Sequence
atgc intronic sequence ATGC exonic sequence...tactctcttttactaaactgtgcctggatgacagtactaatatgatcagctagttgcaaagagaggtttgaaaattgaaacatctgttctctgcttgcagGAGACATTGGTGAGTGGCAACCTGATGGAAGTATGAAAATCATAGATCGCAAAAAGAATATCTTCAAGCTTTCACAAGGAGAATATGTAGCAGTAGAAAA
Basic information
species | Oryza sativa |
transcript | LOC_Os01g46750.4 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g46750.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM5G861300_T01 (Zea mays), 3'ss of exon 15
--------------------------------------------------------------------------tactctcttttactaaact---gtgcctggatgacagtactaatatgatcagctagtt-gcaaagagaggtttgaaaattgaaacatctgttctctgc-ttgcagGAGACATTGGTGAGTGGCAACCTGATGGAAGTATGAAAATCATAGATCGCAAAAAGAATATCTTCAAGCTTTCACAAGGAGAATATGTAGCAGTAGAAAA
| | | | || || | || || | | | | | || ||| || | | | ||| ||| ||||||| | ||||||| ||||||||||||||||||||||||||| ||||||||||||||| || ||||||||||| ||||| |||||||| || |||||||| ||||| |||||
gtagtgtgttgcccgttctactgctctgtttttacatagtgatcactattcatgacacacattgttagtagttaaaattccatgtagaaatccagggttccaatcatataccatgaccaaaatttcctattttgtgctcccgcctataaaacctgacacatctgcctcatctgttgcagGTGACATTGGTGAGTGGCAACCTGATGGATCTATGAAAATCATAGACCGTAAAAAGAATATATTCAAACTTTCACAGGGTGAATATGTGGCAGTTGAAAA
upper sequence: LOC_Os01g46750.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GLYMA05G36910.1 (Glycine max), 3'ss of exon 15
tactctcttttactaaactgtgcctggatgaca-gtactaatatgatcagctagttgcaaagagaggtttgaaaattgaaacatctgttctctgcttgcagGAGACATTGGTGAGTGGCAACCTGATGGAAGTATGAAAATCATAGATCGCAAAAAGAATATCTTCAAGCTTTCACAAGGAGAATATGTAGCAGTAGAAAA
|| ||| | | || || || | | | || || | ||||| | ||| | |||| || ||| | |||| || ||||| ||||||| ||| |||||| |||||||| || ||||| || |||||||| || ||||||||||||||||||||||| || || |||||
---gttcatttttcagtttatgtttgaataagatatgcttctacg-----tggattgcatgatcatattttattcatgaa-----tggtctatttaaacagGGGATATTGGAGAGTGGCTACCCAATGGAACCATGAAAATTATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTTGAAAA
upper sequence: LOC_Os01g46750.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GLYMA01G43470.2 (Glycine max), 3'ss of exon 15
--tactctcttt-tactaaactgtgcctggatgacagtactaatatgatcagctagttgcaaagagaggtttgaaaattgaaacatctgttctctgcttgcagGAGACATTGGTGAGTGGCAACCTGATGGAAGTATGAAAATCATAGATCGCAAAAAGAATATCTTCAAGCTTTCACAAGGAGAATATGTAGCAGTAGAAAA
|| | ||| | | | | | | || |||| | | | | | | | | ||| | ||| || | | | |||| || ||||| |||||||||||| ||||||| |||||||| || ||||| || |||||||| || ||||||||||||||||||||||| || || |||||
gttatttcatttatgttttccaaaattgaggtttatattcttatattagctgttgggttgggtcacaattttccttttattcacaaatgatatat-tcaacagGGGATATTGGAGAGTGGCAACCTAATGGAAGCATGAAAATTATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTCGAAAA
upper sequence: LOC_Os01g46750.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GLYMA11G02030.1 (Glycine max), 3'ss of exon 15
-tactctcttttactaaactgtgcctggatgacagtactaatatgatcagctagttgcaaagagaggtttgaaaattga-aacatctgttctctgcttgcagGAGACATTGGTGAGTGGCAACCTGATGGAAGTATGAAAATCATAGATCGCAAAAAGAATATCTTCAAGCTTTCACAAGGAGAATATGTAGCAGTAGAAAA
| | || |||| | || | || | ||| || |||| |||| | || ||| || |||| || | | | |||| || ||||| |||||||||||| | ||||| |||||||| || ||||| || |||||||| || ||||||||||||||||||||||| || || |||||
gttatttcatttatgttttccaaatttgaggtttatattcttat-attagct-gttg-ggtcacagttttcctttttattaacaaatgatatat-tcaacagGGGATATTGGAGAGTGGCAACCTAACGGAAGCATGAAAATTATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTCGAAAA
upper sequence: LOC_Os01g46750.1 (Oryza sativa), 3'ss of exon 15
lower sequence: AT4G23850.1 (Arabidopsis thaliana), 3'ss of exon 15
-tactctcttttactaaactgtgcctggatgacagtactaatatgatcagctagttgcaaagagaggtttgaaaattgaaacatctgttctctg--cttgcagGAGACATTGGTGAGTGGCAACCTGATGGAAGTATGAAAATCATAGATCGCAAAAAGAATATCTTCAAGCTTTCACAAGGAGAATATGTAGCAGTAGAAAA
|| | || | || ||| | | || | | | |||| | ||| ||| | | | |||| | | || |||| || |||||||||||||||| |||||||| ||||| || || || | || ||||||||||| || || ||||||||||| ||||| || || || ||
gtatttctttctctgaacttgtatacaattagttagaatattg-gtttttgtagtc-cggtgagttcttttcagttctcacactctgcttcttatactctcagGTGATGTTGGTGAGTGGCAACCAGATGGAAGCATGAAGATAATTGACAGGAAGAAGAATATCTTTAAACTCTCACAAGGAGAGTATGTTGCGGTGGAGAA
upper sequence: LOC_Os01g46750.1 (Oryza sativa), 3'ss of exon 15
lower sequence: AT4G11030.1 (Arabidopsis thaliana), 3'ss of exon 15
--tactctcttttactaaactgtgcctggatgacagtacta-atatgatcagctagttgcaaagagaggtttgaa--aattgaaacatctgttctctgcttgc-agGAGACATTGGTGAGTGGCAACCTGATGGAAGTATGAAAATCATAGATCGCAAAAAGAATATCTTCAAGCTTTCACAAGGAGAATATGTAGCAGTAGAAAA
|||| | | ||| || | | | ||| |||| || | | ||| | || | | || | ||| | ||| || |||||||||||||||| ||||||| ||||| || || || || |||||||| |||||||| || | |||||||| ||||| || || || ||
gttactaaaaacctcaacactttgatcattttgctttcctatatatagcattttaaatatcagttcttatttaccttatttaatttaactatgtgtatcttaccagGTGATGTTGGTGAGTGGCAACCAAATGGAAGCATGAAGATAATTGACCGGAAAAAGAACATCTTCAAACTCGCGCAAGGAGAGTATGTCGCTGTTGAGAA
upper sequence: LOC_Os01g46750.1 (Oryza sativa), 3'ss of exon 15
lower sequence: Vv02s0025g01410.t01 (Vitis vinifera), 3'ss of exon 15
tactctcttttacta--aactgtgcctggatgacagtactaatatgatcagctagttgcaaagagaggtttgaaaattgaaac-atctgttctctgcttgcagGAGACATTGGTGAGTGGCAACCTGATGGAAGTATGAAAATCATAGATCGCAAAAAGAATATCTTCAAGCTTTCACAAGGAGAATATGTAGCAGTAGAAAA
| || || | | | | | || || | ||| | | | || | || | ||| | || || || ||| | |||| || |||||||||||||||||||||| || |||||||| || || ||||| ||||| || ||||||||||||||||||||||| || || || || ||
-gtttgctcatattggcatttcttcttgaatta-agttttgaggtcctctattttgtggattcgtttctttaacaaccttgctgatgacttatcttttcacagGGGATGTTGGTGAGTGGCAACCTGATGGGAGCATGAAAATTATCGACCGCAAGAAGAACATATTCAAGCTTTCACAAGGAGAATACGTTGCCGTTGAGAA
upper sequence: LOC_Os01g46750.1 (Oryza sativa), 3'ss of exon 15
lower sequence: PP1S47_161V6.1 (Physcomitrella patens), 3'ss of exon 15
tactctcttttactaaactgtgcctggatgacagtactaatatgatcagctagttgcaaagagaggtttgaaaattgaaacatctgttctctgcttg-cagGAGACATTGGTGAGTGGCAACCTGATGGAAGTATGAAAATCATAGATCGCAAAAAGAATATCTTCAAGCTTTCACAAGGAGAATATGTAGCAGTAGAAAA
| || || | || | || | || | | | || | | | | | | | | | | | ||| | || | |||| || ||||| ||||||||| ||||| | |||| || || |||||||| ||||| |||||||||||||| ||||||||||| || ||||| |||||
caggggctgttcttgaaatatgttgaaaggattatccatctttgggtcgatgaata-agtcaatgatgacatagacaagttctttgtgatgtgtgtatcagGCGATATTGGAGAGTGGCAAAAAGATGGTGCTTTGAAGATTATTGATCGCAAGAAGAACATCTTCAAGCTTTCTCAAGGAGAATACGTTGCAGTCGAAAAMapped 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|87031853|gb|CI272554.1|CI272554EST: ATGGTTCCATACTG GAGACATTGGTGAGTGGCAACCTGATGGAAGTATGAAAATCATAGATCGCA
genomic: ATGGTTCCATACTGgtatgtcttg ... ctgcttgcagGAGACATTGGTGAGTGGCAACCTGATGGAAGTATGAAAATCATAGATCGCA
EST:
gi|58679458|gb|CK068145.1|CK068145EST: GCGTGAAGACCTTACAAAGGATGTTTTGATTGATGGATGGTTCCATACTG GAGACATTGGTGAGTGGCAACCTGATGGAAGTATGAAAATCATAGATCGCA
genomic: GCGTGAAGACCTTACAAAGGATGTTTTGATTGATGGATGGTTCCATACTGgtatgtcttg ... ctgcttgcagGAGACATTGGTGAGTGGCAACCTGATGGAAGTATGAAAATCATAGATCGCA
EST:
gi|87020943|gb|CI269660.1|CI269660EST: GATGGATGGTTCCATACTG GAGACATTGGTGAGTGGCAACCTGATGGAAGTATGAAAATCATAGATCGCT
genomic: GATGGATGGTTCCATACTGgtatgtcttg ... ctgcttgcagGAGACATTGGTGAGTGGCAACCTGATGGAAGTATGAAAATCATAGATCGCA
EST:
gi|27576205|gb|CA998899.1|CA998899EST: GCGTGAAGACCTTACAAAGGATGTTTTGATTGATGGATGGTTCCATACTG GAGACATTGGTGAGTGGCAACCTGATGGAAGTATGAAAATCATAGATCGCA
genomic: GCGTGAAGACCTTACAAAGGATGTTTTGATTGATGGATGGTTCCATACTGgtatgtcttg ... ctgcttgcagGAGACATTGGTGAGTGGCAACCTGATGGAAGTATGAAAATCATAGATCGCA
EST:
gi|29618099|gb|CB623111.1|CB623111EST: GCGTGAAGACCTTACAAAGGATGTTTTGATTGATGGATGGTTCCATACTG GAGACATTGGTGAGTGGCAACCTGATGGAAGTATGAAAATCATAGATCGCA
genomic: GCGTGAAGACCTTACAAAGGATGTTTTGATTGATGGATGGTTCCATACTGgtatgtcttg ... ctgcttgcagGAGACATTGGTGAGTGGCAACCTGATGGAAGTATGAAAATCATAGATCGCA
EST:
gi|56157720|gb|C25972.2|C25972EST: GCGTGAAGACCTTACAAAGGATGTTTTGATTGATGGATGGTTCCATACTG GAGACATTGGTGAGTGGCAACCTGATGGAAGTATGAAA-TCATAGAT
genomic: GCGTGAAGACCTTACAAAGGATGTTTTGATTGATGGATGGTTCCATACTGgtatgtcttg ... ctgcttgcagGAGACATTGGTGAGTGGCAACCTGATGGAAGTATGAAAATCATAGAT
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:
71 (upstream exon),
73 (downstream exon)
Score:
46CGTGGCGAAATCTGCATCAGGGGAGAAACAGTATTCTCAGGATACTACAAGCGTGAAGACCTTACAAAGGATGTTTTGATTGATGGATGGTTCCATACTGgtatgtcttg ... ctgcttgcagGAGACATTGGTGAGTGGCAACCTGATGGAAGTATGAAAATCATAGATCGCAAAAAGAATATCTTCAAGCTTTCACAAGGAGAATATGTAGCAGTAGAAAA
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcagctagttgcaaagagaggtttgaaaattgaaacatctgttctctgcttgcagGAGACATTGGTGAGTGGCAACCTGATGGAAGTATGAAAATCATAGATCGCAAAAAGAATATCTTCAAGCTTTCACAAGGAGAATATGTAGCAGTAGAAAA
tctgttctctgctt CT-rich tract
tttgaaaattgaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tactctcttttactaaactgtgcctggatgacagtactaatatgatcagctagttgcaaagagaggtttgaaaattgaaacatctgttctctgcttgcagGAGACATTGGTGAGTGGCAACCTGATGGAAGTATGAAAATCATAGATCGCAAAAAGAATATCTTCAAGCTTTCACAAGGAGAATATGTAGCAGTAGAAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA