Sequence
atgc intronic sequence ATGC exonic sequencegtttgtatttaaaaccacgttcttttgctgtgctacaaccacaggaagttcaggcttatatacgtgtttacaactttctcaattctcatgcaaatctgcagGAAGAGCAGTGGCTTTTCTAGAGGTGCATCGATCTACAGAGGTGTAACAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os03g19900.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g19900.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G317160_T01 (Zea mays), 3'ss of exon 5
gtttgtatttaaaaccacgttcttttgctgtgctacaaccacaggaagttcaggcttatatacgtgtttacaactttctcaattctcatgcaaatctgcagGAAGAGCAGTGGCTTTTCTAGAGGTGCATCGATCTACAGAGGTGTAACAAG
|| | | |||| ||| | | ||| ||| | || ||| | |||| || | || |||||| || ||| | || ||||| ||||||||||||||||||||||||||| ||||| ||||||||||| |||||||
gtattt-tttataacttcatacttctgcagctacacgtccatggct-------gcttccatgcatgcttacaaatt---caa----cgtgtcaatcttcagGAAGAGCAGTGGCTTTTCTAGAGGAGCATCAATCTACAGAGGAGTAACAAA
upper sequence: LOC_Os03g19900.1 (Oryza sativa), 3'ss of exon 6
lower sequence: EFJ16224 (Selaginella moellendorffii), 3'ss of exon 3
gtttgtatttaaaaccacgttcttttgct---gtgctacaaccacaggaagttcag-gcttatatacg-tgtt-tacaactt---tctcaattctcatgcaaatctgcagGAAGAGCAGTGGCTTTTCTAGAGGTGCATCGATCTACAGAGGTGTAACAAG
|| | | | ||| || |||| || ||| | || | | | |||||| | |||| || | ||| | | | || | | |||||||||||||||||| | ||||||||||||| | ||| |||||||||||
gtgcgaaactttttccattttgctttgtgcgagttctaaagttttgggtgttctaaagtttatatgtggtgttctaaagcttgtatgtgactttgtgtttggaaa-acagGAAGAGCAGTGGCTTCGCGAGAGGTGCATCGAGGTTCAGGGGTGTAACAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agttcaggcttatatacgtgtttacaactttctcaattctcatgcaaatctgcagGAAGAGCAGTGGCTTTTCTAGAGGTGCATCGATCTACAGAGGTGTAACAAG
ttatata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtatttaaaaccacgttcttttgctgtgctacaaccacaggaagttcaggcttatatacgtgtttacaactttctcaattctcatgcaaatctgcagGAAGAGCAGTGGCTTTTCTAGAGGTGCATCGATCTACAGAGGTGTAACAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG