Sequence
atgc intronic sequence ATGC exonic sequenceGTTGCATGGCTTCTCTTTCTGCCATGATTCAGCTTGAACTTCCTCATATCAACATTCTTTCAAAGATGGACCTGGTCTCCAACAAAAAAGATGTGGAAGAgtatgtttatttcatttctcatttatttaaagattcaaccatcctgctttgtattaatatcttgatgtttctag
Basic information
species | Oryza sativa |
transcript | LOC_Os03g50620.2 |
intron # | 6 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g50620.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G154716_T01 (Zea mays), 5'ss of exon 9
GTTGCATGGCTTCTCTTTCTGCCATGATTCAGCTTGAACTTCCTCATATCAACATTCTTTCAAAGATGGACCTGGTCTCCAACAAAAAAGATGTGGAAGAgtatgtttatttcatttctcatttatttaaagattcaa--ccatcctgctttgtat-----taatatcttgatgtttctag---------------------------
|||||||||||||||| ||||| |||||||||||||||||||||||||||||||| |||||||||||||| ||| ||||||||||||||||||| ||||||||||||| || |||| | | || | || | | |||| | ||| || ||| |||| || || |
GTTGCATGGCTTCTCTATCTGCTATGATTCAGCTTGAACTTCCTCATATCAACATCCTTTCAAAGATGGATCTGATCTCCAACAAAAAAGATGTAGAAGAgtatgttttatttctttcctctcttgcaaatgttttatttctttcctcccttgcatagttctaaaggtttgaatttccttgtttgtattaatgttccaatggctctag
upper sequence: LOC_Os03g50620.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G131324_T01 (Zea mays), 5'ss of exon 7
GTTGCATGGCTTCTCTTTCTGCCATGATTCAGCTTGAACTTCCTCATATCAACATTCTTTCAAAGATGGACCTGGTCTCCAACAAAAAAGATGTGGAAGAgtatgttt-atttcatttctc------atttatttaaagattcaaccatcctgctttgtattaatatcttgatgtttctag---------------------------
|||||||||||||||| ||||| |||||||||||||||||||||||||||||||| |||||||||||||| ||||||||||||||||||||||| ||||||||||||| ||||| || ||| || | ||| | | | | ||| | || ||| |||| || || |
GTTGCATGGCTTCTCTATCTGCTATGATTCAGCTTGAACTTCCTCATATCAACATCCTTTCAAAGATGGATCTGGTCTCCAACAAAAAAGATGTAGAAGAgtatgttttatttctttcctctcttgcatatgttttatttctttcctcccttgcatagttctaaaggtttgaatttccttgtctgtattaatgttccaatggctctag
upper sequence: LOC_Os03g50620.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA08G39880.1 (Glycine max), 5'ss of exon 7
GTTGCATGGCTTCTCTTTCTGCCATGATTCAGCTTGAACTTCCTCATATCAACATTCTTTCAAAGATGGACCTGGTCTCCAACAAAAAAGATGTGGAAGAgtatgt-ttatttc----atttctcattta--tttaaagattcaaccatcctgctttg--tattaatatcttgatgtttctag
| |||||||| | ||||||||| ||| |||| |||||||| |||||| | || || || |||||||||||||| || | || || || ||| | ||||||||| | |||| | | |||| | ||| || | | ||| | |||||| | || | |||
GATGCATGGCATGTCTTTCTGCGATGGTTCAACTTGAACTACCTCATGTTAATATCCTCTCAAAGATGGACCTTGTGACTAAAAAGAAGGATCTTGAAGAgtatttactattactaaaacttctttcccaaatttgtcttctccatttcattcatttaatttctaatatacttttgctcttag
upper sequence: LOC_Os03g50620.2 (Oryza sativa), 5'ss of exon 6
lower sequence: PP1S234_26V6.2 (Physcomitrella patens), 5'ss of exon 7
GTTGCATGGCTTCTCTTTCTGCCATGATTCAGCTTGAACTTCCTCATATCAACATTCTTTCAAAGATGGACCTGGTCTCCAACAAAAAAGATGTGGAAGAgtatgtttatttcatttctcatttatttaa---agattcaaccatcctgctttgtattaatatcttgatgtttctag-----------------------
| || |||||||| || ||||| ||||||||||| ||||||||||| ||||| | || | ||| | || || || ||||||| || | || ||| || | | | | || || || | || | | ||| | ||| |||| | | | |
GCTGTATGGCTTCGCTGTCTGCTATGATTCAGCTAGAACTTCCTCACATCAATGTGCTGACGAAGGTTGATCTTCTCCCCAACAAGCGCGACATTGATAGgtaaagttgtgttttcaaacgcttgttgtgcctagtgttgactagtttattttacagtaacctcttccaatgtgtgggttgagcaccatcaacagaatcgMapped 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|86530562|gb|CI170768.1|CI170768EST: AACATTCTTTCAAAGATGGACCTGGTCTCCAACAAAAAAGATGTGGAAGA GTATCTGAATCCAGAGGCGCAGGTTCTCTTGTCACAGCTGAACCGACAGAT
genomic: AACATTCTTTCAAAGATGGACCTGGTCTCCAACAAAAAAGATGTGGAAGAgtatgtttat ... atgtttctagGTATCTGAATCCAGAGGCGCAGGTTCTCTTGTCACAGCTGAACCGACAGAT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTTGCATGGCTTCTCTTTCTGCCATGATTCAGCTTGAACTTCCTCATATCAACATTCTTTCAAAGATGGACCTGGTCTCCAACAAAAAAGATGTGGAAGAgtatgtttatttcatttctcatttatttaaagattcaaccatcctgctttgtattaatatcttgatgtttctag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA