Sequence
atgc intronic sequence ATGC exonic sequencegtacgcttatgttgaagattacttctggttgacaataaaaattaatactcttaagttgtagattacttctggttgacgataaaagttgtgtaacctgtagGCTATCTGCAAAACTGCACAGGATATTGCAAATCCAATTATTGCAGAGAATAAAGAAAAATATAAAATAGATTCTATTGAGTTTGAAACACTTACTCTGG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g60350.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g60350.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G111737_T01 (Zea mays), 3'ss of exon 4
gtacgcttatgttgaagattacttctggttgacaataaaaattaatactcttaagttgtagattacttctggttgacgataaaagttgtgt--aacctgtagGCTATCTGCAAAACTGCACAGGATATTGCAAATCCAATTATTGCAGAGAATAAAGAAAAATATAAAATAGATTCTATTGAGTTTGAAACACTTACTCTGG
|||| | || || | ||| ||||| |||| | ||| | || ||| |||| | | | | || | | |||| | | ||||||||||||||||| ||||||||| ||||| || || ||||||||||| ||||||| | || ||||| ||||| || |||||||||||||||||||| |||
gtacccgcatctt-atcatttgctctgg--gacagcataaaatcattatctctggttg-acactgaatttgccatgctttgtgttttgtttttatcctgtagGCTATCTGCAGAACTGCACAAGATATCGCGAAGCCAATTATTGCTGAGAATACTGCTAAGTATAACATAGACACTGTTGAGTTTGAAACACTTACTTTGG
upper sequence: LOC_Os01g60350.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G050193_T03 (Zea mays), 3'ss of exon 2
----gtacgcttatgttgaagattacttctggttgacaataaaa-attaatactcttaagttgtagattacttctggttgacgataaaagttgtgtaacctgtagGCTATCTGCAAAACTGCACAGGATATTGCAAATCCAATTATTGCAGAGAATAAAGAAAAATATAAAATAGATTCTATTGAGTTTGAAACACTTACTCTGG
|||| ||||| ||| || || | ||| || | |||| | | | ||| || || | | || | | ||||||||||||||| ||||||||||||||| || || ||||||||||| ||||| | | ||| ||||| ||||| ||| ||||||||||| |||||||| |||
caaggtactcttatcttgtcatttgctctgag--aacactagatcattatctccggttgacactgaattttccatgctttgtgttttgtttt---tgccttgtagGCTATCTGCAGAACTGCACAGGATATCGCGAAGCCAATTATTGCTGAGAACACTGCAAAGTATAAGATAGACTCTGTTGAGTTTGAATCACTTACTTTGG
upper sequence: LOC_Os01g60350.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G050193_T02 (Zea mays), 3'ss of exon 4
gtacgcttatgttgaagattacttctggttgacaataaaa-attaatactcttaagttgtagattacttctggttgacgataaaagttgtgtaacctgtagGCTATCTGCAAAACTGCACAGGATATTGCAAATCCAATTATTGCAGAGAATAAAGAAAAATATAAAATAGATTCTATTGAGTTTGAAACACTTACTCTGG
|||| ||||| ||| || || | ||| || | |||| | | | ||| || || | | || | | ||||||||||||||| ||||||||||||||| || || ||||||||||| ||||| | | ||| ||||| ||||| ||| ||||||||||| |||||||| |||
gtactcttatcttgtcatttgctctgag--aacactagatcattatctccggttgacactgaattttccatgctttgtgttttgtttt---tgccttgtagGCTATCTGCAGAACTGCACAGGATATCGCGAAGCCAATTATTGCTGAGAACACTGCAAAGTATAAGATAGACTCTGTTGAGTTTGAATCACTTACTTTGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tactcttaagttgtagattacttctggttgacgataaaagttgtgtaacctgtagGCTATCTGCAAAACTGCACAGGATATTGCAAATCCAATTATTGCAGAGAATAAAGAAAAATATAAAATAGATTCTATTGAGTTTGAAACACTTACTCTGG
gtgtaac putative branch site (score: 3)
ataaaagtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgcttatgttgaagattacttctggttgacaataaaaattaatactcttaagttgtagattacttctggttgacgataaaagttgtgtaacctgtagGCTATCTGCAAAACTGCACAGGATATTGCAAATCCAATTATTGCAGAGAATAAAGAAAAATATAAAATAGATTCTATTGAGTTTGAAACACTTACTCTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA