Sequence
atgc intronic sequence ATGC exonic sequencegttgggttgagttgttaactcgtaatctatatctcttttggtcttgtggtaacagctctgtcgatacttacagttcatatttatttcagATATTGTTAAGATCGGATCTTATCAAATCTAGTTCTGAGGAACGCTCCTTGCTAAAAAATCTGGGAAGCTGGCTAGGAAAATTCACCATCGGGAGGAACC
Basic information
species | Oryza sativa |
transcript | LOC_Os03g01240.1 |
intron # | 18 |
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 18
lower sequence: GRMZM2G419699_T01 (Zea mays), 3'ss of exon 2
gttgggttgagttgttaactcgtaatctatatctcttttggtcttgtggtaacagctctgtcgatacttacagttcatatttatttcagATATTGTTAAGATCGGATCTTATCAAATCTAGTTCTGAGGAACGCTCCTTGCTAAAAAATCTGGGAAGCTGGCTAGGAAAATTCACCATCGGGAGGAACC---------------------------------
| || ||| | | | ||| || |||| | || || || | | ||| | |||| | | ||| | ||| | ||||||||||| || ||||||||||||||||| ||||| |||||||||||||||| || || || ||| | ||||| |||||||| || ||||| |
----gtttttgttctctccaatttgtctgc-cctatttttattttttgctagccattttgtttaaacttgga---tacttttgctgcaggtcttgttaagatcagaccttatcaaatctagTTCCGAGGAGCGCTCCTTGCTAAAAA-CCTAGGCAGTTGGTTGGGAAAGTTCACCATTGGTAGGAATCAGACACTAAGGGCTAAGGAGATTGATCCAAAAT
upper sequence: LOC_Os03g01240.1 (Oryza sativa), 3'ss of exon 18
lower sequence: AC196144.3_FGT002 (Zea mays), 3'ss of exon 2
gttgggttgagttgttaactcgtaatctatatctcttttggtcttgtggtaacagctctgtcgatacttacagttcatatttatttcagATATTGTTAAGATCGGATCTTATCAAATCTAGTTCTGAGGAACGCTCCTTGCTAAAAAATCTGGGAAGCTGGCTAGGAAAATTCACCATCGGGAGGAACC
| || ||| | | | ||| || |||| | || || || | | ||| | |||| | | ||| | ||| | ||||||||||| || ||||||||||||||||| ||||| |||| |||||||||||| || || | ||| | ||||| |||||||| || ||||| |
----gtttttgttctctccaattcgtctgc-cctgtttttattttttgctagccattttgtttaaacttgga---tacttttgctgcagGTCTTGTTAAGATCAGACCTTATCAAATCTAGTTCCGAGGAGCGCTACTTGCTAAAAAACCTAGGCAATTGGTTGGGAAAGTTCACCATTGGTAGGAATC
upper sequence: LOC_Os03g01240.1 (Oryza sativa), 3'ss of exon 18
lower sequence: GRMZM2G457909_T01 (Zea mays), 3'ss of exon 3
gttgggttgagttgttaactcgtaatctatatctcttttggtcttgtggtaacagctctgtcgatacttacagttcatatttatttcagATATTGTTAAGATCGGATCTTATCAAATCTAGTTCTGAGGAACGCTCCTTGCTAAAAAATCTGGGAAGCTGGCTAGGAAAATTCACCATCGGGAGGAACC---------------------------------
| || ||| | | | ||| || |||| | || || || | | ||| | |||| | | ||| | ||| | ||||||||||| || ||||||||||||||||| ||||| |||||||||||||||| || || || ||| | ||||| |||||||| || ||||| |
----gtttttgttctctccaattcgtctgc-cctgtttttattttttgctagccattttgtttaaacttgga---tacttttgctgcaggtcttgttaagatcagaccttatcaaatctagTTCCGAGGAGCGCTCCTTGCTAAAAA-CCTAGGCAGTTGGTTGGGAAAGTTCACCATTGGTAGGAATCAGGCACTAAGGGCTAAGGAGATTGATCCAAAAT
upper sequence: LOC_Os03g01240.1 (Oryza sativa), 3'ss of exon 18
lower sequence: GRMZM2G424289_T01 (Zea mays), 3'ss of exon 5
gttgggttgagttgttaactcgtaatctatatctcttttggtcttgtggtaacagctctgtcgatacttacagttcatatttatttcagATATTGTTAAGATCGGATCTTATCAAATCTAGTTCTGAGGAACGCTCCTTGCTAAAAAA-TCTGGGAAGCTGGCTAGGAAAATTCACCATCGGGAGGAACC
||| ||||| ||| ||| | | | | | || || || | | ||| | |||| | | ||| | ||| | |||| |||||| || |||||||| |||||||| ||||| ||||||||||||||||| || || || ||| | |||||
-----gttt--ttgttctctc-caattcgtctgcccagtttttttttgctagccattttgtttaaacttgga---tacttttgctgcagGTCTTGTGAAGATCAGACCTTATCAATTCTAGTTCCGAGGAGCGCTCCTTGCTAAAAAAACCTAGGCAGTTGGTTGGGAAAG-------------------
upper sequence: LOC_Os03g01240.1 (Oryza sativa), 3'ss of exon 18
lower sequence: GRMZM2G179406_T01 (Zea mays), 3'ss of exon 5
-------------gttgggttgagttgttaactcgtaatctatatctc----ttttggtcttgtggtaacagctctgtcgatacttacagttcatatttatttcagATATTGTTAAGATCGGATCTTATCAAATCTAGTTCTGAGGAACGCTCCTTGCTAAAAAATCTGGGAAGCTGGCTAGGAAAATTCACCATCGGGAGGAACC
| |||| ||||| ||| |||| | | | | |||| | || || || | | ||| | |||| | | ||| | ||| | ||||||||||| || ||||||||||||||||| ||||| ||||||||||||||||| || || || ||| | ||||| |||||||| || ||||| |
acatatgagaactgcaaggttt--ttgttctctc-taatttgtctgccctgtttttatttttttgctagccattttgtttaaacttgga---tacttttgctgcagGTCTTGTTAAGATCAGACCTTATCAAATCTAGTTCCGAGGAGCGCTCCTTGCTAAAAAACCTAGGCAGTTGGTTGGGAAAGTTCACCATTGGTAGGAATC
upper sequence: LOC_Os03g01240.1 (Oryza sativa), 3'ss of exon 18
lower sequence: GRMZM2G414487_T01 (Zea mays), 3'ss of exon 4
gttgggttgagttgttaactcgtaatctatatctcttttggtcttgtggtaacagctctgtcgatacttacagttcatatttatttcagATATTGTTAAGATCGGATCTTATCAAATCTAGTTCTGAGGAACGCTCCTTGCTAAAAAATCTGGGAAGCTGGCTAGGAAAATTCACCATCGGGAGGAACC
| || ||| | | | ||| || |||| | || || || | | ||| | |||| | | ||| | ||| | ||||||||||| || ||||||||||||||||| ||||| ||||||||||||||||| || || || ||| | ||||| |||||||| || ||||| |
----gtttttgttctctccaattcgtctgc-cctgtttttattttttgctagccattttgtttaaacttgga---tacttttgctgcagGTCTTGTTAAGATCAGACCTTATCAAATCTAGTTCCGAGGAGCGCTCCTTGCTAAAAAACCTAGGCAGTTGGTTGGGAAAGTTCACCATTGGTAGGAATC
upper sequence: LOC_Os03g01240.1 (Oryza sativa), 3'ss of exon 18
lower sequence: GRMZM2G481210_T01 (Zea mays), 3'ss of exon 1
--------------gttgggttgagttgttaactcgtaatctatat---ctcttttggtcttgtggtaacagctctgtcgatacttacagttcatatttatttcagATATTGTTAAGATCGGATCTTATCAAATCTAGTTCTGAGGAACGCTCCTTGCTAAAAAATCTGGGAAGCTGGCTAGGAAAATTCACCATCGGGAGGAACC-
| |||| ||||| ||| ||| | | | || |||| | || || || | | ||| | |||| | | ||| | ||| | ||||||||||| || ||||||||||| ||||| ||||| |||||||||||||||| || || || ||| | ||||| |||||||| || ||||| |
cacatatgagaactgcaaggttt--ttgttctctc-caatttgtctgccctgtttttattttttgctagccattttgtttaaacttgga---tacttttgctgcagGTCTTGTTAAGATCAGACCTTATCAAATCAAGTTCCGAGGAGCGCTCCTTGCTAAAAA-CCTAGGCAGTTGGTTGGGAAAGTTCACCATTGGTAGGAATCA
upper sequence: LOC_Os03g01240.1 (Oryza sativa), 3'ss of exon 18
lower sequence: GRMZM2G082573_T01 (Zea mays), 3'ss of exon 5
gttgggttgagttgttaactcgtaatctatatctcttttggtcttgtggtaacagctctgtcgatacttacagttcatatttatttcagATATTGTTAAGATCGGATCTTATCAAATCTAGTTCTGAGGAACGCTCCTTGCTAAAAAATCTGGGAAGCTGGCTAGGAAAATTCACCATCGGGAGGAACC
| || ||| | | | ||| || |||| | || || || | | ||| | |||| | | ||| | ||| | ||||||||||| || ||||||||||||||| | ||||| ||||||||||||||||| || || || ||| | ||||| |||||||| || ||||| |
----gtttttgttctctccaatttgtctgc-cctgtttttattttttgctagccattttgtttaaacttgga---tacttttgctgcagGTCTTGTTAAGATCAGACCTTATCAAATCTAGTCCCGAGGAGCGCTCCTTGCTAAAAAACCTAGGCAGTTGGTTGGGAAAGTTCACCATTGGTAGGAATC
upper sequence: LOC_Os03g01240.1 (Oryza sativa), 3'ss of exon 18
lower sequence: GRMZM2G179406_T01 (Zea mays), 3'ss of exon 4
gttgggttgagttgttaactcgtaatctatatctcttttggtcttgtggtaacagctctgtcgatacttacagttcatatttatttcagATATTGTTAAGATCGGATCTTATCAAATCTAGTTCTGAGGAACGCTCCTTGCTAAAAAATCTGGGAAGCTGGCTAGGAAAATTCACCATCGGGAGGAACC
| || ||| | | | ||| || |||| | || || || | | ||| | |||| | | ||| | ||| | ||||||||||| | ||||||||||||||||| ||||| ||||||||||||||||| || || || ||| | ||||| |||||||| || ||||| |
----gtttttgttctctccaattcgtctgc-cctgtttttattttttgctagccattttgtttaaacttgga---tacttttgctgcagGTCTTGTTAAGATCAAACCTTATCAAATCTAGTTCCGAGGAGCGCTCCTTGCTAAAAAACCTAGGCAGTTGGTTGGGAAAGTTCACCATTGGTAGGAATC
upper sequence: LOC_Os03g01240.1 (Oryza sativa), 3'ss of exon 18
lower sequence: GRMZM2G435765_T01 (Zea mays), 3'ss of exon 5
gttgggttgagttgttaactcgtaatctatatctcttttggtcttgtggtaacagctctgtcgatacttacagttcatatttatttcagATATTGTTAAGATCGGATCTTATCAAATCTAGTTCTGAGGAACGCTCCTTGCTAAAAAATCTGGGAAGCTGGCTAGGAAAATTCACCATCGGGAGGAACC---------------------------------
| || ||| | | | ||| || |||| | || || || | | ||| | |||| | | ||| | ||| | ||||||||||| | ||||||||||||||||| ||||| |||||||||||||||| || || || ||| | ||||| |||||||| || ||||| |
----gtttttgttctctccaattcgtctgc-cctgtttttattttttgctagccattttgtttaaacttgga---tacttttgctgcaggtcttgttaagatcaaaccttatcaaatctagTTCCGAGGAGCGCTCCTTGCTAAAAA-CCTAGGCAGTTGGTTGGGAAAGTTCACCATTGGTAGGAATCAGGCACTAAGGGCTAAGGAGATTGATCCAAAAT
upper sequence: LOC_Os03g01240.1 (Oryza sativa), 3'ss of exon 18
lower sequence: GRMZM2G467385_T01 (Zea mays), 3'ss of exon 4
gttgggttgagttgttaactcgtaatctatatctcttttggtcttgtggtaacagctctgtcgatacttacagttcatatttatttcagATATTGTTAAGATCGGATCTTATCAAATCTAGTTCTGAGGAACGCTCCTTGCTAAAAAATCTGGGAAGCTGGCTAGGAAAATTCACCATCGGGAGGAACC
| || ||| | | ||| |||| | || || || | | ||| | |||| | | ||| | ||| | ||||||||||| || ||||||||||||||||| ||||| ||||||||||||||||| || || || ||| | ||||| |||||||| || ||||| |
----gtttttgttctctctaatttgtctgccctgtttttatttttttgctagccattttgtttaaacttgga---tacttttgctgcagGTCTTGTTAAGATCAGACCTTATCAAATCTAGTTCCGAGGAGCGCTCCTTGCTAAAAAACCTAGGCAGTTGGTTGGGAAAGTTCACCATTGGTAGGAATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttttggtcttgtggtaacagctctgtcgatacttacagttcatatttatttcagATATTGTTAAGATCGGATCTTATCAAATCTAGTTCTGAGGAACGCTCCTTGCTAAAAAATCTGGGAAGCTGGCTAGGAAAATTCACCATCGGGAGGAACC
tacttac putative branch site (score: 1)
tttatttc putative PPT
agttcatatttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgggttgagttgttaactcgtaatctatatctcttttggtcttgtggtaacagctctgtcgatacttacagttcatatttatttcagATATTGTTAAGATCGGATCTTATCAAATCTAGTTCTGAGGAACGCTCCTTGCTAAAAAATCTGGGAAGCTGGCTAGGAAAATTCACCATCGGGAGGAACC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA