Sequence
atgc intronic sequence ATGC exonic sequence...actagcttgtaaattttgttcaagatttctgcctctgtttctgctctgctctgctctgtatggatagccactgaagaggtacaagtgtttgattttgcagCGAGCGGACCAAGGAGGTGCTCATCAGCGCGGCGTTCGTTCACCTGAAGCAAGCGGATTTGTCCAAGCACATCCGCAACCTCTGCGCCGCAAGCCGCGCG
Basic information
species | Oryza sativa |
transcript | LOC_Os05g50750.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g50750.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G013115_T01 (Zea mays), 3'ss of exon 1
actagcttgtaaattttgttcaagatttctgcctctgtttctgct-ctgctctgct-----ctgtatggatagccactgaagaggtacaagtgtttgattttgcagCGAGCGGACCAAGGAGGTGCTCATCAGCGCGGCGTTCGTTCACCTGAAGCAAGCGGATTTGTCCAAGCACATCCGCAACCTCTGCGCCGCAAGCCGCGCG
| | | |||| ||| ||| | | |||| | | || | | | | || ||| | ||| | || ||| ||| |||||||| | ||| | ||||||||||||||||||||| ||||| ||||| ||| | ||||| || |||||| |||| ||||||| |||||| |||| |||
---gcttcttcagtttttttctttgtttgtttgtttgttatcattattactacgatggcactagcaccgacagcgattgaggtagtg-gtgtgattg--cctgcagCGATCAGACGAGGGAGGTGCTCATCAGCGCGGCTTTCGTCCACCTCAAGAACGCGGAGCTGCTGAAGCACGTCCGGAACCTCTCCGCCGCCAGCCACGCC
upper sequence: LOC_Os05g50750.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G013115_T02 (Zea mays), 3'ss of exon 1
---------------actagcttgtaaattttgttcaagatttctgcctctgtttctgct-ctgctctgct-----ctgtatggatagccactgaagaggtacaagtgtttgattttgcagCGAGCGGACCAAGGAGGTGCTCATCAGCGCGGCGTTCGTTCACCTGAAGCAAGCGGATTTGTCCAAGCACATCCGCAACCTCTGCGCCGCAAGCCGCGCG
| | | | |||| ||| ||| | | |||| | | || | | | | || ||| | ||| | || ||| ||| |||||||| | ||| | ||||||||||||||||||||| ||||| ||||| ||| | ||||| || |||||| |||| ||||||
aaaaggccgcagcacatggcttcttcagtttttttctttgtttgtttgtttgttatcattattactacgatggcactagcaccgacagcgattgaggtagTG-GTGTGATTG--CCTGCAGCGATCAGACGAGGGAGGTGCTCATCAGCGCGGCTTTCGTCCACCTCAAGAACGCGGAGCTGCTGAAGCACGTCCGGAACCTC------------------ atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgctctgctctgtatggatagccactgaagaggtacaagtgtttgattttgcagCGAGCGGACCAAGGAGGTGCTCATCAGCGCGGCGTTCGTTCACCTGAAGCAAGCGGATTTGTCCAAGCACATCCGCAACCTCTGCGCCGCAAGCCGCGCG
gtttgat putative branch site (score: 5)
tttgatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
actagcttgtaaattttgttcaagatttctgcctctgtttctgctctgctctgctctgtatggatagccactgaagaggtacaagtgtttgattttgcagCGAGCGGACCAAGGAGGTGCTCATCAGCGCGGCGTTCGTTCACCTGAAGCAAGCGGATTTGTCCAAGCACATCCGCAACCTCTGCGCCGCAAGCCGCGCG
- - gcttgta
- - - - - - - - - - - - - ttctgcc
- - - - - - - - - - - - - - - - - -tgtttct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gccactg