Sequence
atgc intronic sequence ATGC exonic sequencegtaagtttttgtttgcagagaattgaattcttatcctctgagcattcataaatcttgggtccttttgttgctggaagtggagtaaaatttgttccttttgctgttcattttgggggtacagGGATCATCTTCATTGAAGGACATACCAGTTGTGATCATGTCTTCTGAGAATGTGCCTGCAAGGATCAACAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g72330.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g72330.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G156019_T01 (Zea mays), 3'ss of exon 3
gtaagtttttgtttgcagag-------aattgaattcttatcctctgagcattcataaatcttggg------tccttttgttgctggaa----------gtggagtaaaatttgttcctt--ttgct------gttcattttggg--ggtacagGGATCATCTTCATTGAAGGACATACCAGTTGTGATCATGTCTTCTGAGAATGTGCCTGCAAGGATCAACAG-----------------------------
|| ||| | | || | | || | | || || |||| ||| | |||| || | | | | | |||| | || | || || ||||| | || |||| | | ||||| || || || | |||||||| || || ||||||||||| ||||||||||||||||| |||||| |||
gtgagtgtccttaaattaagttaccccaccccacccctcttggtttgggcgctcattaatagctagctgccctcctcctggtccacggaccaccacggcgcagagtgagatctcatctttgcttgctcaaattgccgtttctgggatgatgcagGGGTCCTCCTCGCTCAAGGACATTCCTGTGGTGATCATGTCGTCTGAGAATGTGCCTGCCCGGATCAGCAGGTCAGCTCCCGACCGCATTCAATTTTAAA
upper sequence: LOC_Os01g72330.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA04G29250.1 (Glycine max), 3'ss of exon 3
gtaagtttttgtttgcagagaattgaattcttatcctctgagcattcataaatcttgggtccttttgttgctggaagtggagtaaaatttgttccttttgctgttcattttgggggtacagGGATCATCTTCATTGAAGGACATACCAGTTGTGATCATGTCTTCTGAGAATGTGCCTGCAAGGATCAACAG
| || | ||| || | || | | | | | ||| || || || | | || ||||| | | || | | | ||| ||| || | || ||||||||||| ||||| ||||| || |||||||| || ||||||||||||||
---------aactctcaaaccatt--tttgtgatgtgcattgtaaccttcaattgcttgtatcttccctggtttgatgctagaaaaata----------acagaaagttattgacttgtagGAATCTAAATCTCTTAAAGACATACCAGTGGTGATTATGTCCTCAGAGAATGTCCCAGCAAGGATCAACAG
upper sequence: LOC_Os01g72330.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA11G21650.1 (Glycine max), 3'ss of exon 3
gtaagtttttgtttgcagagaattgaattcttatcctctgagcattcataaatcttgggtccttttgttgctggaagtggagtaaaatttgttccttttgctgttcattttgggggtacagGGATCATCTTCATTGAAGGACATACCAGTTGTGATCATGTCTTCTGAGAATGTGCCTGCAAGGATCAACAG
|| | ||| | | || | | | |||| | |||| | || || | | | || ||||| | | | | || |||| |||| ||| || | || ||||||||||| ||||| ||||| || |||||||| || |||||||| |||||
-------------ctcaaaccatttttgtgatgtcataacaaccttca-attacttgtatatcttccctggtttgattttagaaaaataataacatgaagttattgattt-------gcagGAATCTAAATCTCTTAAAGACATACCAGTGGTGATTATGTCCTCAGAGAATGTCCCAGCAAGGATTAACAG
upper sequence: LOC_Os01g72330.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA15G37770.1 (Glycine max), 3'ss of exon 3
gtaagtttttgtttgcagagaattgaattcttatcctctgagcattcat---aaatcttgggtccttttgttgctggaagtggagtaaaatttgttccttttgctgttcattttgggggtacagGGATCATCTTCATTGAAGGACATACCAGTTGTGATCATGTCTTCTGAGAATGTGCCTGCAAGGATCAACAG
| |||| || | | || | || | | | | || | | || |||| || | | |||| | | || | | | |||| |||| ||| || | || |||||||||||||||| ||||| || |||||||| || |||||||||||||
---------------aatcaaatttgatcatggccatcatggtatatctttgacagcctgtatattctt-ctgcttgatgatgttaaaaaataata--ttaagttccttgatttg------cagGAATCTAAATCTCTTAAAAACATACCAGTTGTGATTATGTCCTCAGAGAATGTACCATCAAGGATCAACAG
upper sequence: LOC_Os01g72330.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA13G26770.1 (Glycine max), 3'ss of exon 3
gtaagtttttgtttgcagagaattgaattcttat-cctctgagcattcataaatcttgggtccttttgttgctggaagtggagtaaaatttgttccttttgctgttcattttgggggtacagGGATCATCTTCATTGAAGGACATACCAGTTGTGATCATGTCTTCTGAGAATGTGCCTGCAAGGATCAACAG
| ||||| | | ||| || ||| | || || | | | || || || || | ||| ||| | |||| | | |||| ||| || | || |||||||||||||||| ||||| || |||||||| || |||||||||||||
----aatcaaatttgctcatggccatcatgatatatctttgacaacctgtatattcttctgcttgatgatgttgaaa----aataatattaagttctttgatt--------------tgcagGAATCTAAATCTCTTAAAAACATACCAGTTGTGATTATGTCCTCAGAGAATGTACCATCAAGGATCAACAG
upper sequence: LOC_Os01g72330.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv13s0067g03430.t01 (Vitis vinifera), 3'ss of exon 3
----------------------------gtaagtttttgt----ttgcagagaattgaattcttatcctctgagcattcataaatcttgggtccttttgttgctggaagtggagtaaaatttgttccttt----------tgctgttcatttt-----gggggtacagGGATCATCTTCATTGAAGGACATACCAGTTGTGATCATGTCTTCTGAGAATGTGCCTGCAAGGATCAACAG
|| ||| | | |||||| | | | | || || | ||| ||| || || | | | ||| || ||| || || | || | | |||| || | || |||| ||||||||||||||||||||||| |||||||| | ||| ||||||| |||||
gtaagatctctcattttgatcttagctttcaaatttctttgatcttgcagctttctcatggacaacatccagatcagtgtgaaaacttcatattttccactgattgggacttgggaaagttaccaattttgaagccaaactgaagtctaaattcatgtgaatctgcagGAGTCTACATCTCTGAAAGACATACCAGTTGTGATCATGTCCTCTGAGAACATCCCTTCAAGGATTAACAG
upper sequence: LOC_Os01g72330.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv08s0007g05390.t01 (Vitis vinifera), 3'ss of exon 3
gtaagtttttgtttgcagagaattgaattcttatcctctgagcattcataaatcttgggtccttttgttgctggaagtggagtaaaatttgttccttttgctgttcattttgggggtacagGGATCATCTTCATTGAAGGACATACCAGTTGTGATCATGTCTTCTGAGAATGTGCCTGCAAGGATCAACAG
| | | ||| | | | || | | || | |||| || |||| ||||| | || ||| || ||| | | ||||| ||||| ||| || || |||| | |||||||| ||||||||||| ||||||||||||||| ||||||||| |||
------taaggcctaaagatacaagggattccatgc---aaacaaacggaaat----gggaaatttg--actggattttttttattttttatttatttatttactgatttt------acagGAATCTTCATCTTTGAGAAATATACCAGTAGTGATCATGTCATCTGAGAATGTGCCTTCAAGGATCACCAG
upper sequence: LOC_Os01g72330.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv13s0067g03450.t01 (Vitis vinifera), 3'ss of exon 2
gtaagtttttgtttgcagagaattgaattcttatcctctgagcattcataaatcttgg-gtccttttgtt--gctggaagtggagtaaaatttgttccttttgctgttcattt---tgggggtacagGGATCATCTTCATTGAAGGACATACCAGTTGTGATCATGTCTTCTGAGAATGTGCCTGCAAGGATCAACAG
| || | || | | ||| | ||| | || | || || || |||| ||| | | |||| || | | ||| || | |||| || | || | || ||||| ||||||||||||||||| ||||||||| | ||| | ||||| |||||
------------------------gtatcttcatttgccta--attattgaatttcaacatcttattattttactccaagtt-agtcagaacagttcattaaaatttaaattaacatgaatctgcagGAGTCTACATCTCTTAAAGACATCCCAGTTGTGATCATGTCCTCTGAGAATATCCCTTCTAGGATTAACAG
upper sequence: LOC_Os01g72330.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv13s0067g03490.t01 (Vitis vinifera), 3'ss of exon 4
gtaagtttttgtttgcagagaattgaattcttatcctctgagcattcataaatcttgggtccttttgttgc-tggaagtggagtaaaatttgttccttttgctgttcat---tttgggggtacagGGATCATCTTCATTGAAGGACATACCAGTTGTGATCATGTCTTCTGAGAATGTGCCTGCAAGGATCAACAG
| || | || | | ||| || || | | || | || || | | | | | | | | || | | | || | || | |||| || || || |||| ||||||||||||||||||||||| |||||||| | ||| ||||||| |||||
------------------------gtatcttcatttgccca--attgttacatttcagatcttattcttccattccaatttactcagaacaattaatgaaaatctaaatgaatgtgattctgcagGAGTCTTCATCTCTGAAAGACATACCAGTTGTGATCATGTCCTCTGAGAACATCCCTTCAAGGATTAACAG
upper sequence: LOC_Os01g72330.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv13s0067g03480.t01 (Vitis vinifera), 3'ss of exon 2
gtaagtttttgtttgcagagaattgaattcttatcctctgagcattcataaatcttgggtccttttgttgctggaagtggagtaaaatttgttcctt--ttgctgttcattttgggggtacagGGATCATCTTCATTGAAGGACATACCAGTTGTGATCATGTCTTCTGAGAATGTGCCTGCAAGGATCAACAG
| | || | || || | || | || | || || | | | ||| | || || |||| || | |||| || | || | || ||||| ||||||||||||||||| ||||||||| | ||| | ||||| | |||
---------------------------gtatcttcatttgcccaattattacatttcagcatcttatttttttcacgccaagttagtcccaacaattaattagaattcaaaatgaatctgcagGAGTCTACATCTCTTAAAGACATCCCAGTTGTGATCATGTCCTCTGAGAATATCCCTTCTAGGATTACCAG
upper sequence: LOC_Os01g72330.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv13s0067g03510.t01 (Vitis vinifera), 3'ss of exon 3
gtaagtttttgtttgcagagaattgaattcttatcctctgagcattcataaatcttgggtccttttgttgctggaagtggagtaaaatttgttccttttgctgttcattttgggggtacagGGATCATCTTCATTGAAGGACATACCAGTTGTGATCATGTCTTCTGAGAATGTGCCTGCAAGGATCAACAG
| || | || ||| ||| || | || ||| || | | | ||| ||| | | |||| ||| || || |||| ||||||||||||||||||||||| ||||||||| | || ||||||| |||||
------------------------gtatcttcattctcctgatg-----aaaactcagaaccattt----ttgaagctaaaactaaa---------------aatcaaatgaattctgcagGAATCTTCATCTCTGAAAGACATACCAGTTGTGATCATGTCCTCTGAGAATATCCCCTCAAGGATTAACAGMapped 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|428412|gb|D24560.1|D24560EST: ACTACTGCATGCCTGGCATGACAGGGTATGATCTGCTCAAGAGGGTGAAG GGATCATCTTCATTGAAGGACATACCAGTTGTGATCATGTCTTCTGAGAAT
genomic: ACTACTGCATGCCTGGCATGACAGGGTATGATCTGCTCAAGAGGGTGAAGgtaagttttt ... gggggtacagGGATCATCTTCATTGAAGGACATACCAGTTGTGATCATGTCTTCTGAGAAT
EST:
gi|29684119|gb|CB680394.1|CB680394EST: ACTACTGCATGCCTGGCATGACAGGGTATGATCTGCTCAAGAGGGTGAAG GGATCATCTTCATTGAAGGACATACCAGTTGTGATCATGTCTTCTGAGAAT
genomic: ACTACTGCATGCCTGGCATGACAGGGTATGATCTGCTCAAGAGGGTGAAGgtaagttttt ... gggggtacagGGATCATCTTCATTGAAGGACATACCAGTTGTGATCATGTCTTCTGAGAAT
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:
67 (upstream exon),
51 (downstream exon)
Score:
7GAGATTGATGTCAACCTGATAATCACTGACTACTGCATGCCTGGCATGACAGGGTATGATCTGCTCAAGAGGGTGAAGgtaagttttt ... gggggtacagGGATCATCTTCATTGAAGGACATACCAGTTGTGATCATGTCTTCTGAGAATGTGCCTGCAAGGATCAACAG
<
<
<
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttgctggaagtggagtaaaatttgttccttttgctgttcattttgggggtacagGGATCATCTTCATTGAAGGACATACCAGTTGTGATCATGTCTTCTGAGAATGTGCCTGCAAGGATCAACAG
taaaatttgtt TA-rich tract