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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTTCTTTGCTGGCATCATTGTCATCTGTCTGGATGAACTTCTCCAGAAAGGTTATGGTTTGGGTTCTGGCATTTCTCTCTTTATTGCTACCAATATCTGgtgagcacattgaactttgttcttctctattgttgacattttctattcaacttgacttatggaaatctttctctgtag

Basic information

species Oryza sativa
transcript LOC_Os03g11440.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g11440.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G073498_T03 (Zea mays), 5'ss of exon 3
TTTTCTTTGCTGGCATCATTGTCATCTGTCTGGATGAACTTCTCCAGAAAGGTTATGGTTTGGGTTCTGGCATTTCTCTCTTTATTGCTACCAATATCTGgtgagcacattgaactttgttcttctctattgttgacattttctattcaacttgacttatggaaatctttctctgtag-----------------
       || || ||  |  ||    ||      |||         |  | | | |||  |  || |||    |      | ||| ||     |   |   |  | |||  |||   | | || |  |||  || |  |||||| |    || |  | || |  |||| |||   |                   
----GAATGGTG-CACAAAAGTTGCTTGGTATCCTGATTGCTATTGGGGAAGCTGTGGCATATGTCCTG----TCTGGAATGTATGGCAGTgtaagccaacttggaacagggaatgctatcct-cattatacttcagcttttcttt---gctggcatcattgtcatctgtctggatgaacttctccagaaaggtt

upper sequence: LOC_Os03g11440.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G130987_T02 (Zea mays), 5'ss of exon 3
TTTTCTTTGCTGGCATCATTGTCATCTGTCTGGATGAACTTCTCCAGAAAGGTTATGGTTTGGGTTCTGGCATTTCTCTCTTTATTGCTACCAATATCTGgtgagcacattgaactttgttcttct-ctattgttgacatt--------------ttctattcaacttgactt----atggaaatctttctctgtag
||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||| ||||| |||||||| || ||||||||||||||||||| ||||  ||| | ||  | ||| |  |  |||||| |||              |||| ||| ||||    |    ||   | |  ||   |||||
TTTTCTTTGCTGGCATCATTGTCATCTGTTTGGATGAACTTCTCCAGAAAGGTTATGGTTTGGGATCTGGTATTTCTCTGTTCATTGCTACCAATATCTGgtaagcatgttggatttaatccttttattgatgttgatattagattgatgtaatgttctgttccacttagtcttataataagactgctttcatgtag

upper sequence: LOC_Os03g11440.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G073498_T02 (Zea mays), 5'ss of exon 2
TTTTCTTTGCTGGCATCATTGTCATCTGTCTGGATGAACTTCTCCAGAAAGGTTATGGTTTGGGTTCTGGCATTTCTCTCTTTATTGCTACCAATATCTGgtgagcacattgaactttgttcttctctattgttgacattttctattcaacttga--cttatgg---aaatctttctctgtag
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||| |||||||||||||| || ||||||||||||||||||| ||||  ||| ||||  | |||   ||||| ||   | |||| ||  |||| |  |||||      |||  ||   |||||
TTTTCTTTGCTGGCATCATTGTCATCTGTCTGGATGAACTTCTCCAGAAAGGTTATGGCTTGGGATCTGGCATTTCTCTGTTCATTGCTACCAATATCTGgtaagcatcttggacttaatccttt--tattgatgtgctgttctgttgcacttaaagcttataataagaattctttcatgtag

upper sequence: LOC_Os03g11440.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G130987_T04 (Zea mays), 5'ss of exon 2
TTTTCTTTGCTGGCATCATTGTCATCTGTCTGGATGAACTTCTCCAGAAAGGTTATGGTTTGGGTTCTGGCATTTCTCTCTT-TATTGCTA-CCAATATCTGgtgagcacattgaactttgttcttctctattgttgacattttctattcaacttgacttatggaaatctttctctgtag-------
       || || ||  |  ||    ||      ||| |       |  | | | |||  |  || ||| |     | | |  || ||  | ||||  |       | |     |   |  || | ||  |   ||    |  |    |||   | |  | |    ||     |||  ||       
----GAATGGTG-CACAAAAGTTGCTTGGTATCTTGATCGCTATTGGGGAAGCTGTGGCATATGTCCTGTCTGGAATGTATGGTAGTgtaagccaacttggaacagggaatgctattctcattatacttcagcttttctttgctggcatcattgtcatctgtttggatgaacttctccagaaaggtt

upper sequence: LOC_Os03g11440.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA13G34370.1 (Glycine max), 5'ss of exon 3
TTTTCTTTGCTGGCATCATTGTCATCTGTCTGGATGAACTTCTCCAGAAAGGTTATGGTTTGGGTTCTGGCATTTCTCTCTTTATTGCTACCAATATCTGgtgagcac--attgaactttgtt----cttctctattgttgacattttctattcaacttgacttatggaaatctttctctgtag---------------------------------------------------
| |  ||||| || || ||||| || ||||| ||||| ||||| || ||||| |||||| |||| ||||| || || || || ||||| ||||||||||||| |      | |   |  || |      | || |   || |  | |  | |||   ||| ||| | | ||    |  |                                                        
TATGTTTTGCGGGTATAATTGTGATATGTCTAGATGAGCTTCTTCAAAAAGGATATGGTCTGGGGTCTGGAATATCCCTATTCATTGCAACCAATATCTGgtaaatttctacttttccctgatgagatatttccagcttttaattataatgttcttgttgtcttctagcaactgctaaccaggatatttaaccatttatctaatacttaaatggaattcccttttcgtttttcag

upper sequence: LOC_Os03g11440.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT1G78720.1 (Arabidopsis thaliana), 5'ss of exon 2
TTTTCTTTGCTGGCATCATTGTCATCTGTCTGGATGAACTTCTCCAGAAAGGTTATGGTTTGGGTTCTGGCATTTCTCTCTTTATTGCTACCAATATCTGgtgagcacattgaacttt---gttcttctctattgttgacatt-ttctattcaacttgact--tatggaaatctttctctgtag
| |  ||||||| ||| || ||  | ||| | ||||| ||||| ||||||||||||||  | |||||||| ||||| || || |||||||| |||||||||||||      | |||     ||    || | | | | | |   || |   ||  |    |  ||  | | | | | |   |||
TCTGTTTTGCTGCCATTATCGTTCTTTGTTTAGATGAGCTTCTTCAGAAAGGTTATGGCCTCGGTTCTGGTATTTCCCTTTTCATTGCTACTAATATCTGgtgagttttaagtactccaacgtctagctttctcggttaaaccgttatgcgcatttcagatgttaatggagtttcttttcttag

upper sequence: LOC_Os03g11440.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv19s0014g01020.t01 (Vitis vinifera), 5'ss of exon 3
TTTTCTTTGCTGGCATCATTGTCATCTGTCTGGATGAACTTCTCCAGAAAGGTTATGGTTTGGGTTCTGGCATTTCTCTCTTTATTGCTACCAATATCTGgtgagcacattgaactttgttct---tctctattgttgacattttctattcaacttg----acttatggaaatctttctctgtag-----------------------------------------------------------------------------------------
| |  |||||||| |||||||| || ||| | ||||||||||| |||||||| |||||  | || ||||| |||||||| || || || || |||||||||||||||  | |  |||| |      | | | || || |  | |  | || ||| ||    | ||   |||   || || | |||                                                                                         
TCTGTTTTGCTGGTATCATTGTGATATGTTTAGATGAACTTCTGCAGAAAGGATATGGGCTTGGCTCTGGAATTTCTCTTTTCATAGCAACTAATATCTGgtgagcatctggttctttttctgggattttttttattaatttatcattttgaacatggaatatttgaagaagctttactatctagcagccagcgtctggtgaatgtggtctcatttctgggttgaccattaactctactgtcaaatagtgacaattgttttgatcaattggcag

upper sequence: LOC_Os03g11440.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv00s1338g00020.t01 (Vitis vinifera), 5'ss of exon 2
TTTTCTTTGCTGGCATCATTGTCATCTGTCTGGATGAACTTCTCCAGAAAGGTTATGGTTTGGGTTCTGGCATTTCTCTCTTTATTGCTACCAATATCTGgtgagcacattgaactttgttc----ttctctattgttgacattttctattcaacttg----acttatggaaatctttctctgtag---------------------------------------------------------------------------------------------------
| | ||||||||| |||||||| || ||| | ||||||||||| |||||||| |||||  | || ||||| |||||||| || || || || |||||||||| ||||  | |  |||| |      || | | |  || |  | |  | || ||| ||    | ||   |||   ||    | |||                                                                                                   
TCTGCTTTGCTGGTATCATTGTGATATGTTTAGATGAACTTCTGCAGAAAGGATATGGCCTTGGCTCTGGAATTTCTCTTTTCATAGCAACTAATATCTGgttagcatctggttctttttctgggattttttttaattaatttatgattttgaacatggaatatttgaagaagctttatcgtctagcagccagtgtctggtgaatggtgggcccattttctgggtgaaccattaactctactgtcaagtagtgattgctaatgaattgttttgatcaattggcag

upper sequence: LOC_Os03g11440.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv00s2574g00010.t01 (Vitis vinifera), 5'ss of exon 2
TTTTCTTTGCTGGCATCATTGTCATCTGTCTGGATGAACTTCTCCAGAAAGGTTATGGTTTGGGTTCTGGCATTTCTCTCTTTATTGCTACCAATATCTGgtgagcacattgaactttgttc----ttctctattgttgacattttctattcaacttg----acttatggaaatctttctctgtag---------------------------------------------------------------------------------------------------
| | ||||||||| |||||||| || ||| | ||||||||||| |||||||| |||||  | || ||||| |||||||| || || || || |||||||||| ||||  |    |||| |      || | | |  || |  | |  | || ||| ||    | ||   |||   ||  | | |||                                                                                                   
TCTGCTTTGCTGGTATCATTGTGATATGTTTAGATGAACTTCTGCAGAAAGGATATGGCCTTGGCTCTGGAATTTCTCTTTTCATAGCAACTAATATCTGgttagcatctgcttctttttctgggattttttttaattaatttatgattttgaacatggaatatttgaagaagctttattgtctagcagccagtgtctggtgaatggtgggcccattttctgggtggaccattaactctactgtcaagtagtgattgctaatgaattgttttgatcaattggcag

upper sequence: LOC_Os03g11440.1 (Oryza sativa), 5'ss of exon 3
lower sequence: PP1S323_56V6.1 (Physcomitrella patens), 5'ss of exon 3
TTTTCTTTGCTGGCATCATTGTCATCTGTCTGGATGAACTTCTCCAGAAAGGTTATGGTTTGGGTTCTGGCATTTCTCTCTTTATTGCTACCAATATCTGgtgagcacattgaactttgttctt-----ctctattgttgacatttt---ctattcaacttgact-tatggaaatctttctctgtag-------------
| ||||| ||||| |||||||| |||||||| |||||  | || ||||| ||||||||  |||| || || |||||||| || ||||| |||||||||||||  || || |   |||| | | |        ||    |||  ||     | | |  ||| | ||   ||  |||     |||| ||             
TCTTCTTCGCTGGAATCATTGTTATCTGTCTTGATGAGTTGCTACAGAAGGGTTATGGACTGGGATCCGGAATTTCTCTTTTCATTGCCACCAATATCTGgtaggctcagttttctttatgcctgcaattcttagaaatgaagttgagagccaatatactcgtctgcttgcgaattgaaatctggagtttatctctatgt

upper sequence: LOC_Os03g11440.1 (Oryza sativa), 5'ss of exon 3
lower sequence: EFJ15673 (Selaginella moellendorffii), 5'ss of exon 2
TTTTCTTTGCTGGCATCATTGTCATCTGTCTGGATGAACTTCTCCAGAAAGGTTATGGTTTGGGTTCTGGCATTTCTCTCTTTATTGCTACCAATATCTGgtgagcacattgaactttgttcttctctattgttgacattttctattcaacttgacttatggaaatctttctctgtag
| ||||| ||||| ||||||||||| || ||||||||||| |||||||| || || ||  | || || || || ||  | || || || ||||| ||||||||||       ||| || | ||| || |    |||   ||||||||     ||  | |  |                
TCTTCTTCGCTGGTATCATTGTCATTTGCCTGGATGAACTCCTCCAGAAGGGATACGGGCTTGGATCGGGAATCTCGTTGTTCATAGCCACCAACATCTGgtgagag----aaaccttttccttttccagctctgattatttctattgtgactg--tgacag----------------

Mapped 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|88294154|gb|CI667128.1|CI667128
EST:     GTTTGGGTTCTGGCATTTCTCTCTTTATTGCTACCAATATCTG                         TGAGAATATCATCTGGAAGGCATTTAGCCCCACAACTATCAACAGTGGCCG
genomic: GTTTGGGTTCTGGCATTTCTCTCTTTATTGCTACCAATATCTGgtgagcacat ... ttctctgtagTGAGAATATCATCTGGAAGGCATTTAGCCCCACAACTATCAACAGTGGCCG
EST: gi|29665156|gb|CB661431.1|CB661431
EST:     GGTTATGGTTTGGGTTCTGGCATTTCTCTCTTTATTGCTACCAATATCTG                         TGAGAATATCATCTGGAAGGCATTTAGCCCCACAACTATCAACAGTGGCCG
genomic: GGTTATGGTTTGGGTTCTGGCATTTCTCTCTTTATTGCTACCAATATCTGgtgagcacat ... ttctctgtagTGAGAATATCATCTGGAAGGCATTTAGCCCCACAACTATCAACAGTGGCCG
EST: gi|29616182|gb|CB621194.1|CB621194
EST:     GGTTATGGTTTGGGTTCTGGCATTTCTCTCTTTATTGCTACCAATATCTG                         TGAGAATATCATCTGGAAGGCATTTAGCCCCACAACTATCAACAGTGGCCG
genomic: GGTTATGGTTTGGGTTCTGGCATTTCTCTCTTTATTGCTACCAATATCTGgtgagcacat ... ttctctgtagTGAGAATATCATCTGGAAGGCATTTAGCCCCACAACTATCAACAGTGGCCG
EST: gi|58661882|gb|CK050562.1|CK050562
EST:     GGTTATGGTTNGGGTTCTGGCATTTCTCTCTTTATTGCTACCAATATCTG                         TGAGAATATCATCTGGAAGGCATTTAGCCCCACA
genomic: GGTTATGGTTTGGGTTCTGGCATTTCTCTCTTTATTGCTACCAATATCTGgtgagcacat ... ttctctgtagTGAGAATATCATCTGGAAGGCATTTAGCCCCACA
EST: gi|33795682|gb|CF323711.1|CF323711
EST:     GGTTATGGTTTGCGTTCTGGCATTTCTCTCTTTATTGCTACCAATATCTG                         TGAGAATATCATC
genomic: GGTTATGGTTTGGGTTCTGGCATTTCTCTCTTTATTGCTACCAATATCTGgtgagcacat ... ttctctgtagTGAGAATATCATC
EST: gi|58691016|gb|CK079703.1|CK079703
EST:     GGTTATGGTTTGGGTTCTGGCATTTCTCTCTTTATTGCTACCAATATCTG                         TGAGAATATCATCTGGAAGGCATTTAGCCCCACAACTATCAACAGTGGCCG
genomic: GGTTATGGTTTGGGTTCTGGCATTTCTCTCTTTATTGCTACCAATATCTGgtgagcacat ... ttctctgtagTGAGAATATCATCTGGAAGGCATTTAGCCCCACAACTATCAACAGTGGCCG
EST: gi|2310203|gb|C26358.1|C26358
EST:     GGTTATGGTTTGGGTTCTGGCATTTCTCTCTTTATTGCTACCAATATCTG                         TGAGAATATCATCTGGAAGGCATTTAGCCCCACAACTATCAACAGTGGCCG
genomic: GGTTATGGTTTGGGTTCTGGCATTTCTCTCTTTATTGCTACCAATATCTGgtgagcacat ... ttctctgtagTGAGAATATCATCTGGAAGGCATTTAGCCCCACAACTATCAACAGTGGCCG

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: 74 (upstream exon), 75 (downstream exon)
Score: 74

TTTTCTTTGCTGGCATCATTGTCATCTGTCTGGATGAACTTCTCCAGAAAGGTTATGGTTTGGGTTCTGGCATTTCTCTCTTTATTGCTACCAATATCTGgtgagcacat ... ttctctgtagTGAGAATATCATCTGGAAGGCATTTAGCCCCACAACTATCAACAGTGGCCGTGGTGCTGAGTTCGAGGGGGCTGTCATTGCATTGTTCCATCTGTTGATT




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