Sequence
atgc intronic sequence ATGC exonic sequence...tcatgtgttaattgcttgctccggtttctgtgccacttacaagctcagttcttacttatgaatgaagccttaatctcattattcctattcatcacgttagGTCTATAGAGTATCGGACATGGAGCTGGTAAGAGTTCTTCCTAGTGCTGAAGATGAAGTAAACGTTGCATGCTTTCATCCTTCCCCTGGAGGTGGTCTTG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g18820.2 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g18820.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G353548_T01 (Zea mays), 3'ss of exon 12
--tcatgtgttaattgcttgctccggtttct-gtgccacttacaagctcagttcttacttatgaatgaagccttaatctcattattcctattcatcacgttagGTCTATAGAGTATCGGACATGGAGCTGGTAAGAGTTCTTCCTAGTGCTGAAGATGAAGTAAACGTTGCATGCTTTCATCCTTCCCCTGGAGGTGGTCTTG
| || || | ||| | | | || | || | | || || | | | | || | | | || || ||| || || |||||| |||||||| || || |||||||| || ||||| ||||||||||| ||||||||||| || ||||||||||||||||||| || |||||||| ||||
aatgatttgcttattatcctccacaactactcatattgctcata--ctttgtgtacaat-gtaagccaaactatcaatctttttttttaatttattactttagGTATATAGAGTTTCAGATATGGAGCTTGTGAGAGTGCTTCCTAGTGCCGAAGATGAAGTCAATGTTGCATGCTTTCATCCTTTACCAGGAGGTGGCCTTG
upper sequence: LOC_Os02g18820.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G007229_T01 (Zea mays), 3'ss of exon 12
tcatgtgttaattgcttgctccggtttctgtgccacttacaa-gctcagttcttacttatgaatgaagccttaatctcattattcctattcatcacgtt-agGTCTATAGAGTATCGGACATGGAGCTGGTAAGAGTTCTTCCTAGTGCTGAAGATGAAGTAAACGTTGCATGCTTTCATCCTTCCCCTGGAGGTGGTCTTG
||| | | || ||| | | || | ||| | | ||||| || || | ||| | | | ||||| | ||| || || || |||| |||||||| || || |||||||| || ||||| |||||||| |||||||||||||| || |||||||||||||||||||| || |||||||| ||||
tca-aaataatttacttattatc-ctcctcaactactaatattgctcatactttgtgtacaatgtaagtcaaattatcattttcttcatttattacttttagGTATATAGAGTTTCAGATATGGAGCTTGTGAGAGTGCTTCCTAGCGCTGAAGATGAAGTTAATGTTGCATGCTTTCATCCTTCACCAGGAGGTGGCCTTG
upper sequence: LOC_Os02g18820.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA19G35370.3 (Glycine max), 3'ss of exon 11
tcatgtgttaattgct--tgctccggtt-tctgtgccacttacaagctcagttcttact-tatgaatgaagccttaatctcattattcctattcatcacgttagGTCTATAGAGTATCGGACATGGAGCTGGTAAGAGTTCTTCCTAGTGCTGAAGATGAAGTAAACGTTGCATGCTTTCATCCTTCCCCTGGAGGTGGTCTTG
| | ||||| | || | ||| |||| || |||||| | | | | | ||||| || || | | |||||| || ||||| || || ||||| || || || || ||||||||||| |||||||| || || || |||||||||||||||| | ||||| || || |
gccggcacaaattgttgtcattcatatcatctatgccctttttg----tagttctaatggttttagtctgaatttaatgtctttgaatttgctttgtcttttagGTATACAGAGTGTCAGATATGGAACTTGTTAGGGTGCTTCCTAGTGCAGAAGATGAGGTCAATGTGGCATGCTTTCATCCTTTTGCCGGAGGAGGACTAG
upper sequence: LOC_Os02g18820.2 (Oryza sativa), 3'ss of exon 13
lower sequence: AT1G04140.1 (Arabidopsis thaliana), 3'ss of exon 11
----------------------------------------tcatgtgttaattgcttgctccggtttctgtgccacttacaagctcagttcttacttatgaatgaagccttaatct-cattattcctattc-atcacgttagGTCTATAGAGTATCGGACATGGAGCTGGTAAGAGTTCTTCCTAGTGCTGAAGATGAAGTAAACGTTGCATGCTTTCATCCTTCCCCTGGAGGTGGTCTTG
| || | | | ||| | | || | || | | | | | | | ||| || || |||| ||| || | | || | || ||||| || || ||||| ||||| ||||| ||||| || | || |||||||| || ||||| |||||||||||||| ||||| || |||||||
gtaacgtctatgctccagtagttatgaatttctagaccagcagaacaatgtttagcagatgccattt-tatatcattaactatatacacttggaatatcatacaagagtttagactgtgtttttccctttctattccttcagATTTACAGAGTTTCAGATATGGAACTGGTGAGAGTACTTCCAAGCTCAGAGGATGAAGTTAATGTTGCTTGCTTTCATCCTTCTCCTGGGGGAGGTCTTG
upper sequence: LOC_Os02g18820.2 (Oryza sativa), 3'ss of exon 13
lower sequence: AT5G43930.1 (Arabidopsis thaliana), 3'ss of exon 11
tcatgtgttaattgcttgctccggtttctgtgccacttacaagctca-gttctta-cttatgaatgaagccttaatctcattattcctattcatcacgttagGTCTATAGAGTATCGGACATGGAGCTGGTAAGAGTTCTTCCTAGTGCTGAAGATGAAGTAAACGTTGCATGCTTTCATCCTTCCCCTGGAGGTGGTCTTG
| ||| ||| | || |||| | ||| || | | | | || || | | | || || | || ||||| || || |||||||| || ||||| || || ||| | || |||||||| |||||||| || ||||||||||| |||||||| |||||||
-------------------gtaaagccttatgctactagtacatccatgttcagaacttggagatataacacagaac---ttgtttgtgtgggccg-gtcagATATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTGCCAAGTTCAGAGGATGAAGTGAACGTTGCGTGTTTTCATCCTTCTCCTGGAGGAGGTCTTG
upper sequence: LOC_Os02g18820.2 (Oryza sativa), 3'ss of exon 13
lower sequence: Vv05s0077g00140.t01 (Vitis vinifera), 3'ss of exon 11
------tcatgtgttaattgcttgctccggtttctgtgccacttacaagctcagttcttacttatgaatgaagccttaatctcattattcctattcatcacgttagGTCTATAGAGTATCGGACATGGAGCTGGTAAGAGTTCTTCCTAGTGCTGAAGATGAAGTAAACGTTGCATGCTTTCATCCTTCCCCTGGAGGTGGTCTTG
| |||| | ||| | ||| | | || | | || ||| || | | | || | || | | || |||| | ||||||| ||||| || || ||||| || || ||||||||||||||||| || ||||| || || || || |||||||||||||| ||||||||| ||||
tgctacttatgttgtgattataggaataaaactcttgg--attttttatttatttttttatttctatttta---tttcaactttcaaaatatttttatcatgc-agGTCTACAGAGTTTCTGATATGGAACTTGTGAGAGTTCTTCCTAGTGCAGAGGATGAGGTTAATGTAGCTTGCTTTCATCCTTCTGTTGGAGGTGGCCTTG
upper sequence: LOC_Os02g18820.2 (Oryza sativa), 3'ss of exon 13
lower sequence: Vv07s0005g04630.t01 (Vitis vinifera), 3'ss of exon 11
----------------------------------tcatgtgttaattgcttgctccggtttctgtgccacttacaagctcagttctta--------cttatgaatgaagcctt---aatctcattattcctattcatcacgttagGTCTATAGAGTATCGGACATGGAGCTGGTAAGAGTTCTTCCTAGTGCTGAAGATGAAGTAAACGTTGCATGCTTTCATCCTTCCCCTGGAGGTGGTCTTG
|| || || | |||| || |||| | | || || | |||| | ||| ||||| || || |||| | |||| || |||| || || ||||| || || ||||| ||||| |||||||||||||| || || || || ||||||||||||| |||||||| |||||||
gtaacacttcaaaattttaatagcattaggcagtaaatatggtactgaagatctccaattgaagtgctggtcaagtactttattatctgttcaaatcttactgttctgatctttcaggtctcacaggctctttttgtcac-tcagGTTTACCGAGTCTCAGATATGGAACTTGTTAGAGTGCTTCCCAGTGCTGAAGATGAGGTCAATGTAGCTTGCTTTCATCCTTTACCTGGAGGAGGTCTTG
upper sequence: LOC_Os02g18820.2 (Oryza sativa), 3'ss of exon 13
lower sequence: EFJ26270 (Selaginella moellendorffii), 3'ss of exon 12
tcatgtgttaattgcttgctccggtttctgtgccacttacaagctcagttcttacttatgaatgaagccttaatctcattattcctattcatcacgttagGTCTATAGAGTATCGGACATGGAGCTGGTAAGAGTTCTTCCTAGTGCTGAAGATGAAGTAAACGTTGCATGCTTTCATCCTTCCCCTGGAGGTGGTCTTG
|| | ||| ||| || || | || || | | ||||| || | | | || | |||||| |||| || || | || || ||||||| || ||||||||||||||||| || || || |||||||||||| ||| || || ||||
----------------------------------gtttgcgctctctgttttt-----tgga------ctccattgaaattttcct-tttgtttc-tcagATTTATAGAATATCAGATTTGAAACTAGTGCGAGTTCTCCCAAGTGCTGAAGATGAAGTTAATGTAGCGTGCTTTCATCCTCGAGTTGGCGGAGGGCTTG
upper sequence: LOC_Os02g18820.2 (Oryza sativa), 3'ss of exon 13
lower sequence: EFJ14567 (Selaginella moellendorffii), 3'ss of exon 11
tcatgtgttaattgcttgctccggtttctgtgccacttacaagctcagttcttacttatgaatgaagccttaatctcattattcctattcatcacgttagGTCTATAGAGTATCGGACATGGAGCTGGTAAGAGTTCTTCCTAGTGCTGAAGATGAAGTAAACGTTGCATGCTTTCATCCTTCCCCTGGAGGTGGTCTTG
| | || || | || | || || | | ||||| || | | | || | |||||| |||| || || | || || ||||||| || ||||||||||||||||| || || || |||||||||||| ||| || || ||||
-------------------------------------------gtttgcgctctctattttttgga--ctccattgaaattttcct-tttgtttc-tcagATTTATAGAATATCAGATTTGAAACTAGTGCGAGTTCTCCCAAGTGCTGAAGATGAAGTTAATGTAGCGTGCTTTCATCCTCGAGTTGGCGGAGGGCTTGMapped 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|58691171|gb|CK079858.1|CK079858EST: GCATTGTGATGGATGGGGAAACTGGAATTCCTGTATATACTATCTTGGAG GTCTATAGAGTATCGGACATGGAGCTGGTAAGAGT-CTTCCTAGTGCTGAA
genomic: GCATTGTGATGGATGGGGAAACTGGAATTCCTGTATATACTATCTTGGAGgtacatatag ... atcacgttagGTCTATAGAGTATCGGACATGGAGCTGGTAAGAGTTCTTCCTAGTGCTGAA
EST:
gi|33799429|gb|CF325571.1|CF325571EST: GCATTGTGATGGATGGGGAAACTGGAATTCCTGTATATACTATCTTGGAG GTCTATAGAGTATCGGCCATGGAGCTGGTAAGAGTTCTTCCTAGTGCTGAA
genomic: GCATTGTGATGGATGGGGAAACTGGAATTCCTGTATATACTATCTTGGAGgtacatatag ... atcacgttagGTCTATAGAGTATCGGACATGGAGCTGGTAAGAGTTCTTCCTAGTGCTGAA
EST:
gi|29674171|gb|CB670446.1|CB670446EST: GCATTGTGATGGATGGGGAAACTGGAATTCCTGTATATACTATCTTGGAG GTCTATAGAGTATCGGACATGGAGCTGGTAAGAGTTCTTCCTAGTGCTGAA
genomic: GCATTGTGATGGATGGGGAAACTGGAATTCCTGTATATACTATCTTGGAGgtacatatag ... atcacgttagGTCTATAGAGTATCGGACATGGAGCTGGTAAGAGTTCTTCCTAGTGCTGAA
EST:
gi|58592710|gb|CF991018.1|CF991018EST: GCATTGTGATGGATGGGGAAACTGGAATTCCTGTATATACTATCTTGGAG GTCTATAGAGTATCGGACATGGAGCTGGTAAGAGTTCTTCCTAGTGCTGAA
genomic: GCATTGTGATGGATGGGGAAACTGGAATTCCTGTATATACTATCTTGGAGgtacatatag ... atcacgttagGTCTATAGAGTATCGGACATGGAGCTGGTAAGAGTTCTTCCTAGTGCTGAA
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:
72 (upstream exon),
68 (downstream exon)
Score:
19AGAGCACATACTATTGGCATATGGTCGTCGTCATAACTCTATGCTTAGGAGCATTGTGATGGATGGGGAAACTGGAATTCCTGTATATACTATCTTGGAGgtacatatag ... atcacgttagGTCTATAGAGTATCGGACATGGAGCTGGTAAGAGTTCTTCCTAGTGCTGAAGATGAAGTAAACGTTGCATGCTTTCATCCTTCCCCTGGAGGTGGTCTTG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cagttcttacttatgaatgaagccttaatctcattattcctattcatcacgttagGTCTATAGAGTATCGGACATGGAGCTGGTAAGAGTTCTTCCTAGTGCTGAAGATGAAGTAAACGTTGCATGCTTTCATCCTTCCCCTGGAGGTGGTCTTG
ttaatctcattatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcatgtgttaattgcttgctccggtttctgtgccacttacaagctcagttcttacttatgaatgaagccttaatctcattattcctattcatcacgttagGTCTATAGAGTATCGGACATGGAGCTGGTAAGAGTTCTTCCTAGTGCTGAAGATGAAGTAAACGTTGCATGCTTTCATCCTTCCCCTGGAGGTGGTCTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
-catgtgt
- - - - - - tgcttgc
- - - - - - - - - - - - - -ctgtgcc
- - - - - - - - - - - - - - - - - - - -caagctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgaatg