Sequence
atgc intronic sequence ATGC exonic sequencegtacggttcttcatggcatctgctccctcccgtgtgttgaccttttagtcaacgtgttgacctgtggttttgactttgtggcagGTTGACCTCACCGGCGGCTACTACGACGGCGGCGACAACGTCAAGTTCGGGTTCCCGATGGCGTTCACGACGACGATGCTGTCGTGGGGCGTCGTGGAGT
Basic information
species | Oryza sativa |
transcript | LOC_Os04g36610.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g36610.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G125436_T01 (Zea mays), 3'ss of exon 1
--------------------------------------------------------------gtacggttcttcatggcatctgctccctcccgtgtgttgacctt-ttagtcaacgtgttgacctgtggttttgactttgtggcagGTTGACCTCACCGGCGGCTACTACGACGGCGGCGACAACGTCAAGTTCGGGTTCCCGATGGCGTTCACGACGACGATGCTGTCGTGGGGCGTCGTGGAGT
| | | || | | | | | | |||||| |||||| | | |||| | || | ||||||| |||||||||||||| |||||||||||||||||||||| ||||||||| ||||||||||| |||||||||||||||||||||||| |||| |||||
gtacgtacttccttcctgctgtgtcttgttcgaaaacatgggtcagcgcgctgacggctgacggctgacctgacctgacctggggcttggactggacctggaccttcttagtctctctatctgtctgttgacgtgcgcgcgcggcagGTCGACCTCACCGGCGGGTACTACGACGGCGGCGACAACGCCAAGTTCGGCTTCCCGATGGCCTTCACGACGACGATGCTGTCGTGGAGCGTGCTGGAGC
upper sequence: LOC_Os04g36610.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ16113 (Selaginella moellendorffii), 3'ss of exon 1
gtacggttcttcatggcatctgctccctcccgtgtgttgaccttttagtcaacgtgttgacctg--tggttttgactttgtggcagGTTGACCTCACCGGCGGCTACTACGACGGCGGCGACAACGTCAAGTTCGGGTTCCCGATGGCGTTCACGACGACGATGCTGTCGTGGGGCGTCGTGGAGT
|| | | | | | | | |||| ||| | || || | | | | | |||| || ||||| | ||||| || ||||||||||| ||||||||||||||||| || ||||||||||||||||||| ||| ||||||||||| |||| ||||| |
-----gtaccttagaatcttttgctcgtttgaaatgtttttcttgtggtttacctttctagtcgatcgattttcgctgctgctcagGTGAATCTCACGGGAGGCTACTACGATTCAGGCGACAACGTCAAGTTTGGCTTCCCGATGGCGTTCACGATCACGCTGCTGTCGTGGAGCGTGGTGGAAT
upper sequence: LOC_Os04g36610.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ08014 (Selaginella moellendorffii), 3'ss of exon 1
gtacggttcttcatggcatctgctccctcccgtgtgttgaccttttagtcaacgtgttgacctg--tggttttgactttgtggcagGTTGACCTCACCGGCGGCTACTACGACGGCGGCGACAACGTCAAGTTCGGGTTCCCGATGGCGTTCACGACGACGATGCTGTCGTGGGGCGTCGTGGAGT
|| | | | | | | |||| ||| | || || | | | | | |||| || ||||| | ||||| || ||||||||||| |||||||||||||||||| || ||||||||||||||||||| ||| ||||||||||| |||| ||||| |
-----gtaccatagaatcttttgctcgtttgaaatgtttttcttgtggtttacctttctagtcgatcgattttcgctgctgctcagGTGAATCTCACGGGAGGCTACTACGATTCCGGCGACAACGTCAAGTTTGGCTTCCCGATGGCGTTCACGATCACGCTGCTGTCGTGGAGCGTGGTGGAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccgtgtgttgaccttttagtcaacgtgttgacctgtggttttgactttgtggcagGTTGACCTCACCGGCGGCTACTACGACGGCGGCGACAACGTCAAGTTCGGGTTCCCGATGGCGTTCACGACGACGATGCTGTCGTGGGGCGTCGTGGAGT
ttttgac putative branch site (score: 3)
ttttagt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacggttcttcatggcatctgctccctcccgtgtgttgaccttttagtcaacgtgttgacctgtggttttgactttgtggcagGTTGACCTCACCGGCGGCTACTACGACGGCGGCGACAACGTCAAGTTCGGGTTCCCGATGGCGTTCACGACGACGATGCTGTCGTGGGGCGTCGTGGAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG