Sequence
atgc intronic sequence ATGC exonic sequencegtatgaagtaaaatttgttaaaaagtttccggttggaattggatctttcaaacatctgttatttgtaatagtgtcaagagcttgttttgttcccttggaaaattatttcacttatttgatttgcctgatgatgttccagACCTTGTTGTTCGATCCCATGAAGTGAAAGATGAAGGCTATGAAATTGAACATGATGGAAAGCTTATAACGGTGTTCTCTGCTCCCAATTATTGCGACCA
Basic information
species | Oryza sativa |
transcript | LOC_Os05g11550.2 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g11550.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G126435_T02 (Zea mays), 3'ss of exon 9
gtatgaagtaaaatttgttaaaaagtttccggttggaattggatctttcaaacatc-tgttatttgtaatagtgtcaagagcttgttttgttcccttggaaaattatttcacttatttgatttgcctgatgatgttccagACCTTGTTGTTCGATCCCATGAAGTGAAAGATGAAGGCTATGAAATTGAACATGATGGAAAGCTTATAACGGTGTTCTCTGCTCCCAATTATTGCGACCA
||| || || || | | || || | ||| || | | || || ||||| | || ||| | | |||| | ||||| ||| |||| || || |||||||| || ||||||||| ||||||||||||||||||||||||||||||| || |||||||| || ||||| || |||||
-----------------------------------------------gtaaatattgtgggatctcaattactga-aggaga-------atttacacgtgaatttttttcatct--tttgttttcttaatgagttgccagATCTTATTGTCCGGTCTCATGAAGTAAAGGATGAAGGCCATGAAATTGAACATGATGGAAAGCTTATAACAGTCTTCTCTGCGCCTAATTACTGTGACCA
upper sequence: LOC_Os05g11550.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA18G12440.1 (Glycine max), 3'ss of exon 10
gtatgaagtaaaatttgttaaaaagtttccggttggaattggatctttcaaacatctgttatttgtaatagtgtcaagagcttgttttgttcccttggaaaattatttcacttatttgatttgcctgatgatgttccagACCTTGTTGTTCGATCCCATGAAGTGAAAGATGAAGGCTATGAAATTGAACATGATGGAAAGCTTATAACGGTGTTCTCTGCTCCCAATTATTGCGACCA-
| | |||| | |||| | | | | | || | ||| || ||| | || | | | | | || |||| | ||||| ||||| |||||||| || || || || ||||| |||||||||||||| || || ||||| ||||| |||||||| ||||| || |||||
--------------------------------------------------------tatgttttgcattagtctgatgttttattaatgcttatttgttc--tttaatcagtggcttcacataaattaccaatttacagaTTTAGTTGTGCGATCTCATGAAGTAAAGGACGAGGGTTATGAGATTGAACATGATGGTAAACTCATAACTGTGTTTTCTGCTCCAAATTACTGTGACCAG
upper sequence: LOC_Os05g11550.1 (Oryza sativa), 3'ss of exon 10
lower sequence: AT2G42810.2 (Arabidopsis thaliana), 3'ss of exon 11
gtatgaagtaaaatttgttaaaaagtttccggttggaattggatctttcaaacatctgttatttgtaatagtgtcaagagcttgttttgttcccttggaaaattatttcacttatttgatttgcctgatgatgttccagACCTTGTTGTTCGATCCCATGAAGTGAAAGATGAAGGCTATGAAATTGAACATGATGGAAAGCTTATAACGGTGTTCTCTGCTCCCAATTATTGCGACCA
||| | |||| | ||| | |||| || || | || | || |||| | | || |||| |||| | |||| ||| |||| | | || || || |||||||| ||||||||||| ||||| |||||||||| || || || ||||| || |||||||| || ||||| || || ||
-------------------------------gttagttcactgtcttgttattatcggg-gtttg-----gtttcgcaaactaat---atttacttgagatagctattaacttgc---attttcatgat--tgtggcagATTTGTTGGTCCGGTCACATGAAGTAAAAGATGAAGGTTATGAGGTTGAACATGACGGTAAACTCATAACTGTCTTCTCTGCGCCAAATTACTGTGATCA
upper sequence: LOC_Os05g11550.1 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv12s0142g00720.t01 (Vitis vinifera), 3'ss of exon 4
gtatgaagtaaaatttgttaaaaagtttccggttggaattggatctttcaaacatctgttatttgtaatagtgtcaagagct-tgttttgttcccttggaaaattatttcacttatttgatttgcctgatgatgttccagACCTTGTTGTTCGATCCCATGAAGTGAAAGATGAAGGCTATGAAATTGAACATGATGGAAAGCTTATAACGGTGTTCTCTGCTCCCAATTATTGCGACCA
| ||| || || ||| | | | | | ||||||| | | | |||| | || ||| ||| |||| | ||||| ||||| |||||||| || |||||||||||||| |||||||||||||| |||||||| || ||||| |||||||| || ||||| || ||
-----------------------------------------------gtacttctctactaatttgtatattatttatggtcatattttgttga---agtcactctcttcatgcacatggcttgtttga--------cagATTTAGTTGTGCGATCTCATGAAGTAAAGGATGAAGGCTATGAGATTGAACATGATGGCAAGCTTATTACTGTGTTTTCTGCTCCAAACTATTGTGATCA
upper sequence: LOC_Os05g11550.1 (Oryza sativa), 3'ss of exon 10
lower sequence: PP1S80_144V6.1 (Physcomitrella patens), 3'ss of exon 9
gtatgaagtaaaatttgttaaaaagtttccggttggaattggatctttcaaacatctgttatttgtaatagtgtcaagagcttgttttgttcccttggaaaattatttcacttatttgatttgcctgatgatgttccagACCTTGTTGTTCGATCCCATGAAGTGAAAGATGAAGGCTATGAAATTGAACATGATGGAAAGCTTATAACGGTGTTCTCTGCTCCCAATTATTGCGACCA
| | | ||| | | ||| || | | ||| || || | | || || ||| | | | | ||| | | | || |||| ||||| || || |||||||| ||||| ||||| || |||||| |||| || | ||| || ||||| || || ||||||||||||||||| ||||| ||
------------------------------------atgagtgtattttagttcatttttaattctgttcgtggcatgaattagaaacgtaattttctgtt-ctatcttgcggggtggttttactt--ttctggaacagAACTTGTGGTGCGGTCCCATGAGGTGAAGGATGAGGGTTATGAACTTGACCACGGTGGCAAACTTATTACCGTCTTCTCTGCTCCCAATTACTGCGATCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttgttcccttggaaaattatttcacttatttgatttgcctgatgatgttccagACCTTGTTGTTCGATCCCATGAAGTGAAAGATGAAGGCTATGAAATTGAACATGATGGAAAGCTTATAACGGTGTTCTCTGCTCCCAATTATTGCGACCA
gcctgat putative branch site (score: 4)
aaaattatttcactta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgaagtaaaatttgttaaaaagtttccggttggaattggatctttcaaacatctgttatttgtaatagtgtcaagagcttgttttgttcccttggaaaattatttcacttatttgatttgcctgatgatgttccagACCTTGTTGTTCGATCCCATGAAGTGAAAGATGAAGGCTATGAAATTGAACATGATGGAAAGCTTATAACGGTGTTCTCTGCTCCCAATTATTGCGACCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA