Sequence
atgc intronic sequence ATGC exonic sequencegtacgtacgtgagcgttgatttggttgcacgcgcgcgcgttcgtgtgtgccatgtcgcgatctgatgggtggtctggttggttgggtgcagcagGATCAGGAGTGGGTGCTGTGCAGGGTGTTCAAGAAGAGCCTCGAGCTGGCGCCGGCGGCGGCGGCGGCGGTCGGCAGGAGAGGCGCGGGCGCGGGGACGG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g36880.4 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g36880.4 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G898290_T02 (Zea mays), 3'ss of exon 3
--------------------------------------------gtacgtacgtgagcgttgatttggt---tgcacgcgcgcgcgttcgtgtgtgc--catgtcgcgatctgatgggtg-gtctggt---tggttgggtgca-gcagGATCAGGAGTGGGTGCTGTGCAGGGTGTTCAAGAAGAGCCTCGAGCTGGCGCCGGCGGCGGCGGCGGCGGTCGGCAGGAGAG-GCGCGGGCGCGGGGACGG---
| | | | | || ||| || | || ||| ||| | | | ||| || ||| | || | ||||||||| | |||||| ||||||||||||||||||||||||||||||||| |||||| | ||||| | | || | | ||||| | | | | || |||| || | ||
gtgccgcccgcagtatatagcttcagtttattggtcgatggagagcatattctccaacgaccgagtggcgtgtggatccgtctaacctcgcttgttcatctttatgcgtcctcttggccgcatccattccatggttgggtactcgcagGAC---GAGTGGGTGCTGTGCAGGGTGTTCAAGAAGAGCATCGAGCCGCCGCCGTCAGTGG-GCAAGAGGTCGTCGGTCGCGTGCACGGGGACGATGGTGGTGG
upper sequence: LOC_Os02g36880.4 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G146380_T01 (Zea mays), 3'ss of exon 1
-----------------------------------------------------------------gtacgtacgtgagcgttgatttggttgcacgcgcgcgcgtt-cgtgtgtgcca---tgtcgcgatctg----atgggtg-gtctggttggttgggtgca-----gcagGATCAGGAGTGGGTGCTGTGCAGGGTGTTCAAGAAGAGCCTCGAGCTGGCGCCGGCGGC-GGCGGCG-GCGGTCGGCAGGAGAGGCGCGGGCGCGGGGACGG---
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gtacgtacggtgctagcttttttttgttgcttgcgcgtgcatgttacgtaccggtcgatccatccatccatcggttgcggttggttggtcgagacaca-gcgagtggcgtgtggatccgtctaactccatctgtgctgtgtgtgtgccttgccgctgcactacatgctggcagcagGACGAGTGGGTGCTGTGCAGGGTGTTCAAGAAGAGCATCGAGCCGCCATCCGTGCCCGGCAGCAAGAGGTCATC--GTCGGTTGCGTGCATGGGGACGGAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcgtgtgtgccatgtcgcgatctgatgggtggtctggttggttgggtgcagcagGATCAGGAGTGGGTGCTGTGCAGGGTGTTCAAGAAGAGCCTCGAGCTGGCGCCGGCGGCGGCGGCGGCGGTCGGCAGGAGAGGCGCGGGCGCGGGGACGG
atctgat putative branch site (score: 4)
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgtacgtgagcgttgatttggttgcacgcgcgcgcgttcgtgtgtgccatgtcgcgatctgatgggtggtctggttggttgggtgcagcagGATCAGGAGTGGGTGCTGTGCAGGGTGTTCAAGAAGAGCCTCGAGCTGGCGCCGGCGGCGGCGGCGGCGGTCGGCAGGAGAGGCGCGGGCGCGGGGACGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG