Sequence
atgc intronic sequence ATGC exonic sequencegtgagctcgccgttcgtgctagtgctagctccggtggccggagttcgatcttactaatggttcttgtggttttgcagCGATAACGCCGGTGGGGAGGAGGAGCATGCTGAAGCTGGCGCAGCGGATGACGGACAACTTCTGCGCGGGGGTGTGCGCGTCGGCGGCGCAGAAGTGGCG
Basic information
species | Oryza sativa |
transcript | LOC_Os09g35760.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os09g35760.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G116658_T01 (Zea mays), 3'ss of exon 7
------------------gtgagctcgccgttcgtgctagtg-ctagctc----cggtggccggagttcgatcttactaa---tggttct-tgtggtttt--gcagCGATAACGCCGGTGGGGAGGAGGAGCATGCTGAAGCTGGCGCAGCGGATGACGGACAACTTCTGCGCGGGGGTGTGCGCGTCGGCGGCGCAGAAGTGGCG
| | | |||| ||| ||| || || | ||| | | ||| | | ||| | | | ||| ||| |||||||| |||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||| || ||||| |||||||||||||||||||||||
gtgagtaataacttactaatcactccatcgttggtgtgagtaacttgcacgagatggttaaccaatggcgacggcggtgagcatggatatatatggatttatgcagCGATCACGCCGGTGGGGCGGAGGAGCATGCTGAAGCTGGCGCAGCGGATGACGGACAACTTCTGCGCCGGTGTGTGTGCGTCGGCGGCGCAGAAGTGGCG
upper sequence: LOC_Os09g35760.1 (Oryza sativa), 3'ss of exon 7
lower sequence: EFJ10492 (Selaginella moellendorffii), 3'ss of exon 8
--------------------------------------------------------------------------------gtgagctcgccgttcgtgctagtgctagctc-cggtggccggagttcgatctta-------ctaatggttcttgtggttttgcagCGA-TAACGCCGGTGGGGAGGAG------GAGCATGCTGAAGCTGGCGCAGCGGATGACGGACAACTTCTGCGCGGGGGTGTGCGCGTCGGCGGCGCAGAAGTGGCG
| | || | | || | | || ||| | ||| || |||||||| | | | ||||| || | | | || | ||| | ||||||||| ||| |||||||||| |||||| | |||||||||||||| ||| | ||||| | | ||| | ||
gtagtactttctttcctcttccatcttttctttcgaagaacttagagagaggagggaacaaaaaaatgctttttttctcagctggttcttccccctcctctttgtttgttcacgggcattgtttttcttcctcggctttgtttaatggtttgttttgctttgctgccagTGATACCCAATGCGAGTGGCCGCCGGAGCATGCTCAAGTTGGCGCAGCGCATGACGAATAACTTCTGCGCGGGCGTGAGTGCGTCCACTGTGCACACTTG---
upper sequence: LOC_Os09g35760.1 (Oryza sativa), 3'ss of exon 7
lower sequence: EFJ19972 (Selaginella moellendorffii), 3'ss of exon 8
--------------------------------------------------------------------------------gtgagctcgccgttcgtgctagtgctagctc-cggtggccggagttcgatctta-------ctaatggttcttgtggttttg----cagCGATA----ACGCCGGTGGGGAGGAGGAGCATGCTGAAGCTGGCGCAGCGGATGACGGACAACTTCTGCGCGGGGGTGTGCGCGTCGGCGGCGCAGAAGTGGCG
| | || | | || | | || ||| | ||| || |||||||| | | | |||| ||| |||| | || |||| | |||||||||| ||| |||||||||| |||||| | |||||||||||||| ||| | ||||| | | ||| | ||
gtagtactttctttcctcttccatcttttctttcgaagaacttagagagaggagggaacaaaaaaatgctttttttctcagctggttcttccccctcctctttgtttgttcacgggcattgtttttcttcctcggctttgtttaatggtttgttttgctttggtgccagTGATACCCAATGCGAGTGGCC-GCCGGAGCATGCTCAAGTTGGCGCAGCGCATGACGAATAACTTCTGCGCGGGCGTGAGTGCGTCCACTGTGCACACTTG--- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgctagctccggtggccggagttcgatcttactaatggttcttgtggttttgcagCGATAACGCCGGTGGGGAGGAGGAGCATGCTGAAGCTGGCGCAGCGGATGACGGACAACTTCTGCGCGGGGGTGTGCGCGTCGGCGGCGCAGAAGTGGCG
tactaat putative branch site (score: 1)
ttactaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagctcgccgttcgtgctagtgctagctccggtggccggagttcgatcttactaatggttcttgtggttttgcagCGATAACGCCGGTGGGGAGGAGGAGCATGCTGAAGCTGGCGCAGCGGATGACGGACAACTTCTGCGCGGGGGTGTGCGCGTCGGCGGCGCAGAAGTGGCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT