagtgcaattttccgttcagttattacaagctcggtttggttgtctgtcgagtaggtggccgcctgaca-taattagcatcgctgatagaggtggttcatgtct--acctggcaaaatctgcagGGCTTTGATCCGGAGGCTTTCATCGGTTGACCTGACGGGGCTCTCCCATCAGCAGAAGCTGGCATTCTGGATCAACATCTACAATTCGTGCATGATGAAT
| ||||| || | | | || | | | | | ||||| | || | | | | | || | | | |||||| |||||| | | | | | || | | || || | | ||| ||| ||| ||||||| || ||||||||||||||||||||||| || |||||||||
---------------------------gtatgttatattcttttcaaactagattactattacattccttttc-cttgacacttatcaaccgtgtcacttagattttacaatattctaatattccaaaatttgcagGCTTCTTCTGAGAAAACTAGCTTGTGTCAACATCGAGAACCTCAACCACCAGGAGAAGCTTGCCTTCTGGATCAACATCTACAATTCATGTATGATGAAT
upper sequence: LOC_Os09g28850.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA17G36350.1 (Glycine max), 3'ss of exon 7
gtgcgttcttgctagtgcaatt-ttccgttcagttattacaagctcggtttggttgtctgtcgagtaggtggccgcctgacataattagcatcgctgatagaggtggttcatgtctacctggcaaaatctgcagGGCTTTGATCCGGAGGCTTTCATCGGTTGACCTGACGGGGCTCTCCCATCAGCAGAAGCTGGCATTCTGGATCAACATCTACAATTCGTGCATGATGAAT-
||| ||| ||| |||| | | ||| ||| || || | | | | || | ||| | | | | || | || | | | | ||||| ||||| | | ||| | | || || || || ||| ||||||| ||||||| ||||||||||||||||||||||||||||| |||||||||
-----------tatgtgagattgttctattca---aattcaaatcatttttacttttccatgacattgat------ttgttgttatttctgtaaattaga-agttaaagtattttgattttggaaaatttgcagaCTACTTTTTAGGAAAGTAGCCTCTGTCAACTTGGAAAACCTCAACCATCAGGAGAAGCTTGCATTCTGGATCAACATCTACAATTCGTGTATGATGAATG
upper sequence: LOC_Os09g28850.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA04G03930.1 (Glycine max), 3'ss of exon 5
gtgcgttcttgctagtgcaattttccgtt-cagttattacaagctcggtttggttgtctgtcgagtaggtggccgcctgacataattagcatcgctgatagaggtggtt-catgtctacctggcaaaatctgcagGGCTTTGATCCGGAGGCTTTCATCGGTTGACCTGACGGGGCTCTCCCATCAGCAGAAGCTGGCATTCTGGATCAACATCTACAATTCGTGCATGATGAAT
| ||| | | || ||| || | || | || | | | | | | | || | | | || || |||| || || | | |||||| |||||| | | | | | || | | || || | | ||| ||| ||| ||||||| || ||||||||||||||||||||||| || |||||||||
----------------------gtatgttatattcttttcaaactagaattcactttcctt----ttccttgacactt---atcaatcgagtcact--tagatgttacaatattctaattttccaaaatttgcagGCTTCTTCTGAGAAAACTAGCCTGTGTCAACATTGAGAACCTCAACCACCAGGAGAAGCTTGCCTTCTGGATCAACATCTACAATTCATGTATGATGAAT
upper sequence: LOC_Os09g28850.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA14G08820.1 (Glycine max), 3'ss of exon 6
gtgcgttcttgctagtgcaatt-ttccgttcagttattacaagctcggtttggttgtctgtcgagtaggtggccgcctgacataattagcatcgctgatagaggtggttcatgtctacctggcaaaatctgcagGGCTTTGATCCGGAGGCTTTCATCGGTTGACCTGACGGGGCTCTCCCATCAGCAGAAGCTGGCATTCTGGATCAACATCTACAATTCGTGCATGATGAAT
| ||| ||| ||| |||| | | ||| | |||| || || | | || || ||| | | | | || | || | | | | |||| ||||| | | ||| || | ||||| || || ||| ||||||| ||||||| ||||||||||||||||||||||| || || |||||||||
----------gtatgtgacattgttctattca---aattcaaatactgtttacttttcaat------gacattaatttgttattatttgtgtaaattgga-agttaaagtattttgattttgggaaatttgcagACTACTTTTTAGGAAACTAGCCTCGGTCAACTTGGAAAACCTCAACCATCAGGAGAAGCTTGCATTCTGGATCAACATCTACAACTCTTGTATGATGAAT
upper sequence: LOC_Os09g28850.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv00s0804g00020.t01 (Vitis vinifera), 3'ss of exon 4
gtgcgttcttgctagtgcaattttccgttcagttattacaagctcggtttggttgtctgtcgagtaggtggccgcctgacataattagcatcgctgatagaggtggttcatgtctacctggcaaaatctgcagGGCTTTGATCCGGAGGCTTTCATCGGTTGACCTGACGGGGCTCTCCCATCAGCAGAAGCTGGCATTCTGGATCAACATCTACAATTCGTGCATGATGAAT
|| ||| | || | | | | || | | || ||||| || | || | | | ||| | | ||| || || || || | |||| |||| | | ||| |||| | | || || | ||| || |||||||||||||||| ||||| ||||| ||||| |||||||| ||||||||||||
gtaagttttat---gtttcttcctatgatttaatacttccagtaatttttggactaaagtaagttttatgttttttcgtctgatttaatacttccaatatttgtatttaccttc--ccattctaaataatcagGCTCCTACTGGGGAAGCTTGCCTGTGTCAACTTAGAGGGTCTTACCCATCAGCAGAAGCTCGCATTTTGGATAAACATATACAATTCCTGCATGATGAAT
upper sequence: LOC_Os09g28850.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv18s0001g11120.t01 (Vitis vinifera), 3'ss of exon 7
gtgcgttcttgctagtgcaattttccgttcagttattacaagctcggtttggttgtctgtcgagtaggtggccgcctgacataattagcatcgctgatagaggtggttcatgtctacctggcaaaatctgcagGGCTTTGATCCGGAGGCTTTCATCGGTTGACCTGACGGGGCTCTCCCATCAGCAGAAGCTGGCATTCTGGATCAACATCTACAATTCGTGCATGATGAAT
|| | | | | |||| |||| | | | | | || | |||| | |||| | | || | |||| || || | | |||| | || ||| ||| | || ||| || | ||| || |||||||| ||||||| || ||||||||||||| ||| ||||| ||||||||||||
----------------------------gtaggtttcttatttttggtt-ggtttcttatttactt--ttaatgcattctataa--atcatc--taacagttata-ttcac-cttatcttcta---ttctcagGCGCCTCCTCGGGAAACTTGCCTCTGTTAACTTACAGGGCCTAACCCATCAGGAGAAGCTTGCTTTCTGGATCAACACCTATAATTCCTGCATGATGAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acataattagcatcgctgatagaggtggttcatgtctacctggcaaaatctgcagGGCTTTGATCCGGAGGCTTTCATCGGTTGACCTGACGGGGCTCTCCCATCAGCAGAAGCTGGCATTCTGGATCAACATCTACAATTCGTGCATGATGAAT
aaaatct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgcgttcttgctagtgcaattttccgttcagttattacaagctcggtttggttgtctgtcgagtaggtggccgcctgacataattagcatcgctgatagaggtggttcatgtctacctggcaaaatctgcagGGCTTTGATCCGGAGGCTTTCATCGGTTGACCTGACGGGGCTCTCCCATCAGCAGAAGCTGGCATTCTGGATCAACATCTACAATTCGTGCATGATGAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG