Sequence
atgc intronic sequence ATGC exonic sequence...ttttcatatcaaaagagactgacctgttaacagaatgctttgacatttccccctgattgaatgcttcttgtaaccggctcactttgatatcttactgtagGAGACATTGGTGAGTGGCAGTCTGATGGAAGCATGAAGATCATTGATCGCAAGAAGAACATCTTCAAGCTCTCCCAAGGAGAATATGTCGCTGTGGAGAA
Basic information
species | Oryza sativa |
transcript | LOC_Os01g48910.1 |
intron # | 15 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g48910.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G152127_T01 (Zea mays), 3'ss of exon 15
-ttttcatatcaaaagagact-gacctgttaacagaa-tgctttgacatttccccctgattgaatgcttcttgtaaccggctcactttgatatcttactgtagGAGACATTGGTGAGTGGCAGTCTGATGGAAGCATGAAGATCATTGATCGCAAGAAGAACATCTTCAAGCTCTCCCAAGGAGAATATGTCGCTGTGGAGAA
| || | | | || | || || | ||||| ||| || | || ||| | || | || || || | | | || |||| |||||| ||||||||||||||||||||||||||| |||||||||||||||||||| |||||||||||||||||||||||||| || ||||| || || || || |||||
gtcttgaaagagatcctgatttaacttgccatcagaaatgcctttgaaattttcccaagtctaacgtttgtt--cactgccaaatattaatat-ttactgcagGAGACATTGGTGAGTGGCAGTCTGACGGAAGCATGAAGATCATTGACCGCAAGAAGAACATCTTCAAGCTCTCACAGGGAGAGTACGTTGCGGTTGAGAA
upper sequence: LOC_Os01g48910.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GLYMA05G36910.1 (Glycine max), 3'ss of exon 15
ttttcatatcaaaagagactgacctgttaacagaatgctttgacatttccccc-tgattgaatgcttcttgtaaccggctcactttgatatcttactgtagGAGACATTGGTGAGTGGCAGTCTGATGGAAGCATGAAGATCATTGATCGCAAGAAGAACATCTTCAAGCTCTCCCAAGGAGAATATGTCGCTGTGGAGAA
||||| | | | || | |||||| || | | |||| || | | | | || | || | | || || ||||| ||||||| | |||||| |||||| || |||||||| |||||||| || || ||||| || |||||||||||||| ||||| || ||
-gttcatttttcagtttat--gtttgaataagatatgcttctacgtggattgcatgatcatattttattcatgaatggtctatttaaaca----------gGGGATATTGGAGAGTGGCTACCCAATGGAACCATGAAAATTATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTTGAAAA
upper sequence: LOC_Os01g48910.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GLYMA01G43470.2 (Glycine max), 3'ss of exon 15
-------ttttcatatcaaaagagactgacctgttaacagaatgctttgacatttccccctgattgaatgcttcttgtaaccggctcactttgatatcttactgtagGAGACATTGGTGAGTGGCAGTCTGATGGAAGCATGAAGATCATTGATCGCAAGAAGAACATCTTCAAGCTCTCCCAAGGAGAATATGTCGCTGTGGAGAA
|| || | | | ||| | ||| | || | || | | | ||| | | | | | |||||| || | ||| || ||||| |||||||| || ||||||||||||| || |||||||| |||||||| || || ||||| || |||||||||||||| ||||| || ||
gttatttcatttatgttttccaaaattgaggt-ttatattcttatattagctgttgggttgggtcacaattttccttttattcacaaa---tgatatatt-caacagGGGATATTGGAGAGTGGCAACCTAATGGAAGCATGAAAATTATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTCGAAAA
upper sequence: LOC_Os01g48910.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GLYMA11G02030.1 (Glycine max), 3'ss of exon 15
-ttttcatatcaaaagagactgacctgttaacagaatgctttgacatttccccctgattgaatgctt--cttgtaaccggctcactttgatatcttactgtagGAGACATTGGTGAGTGGCAGTCTGATGGAAGCATGAAGATCATTGATCGCAAGAAGAACATCTTCAAGCTCTCCCAAGGAGAATATGTCGCTGTGGAGAA
|| | || | | | | | | || | | | ||| | || | | | || ||| | | | | |||||| || | ||| || ||||| |||||||| || | ||||||||||| || |||||||| |||||||| || || ||||| || |||||||||||||| ||||| || ||
gttatttcatttatgttttccaaatt-tgaggtttatattcttatattagctgttgggtcacagttttcctttttattaacaaa---tgatatatt-caacagGGGATATTGGAGAGTGGCAACCTAACGGAAGCATGAAAATTATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTCGAAAA
upper sequence: LOC_Os01g48910.1 (Oryza sativa), 3'ss of exon 15
lower sequence: AT4G23850.1 (Arabidopsis thaliana), 3'ss of exon 15
---ttttcatatcaaaagagactgacctgttaacagaatgctttgacatttccccctgattgaatgcttcttgtaaccggctcactttgatatct-tactgt-agGAGACATTGGTGAGTGGCAGTCTGATGGAAGCATGAAGATCATTGATCGCAAGAAGAACATCTTCAAGCTCTCCCAAGGAGAATATGTCGCTGTGGAGAA
||| | || || || | ||||| ||| ||| ||| | ||| | | | |||| || | | |||| | ||| || ||||||||||||| | ||||||||||||||||| ||||| | |||||||| ||||| || ||||| |||||||| ||||| || ||||||||
gtatttctttctctgaacttgtatacaattagttagaata--ttggtttttgtagtccggtgagttcttttc--agttctcacactctgcttcttatactctcagGTGATGTTGGTGAGTGGCAACCAGATGGAAGCATGAAGATAATTGACAGGAAGAAGAATATCTTTAAACTCTCACAAGGAGAGTATGTTGCGGTGGAGAA
upper sequence: LOC_Os01g48910.1 (Oryza sativa), 3'ss of exon 15
lower sequence: AT4G11030.1 (Arabidopsis thaliana), 3'ss of exon 15
ttttcatatcaaaagagactgacctgttaacagaatgctttgacatttccccctgattgaatgc---ttcttgt--aaccggctcactttga-------tatcttactgtagGAGACATTGGTGAGTGGCAGTCTGATGGAAGCATGAAGATCATTGATCGCAAGAAGAACATCTTCAAGCTCTCCCAAGGAGAATATGTCGCTGTGGAGAA
|| |||| | || | | || |||||| || | | || ||| ||||| | | | | | ||| | |||||||| ||| || ||||||||||||| | |||||||||||||||| ||||| || || |||||||||||||| ||| | |||||||| ||||||||||| |||||
----gttactaaaaacctcaacactttgatcattttgctttcctatatatagcattttaaatatcagttcttatttaccttatttaatttaactatgtgtatcttacc--agGTGATGTTGGTGAGTGGCAACCAAATGGAAGCATGAAGATAATTGACCGGAAAAAGAACATCTTCAAACTCGCGCAAGGAGAGTATGTCGCTGTTGAGAA
upper sequence: LOC_Os01g48910.1 (Oryza sativa), 3'ss of exon 15
lower sequence: Vv02s0025g01410.t01 (Vitis vinifera), 3'ss of exon 15
ttttcatatcaaaagagactgacctgttaacagaatgctttgacatttccccctgattgaatgc-ttcttgtaaccggctcactt-tga--tatcttactgtagGAGACATTGGTGAGTGGCAGTCTGATGGAAGCATGAAGATCATTGATCGCAAGAAGAACATCTTCAAGCTCTCCCAAGGAGAATATGTCGCTGTGGAGAA
|| ||| | | | | | || | | | | ||||| | | | || || | || | |||| || || ||| |||||| ||| || ||||||||||||| ||||||| |||||||| || || || |||||||||||||| |||||||| || ||||||||||| || || || |||||
-gtttgc-tcatattggcatttcttcttga-attaagttttgaggtcctctattttgtggattcgtttctttaacaaccttgctgatgacttatcttttcacagGGGATGTTGGTGAGTGGCAACCTGATGGGAGCATGAAAATTATCGACCGCAAGAAGAACATATTCAAGCTTTCACAAGGAGAATACGTTGCCGTTGAGAA
upper sequence: LOC_Os01g48910.1 (Oryza sativa), 3'ss of exon 15
lower sequence: EDO96800 (Chlamydomonas reinhardtii), 3'ss of exon 12
-----------------------ttttcatatcaaaagagactgacctgttaaca-gaatgctttgacatttccccctgattgaatgcttcttgtaaccggctcactttgatatcttactgtagGAGACATTGGTGAGTGGCAGTCTGATGGAAGCATGAAGATCATTGATCGCAAGAAGAACATCTTCAAGCTCTCCCAAGGAGAATATGTCGCTGTGGAGAA
|| | | | | || || ||| | | || || | | | || | | || | | | | | | || ||| | || ||| | | | || |||| | | |||||||| || |||||||||||||||||||||||| |||
tgttttccttgtgctctttaacacacacacacacacacacacacacacacacacacgcacgcacgcacgcacgcacacaaacaaacacgtacacacacagACGCGGACGGCTTCTTCCACACGGGCGACGTGGGCGAGCTGGTGACGGACGGAACCCTCAAGATCATCGACCGCAAGAAGAACATCTTCAAGCTCAGCCA------------------------
upper sequence: LOC_Os01g48910.1 (Oryza sativa), 3'ss of exon 15
lower sequence: PP1S47_161V6.1 (Physcomitrella patens), 3'ss of exon 15
----ttttcatatcaaaagagactgacctgttaacagaatgctttgacatttccccctgattgaatgcttcttgtaaccggctcactttgatatcttactgtagGAGACATTGGTGAGTGGCAGTCTGATGGAAGCATGAAGATCATTGATCGCAAGAAGAACATCTTCAAGCTCTCCCAAGGAGAATATGTCGCTGTGGAGAA
| | | ||| | ||| | | | | ||||| | | | | |||| | || | || | |||| | | ||| || ||||| |||||||| ||||| ||||||| ||||||||||||||||||||||||||||| || ||||||||||| || || || || ||
caggggctgttcttgaaatatgttgaaaggattatccat--ctttgg-gtcgatgaataagtcaatgatgacatagacaagttctttgtgatgtgt-gtatcagGCGATATTGGAGAGTGGCAAAAAGATGGTGCTTTGAAGATTATTGATCGCAAGAAGAACATCTTCAAGCTTTCTCAAGGAGAATACGTTGCAGTCGAAAA
upper sequence: LOC_Os01g48910.1 (Oryza sativa), 3'ss of exon 15
lower sequence: PP1S108_163V6.1 (Physcomitrella patens), 3'ss of exon 15
ttttcatatcaaaagagactgacctgttaacagaatgctttgacatttccccctgattgaatgc-ttcttgtaaccggctcactttgatat-cttactgtagGAGACATTGGTGAGTGGCAGTCTGATGGAAGCATGAAGATCATTGATCGCAAGAAGAACATCTTCAAGCTCTCCCAAGGAGAATATGTCGCTGTGGAGAA
| | || | || | | | ||| | | || | ||| || || | |||| | | | ||| || | | ||| || ||||| ||||||||| | ||||| ||||||||||| ||||| || |||||||| || |||||||| || || ||||||||| | || || || ||
gtcaccaatatacgtggaaaaaacgat--gcagtttatgtaaacgaatggtgctggaggagagcgctgatgtattctgattcttttataatgcatgaatcagGTGATATTGGAGAGTGGCAGGCAGATGGTAGCATGAAGATTATTGACCGTAAGAAGAATATTTTCAAGCTTTCTCAGGGAGAATATATTGCAGTCGAAAA
upper sequence: LOC_Os01g48910.1 (Oryza sativa), 3'ss of exon 15
lower sequence: EFJ23443 (Selaginella moellendorffii), 3'ss of exon 15
ttttcatatcaaaagagactgacctgttaacagaatgctttgacatttccccctgattgaatgcttcttgtaaccggctcactttgatatcttactgtagGAGACATTGGTGAGTGGCAGTCTGATGGAAGCATGAAGATCATTGATCGCAAGAAGAACATCTTCAAGCTCTCCCAAGGAGAATATGTCGCTGTGGAGAA
| | | ||| ||| | || ||| | || | ||||||| || || ||||||| | | ||| | |||| ||||| || | ||||||||||| ||||| ||||| ||||| ||||| |||||||| |||||
--------------------------------------------gtagggactcaaaagaa-acttgctacgtggttcttactgaacgaggtttttatagGAGATATCGGAGAGTGGCTACCAAACGGAGCCTTGAAAATCATAGACAGGAAGAAGAACATTTTCAAACTCTCGCAAGGCGAATACGTCGCTGTAGAGAA
upper sequence: LOC_Os01g48910.1 (Oryza sativa), 3'ss of exon 15
lower sequence: EFJ25426 (Selaginella moellendorffii), 3'ss of exon 15
ttttcatatcaaaagagactgacctgttaacagaatgctttgacatttccccctgattgaatgcttcttgtaac-cggctcactttgat--atcttactgtagGAGACATTGGTGAGTGGCAGTCTGATGGAAGCATGAAGATCATTGATCGCAAGAAGAACATCTTCAAGCTCTCCCAAGGAGAATATGTCGCTGTGGAGAA
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------------------------------------------------gtagggactcaaaagaaacttgctacgtggttcgtactgaacgaggtttttacagGAGATATCGGAGAGTGGCTACCAAACGGAGCCTTGAAAATCATAGACAGGAAGAAGAACATTTTCAAACTCTCGCAAGGCGAATACGTCGCTGTAGAGAAMapped 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|29616396|gb|CB621408.1|CB621408EST: TTTAGTCGATGGATGGTTTCACACAG GAGACATTGGTGAGTGGCAGTCTGATGGAAGCATGAAGATCATTGATCGCA
genomic: TTTAGTCGATGGATGGTTTCACACAGgtatgccaac ... cttactgtagGAGACATTGGTGAGTGGCAGTCTGATGGAAGCATGAAGATCATTGATCGCA
EST:
gi|86910803|gb|CI294794.1|CI294794EST: ACGAGAAGACCTCACCAAGGAAGTTTTAGTCGATGGATGGTTTCACACAG GAGACATTGGTGAGTGGCAGTCTGATGGAAGCATGAAGATCATTGATCGCA
genomic: ACGAGAAGACCTCACCAAGGAAGTTTTAGTCGATGGATGGTTTCACACAGgtatgccaac ... cttactgtagGAGACATTGGTGAGTGGCAGTCTGATGGAAGCATGAAGATCATTGATCGCA
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:
54 (upstream exon),
57 (downstream exon)
Score:
6CGTGGGGAGATTTGCATCAGAGGGGACACCTTGTTCTCAGGGTACCACAAACGAGAAGACCTCACCAAGGAAGTTTTAGTCGATGGATGGTTTCACACAGgtatgccaac ... cttactgtagGAGACATTGGTGAGTGGCAGTCTGATGGAAGCATGAAGATCATTGATCGCAAGAAGAACATCTTCAAGCTCTCCCAAGGAGAATATGTCGCTGTGGAGAA
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttccccctgattgaatgcttcttgtaaccggctcactttgatatcttactgtagGAGACATTGGTGAGTGGCAGTCTGATGGAAGCATGAAGATCATTGATCGCAAGAAGAACATCTTCAAGCTCTCCCAAGGAGAATATGTCGCTGTGGAGAA
tcttact CT-rich tract
tttgatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttttcatatcaaaagagactgacctgttaacagaatgctttgacatttccccctgattgaatgcttcttgtaaccggctcactttgatatcttactgtagGAGACATTGGTGAGTGGCAGTCTGATGGAAGCATGAAGATCATTGATCGCAAGAAGAACATCTTCAAGCTCTCCCAAGGAGAATATGTCGCTGTGGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - -atcaaaa
- - - - - - - - - -tgacctg
- - - - - - - - - - - - - - - -agaatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgaatgc