Sequence
atgc intronic sequence ATGC exonic sequence...aatagaaatgttgctacggagcaaagcattattctgggcatgcatttttggttcaatttctttatagctcaataatatttaaccttttgttgcaaagtagGGAGCAAAACAAATTGTTGAAAAAGGCGAGTTCCCTTGCACAGCATCAACACTCCGTGAAGTTCGTGGCATTGGGGATTACACAGCAGGAGCCATTGCTT
Basic information
species | Oryza sativa |
transcript | LOC_Os12g10850.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g10850.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G425986_T01 (Zea mays), 3'ss of exon 3
---------------------------------------------------aatagaaatgtt-gctacggagcaaagcattattctgg-gcatgcatttttggttcaatttctttatagctcaataatatttaaccttttgttgcaaagtagGGAGCAAAACAAATTGTTGAAAAAGGCGAGTTCCCTTGCA-CAGCAT-CAACACTCCGTGAAGTTCGTGGCATTGGGGATTACACAGCAG-GAGCCATTGCTT
|| |||| | ||||| | | | | | | |||||||| ||| ||| || || | | ||| || ||| | | | | |||| || | | | | | || ||||| | || || | | | | ||| | | || ||| || | ||
gttcgtggcattggggattacacagctggagcaatcgcttcaattgccttcaacgaggttgttcacagtttagcaactcgtgaaattagtgtgtgcattttcttttcctttttcgaatgactttgtgaattttctatcattattgtagGTTGTC--------CCAGTTGTGGATGGAAATGTGATACGAGTCATCAGCAGGCTTTACACCAT--TGCTGACAACCCAAAGGAATCCTCAACAGTGAAGAGATTCTG
upper sequence: LOC_Os12g10850.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G425986_T02 (Zea mays), 3'ss of exon 2
------aatagaaatgttgctacggagcaaagcattattctgggcatgcatttttggttcaatttctttatagctcaataatatttaaccttttgttgcaaagtagGGAGCAAAACAAATTGTTGAAAAAGGCGAGTTCCCTTGCACAGCATCAACACTCCGTGAAGTTCGTGGCATTGGGGATTACACAGCAGGAGCCATTGCTT
|| ||| | || | || || || ||| || | | | ||||| | || | | | | | | || |||||||||| || || | ||||| || ||| |||||||| || | | | || ||||| |||||||||||||||||||||||||| ||||| || ||||
aaattttgcagttttgtggtctttacataacactataaactaggaatggatgatctctatctgtggtttatggtcca------tcttctttatgatggagaaacagGGAGCAAAGCAGATCATCGAAAAGGGGTTGTTTCCTTGCACGGCGTTAGCCCTTCGTGAGGTTCGTGGCATTGGGGATTACACAGCTGGAGCAATCGCTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttggttcaatttctttatagctcaataatatttaaccttttgttgcaaagtagGGAGCAAAACAAATTGTTGAAAAAGGCGAGTTCCCTTGCACAGCATCAACACTCCGTGAAGTTCGTGGCATTGGGGATTACACAGCAGGAGCCATTGCTT
atttaac putative branch site (score: 3)
ccttttgtt CT-rich tract
aatttctttatagctc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatagaaatgttgctacggagcaaagcattattctgggcatgcatttttggttcaatttctttatagctcaataatatttaaccttttgttgcaaagtagGGAGCAAAACAAATTGTTGAAAAAGGCGAGTTCCCTTGCACAGCATCAACACTCCGTGAAGTTCGTGGCATTGGGGATTACACAGCAGGAGCCATTGCTT
aatagaaa
- - - - tgttgct
- - - - - - - - - gagcaaa
- - - - - - - - - - - - - - -tattctg
- - - - - - - - - - - - - - - - - - ggcatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttttgt