Sequence
atgc intronic sequence ATGC exonic sequencegtgacgctgctttaccctttgttaattcttgttaaatgtgtttggattattgtctgatcaatgcattcctgattttagGAAGGGAGATTACTACCGGTACCTTGCAGAGTTCAAGACTGGGACTGAGAAGATTGAAGTGTCTGAACTGTCACTCAATGCTTATGAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g11110.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g11110.2 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S67_176V6.1 (Physcomitrella patens), 3'ss of exon 2
----------------------------------------------------------------------------------------gtgacgctgctttaccctttgttaattcttgttaaatgtgtttggattattgtctgatcaatgcattcc-----tgattttagGAAGGGAGATTACTACCGGTACCTTGCAGAGTTCAAGACTGGGACTGAGAAGATTGAAGTGTCTGAACTGTCACTCAATGCTTATGAG
| | | | | || | || | | | | | | | | ||| || | | || | |||||||| |||||||| || |||||||| ||||||||||| || | || | || |||| |||| | || | || |||||| ||
gtacgtgatgttctgagagagaagttattagtgttttgttaggagttttgtttgtgatttatcacaatgtggactacgtggaaaagtgatcataactgctcagattcagtgcgcaagtcttcatttcgcgttggtggtaatttgactaaagatctatgggaatggtaccagGAAGGGTGATTACTATCGTTACCTTGCCGAGTTCAAGACCGGAAACGATAGGAAAGAAGCCGCTGACCAATCTTTGAAGGCTTATCAG
upper sequence: LOC_Os01g11110.2 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S201_25V6.1 (Physcomitrella patens), 3'ss of exon 2
-----gtgacgct-gctttaccctttgttaattcttgttaaatgtgtttggattat--tgtctga---tcaatgcattcctg-----------attttagGAAGGGAGATTACTACCGGTACCTTGCAGAGTTCAAGACTGGGACTGAGAAGATTGAAGTGTCTGAACTGTCACTCAATGCTTATGAG
| | || | ||| | | | | | |||| ||| || | || | || ||| | ||| || |||||||||||| |||||||||||||| || |||||||| |||||| |||||| | |||| |||| | || | || || || ||
atcggttaattcttgaccggtcctatagtcgtcttcaagaggagtgtctggtttgtgctgacagaagtctgatgtttgtctgtgatgggcggggttctagGAAGGGAGACTACTACCGGTACCTGGCGGAGTTCAAAACTGGGGCTGAGAGAAAAGAAGCTGCTGACCAATCTTTGAAGGCCTACCAG
upper sequence: LOC_Os01g11110.2 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S46_127V6.1 (Physcomitrella patens), 3'ss of exon 2
---------------gtgacgctgctttaccctttgttaattcttgttaa-atgtg-tttggattattgtctgatcaatgcattcctgattt-----tagGAAGGGAGATTACTACCGGTACCTTGCAGAGTTCAAGACTGGGACTGAGAAGATTGAAGTGTCTGAACTGTCACTCAATGCTTATGAG
| | | | | || | | ||| || | | ||| || | | | | |||| |||| | | | |||||||||||||||||| |||||||| || ||||||||||| |||| ||||| || || | |||| | || | || || || ||
cgagaaggataatctgcggatcgcatccgcagttagctctgactttttgagacgtgacctgaaatctgttttgatatatgcgtgatgggtggggtgatagGAAGGGAGATTACTATCGGTACCTGGCGGAGTTCAAGACCGGGAATGAGAGGAAAGAGGCCGCTGACCAATCTTTGAAGGCATACCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aattcttgttaaatgtgtttggattattgtctgatcaatgcattcctgattttagGAAGGGAGATTACTACCGGTACCTTGCAGAGTTCAAGACTGGGACTGAGAAGATTGAAGTGTCTGAACTGTCACTCAATGCTTATGAG
tcctgat putative branch site (score: 3)
cattcct CT-rich tract
ttgttaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgacgctgctttaccctttgttaattcttgttaaatgtgtttggattattgtctgatcaatgcattcctgattttagGAAGGGAGATTACTACCGGTACCTTGCAGAGTTCAAGACTGGGACTGAGAAGATTGAAGTGTCTGAACTGTCACTCAATGCTTATGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG