Sequence
atgc intronic sequence ATGC exonic sequencegtaagcaagtgtttcaattgagtatacatgattaataaattgttaattagtacataaatcttcaccaaacagctaatttcttatgtggtgaatggtgagttgagaactgaagattattggctgatcattattattgactgtccaaccagATTATGATAGAATTATCAAGAATATTGAAAGGGGAGAGGCCAGGATATCACGGAAGGATGAAATTATGAGAGCCATCGGGAAGAAGTTAGACCGCTATAA
Basic information
species | Oryza sativa |
transcript | LOC_Os01g27040.1 |
intron # | 21 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g27040.1 (Oryza sativa), 3'ss of exon 21
lower sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 21
gtaagcaagtgtttcaattgagtatacatgattaataaattgttaattagtacataaatcttcaccaaacagctaatttcttatgtggtgaatggtgagttgagaactgaagattattggctgatcat---tattattgactgtccaaccagATTATGATAGAATTATCAAGAATATTGAAAGGGGAGAGGCCAGGATATCACGGAAGGATGAAATTATGAGAGCCATCGGGAAGAAGTTAGACCGCTATAA
|||| || | || ||| | | | | | || || ||| |||| || | || | ||| | | || | | ||| |||| |||||||||||||||||| || |||||||||||||| || || || ||||| || |||||||| ||||||| || || |||||||||||||||||||| ||
---------------------------------------------------ttataacattttaattaaaagcaactgtttgcaattttgcatactgaagatcaaacttttcat-actgacagattttgtgttttgatcattgttcaactagATTATGATAGAATTATAAAAAATATTGAAAGGGGGGAAGCAAGAATATCCCGCAAGGATGAGATTATGAAGGCTATTGGGAAGAAGTTAGACCGCTACAA
upper sequence: LOC_Os01g27040.1 (Oryza sativa), 3'ss of exon 21
lower sequence: GRMZM2G010085_T02 (Zea mays), 3'ss of exon 13
gtaagcaagtgtttcaattgagtatacatgattaataaattgttaattagtacataaatcttcaccaaacagctaatttcttatgtggtgaatggtgagttgagaactgaagattattggctgatcat-tattattgactgtccaaccagATTATGATAGAATTATCAAGAATATTGAAAGGGGAGAGGCCAGGATATCACGGAAGGATGAAATTATGAGAGCCATCGGGAAGAAGTTAGACCGCTATAA
| | || || | || || ||| || | || | |||| | | | | || | || || | || | | ||| ||||||||||||||||||||||| || |||||||||||||| || || |||||||| || |||||||| ||||||| || || ||||||||| |||||||||| ||
---------------------------------------------accattatattttttttttaataaaagc-aactgtttgcatactgaagatcaaactt----tccatactgatggattgtgtatgttttgatcattgtacaaccagATTATGATAGAATTATAAAAAATATTGAAAGGGGGGAAGCAAGGATATCCCGCAAGGATGAGATTATGAAGGCTATTGGGAAGAAGCTAGACCGCTACAA
upper sequence: LOC_Os01g27040.1 (Oryza sativa), 3'ss of exon 21
lower sequence: GLYMA07G38050.1 (Glycine max), 3'ss of exon 21
gtaagcaagtgtttcaattgagtatacatgattaataaattgttaattagtacataaatcttcaccaaacagctaatttcttatgtggtgaatggtgagttgagaactgaagattattggctgatcattattattgactgtccaaccagATTATGATAGAATTATCAAGAATATTGAAAGGGGAGAGGCCAGGATATCACGGAAGGATGAAATTATGAGAGCCATCGGGAAGAAGTTAGACCGCTATAA
| || || | | | || | || || ||| | | || ||| || | || || | ||| | | || | | | ||| | || ||||||||||||||||||| || || |||||||| || ||||| || ||||| ||||| ||||| || |||| ||| || ||||||||||| |||||||| ||
-----------------------------gtttgatgtgtgttgatttgccaaatgaagcttga------atttagttttccattaag---atatcaag----ggtctg-----tctgatttgtgtactttgatttatggtttg--cagATTATGATAGAATTATTAAAAACATTGAAAGAGGGGAGGCAAGAATATCCCGGAAAGATGAGATCATGAAAGCTATTGGGAAGAAGTTGGACCGCTACAA
upper sequence: LOC_Os01g27040.1 (Oryza sativa), 3'ss of exon 21
lower sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 21
gtaagcaagtgtttcaattgagtatacatgattaataaattgttaattagtacataaatcttcaccaaacagctaatttcttatgtggtgaatgg--tgagttgagaactgaagattattggctgatcattattattgactgtccaacc---agATTATGATAGAATTATCAAGAATATTGAAAGGGGAGAGGCCAGGATATCACGGAAGGATGAAATTATGAGAGCCATCGGGAAGAAGTTAGACCGCTATAA
|||| ||| | | | | || || ||||| ||| || | | | ||| | || ||||| | | || | | |||||||||||||||||| || || |||||||| || ||||| || ||||| ||||| ||||| || |||| ||| || ||||||||||| |||||||| |
-----------------------------------------------------ttaaaatatcaagggtttgatgtgtgttgatttgccaaatggcttgaattaaaatataaagggt-ctgtctgatttgtgtactttggtttatggtttgtagATTATGATAGAATTATTAAAAACATTGAAAGAGGGGAGGCAAGAATATCCCGGAAAGATGAGATCATGAAAGCTATTGGGAAGAAGTTGGACCGCTACAG
upper sequence: LOC_Os01g27040.1 (Oryza sativa), 3'ss of exon 21
lower sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 21
gtaagcaagtgtttcaattgagtatacatgattaataaattgttaattagtacataaatcttcaccaaacagctaatttcttatgtggtgaatggtgagttgagaactgaagattattggctgatcattattattgactgtccaaccagATTATGATAGAATTATCAAGAATATTGAAAGGGGAGAGGCCAGGATATCACGGAAGGATGAAATTATGAGAGCCATCGGGAAGAAGTTAGACCGCTATAA
|| || | | | ||| || | | | || ||||| || ||||| | | | | | ||||| || || ||| | | |||| |||||||||| |||||||| || || ||||||||||| ||||| || || || ||||| ||||| || |||| || || || |||||||| |||||||| ||
-------------------------------------gataaggctttgttgctttaattttttctgga-aattagtttct---gtttagaatgtt----tcaaggttctgcctaattggtgcat--tttttaatcattgtctg--cagATTATGACAGAATTATTAAAAACATTGAAAGGGGGGAGGCAAGAATTTCTCGGAAAGATGAGATCATGAAGGCTATTGGAAAGAAGTTGGACCGCTACAA
upper sequence: LOC_Os01g27040.1 (Oryza sativa), 3'ss of exon 21
lower sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 21
gtaagcaagtgtttcaattgagtatacatgattaataaattgttaattagtac-ataaatcttcaccaaacagctaatttcttatgtggtgaatggtgagttgagaactgaagattattggctgat-----cattattattgactgtccaaccagATTATGATAGAATTATCAAGAATATTGAAAGGGGAGAGGCCAGGATATCACGGAAGGATGAAATTATGAGAGCCATCGGGAAGAAGTTAGACCGCTATAA
||| |||| ||| | ||| || || || | | ||| |||| | | || || || |||| | | | | |||| |||||||||| |||||||| || || ||||||||||| ||||| || || || ||||| ||||| || |||| ||| || || |||||||| |||||||| ||
------------------------------------------------agtgggataaggctttgtta-----ttaactttttttggaaattactttctgtttagaatgtcaaggttctgcctaatttgtgcattttgaatcattgtctg--cagATTATGACAGAATTATTAAAAACATTGAAAGGGGGGAGGCAAGAATTTCTCGGAAAGATGAGATCATGAAAGCTATTGGAAAGAAGTTGGACCGCTACAA
upper sequence: LOC_Os01g27040.1 (Oryza sativa), 3'ss of exon 21
lower sequence: AT3G06400.3 (Arabidopsis thaliana), 3'ss of exon 21
gtaagcaagtgtttcaattgagtatacatgattaataaattgttaattagtacataaatcttcaccaaacagctaatttcttatgtggtgaatggtgagttgagaactgaagattattggctgatcattattattgactgtccaaccagATTATGATAGAATTATCAAGAATATTGAAAGGGGAGAGGCCAGGATATCACGGAAGGATGAAATTATGAGAGCCATCGGGAAGAAGTTAGACCGCTATAA
| |||| | || | | | | | || | |||| | | | | | | || ||| | | | | ||| | ||| ||| |||| ||| || | | | | ||| ||||||||||| || ||||| ||||| ||||||||||| ||||| || |||| || ||||| |||| ||||| |||||||| | || ||||| |
----gtaagtaacacctttcaatgc---taagttatgcagtgtt------tttacatgtttctaagtaattcctacctccaaaaagagcttatgctaagt---------aagtttatc-----atctttccctctaaatatgt----agACTATGATAGAATCATTAAGAACATTGAGAGGGGAGAGGCAAGGATCTCTAGGAAAGACGAAATCATGAAGGCCATAGGGAAGAAACTGGATCGCTACAG
upper sequence: LOC_Os01g27040.1 (Oryza sativa), 3'ss of exon 21
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 21
gtaagcaagtgtttcaattgagtatacatgattaataaattgttaattagtacataaatcttcaccaaacagctaatttcttatgtggtgaatggtgagttgagaactgaagattattggctgatcattattattgactgtccaaccagATTATGATAGAATTATCAAGAATATTGAAAGGGGAGAGGCCAGGATATCACGGAAGGATGAAATTATGAGAGCCATCGGGAAGAAGTTAGACCGCTATAA
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-----------------------------ggttgatatattgtcag-------atgcatctt-ac--aacatccatttgtttttcatcaaaatggtgattttt----------tcgtctgcttttaaccattaaatacaatttctccagATTATGATAGGATCATCAAGAACATTGAAAGAGGAGAGGCTAGAATTTCTAGGAAAGATGAGATCATGAAAGCAATTGGGAAGAAGTTGGATCGCTACAAMapped 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|58682000|gb|CK070687.1|CK070687EST: AGTTCAACGATATGCTAAAGTTTTCAAGGAGAGATACAAGGAACTGAGTG ATTATGATAGAATTATCAAGAATATTGAAGAGGGGAGAGGCCAGGATATCA
genomic: AGTTCAACGATATGCTAAAGTTTTCAAGGAGAGATACAAGGAACTGAGTGgtaagcaagt ... gtccaaccagATTATGATAGAATTATCAAGAATATTGAA-AGGGGAGAGGCCAGGATATCA
EST:
gi|84117441|gb|CD151208.1|CD151208EST: AGTTCAACGATATGCTAAAGTTTTCAAGGAGAGATACAAGGAACTGAGTG ATTATGATAGAATTATCAAGAATATTGAAAGGGGAGAGGCCAGGATATCAC
genomic: AGTTCAACGATATGCTAAAGTTTTCAAGGAGAGATACAAGGAACTGAGTGgtaagcaagt ... gtccaaccagATTATGATAGAATTATCAAGAATATTGAAAGGGGAGAGGCCAGGATATCAC
EST:
gi|396941444|gb|HO188653.1|HO188653EST: GTTCAACGATATGCTAAAGTTTTCAAGGAGAGATACAAGGAACTGAGTG ATTATGATAGAATTATCAAGAATATTGAAAGGGGAGAGGCCAGGATATCAC
genomic: GTTCAACGATATGCTAAAGTTTTCAAGGAGAGATACAAGGAACTGAGTGgtaagcaagt ... gtccaaccagATTATGATAGAATTATCAAGAATATTGAAAGGGGAGAGGCCAGGATATCAC
EST:
gi|58683001|gb|CK071688.1|CK071688EST: AGTTCAACGATATGCTAAAGTTTTCAAGGAGAGATACAAGGAACTGAGTG ATTATGATAGAATTATCAAGAATATTGAAAGGGGAGAGGCCAGGATATCAC
genomic: AGTTCAACGATATGCTAAAGTTTTCAAGGAGAGATACAAGGAACTGAGTGgtaagcaagt ... gtccaaccagATTATGATAGAATTATCAAGAATATTGAAAGGGGAGAGGCCAGGATATCAC
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:
75 (upstream exon),
75 (downstream exon)
Score:
34AATGATATTAGGAGTATTGCCGCTGAAATGGAGGGGAAGACAGAGGAGGAAGTTCAACGATATGCTAAAGTTTTCAAGGAGAGATACAAGGAACTGAGTGgtaagcaagt ... gtccaaccagATTATGATAGAATTATCAAGAATATTGAAAGGGGAGAGGCCAGGATATCACGGAAGGATGAAATTATGAGAGCCATCGGGAAGAAGTTAGACCGCTATAA
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgagttgagaactgaagattattggctgatcattattattgactgtccaaccagATTATGATAGAATTATCAAGAATATTGAAAGGGGAGAGGCCAGGATATCACGGAAGGATGAAATTATGAGAGCCATCGGGAAGAAGTTAGACCGCTATAA
tattgac putative branch site (score: 34)
tgatcattattatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcaagtgtttcaattgagtatacatgattaataaattgttaattagtacataaatcttcaccaaacagctaatttcttatgtggtgaatggtgagttgagaactgaagattattggctgatcattattattgactgtccaaccagATTATGATAGAATTATCAAGAATATTGAAAGGGGAGAGGCCAGGATATCACGGAAGGATGAAATTATGAGAGCCATCGGGAAGAAGTTAGACCGCTATAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT