Sequence
atgc intronic sequence ATGC exonic sequencegtatgtccttattggtattcatttcatgctcaacctgttcgtcagttctatccttgcagtgttaaagaagaaattaatgataaaattttcatgtttcagTTTACAAGAAGCATCATCCTCCTGCACTAGCTGATGACGTTTGGCGTTTGGAGAAAATTGGGAAAGACGGCGTTTTCCACAAGAAGCTTGCAGACTTTGG
Basic information
species | Oryza sativa |
transcript | LOC_Os03g18960.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g18960.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G006714_T01 (Zea mays), 3'ss of exon 4
-----------gtatgtccttattggtattcatttcatgctcaacc---tgttcgtcagttctatccttgcagtgttaaagaagaaattaatgataaaattttcat--gtttcagTTTACAAGAAGCATCATCCTCCTGCACTAGCTGATGACGTTTGGCGTTTGGAGAAAATTGGGAAAGACGGCGTTTTCCACAAGAAGCTTGCAGACTTTGG
|| | || | | ||| || |||| ||| ||| | | || || || | ||| | | | || ||||| ||||||||||| ||||| |||||| |||| || ||||| |||||| ||||||| || |||||||||||||| |||||||||||||| || ||||| ||
gtaattgaatataattgctctacacttggtttttttttgttcaattctttgtccgttcacgagacacggatagcgtagcgtctgatacaaattttggttcctgaactcgtgtcagTGTACAAGAAGCACCATCCACCTGCATTAGCCGACGACGTGTGGCGTCTGGAGAAGATCGGGAAAGACGGCGTGTTCCACAAGAAGCTGGCGGACTTCGG
upper sequence: LOC_Os03g18960.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G427418_T01 (Zea mays), 3'ss of exon 4
gtatgtccttattggtattcatttcatgctcaacctgttcgtcagttctatccttgcagtgttaaagaagaaattaatgataaaattttcatgtt-------tcagTTTACAAGAAGCATCATCCTCCTGCACTAGCTGATGACGTTTGGCGTTTGGAGAAAATTGGGAAAGACGGCGTTTTCCACAAGAAGCTTGCAGACTTTGG
||| | | | ||| | ||| | | || || | || || | || | | || ||| || | | | |||| ||||||||||| ||||| |||||| |||| || ||||| ||||| ||||||| || |||||||||||||| |||||||||||||| || ||||| ||
--------gtataaatttctgtgccattattttccttgccacgaatt--gcttgtgtttttttgaactctagat-acttatgaaacttccgtcctgataaatccagTGTACAAGAAGCACCATCCACCTGCATTAGCCGACGACGTGTGGCGCCTGGAGAAGATCGGGAAAGACGGCGTGTTCCACAAGAAGCTGGCTGACTTCGG
upper sequence: LOC_Os03g18960.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S34_132V6.1 (Physcomitrella patens), 3'ss of exon 4
------gtatgtccttattggtattcatttcatgctcaacctgttcgtcagttctatccttgcagtgttaaagaagaaattaatgataaaattttcatgtttcagTTTACAAGAAGCATCATCCTCCTGCACTAGCTGATGACGTTTGGCGTTTGGAGAAAATTGGGAAAGACGGCGTTTTCCACAAGAAGCTTG--CAGACTTTGG
|| ||| ||| | ||| | | | | | || | | || || | | |||| || | || | |||||||||||||||||| |||| || || | ||| || |||||||| ||||| || |||||||||||||| | |||||||||| || || ||
tctgccagatttccaagttg-tgatcagaagaagaaagaagggatggtgaa----agcccaacatatctgtatttttgattattgttgttgattactctgttcagTTTACAAGAAGCACTATCCACCAGCCTTGAATGACGAGGTTTGGCGATTGGACAAGATTGGGAAAGACGGTGCTTTCCACAAGCGTCTAAATCAAGCTCA-- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttctatccttgcagtgttaaagaagaaattaatgataaaattttcatgtttcagTTTACAAGAAGCATCATCCTCCTGCACTAGCTGATGACGTTTGGCGTTTGGAGAAAATTGGGAAAGACGGCGTTTTCCACAAGAAGCTTGCAGACTTTGG
aattaat putative branch site (score: 3)
ttttcat putative PPT
ttaaagaagaaattaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtccttattggtattcatttcatgctcaacctgttcgtcagttctatccttgcagtgttaaagaagaaattaatgataaaattttcatgtttcagTTTACAAGAAGCATCATCCTCCTGCACTAGCTGATGACGTTTGGCGTTTGGAGAAAATTGGGAAAGACGGCGTTTTCCACAAGAAGCTTGCAGACTTTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC