Sequence
atgc intronic sequence ATGC exonic sequence...tcttgtcaatctgcaacataatattttcttgtggcaatatcatatgtatattgagttgtgccactaaaatatttgactgattgactcctttcgcttccagGCAGGAATTGGCACTGATGCAACGATGCATGATCACATAAAAAAGTTACTTGACCGTTGTTATGCAACCAAAGATGCAAATACACGGTTCTCCCCAACAA
Basic information
species | Oryza sativa |
transcript | LOC_Os03g06900.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g06900.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G470438_T02 (Zea mays), 3'ss of exon 12
------------tcttgtcaatctgcaacataatattttcttgtggcaatatcatatgta----tattgagttgtgccactaaa---------atatt--tgactga-------------ttgactcctttc------gcttccagGCAGGAATTGGCACTGATGCAACGATGCATGATCACATAAAAAAGTTACTTGACCGTTGTTATGCAACCAAAGATGCAAATACACGGTTCTCCCCAACAA
| | | || | | || | |||| | | || || ||| | | || |||||||||| || |||| | | | | ||||| || ||||||||||||||||||||||||||||| ||||||||||||||||||||||| |||||||||||||||||||||||||||| ||| ||||| |||||||| ||||
gtaaaaaaatccttcttttaacccacgttgtatttttttatggcaataacttcgtattcagaattggtggattgtgccacttaatgcatctacatatccataatttaaaatcatgcagatttgacattttcttattatatttccagGCAGGAATTGGCACTGATGCAACCATGCATGATCACATAAAAAAGTTGCTTGACCGTTGTTATGCAACCAAAGATGAAAACACACGTTTCTCCCCGACAA
upper sequence: LOC_Os03g06900.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G470438_T05 (Zea mays), 3'ss of exon 4
------------tcttgtcaatctgcaacataatattttcttgtggcaatatcatatgta----tattgagttgtgccactaaa---------atatt--tgactga-------------ttgactcctttc------gcttccagGCAGGAATTGGCACTGATGCAACGATGCATGATCACATAAAAAAGTTACTTGACCGTTGTTATGCAACCAAAGATGCAAATACACGGTTCTCCCCAACAA
| | | || | | || | |||| | | || || ||| | | || |||||||||| || |||| | | | | ||||| || ||||||||||||||||||||||||||||| ||||||||||||||||||||||| ||||||||||||||||||||
gtaaaaaaatccttcttttaacccacgttgtatttttttatggcaataacttcgtattcagaattggtggattgtgccacttaatgcatctacatatccataatttaaaatcatgcagatttgacattttcttattatatttccagGCAGGAATTGGCACTGATGCAACCATGCATGATCACATAAAAAAGTTGCTTGACCGTTGTTATGCAAC--------------------------------
upper sequence: LOC_Os03g06900.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G470438_T04 (Zea mays), 3'ss of exon 4
------------tcttgtcaatctgcaacataatattttcttgtggcaatatcatatgta----tattgagttgtgccactaaa---------atatt--tgactga-------------ttgactcctttc------gcttccagGCAGGAATTGGCACTGATGCAACGATGCATGATCACATAAAAAAGTTACTTGACCGTTGTTATGCAACCAAAGATGCAAATACACGGTTCTCCCCAACAA----
| | | || | | || | |||| | | || || ||| | | || |||||||||| || |||| | | | | ||||| || ||||||||||||||||||||||||||||| ||||||||||||||||||||||| |||||||||||||||||||||||||||| ||| ||||| |||||||| ||||
gtaaaaaaatccttcttttaacccacgttgtatttttttatggcaataacttcgtattcagaattggtggattgtgccacttaatgcatctacatatccataatttaaaatcatgcagatttgacattttcttattatatttccaggcagGAATTGGCACTGATGCAACCATGCATGATCACATAAAAAAGTTGCTTGACCGTTGTTATGCAACCAAAGATGAAAACACACGTTTCTCCCCGACAAATCT
upper sequence: LOC_Os03g06900.1 (Oryza sativa), 3'ss of exon 11
lower sequence: AT5G63920.1 (Arabidopsis thaliana), 3'ss of exon 12
--------------------------tcttgtcaatctgcaacataatattttcttgtggcaatatca-tatgtat-attgagttgtgccactaaaatatttgactgattgactcctttcgcttccagGCAGGAATTGGCACTGATGCAACGATGCATGATCACATAAAAAAGTTACTTGACCGTTGTTATGCAACCAAAGATGCAAATACACGGTTCTCCCCAACAA
|| | || || | || |||||| || | || ||| || || || ||| | ||| | || | | | ||||||| |||||||| ||||| || ||||| || |||||||| || | ||||| || |||||||||| || ||||| ||||||||||| || ||||| |
gtttttaaaattttcttgtttccccttcctttcgtggtggtgt-ttgcatactcttgttcacctacccctacttatcatccgattatgtttgtaac-tctttattatcctaccttttgtgaatgttagGCAGGCATTGGCACCGATGCGACAATGCACGACCACATAAAGAAACTCCTTGATCGGGGTTATGCAACAAAGGATGCTAATACACGGTTTTCTCCAACCA
upper sequence: LOC_Os03g06900.1 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv04s0044g01570.t01 (Vitis vinifera), 3'ss of exon 5
---------------------------------------------tcttgtcaatctgcaacataatattttcttgtggcaatatcatatgtatattgagttgt-gccactaaaatatttgactgattgactcctttcgcttccagGCAGGAATTGGCACTGATGCAACGATGCATGATCACATAAAAAAGTTACTTGACCGTTGTTATGCAACCAAAGATGCAAATACACGGTTCTCCCCAACAA
||||| | | || ||||| | | | ||| | | || || | | | | || |||| | || | | || | |||| || ||||| || |||||||| ||||||||||||||||||||| | || || || | ||||||||| || || ||||||| || ||||| |||||||
gtaatgaagattaagtatctgtttttagcttaaggttggttattgaattgtctttttatggtctataattttgaattactagt--catttactttttcagacattgaaagtgaactattccttttcttt-tacttgtctttcttagGCTGGCATTGGTACAGATGCAACAATGCATGATCACATAAAAAAGCTGCTGGATCGGTTTTATGCAACTAAGGACTCAAATACTCGTTTCTCACCAACAA
upper sequence: LOC_Os03g06900.1 (Oryza sativa), 3'ss of exon 11
lower sequence: EFJ13984 (Selaginella moellendorffii), 3'ss of exon 12
tcttgtcaatctgcaacataatattttcttgtggcaatatcatatgtatattgagttgtgccactaaaatatttgactgattgactcctttcgcttccagGCAGGAATTGGCACTGATGCAACGATGCATGATCACATAAAAAAGTTACTTGACCGTTGTTATGCAACCAAAGATGCAAATACACGGTTCTCCCCAACAA
| | | | | | || || | | | || | || ||||| |||||||| || ||||| || ||||||||||||||||||||| | || ||||| | || || ||||||||||| | ||||| || | || ||||
-------------------------------------------------gtggtttcttagttccagcattttcaagacctgaattctctgtgcggccagGAGGGAATTGGAACGGATGCTACTATGCATGATCACATAAAAAAGCTGCTGGACCGGCGCTACGCTACCAAAGATGCGCAGACACGCTTTTGTCCCACAA
upper sequence: LOC_Os03g06900.1 (Oryza sativa), 3'ss of exon 11
lower sequence: EFJ28114 (Selaginella moellendorffii), 3'ss of exon 12
tcttgtcaatctgcaacataatattttcttgtggcaatatcatatgtatattgagttgtgccactaaaatatttgactgattgactcctttcgcttccagGCAGGAATTGGCACTGATGCAACGATGCATGATCACATAAAAAAGTTACTTGACCGTTGTTATGCAACCAAAGATGCAAATACACGGTTCTCCCCAACAA
| | | | | | || || | | | || | | ||||| |||||||| || ||||| || ||||||||||||||||||||| | || ||||| | || || ||||||||||| | ||||| || | || ||||
-------------------------------------------------gtggtttcttagttccagcattttcaagacctgaattctctgtgtggccagGAGGGAATTGGAACGGATGCTACTATGCATGATCACATAAAAAAGCTGCTGGACCGGCGCTACGCTACCAAAGATGCGCAGACACGCTTTTGTCCCACAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtatattgagttgtgccactaaaatatttgactgattgactcctttcgcttccagGCAGGAATTGGCACTGATGCAACGATGCATGATCACATAAAAAAGTTACTTGACCGTTGTTATGCAACCAAAGATGCAAATACACGGTTCTCCCCAACAA
ctcctttcgcttcc CT-rich tract
actaaaatatttga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcttgtcaatctgcaacataatattttcttgtggcaatatcatatgtatattgagttgtgccactaaaatatttgactgattgactcctttcgcttccagGCAGGAATTGGCACTGATGCAACGATGCATGATCACATAAAAAAGTTACTTGACCGTTGTTATGCAACCAAAGATGCAAATACACGGTTCTCCCCAACAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - atctgca
- - - - - - - - - - - - tttcttg
- - - - - - - - - - - - - - - - - - - - - tatgtat
- - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgtgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - actaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgattg