Sequence
atgc intronic sequence ATGC exonic sequencegtaacacaaaacacatactcattatctcattatttcgagatgattttgcatctgtgattgatgtggatggatgcatcatatgctgtcacgtatgggggcagTGAACAACTTCATGCAGTACACGGCCTACTTCGGGGTGTCGACGAACCTGGTGAACTACCTCAAGTACAGGCTGCACGAGGGCAGCAAGTCGGCGGCGAA
Basic information
species | Oryza sativa |
transcript | LOC_Os01g67630.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g67630.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G817436_T02 (Zea mays), 3'ss of exon 2
----------------------------------------------------------------gtaacacaa---aacacatactcattatctcattatttcgagatgattttgcatct----gtgattgatgtggatggatgcatcatatgc-tgtcacgtatgggggcagTGAACAACTTCATGCAGTACACGGCCTACTTCGGGGTGTCGACGAACCTGGTGAACTACCTCAAGTACAGGCTGCACGAGGGCAGCAAGTCGGCGGCGAA
||| | | | || || || || || | | | | ||| | || | ||| | |||| | ||| | ||| |||||||| | | |||| || ||||||||||| |||||||||||||||||||||||||||||| || ||||||||||||||||||| | || |||||
gtaatactgcatacacctagcctgatttttctttctttcgtcgtcgtgtagatgagcactcaacttaattcgctctggcctgcatatgcgctcctatacgcgcgtgacgacgtggtgaataatggcgatggttgggctcggacatgt-atatatataccacacacatcatcagCGAACAACTGCTTCCAGTTCATCGCCTACTTCGGCGTGTCGACGAACCTGGTGAACTACCTCAAGGACCGGCTGCACGAGGGCAGCAAAGCCGCCGCGAA
upper sequence: LOC_Os01g67630.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G419328_T01 (Zea mays), 3'ss of exon 2
----------------------------------gtaacacaaaacacatactcattatctc----attatttcgagatgattt----------tgcatctgtg-----attgatgtggatggatgcatcatatgctgtcacgtatgggggcagTGAACAACTTCATGCAGTACACGGCCTACTTCGGGGTGTCGACGAACCTGGTGAACTACCTCAAGTACAGGCTGCACGAGGGCAGCAAGTCGGCGGCGAA
||| | | | | ||| | | | | | | | || | |||| | || ||| ||| | | || | | | | || ||| || |||| | | |||| || |||||||||| |||||||||||||||||||||||||||||| || | |||||| |||||||||| | || |||||
gtaataatggcatgtctcacatacacatctgttcgtagctttatatatggcctcgctcgccctcaaaccgtctggctgtggcctctgcactgcatgcacccgtacatgcattcatggcggcgatggcg--ggactcggccggacatcacaccagCGAGTAACTGCTTCCAGTTCATCGCCTACTTCGCCGTGTCGACGAACCTGGTGAACTACCTCAAGGACCGCCTGCACCAGGGCAGCAAAGCCGCCGCGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcatctgtgattgatgtggatggatgcatcatatgctgtcacgtatgggggcagTGAACAACTTCATGCAGTACACGGCCTACTTCGGGGTGTCGACGAACCTGGTGAACTACCTCAAGTACAGGCTGCACGAGGGCAGCAAGTCGGCGGCGAA
gattgat putative branch site (score: 4)
atcatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaacacaaaacacatactcattatctcattatttcgagatgattttgcatctgtgattgatgtggatggatgcatcatatgctgtcacgtatgggggcagTGAACAACTTCATGCAGTACACGGCCTACTTCGGGGTGTCGACGAACCTGGTGAACTACCTCAAGTACAGGCTGCACGAGGGCAGCAAGTCGGCGGCGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG