Sequence
atgc intronic sequence ATGC exonic sequence...ctgtaagcatgtatactttgcagttgacctaatgacctgtgcgctcggctcaactaacttggcgatacgatggttcgttgggtggttgtgatggatacagGGGATACTACAAGTGCAGCAGCATGAAGGGGTGCATGGCCAGGAAGATGGTGGAGCGCAGCCCGGCCAAGCCCGGGATGCTCGTCGTCACCTACATGGCC
Basic information
species | Oryza sativa |
transcript | LOC_Os01g43550.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g43550.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G105140_T01 (Zea mays), 3'ss of exon 2
-ctgtaagcatgtatactttgcagttgacctaatgacctgtgcgctcggctcaactaacttggcgatacgatggtt-cgttgggtggttgtg-atggatacagGGGATACTACAAGTGCAGCAGCATGAAGGGGTGCATGGCCAGGAAGATGGTGGAGCGCAGCCCGGCCAAGCCCGGGATGCTCGTCGTCACCTACATGGCC
| || | ||| |||||||||| || | || || || | | | | | ||| ||| || |||| | | ||| |||||| ||||||||||||||||||||||||||||||||||| ||||| |||||||||||||||| || ||||||||| ||||| ||||||||||||||||
atagccgtactgcgtgctt-gcagttgaccctgtggc-tgctggcccg-cacgctcagcgaactaacgcgactgttgcgatgggaattgatctgtggccgcagGGGGTACTACAAGTGCAGCAGCATGAAGGGGTGCATGGCGCGGAAGCTGGTGGAGCGCAGCCCAGCGAAGCCCGGGGTGCTCATCGTCACCTACATGGCG
upper sequence: LOC_Os01g43550.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G149683_T01 (Zea mays), 3'ss of exon 2
---------------------------------------------------------------------------------------------ctgtaagcatgtatactttgcagttgacctaatgacctgtgcgct--cggctcaactaacttggcgat---acgatggttcgttggg--tggttgtgatggatacagGGGATACTACAAGTGCAGCAGCATGAAGGGGTGCATGGCCAGGAAGATGGTGGAGCGCAGCCCGGCCAAGCCCGGGATGCTCGTCGTCACCTACATGGCC
| | | || | ||| ||||| ||| | || || || | | | | || ||| | ||| | ||||| | | | || |||||| ||||||||||||||||||||||||||||||| ||| ||||| |||||||||||||||| |||||||||||| ||||| ||||||| |||||||||
gtaactacgttgttttttactttgacctcgccttccatactgcgtgcttgctagtgttaggagctttgataattcagccacaagacaattcgacagcagtagtgcgtgctt-gcagtcgacattgtggccgctgaggcgctgacccgcagggctcaccgaactaataatgctccgttgcgattcgaatctgtgaccgcagGGGGTACTACAAGTGCAGCAGCATGAAGGGGTGCACGGCGCGGAAGCTGGTGGAGCGCAGCCCAGCCAAGCCCGGGGTGCTCATCGTCACGTACATGGCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cggctcaactaacttggcgatacgatggttcgttgggtggttgtgatggatacagGGGATACTACAAGTGCAGCAGCATGAAGGGGTGCATGGCCAGGAAGATGGTGGAGCGCAGCCCGGCCAAGCCCGGGATGCTCGTCGTCACCTACATGGCC
aactaac putative branch site (score: 1)
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctgtaagcatgtatactttgcagttgacctaatgacctgtgcgctcggctcaactaacttggcgatacgatggttcgttgggtggttgtgatggatacagGGGATACTACAAGTGCAGCAGCATGAAGGGGTGCATGGCCAGGAAGATGGTGGAGCGCAGCCCGGCCAAGCCCGGGATGCTCGTCGTCACCTACATGGCC
- - - gcatgta
- - - - - - - -ctttgca
- - - - - - - - - - - - - - - - - -cctgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - caactaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtggttg