Sequence
atgc intronic sequence ATGC exonic sequence...ttcttactaacagacaggagaaataaagtgctcttgttgtctatctttaccattacacctgagagtggcatcaaacaccaatacaagttttccttggcagGTAAGAATGGATCCTCGGAACAACGAAACTGATCTTGATAGTTTAATGTATGGTGCGATAGGAAGACTAACAGAACAAGAGCTAAAAAAACAAGAAGCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os03g19690.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g19690.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G135968_T01 (Zea mays), 3'ss of exon 4
ttcttactaacagacaggagaaataaagtgctcttg----ttgtctatctttaccattacacctgagagtggcatcaaacaccaatacaagttttccttggcagGTAAGAATGGATCCTCGGAACAACGAAACTGATCTTGATAGTTTAATGTATGGTGCGATAGGAAGACTAACAGAACAAGAGCTAAAAAAACAAGAAGCAG
|| ||| | |||| ||| ||||||||| | |||| |||| || | ||||| | | | | |||| |||| ||||||||||||||| |||||||||||||| ||||| ||| | |||| |||||||||||||||||| | || || |||||||||||||||| |||||||||||||||||||
-cctgactt-tactaaggacaaaactagtgctcttcatcttcgtcttcctttcttgtt-cttttgagatttgtaactaacat-ggtacatattttccttggcagGTTAGAATGGATCCTCGAAACAAAGAAGTTAATCTCGATAGTTTAATGTATGGTACAATTGGTGGACTAACAGAACAAGAACTAAAAAAACAAGAAGCAG
upper sequence: LOC_Os03g19690.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv05s0077g00250.t01 (Vitis vinifera), 3'ss of exon 4
ttcttactaacagacaggagaaataaagtgctcttgttgtctatct--ttaccattacacctgagagtggcat-caaacaccaatacaagttttccttggcagGTAAGAATGGATCCTCGGAACAACGAAACTGATCTTGATAGTTTAATGTATGGTGCGATAGGAAGACTAACAGAACAAGAGCTAAAAAAACAAGAAGCAG
|| || | || | || | | |||||| | || | ||| | || |||| | | | | |||||| |||||||||||| ||||||| || | |||||| || |||||||||||||| || | ||| || ||||| | |||| ||| || | |
--gtttcttgaaaccatgtgatttgat-catctacactgtctaataaacttccttccttcctttttttaatattcaaatttgggtggttctactttattgcagGTGAGAATGGATCCTAGGAACAAGGAGATTGATCTCGACAGTTTAATGTATGGAAAAATTACCCAGCGAACTGAGGAAGAGATGAAAAGACAGGAGGGGG
upper sequence: LOC_Os03g19690.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv05s0077g00200.t01 (Vitis vinifera), 3'ss of exon 3
ttcttactaacagacaggagaaataaagtgctcttgttgtctatct--ttaccattacacctgagagtggcat-caaacaccaatacaagttttccttggcagGTAAGAATGGATCCTCGGAACAACGAAACTGATCTTGATAGTTTAATGTATGGTGCGATAGGAAGACTAACAGAACAAGAGCTAAAAAAACAAGAAGCAG
|| || | || | || | | |||||| | || | ||| | || |||| | | | | | |||||| |||||||||||| ||||||| || | |||||| || |||||||||||||| || ||||| || ||||| | |||| ||| || | |
--gtttcttgaaaccatgtgatttgat-catctacactgtctaataaacttccttccttcctttttttaatattcaaatttgggtggttctacttcattgcagGTGAGAATGGATCCTAGGAACAAGGAGATTGATCTCGACAGTTTAATGTATGGAAAAATTACCCAGCTAACTGAGGAAGAGATGAAAAGACAGGAGGGGG
upper sequence: LOC_Os03g19690.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv05s0077g00820.t01 (Vitis vinifera), 3'ss of exon 4
ttcttactaacagacaggagaaataaagtgctcttgttgtctatct--ttaccattacacctgagagtggcat-caaacaccaatacaagttttccttggcagGTAAGAATGGATCCTCGGAACAACGAAACTGATCTTGATAGTTTAATGTATGGTGCGATAGGAAGACTAACAGAACAAGAGCTAAAAAAACAAGAAGCAG
|| || | || | | | | |||||| | | | ||| | || |||| | | | | |||||| |||||||||||| ||||||| || | |||||| || |||||||||||||| || ||||| || ||||| | |||| ||| || | |
--gtttcttg-aaaccatatgatttgatcatctacactgtctaataaacaaacttccttcctttttttaatattcaaatttgggtggttctactttattgcagGTGAGAATGGATCCTAGGAACAAGGAGATTGATCTCGACAGTTTAATGTATGGAAAAATTACCCAGCTAACTGAGGAAGAGATGAAAAGACAGGAGGGGGMapped 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|25800195|gb|CA756156.1|CA756156EST: AGATGGATAGGCCTGCGCCTGTTGCAATATTTGTCGTTAATTTTGATAAG GTAAGAATGGATCCTCGGAACAACGAAACTGATCTTGATAGTTTAATGTAT
genomic: AGATGGATAGGCCTGCGCCTGTTGCAATATTTGTCGTTAATTTTGATAAGgtatggggat ... tccttggcagGTAAGAATGGATCCTCGGAACAACGAAACTGATCTTGATAGTTTAATGTAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttaccattacacctgagagtggcatcaaacaccaatacaagttttccttggcagGTAAGAATGGATCCTCGGAACAACGAAACTGATCTTGATAGTTTAATGTATGGTGCGATAGGAAGACTAACAGAACAAGAGCTAAAAAAACAAGAAGCAG
ttttcctt CT-rich tract
aatacaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttcttactaacagacaggagaaataaagtgctcttgttgtctatctttaccattacacctgagagtggcatcaaacaccaatacaagttttccttggcagGTAAGAATGGATCCTCGGAACAACGAAACTGATCTTGATAGTTTAATGTATGGTGCGATAGGAAGACTAACAGAACAAGAGCTAAAAAAACAAGAAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC