Sequence
atgc intronic sequence ATGC exonic sequence...ttatgaatcatgaatgcatttggtagctgagatatatatggatcattgataattgattagggttcttacgtttgtgtgatggatggatggatgggtgcagGAGCTACTACCGGTGCACGACGCAGAAGTGCCCGGTGAAGAAGAGGGTGGAGCGGTCGTACCAGGACGCGGCGGTGGTGATCACCACCTACGAGGGGAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os05g49100.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g49100.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G453571_T01 (Zea mays), 3'ss of exon 2
ttatgaatcatgaatg-catttggtagctgagatatatatggatcattgataattgattagggttcttacgtttgtgtgatggatggatggatgggtgc--agGAGCTACTACCGGTGCACGACGCAGAAGTGCCCGGTGAAGAAGAGGGTGGAGCGGTCGTACCAGGACGCGGCGGTGGTGATCACCACCTACGAGGGGAAG
|| | || | | || | ||| | || || || | | | | | | ||| | || | | |||| ||||| || ||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||| |||||||| |||
-tagggttcccacacgacacgagcgagcagcaatgagcat--atggtgaccacgtcgtactgactgatacaataatgcaacgatatgatgcatgggcgcgcagGAGCTACTACCGGTGCACGACGCAGAAGTGCCCGGTGAAGAAGCGGGTGGAGCGGTCGTACCAGGACGCGGCGGTGGTGATCACCACGTACGAGGGCAAG
upper sequence: LOC_Os05g49100.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA08G08720.1 (Glycine max), 3'ss of exon 2
ttatgaatcatgaatgcatttggtagctgagatatatatggatcattgataattgattagggttcttacgtttgt---gtgatggatggatggatgggtgcagGAGCTACTACCGGTGCACGACGCAGAAGTGCCCGGTGAAGAAGAGGGTGGAGCGGTCGTACCAGGACGCGGCGGTGGTGATCACCACCTACGAGGGGAAG
| | || | || | | | |||| || | | | || | | | | |||| ||||| || ||| ||||||||||||||| ||||||| || ||||||||| | |||||||| | |||||| |||| | |||||| | | ||||| || || || || || |
--aatggtttcgatttgtttaatttaattaccaatat-tgtagtagtaatggccaaagtgaaaaatgaagtttaatagatgatgaatatgatgataattgcagGAGCTACTACAGGTGCACTACACAGAAGTGCACAGTGAAGAAACGCGTGGAGAGGTCATTTCAGGACCCAACCACTGTGATAACAACGTATGAAGGTCAA
upper sequence: LOC_Os05g49100.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA05G25770.1 (Glycine max), 3'ss of exon 2
ttatgaatcatgaatgca-tttggtagctgagatatatatggatcattgataattgattagggttcttacgtttgtgtgatggat--ggatggatggg-----tgcagGAGCTACTACCGGTGCACGACGCAGAAGTGCCCGGTGAAGAAGAGGGTGGAGCGGTCGTACCAGGACGCGGCGGTGGTGATCACCACCTACGAGGGGAAG
||| | || ||| | | | || |||| || | | | || | | | | ||||| | || || || || ||| ||||||||||||||| ||||||| || ||||||||| | |||||||| | |||||| |||| | |||||| | | ||||| || || || || || ||
-------caatggcttcaatttcttggtttagcaatat-tgtagtagtaatggccaaagtgaaaaatgaagtttgatagctgaataagggtgaatgataatattgcagGAGCTACTACAGGTGCACAACACAGAAGTGCACAGTGAAGAAACGCGTGGAGAGGTCATTTCAGGACCCAACCACTGTGATAACAACGTATGAAGGTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgataattgattagggttcttacgtttgtgtgatggatggatggatgggtgcagGAGCTACTACCGGTGCACGACGCAGAAGTGCCCGGTGAAGAAGAGGGTGGAGCGGTCGTACCAGGACGCGGCGGTGGTGATCACCACCTACGAGGGGAAG
ttcttac putative branch site (score: 2)
aattgatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttatgaatcatgaatgcatttggtagctgagatatatatggatcattgataattgattagggttcttacgtttgtgtgatggatggatggatgggtgcagGAGCTACTACCGGTGCACGACGCAGAAGTGCCCGGTGAAGAAGAGGGTGGAGCGGTCGTACCAGGACGCGGCGGTGGTGATCACCACCTACGAGGGGAAG
- -tgaatca
- - - - - tgaatgc
- - - - - - - - - - - gtagctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atggatg