Sequence
atgc intronic sequence ATGC exonic sequencegttcaatccgtcgtcatatgacatgacatgacactctcatggcgatcactacgatcgatcttgacgtcatcaatggcgtgattctgtgcagGTGGCGCAGGTGCTGCTGACGCTGCCCTACTCCTTCTCGCAGCTGGGCATGGCGTCCGGGGTGGCGTTCCAGGTGTTCTACGGGCTGATGGGGTCGTGGA
Basic information
species | Oryza sativa |
transcript | LOC_Os11g06820.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os11g06820.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G045057_T02 (Zea mays), 3'ss of exon 1
gttcaatccgtcgtcatatgacatgacatgacactctcatggcgatcactacgatcgatcttgacgtcatcaatggcgtgattctgtgcagGTGGCGCAGGTGCTGCTGACGCTGCCCTACTCCTTCTCGCAGCTGGGCATGGCGTCCGGGGTGGCGTTCCAGGTGTTCTACGGGCTGATGGGGTCGTGGA------------------------------------------------------------
|| | ||| | | || ||| ||| | || |||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||| ||||||| | |||||||| || ||||| ||||
--------------------------------------------gtcggtgta--cga-cgcgtggt--tcagctgcgcg--tcgaaccaggtggcgcaggtgctgctgacgctgccctactccttctcgcagctgggcatggcatccgggGTGGTGTTCCAGCTCTTCTACGGCCTCATGGGCAGCTGGACCGCCTACCTCATCAGCATCCTCTACGTCGAGTACCGCACCAGGAAGGAGCGCGAGAAGG
upper sequence: LOC_Os11g06820.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S90_46V6.1 (Physcomitrella patens), 3'ss of exon 1
--gttcaatccgtcgtcatatgacatgacatgacactctca-----tggcgatcactacgatcgatcttgacgtc--atcaatggcgtgattctgtgcagGTGGCGCAGGTGCTGCTGACGCTGCCCTACTCCTTCTCGCAGCTGGGCATGGCGTCCGGGGTGGCGTTCCAGGTGTTCTACGGGCTGATGGGGTCGTGGA
| | | || | | | | | | | | |||| || || | ||||| |||| || | | | | || ||||||| ||||| ||||||||||||||||||||||||||| | ||||| || | || ||||| | ||||||||| | |||||||| | || || | |||
accgacgttttgaggtggaaggtaactgcgtcggatttttcaggattggccatggctgtgtctaatcttttcgtctgatgggtcggttcaatcgatgcagGTCGCGCAAGTGCTGCTGACGCTGCCCTACTCCTTCGCACAGCTCGGGTTTGCCTCCGGAATTGCGTTCCAGTTTTTCTACGGTGTAATCGGCTGCTGGT
upper sequence: LOC_Os11g06820.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ21839 (Selaginella moellendorffii), 3'ss of exon 1
----gttcaatccgtcgtcatatgacatgacatgacactc-tcatggcgatcactacgatcg--atcttgacgtca---tcaatggcgtgattctgtgcagGTGGCGCAGGTGCTGCTGACGCTGCCCTACTCCTTCTCGCAGCTGGGCATGGCGTCCGGGGTGGCGTTCCAGGTGTTCTACGGGCTGATGGGGTCGTGGA
| ||| | | || | ||| | | || || | | | | | | ||||| | ||| | | ||| | | | |||||||| || |||||||| |||||||| |||||||||||||||||||| | ||||| || | | |||||| | ||||| || ||| | ||| | ||||
gtgaggacaaacaga-gttttgggacttttttttttcttcctcttcttcgttgttgtgcttgtgatcttcgcctcacggtttcttctgtggtgatttccagGTGGCTCAAGTGCTGCTCACGCTGCCATACTCCTTCTCGCAGCTGGGATTCGCGTCGGGCATTGTCTTCCAGATCTTCTATGGCCTGCTCGGGGCCTGGA
upper sequence: LOC_Os11g06820.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ36050 (Selaginella moellendorffii), 3'ss of exon 1
-----gttcaatccgtcgtcatatgacatgaca---tgacactctcatggcgatcactacg-atcgatcttgacgtcatcaatggcgtgattctgtgcagGTGGCGCAGGTGCTGCTGACGCTGCCCTACTCCTTCTCGCAGCTGGGCATGGCGTCCGGGGTGGCGTTCCAGGTGTTCTACGGGCTGATGGGGTCGTGGA
|||| | || | | || | | || | || | ||| | || | | | |||| ||||| || |||||||| |||||||||| ||||| ||||||||||||||||| | || ||||| | ||||| ||||| |||||||| |||| || ||||
tccactttcagtatagcgaacaccaaaaagaaacctttgttcttcttcttccttcgttgtttgtcggaacttacttgtttttctcttttcttctccacagGTCGCACAGGTGCTTTTGACGCTGCCATACTCTTTCTCGCAGCTGGGCATTGTGTGGGGGGTCACCTTCCAAGTGTTTTACGGGCTTTTGGGCTCCTGGA
upper sequence: LOC_Os11g06820.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ34222 (Selaginella moellendorffii), 3'ss of exon 1
gttcaatccgtcgtcatatgacatgacatgacactct----catggcgatcactacgatcg--atcttgacgtca---tcaatggcgtgattctgtgcagGTGGCGCAGGTGCTGCTGACGCTGCCCTACTCCTTCTCGCAGCTGGGCATGGCGTCCGGGGTGGCGTTCCAGGTGTTCTACGGGCTGATGGGGTCGTGGA
| || | || | ||| | | ||| | | | | | | | ||||| | ||| | | ||| | | | |||||||| || |||||||| |||||||| |||||||||||||||||||| | ||||| || | | |||||||| ||||| || ||| | ||| | ||||
gacaaacacacagttttgggacttttttttttcttcttcctcttcttcgttgttgtgcttgtgatcttcgcctcacggtttcttctgtggtgatttccagGTGGCTCAAGTGCTGCTCACGCTGCCATACTCCTTCTCGCAGCTGGGATTCGCGTCGGGCATTGTCTTCCAGGTCTTCTATGGCCTGCTCGGGGCCTGGA
upper sequence: LOC_Os11g06820.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ18760 (Selaginella moellendorffii), 3'ss of exon 1
-gttcaatccgtc-gtcatatgacatgacatgacactc-tcatggcgatcactacg------atcgatcttgacgtcatcaatggcgtgattctgtgcagGTGGCGCAGGTGCTGCTGACGCTGCCCTACTCCTTCTCGCAGCTGGGCATGGCGTCCGGGGTGGCGTTCCAGGTGTTCTACGGGCTGATGGGGTCGTGGA
||| || | || | || || | || || | | | || || ||| | || | | | |||| ||||| || |||||||| |||||||||| ||||| ||||||||||||||||| | || ||||| | ||||| ||||| |||||||| |||| || ||||
gcttcgattcctccactttctgtcaaaaagaaaccttcgttcttcttcttccttcgttgtttgtcggaacttacttgtttttctcttttcttctccacagGTCGCACAGGTGCTTTTGACGCTGCCATACTCTTTCTCGCAGCTGGGCATTGTGTGGGGGGTCACCTTCCAAGTGTTTTACGGGCTTTTGGGCTCCTGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatggcgatcactacgatcgatcttgacgtcatcaatggcgtgattctgtgcagGTGGCGCAGGTGCTGCTGACGCTGCCCTACTCCTTCTCGCAGCTGGGCATGGCGTCCGGGGTGGCGTTCCAGGTGTTCTACGGGCTGATGGGGTCGTGGA
tcttgac putative branch site (score: 3)
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcaatccgtcgtcatatgacatgacatgacactctcatggcgatcactacgatcgatcttgacgtcatcaatggcgtgattctgtgcagGTGGCGCAGGTGCTGCTGACGCTGCCCTACTCCTTCTCGCAGCTGGGCATGGCGTCCGGGGTGGCGTTCCAGGTGTTCTACGGGCTGATGGGGTCGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT