Sequence
atgc intronic sequence ATGC exonic sequencegtagcttcaatttattcttctcctcctctttatggtcatatcgtttattagatatgtatggtgcattggtgctgactgttagtttgattctggagggactagggtatgtcagatttgagctagacatatcaggattcagattgtttggatatatcaactgatatctgtcttcttattgattctttttaacaacattcagGCTCTAAACATGGTCTGCTGCTGGGCGGAAGATCCCAATTCAGACGCATTCAAGCAGCATCTTGCGAGAGTACCTGATTTCTTGTGGCTTTCAGAAGATG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g04750.3 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g04750.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G468929_T01 (Zea mays), 3'ss of exon 6
gtagcttcaatttattcttctcctcctctttatggtcatatcgtttattagatatgtatggtgcattggtgctgactgttagtttgattctggagggactagggtatgtcagatttgagctagacatatcaggat-tcagattgtttggatatatcaactgatatctgtcttcttattgattctttttaacaacattcagGCTCTAAACATGGTCTGCTGCTGGGCGGAAGATCCCAATTCAGACGCATTCAAGCAGCATCTTGCGAGAGTACCTGATTTCTTGTGGCTTTCAGAAGATG
| | || || | || | | | | | | || | || || ||| || | || || ||| | | | | | | ||| || || | | ||| | | | ||| || || | | | || | | || || ||| ||| ||| | || || ||||||||||||||||||||||| |||||||| |||||||||||||||||| |||||||| || ||||||||||||||||||| ||||||||||
-----gtaatattgttgaggcctcactgtctgcacttgaactatatgc---atgggcattttgtcctgg--cttggtcttgtttctattatt-atgttccatgatatagcatatgaactattgtcatgtttgtttgtcatatctttgtggtctgattcttggtttttg--ttaagattaattaattt----gatgtttagATTCTAAACATGGTCTGCTGCTGGGTAGAAGATCCAAATTCAGACGCATTCAAGTGTCATCTTGCAAGGATACCTGATTTCTTGTGGCTCTCAGAAGATG
upper sequence: LOC_Os02g04750.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G006937_T01 (Zea mays), 3'ss of exon 7
----gtagcttcaatttattcttctcctcctctttatggtcatatcgtttattagatatgtatggtgcattggtgctgactgttagtttgatt-ctggagggactagggtatgtcagatttgagctagacatatcaggattcagattgtttggatatatcaactgatatctgtcttcttattgattctttttaacaacattcagGCTCTAAACATGGTCTGCTGCTGGGCGGAAGATCCCAATTCAGACGCATTCAAGCAGCATCTTGCGAGAGTACCTGATTTCTTGTGGCTTTCAGAAGATG
|| || ||| || | || | | | | || || || | || || |||| || | | ||| || | || | | ||| || | | | || | || ||| | ||| | || | | || | || || ||||| || ||| |||| ||||||||||||||||||||||||||| |||||||| |||||||| |||||||||| || ||||| || |||| || ||||||||| ||||||||||||
gtaaatatctccaaaagtttgatgtcttgttactggaactttaattgtccatgcttctgttctgttgttgtggt-cttattattaattctcctacttcatgatttagtgttta-ctgtttcttgttaa--ttattgtcttgtggatgat---gaacttctgattggtgccta--ttaatattggttacttt----gccatttagGCTCTAAACATGGTCTGCTGCTGGGTAGAAGATCCAAATTCAGATGCATTCAAGCGTCACCTTGCAAGGATACCAGACTTCTTGTGGATTTCAGAAGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttggatatatcaactgatatctgtcttcttattgattctttttaacaacattcagGCTCTAAACATGGTCTGCTGCTGGGCGGAAGATCCCAATTCAGACGCATTCAAGCAGCATCTTGCGAGAGTACCTGATTTCTTGTGGCTTTCAGAAGATG
ttttaac putative branch site (score: 2)
ttattgattcttttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagcttcaatttattcttctcctcctctttatggtcatatcgtttattagatatgtatggtgcattggtgctgactgttagtttgattctggagggactagggtatgtcagatttgagctagacatatcaggattcagattgtttggatatatcaactgatatctgtcttcttattgattctttttaacaacattcagGCTCTAAACATGGTCTGCTGCTGGGCGGAAGATCCCAATTCAGACGCATTCAAGCAGCATCTTGCGAGAGTACCTGATTTCTTGTGGCTTTCAGAAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG