Sequence
atgc intronic sequence ATGC exonic sequence...agttgactatactattaaacttgctcttatctgtagaaaaaaaatacatttgcatatgtaaatttatatttgtgttgatggtgttctcctataatcatagGCTGCGAACATCCCGAAGAAGTATACTCCGACCATTGGAATTTCCGTGGACCACCGCCGCAAGAACCGCTCACTTGAGGGCTCCAGGCTAAT
Basic information
species | Oryza sativa |
transcript | LOC_Os08g06560.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g06560.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G081102_T03 (Zea mays), 3'ss of exon 3
-agttgactatactattaaacttgctcttatctgtagaaaaaaaatacatttgcatatgtaaatttatatttgtgttgatggtgttctcctataatcatagGCTGCGAACATCCCGAAGAAGTATACTCCGACCATTGGAATTTCCGTGGACCACCGCCGCAAGAACCGCTCACTTGAGGG-CTCCAGGCTAAT-------
| || |||| || || | || |||| | || || | |||| || | || || | | || |||||||| ||| || || | | | |||| |||||||| ||||| ||||| ||||||||||||||| || |||||||| || ||||| |||
aattttgctatctcatggtgtttaatttttgctgttccttttctacttgttgaattaccttgtgttatcttgatattagaagtaactatgt-tgattgcagGCTGCGGGCATTCCAAAAAGGCTTGCTCCAACCATTGGCATTTCTGTGGATCACCGCCGCAAGAACAAATCCCTTGAGGGGCTGCAGGCCAATGTCCAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acatttgcatatgtaaatttatatttgtgttgatggtgttctcctataatcatagGCTGCGAACATCCCGAAGAAGTATACTCCGACCATTGGAATTTCCGTGGACCACCGCCGCAAGAACCGCTCACTTGAGGGCTCCAGGCTAAT
tgttgat putative branch site (score: 4)
ttctcctat putative PPT
atatgtaaatttatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agttgactatactattaaacttgctcttatctgtagaaaaaaaatacatttgcatatgtaaatttatatttgtgttgatggtgttctcctataatcatagGCTGCGAACATCCCGAAGAAGTATACTCCGACCATTGGAATTTCCGTGGACCACCGCCGCAAGAACCGCTCACTTGAGGGCTCCAGGCTAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - -cttgctc
- - - - - - - - - - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - catttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - -atatgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttgatg