Sequence
atgc intronic sequence ATGC exonic sequencegttgttttttttaaatgaacttttttcccatagcatatgcccctgtaggaggaaacataacttgggctcactgattgattcttttttcttcacctagTCTCCTCCATCTGAAGTTCAGGACAAGATCATGTTTATGATTAATAATATATCAATCTCAAATATGGAGGCTAAGGCAAAAGAATGTATTGAGGTACTCC
Basic information
species | Oryza sativa |
transcript | LOC_Os03g01240.1 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g01240.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G435765_T01 (Zea mays), 3'ss of exon 3
gttgttttttttaaatgaacttttttcccatagcatatgcccctgtaggaggaaacataacttgggctcactgattgattcttttttcttcacctagTCTCCTCCATCTGAAGTTCAGGACAAGATCATGTTTATGATTAATAATATATCAATCTCAAATATGGAGGCTAAGGCAAAAGAATGTATTGAGGTACTCC---------------------
| ||| || | || | | | | | | || | |||||||| || | | || || |||| ||||| |||||| ||||||||||||||||||| | |||||||| || |||||||| |||||||||||||| ||||||||||| |||| || ||||| | |
--------------gttggttttgttttctgag--tttcctcttttgggttaatacataactca---tcccgtgctaatggacttctcttaacctaaatacctccacctgaagttcagGACAAGATTCTTTTTATGATCAACAATATATCCATCTCAAATATGGAAGCTAAGGCAAAGGAATTTAACGAGGTCATACAGGAACAGCATTATCCTTGGT
upper sequence: LOC_Os03g01240.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G414487_T01 (Zea mays), 3'ss of exon 2
gttgttttttttaaatgaacttttttcccatagcatatgcccctgtaggaggaaacataacttgggctcactgattgattcttttttcttcacctagTCTCCTCCATCTGAAGTTCAGGACAAGATCATGTTTATGATTAATAATATATCAATCTCAAATATGGAGGCTAAGGCAAAAGAATGTATTGAGGTACTCC
|| || ||| || | | | | | | | || | |||||||| || | | || || |||| | |||| | |||||| || |||||||||||||||| | |||||||| || |||||||| |||||||||||||| ||||||||||| |||| || |||||| | |
-------------gttggttttgttttcc---gagtttcctcttttgggttaatacataactca---tcccgtgctaatggacttctcttaaactagACACCTCCACCTAAAGTTCAGGACAAGATTCTTTTTATGATCAACAATATATCCATCTCAAATATGGAAGCTAAGGCAAAGGAATTTAATGAGGTCATAC
upper sequence: LOC_Os03g01240.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G467385_T01 (Zea mays), 3'ss of exon 2
gttgttttttttaaatgaacttttttcccatagcatatgcccctgtaggaggaaacataacttgggctcactgattgattcttttttcttcacctagTCTCCTCCATCTGAAGTTCAGGACAAGATCATGTTTATGATTAATAATATATCAATCTCAAATATGGAGGCTAAGGCAAAAGAATGTATTGAGGTACTCC---------------------
| ||| || | || | | | | | | || | |||||||| || | | || || |||| |||||| | |||||| ||||||||||||||||||| | |||||||| || |||||||| |||||||||||||| ||||||||||| |||| || |||||| | |
--------------gttggttttgttttctgag--tttcctcttttgggttaatacataactca---tcccgtgctaatagacttctcttaacctagacacctccacctgaagttcagGACAAGATTCTTTTTATGATCAACAATATATCCATCTCAAATATGGAAGCTAAGGCAAAGGAATTTAATGAGGTCATACAGGAACAGTATTATACTTGGT
upper sequence: LOC_Os03g01240.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G424289_T01 (Zea mays), 3'ss of exon 3
gttgttttttttaaatgaacttttttcccatagcatatgcccctgtaggaggaaacataacttgggctcactgattgattcttttttcttcacctagTCTCCTCCATCTGAAGTTCAGGACAAGATCATGTTTATGATTAATAATATATCAATCTCAAATATGGAGGCTAAGGCAAAAGAATGTATTGAGGTACTCC
| ||| || | || | | | | | | || | |||||||| || | | || || |||| || ||| | |||||| ||||||||||||||||||| | |||||||| || |||||||| |||||||||||||| ||||||||||| |||| || |||| | |
--------------gttggttttgttttctgag--tttcctcttttgggttaatacataactca---tcccgtgctaatgaacttctcttaacttagACACCTCCACCTGAAGTTCAGGACAAGATTCTTTTTATGATCAACAATATATCCATCTCAAATATGGAAGCTAAGGCAAAGGAATTTAACAAGGTCATAC
upper sequence: LOC_Os03g01240.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G082573_T01 (Zea mays), 3'ss of exon 3
gttgttttttttaaatgaacttttttcccatagcatatgcccctgtaggaggaaacataacttgggctcactgattgattcttttttcttcacctagTCTCCTCCATCTGAAGTTCAGGACAAGATCATGTTTATGATTAATAATATATCAATCTCAAATATGGAGGCTAAGGCAAAAGAATGTATTGAGGTACTCC
| ||| || | || | | | | | | || | |||||||| || | | || || |||| || ||| | |||||| ||||||||||||||||||| | |||||||| || |||||||| |||||||||||||| ||||||||||| |||| || ||||| | |
--------------gttggttttgttttctgag--tttcctcttttgggttaatacataactca---tcccgtgctaatggacttctcttaacttagACACCTCCACCTGAAGTTCAGGACAAGATTCTTTTTATGATCAACAATATATCCATCTCAAATATGGAAGCTAAGGCAAAGGAATTTAACGAGGTCATAC
upper sequence: LOC_Os03g01240.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G179406_T01 (Zea mays), 3'ss of exon 2
gttgttttttttaaatgaacttttttcccatagcatatgcccctgtaggaggaaacataacttgggctcactgattgattcttttttcttcacctagTCTCCTCCATCTGAAGTTCAGGACAAGATCATGTTTATGATTAATAATATATCAATCTCAAATATGGAGGCTAAGGCAAAAGAATGTATTGAGGTACTCC---------------------
| ||| || | || | | | | | | || | ||| |||| || | | || || |||| ||||| | |||||| ||||||||||||||||||| | |||||||| || |||||||| |||||||||||||| ||||||||||| |||| || ||||| | |
--------------gttggttttgttttctgag--tttcctcttttgggttaatacaaaactca---tcccgtgctaatggacttctcttaacctaaacacctccacctgaagttcagGACAAGATTCTTTTTATGATCAACAATATATCCATCTCAAATATGGAAGCTAAGGCAAAGGAATTTAACGAGGTCATACAGGAACAGTATTATCCTTGGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgtaggaggaaacataacttgggctcactgattgattcttttttcttcacctagTCTCCTCCATCTGAAGTTCAGGACAAGATCATGTTTATGATTAATAATATATCAATCTCAAATATGGAGGCTAAGGCAAAAGAATGTATTGAGGTACTCC
ttgattcttttttctt CT-rich tract
attgattctttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgttttttttaaatgaacttttttcccatagcatatgcccctgtaggaggaaacataacttgggctcactgattgattcttttttcttcacctagTCTCCTCCATCTGAAGTTCAGGACAAGATCATGTTTATGATTAATAATATATCAATCTCAAATATGGAGGCTAAGGCAAAAGAATGTATTGAGGTACTCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA