Sequence
atgc intronic sequence ATGC exonic sequencegtttgtttgtgaaaatacatgatatatcttctcgtttgcttttcttacatcataaatgttttttttggtactattgtccagGTTCTGTTCGATTTAATCTGGATCCTTTTAATGAGCACAATGATGCGGATCTCTGGGAAGCGCTTGAAAGGGCTCATCTAAAAGATGTCATAAGGAGGAA
Basic information
species | Oryza sativa |
transcript | LOC_Os04g52900.2 |
intron # | 24 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g52900.2 (Oryza sativa), 3'ss of exon 24
lower sequence: GRMZM2G084181_T01 (Zea mays), 3'ss of exon 23
gtttgtttgtgaaaa-tacatgatatatcttctcgtttgcttttcttacatcata-----aatgttttttttggtactattgtc-cagGTTCTGTTCGATTTAATCTGGATCCTTTTAATGAGCACAATGATGCGGATCTCTGGGAAGCGCTTGAAAGGGCTCATCTAAAAGATGTCATAAGGAGGAA
|| || | ||||||| |||||| || | | | || |||| | || | | | || | ||| || | | ||||||||||||| |||||||||||||| ||||||||||||||||||||||| |||||||| || || ||||||||||||||||||||||| |||||||||||
gtatgctagtgaaaaatacatgttagctgctggagcttctttttttggcaacttgggtttagtgaaatatttattaatgccctttcagGTTCTGTTCGGTTTAATCTGGATCCCTTTAATGAGCACAATGATGCGGACCTCTGGGAGGCTCTGGAAAGGGCTCATCTAAAAGATGTTATAAGGAGGAA
upper sequence: LOC_Os04g52900.2 (Oryza sativa), 3'ss of exon 24
lower sequence: GLYMA13G29180.1 (Glycine max), 3'ss of exon 23
---gtttgtttgtgaaaatacatgatatatcttctcgtttgcttttcttacatcata-aatgttttttt--tggtacta-------------ttgtccagGTTCTGTTCGATTTAATCTGGATCCTTTTAATGAGCACAATGATGCGGATCTCTGGGAAGCGCTTGAAAGGGCTCATCTAAAAGATGTCATAAGGAGGAA
|| || |||| | | | || | | || | | |||| | ||||| || | | || || | | ||| |||| |||||||||| ||||| |||||||| ||||||||||| || |||||||| || || || ||||| ||| | || ||||| ||| |||||||
tcatttaacttctgaatcaatgttttgtaggtaattaattagaatataaaaatcaaataatgtcattgtaataatattaagctcaccttactctttatagGAACTGTGAGATTTAATCTTGATCCATTTAATGAACACAATGATGCTGACCTCTGGGAGGCTCTGGAGAGGGCACATTTGAAGGATGTGATACGGAGGAA
upper sequence: LOC_Os04g52900.2 (Oryza sativa), 3'ss of exon 24
lower sequence: GLYMA15G09900.1 (Glycine max), 3'ss of exon 23
-------------------gtttgt-ttgtgaaaatacatgatatatcttctcgtttgcttttcttacatcataaatgttttttttggtac-tattgtccagGTTCTGTTCGATTTAATCTGGATCCTTTTAATGAGCACAATGATGCGGATCTCTGGGAAGCGCTTGAAAGGGCTCATCTAAAAGATGTCATAAGGAGGAA
|| | || || | || ||| |||| | || | | | | | ||| || | | | ||| |||| |||||||||| ||||| || ||||| ||||||||||| || |||||||| || || || ||||| ||| | || ||||| ||| |||||||
agaatattttaacttctgaattaatgttttgcaggtaattgaaatataaaat--ttaaataatgtcattgtaataatattaagctcatcttacacttcatagGAACTGTGAGATTTAATCTCGATCCATTCAATGAACACAATGATGCTGACCTCTGGGAGGCTCTGGAGAGGGCACATTTGAAGGATGTGATACGGAGGAA
upper sequence: LOC_Os04g52900.2 (Oryza sativa), 3'ss of exon 24
lower sequence: AT1G30420.1 (Arabidopsis thaliana), 3'ss of exon 23
gtttgtttgtgaaaatacatgatatatcttctcgtttgcttttcttacatcataaatgttttttttggtactattgtccagGTTCTGTTCGATTTAATCTGGATCCTTTTAATGAGCACAATGATGCGGATCTCTGGGAAGCGCTTGAAAGGGCTCATCTAAAAGATGTCATAAGGAGGAA
|||||| ||| | | ||||| | || || | | | | ||| || || | || ||| | || |||| ||| | ||||| |||| ||| ||||||||||| || |||||||| || || |||||||| ||| ||||||||||||| |||||
gtttgtgtgtagtttaagacgatat---tgtaagtatgatcctgaattctgagaaacagttcttcttgt---------tagGGACGGTGAGATTCAATATCGATCCATTTAGTGAACACAATGATGCTGACCTCTGGGAGGCTCTAGAAAGGGCGCATATAAAAGATGTCATCGATAGGAA
upper sequence: LOC_Os04g52900.2 (Oryza sativa), 3'ss of exon 24
lower sequence: Vv10s0003g04460.t01 (Vitis vinifera), 3'ss of exon 5
gtttgtttgtgaaa--atacatgata-----tatcttctc--gtttgcttttctt-----------acatcataaatgttttttttggtactattgtccagGTTCTGTTCGATTTAATCTGGATCCTTTTAATGAGCACAATGATGCGGATCTCTGGGAAGCGCTTGAAAGGGCTCATCTAAAAGATGTCATAAGGAGGAA
||| |||||| | |||||||| || ||| | ||||||| || |||| | | || | | ||| | |||| |||| |||||||||| |||||||| ||||||||||||||||| || || ||| | || || | || || ||||| || || |||| |||| |||
-tttcacggtgaaacaaaacatgataaaaatcattttcctcaacatatttttctttccgagaatatactgtataattctaattgtcatttttataatgtagGTACTGTGAGATTTAATCTTGATCCTTTCAATGAGCACAATGATGCTGACCTTTGGAAGGCTCTAAAGAGAGCACATCTCAAGGACTTCATTAGGATGAA
upper sequence: LOC_Os04g52900.2 (Oryza sativa), 3'ss of exon 24
lower sequence: Vv10s0003g04390.t01 (Vitis vinifera), 3'ss of exon 23
-----------gtttgtttgtgaa-aatacatgatatatcttctcgtttgcttttctta-catcataaatgttttttttggtacta-ttgtcc-----agGTTCTGTTCGATTTAATCTGGATCCTTTTAATGAGCACAATGATGCGGATCTCTGGGAAGCGCTTGAAAGGGCTCATCTAAAAGATGTCATAAGGAGGAA
| | | || | ||| || | || | | | |||| ||| | |||| || | | | |||| ||| |||| ||||| ||||| |||||||| || |||||||||||||| || |||||||| || | || ||||| ||| | || ||||| || ||||||||
attactgataagatcctaagttatcaattcaatacattttagttaataaattttttttaatgaagtttgtgttattctaatgatcacttgtttcacatagGAACTGTGCGATTCAATCTTGATCCTTTCAACGAGCACAATGATGCTGACCTCTGGGAGGCTTTAGAGAGGGCACATTTGAAGGATGTTATCAGGAGGAAMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|58690744|gb|CK079431.1|CK079431EST: CCTACGAAAAGTACTAGGAATAATACCACAGGCACCTGTCCTATTTTCAG GTTCTGTTCGATTTAATCTGGATCCTTTTAATGAGCACAATGATGCGGATC
genomic: CCTACGAAAAGTACTAGGAATAATACCACAGGCACCTGTCCTATTTTCAGgtttgtttgt ... tattgtccagGTTCTGTTCGATTTAATCTGGATCCTTTTAATGAGCACAATGATGCGGATC
EST:
gi|29680004|gb|CB676279.1|CB676279EST: CCTACGAAAAGTACTAGGAATAATACCACAGGCACCTGTCCTATTTTCAG GTTCTGTTCGATTTAATCTGGATCCTTTTAATGAGCACAATGATGCGGATC
genomic: CCTACGAAAAGTACTAGGAATAATACCACAGGCACCTGTCCTATTTTCAGgtttgtttgt ... tattgtccagGTTCTGTTCGATTTAATCTGGATCCTTTTAATGAGCACAATGATGCGGATC
EST:
gi|33793897|gb|CF322837.1|CF322837EST: CCTACGAAAAGTACTAGGAATAATACCACAGGCACCTGTCCTATTTTCAG GTTCTGTTCGATTTAATCTGGATCCTTTTAATGAGCACAATGA
genomic: CCTACGAAAAGTACTAGGAATAATACCACAGGCACCTGTCCTATTTTCAGgtttgtttgt ... tattgtccagGTTCTGTTCGATTTAATCTGGATCCTTTTAATGAGCACAATGA
EST:
gi|58689770|gb|CK078457.1|CK078457EST: CCTACGAAAAGTACTAGGAATAATACCACAGGCACCTGTCCTATTTTCAG GTTCTGTTCGATTTAATCTGGATCCTTTTAATGAGCACAATGATGCGGATC
genomic: CCTACGAAAAGTACTAGGAATAATACCACAGGCACCTGTCCTATTTTCAGgtttgtttgt ... tattgtccagGTTCTGTTCGATTTAATCTGGATCCTTTTAATGAGCACAATGATGCGGATC
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 1 RNA-Seqlibrary.
Block sizes:
73 (upstream exon),
72 (downstream exon)
Score:
44GGGAGAATATTGGTTGATGATTGTGACACTTCTAAATTTGGAATTTGGGACCTACGAAAAGTACTAGGAATAATACCACAGGCACCTGTCCTATTTTCAGgtttgtttgt ... tattgtccagGTTCTGTTCGATTTAATCTGGATCCTTTTAATGAGCACAATGATGCGGATCTCTGGGAAGCGCTTGAAAGGGCTCATCTAAAAGATGTCATAAGGAGGAA
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttctcgtttgcttttcttacatcataaatgttttttttggtactattgtccagGTTCTGTTCGATTTAATCTGGATCCTTTTAATGAGCACAATGATGCGGATCTCTGGGAAGCGCTTGAAAGGGCTCATCTAAAAGATGTCATAAGGAGGAA
ttcttac putative branch site (score: 44)
ttttcttacatcataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtttgtgaaaatacatgatatatcttctcgtttgcttttcttacatcataaatgttttttttggtactattgtccagGTTCTGTTCGATTTAATCTGGATCCTTTTAATGAGCACAATGATGCGGATCTCTGGGAAGCGCTTGAAAGGGCTCATCTAAAAGATGTCATAAGGAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA