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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGAAAAGGATGTATGGGTCATGAATGTTGTTCCACATGATGGACCAAGCACTCTCAAGATAATCTATGACAGAGGGCTTATAGGTTCTACTCATGACTGgtatgtgtcattttatataaagaaaattgtgcttggcatatcagtagttgagcattatgctagtttgttaggttaaggcaactcagtagctctctgccac...

Basic information

species Oryza sativa
transcript LOC_Os10g33720.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g33720.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G107629_T05 (Zea mays), 5'ss of exon 3
AGGAAAAGGATGTATGGGTCATGAATGTTGTTCCACATGATGGACCAAGCACTCTCAAGATAATCTATGACAGAGGGCTTATAGGTTCTACTCATGACTGgtatgtgtcattt-tatataaagaaaattgtgcttggcatatcagtagttgagcattatgctagtttgttaggttaaggcaactcagtagctctctgccac
||||||| || |||||||| ||||||||||| |||||||||||||||||||| ||||||||||||||||| |||||||| |||||    | ||||||||||||||||| |      ||||||   |    |  ||   ||   ||     |     |    | || ||  | | |  |    || |     |   |     
AGGAAAAAGACGTATGGGTGATGAATGTTGTGCCACATGATGGACCAAGCACCCTCAAGATAATCTATGATAGAGGGCTGATAGGCAGCAATCATGACTGgtatgtgttaagcacctataaatttatccattgttattattcaagggcaggcctggtgcagtggtgtgccatgctttgtgcccttacgttttagttaatt-

upper sequence: LOC_Os10g33720.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G067764_T02 (Zea mays), 5'ss of exon 7
AGGAAAAGGATGTATGGGTCATGAATGTTGTTCCACATGATGGACCAAGCACTCTCAAGATAATCTATGACAGAGGGCTTATAGGTTCTACTCATGACTGgtatgtgtcattttatataaagaaaattgtgcttggcatatcagtagttgagcattatgctagtttgttaggttaaggcaactcagtagctctctgccac-------------
|||| || || |||||||| ||||||||||| |||||||||||||||||||| ||||||||||||||||| |||||||| |||||    | ||| ||||||||||||| |      |   | ||  || | | | |  ||| |    ||||   || | |      | || |  |   |||| | ||| |  | |||||              
AGGAGAAAGACGTATGGGTGATGAATGTTGTGCCACATGATGGACCAAGCACCCTCAAGATAATCTATGATAGAGGGCTGATAGGCAGCAATCACGACTGgtatgtgttaa---gaacctataagtttattcattg-gtatta----ttgaattttgtaca-----gctaagagatatcaacacggtaccattttgccatgccttatgccctt

upper sequence: LOC_Os10g33720.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA10G00880.2 (Glycine max), 5'ss of exon 7
AGGAAAAGGATGTATGGGTCATGAATGTTGTTCCACATGATGGACCAAGCACTCTCAAGATAATCTATGACAGAGGGCTTATAGGTTCTACTCATGACTGgtatgtgtcattttatataaagaaaattgtgcttggcatatcagtagttgagcattatgctagtttgttaggttaaggcaactcagtagctctctgccac--
  |  || ||||| ||||| ||||||||||| || | ||||||||| | ||| || ||| | || ||||||||||| || ||||| ||||  ||||||||||||      ||   | |   |||   |    ||     |||  |  |      ||||||   |||| |   ||    |   |  ||  |  |     |   
GAGGCAAAGATGTTTGGGTGATGAATGTTGTACCTCGTGATGGACCTAACACACTAAAGCTTATATATGACAGAGGCCTCATAGGGTCTATCCATGACTGgtattaaaacttgattttcctgaagcataaatttattgcatctttgatatctttttatgc--atttgattcatttcaccttttttgtctcatttgatgatat

upper sequence: LOC_Os10g33720.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA10G32470.1 (Glycine max), 5'ss of exon 7
AGGAAAAGGATGTATGGGTCATGAATGTTGTTCCACATGATGGACCAAGCACTCTCAAGATAATCTATGACAGAGGGCTTATAGGTTCTACTCATGACTGgtat--gtgtcattttatataaagaaaattgtgcttggcatatcagtagttgagcattatgctagtttgttaggttaaggcaactcagtagctctctgccac
  || ||| | || ||||| ||||||||||| || || |||||||||| ||| || ||| | || ||||||||||| ||||||||  |||||||||||||||||    |  |  ||   | ||  | |      |||     |   ||  |   |||     |      ||   ||     |||  |  |  |      |  
GAGACAAGAAAGTTTGGGTAATGAATGTTGTACCTCAAGATGGACCAAACACACTTAAGCTCATATATGACAGAGGCCTTATAGGAACTACTCATGACTGgtattgaagctagattgcttgaattataaatctattgcttctttgataactttccatgcatttgaggcatttcatttttataacctatgaatttctgatc--

upper sequence: LOC_Os10g33720.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA20G35120.1 (Glycine max), 5'ss of exon 6
AGGAAAAGGATGTATGGGTCATGAATGTTGTTCCACATGATGGACCAAGCACTCTCAAGATAATCTATGACAGAGGGCTTATAGGTTCTACTCATGACTGgtat--gtgtcattttatataaagaaaattgtgcttggcatatcagtagttgagcattatgctagtttgttaggttaaggcaactcagtagctctctgccac
  || |||||||| ||||| ||||||||||| || || |||||||||| ||| || ||| | || ||||||||||| || || ||  |||||||||||||||||    |  |  ||   | ||  | |      ||||    |   ||  |   | |     |      ||   ||     |||  | ||  |   |     
GAGACAAGGATGTTTGGGTGATGAATGTTGTACCTCAAGATGGACCAAACACACTTAAGCTCATATATGACAGAGGCCTCATTGGAACTACTCATGACTGgtattgaagctagattgcttgaattataaatctattggttctttgataacttgccgtgcatttgaggcatttcatttttataacctaataatttcttata--

upper sequence: LOC_Os10g33720.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA13G18630.1 (Glycine max), 5'ss of exon 6
AGGAAAAGGATGTATGGGTCATGAATGTTGTTCCACATGATGGACCAAGCACTCTCAAGATAATCTATGACAGAGGGCTTATAGGTTCTACTCATGACTGgtatgtgtcat-------tttatataaagaaaattgtgcttggcatatcagtagttgagcattatg--ctagtttgttaggttaaggcaactcagtagctctctgccac
|||| || ||||| ||||| |||||||| || ||| |  ||||||||| |||||||||||| || ||||||||||||||  ||||  |   |||  |||||||||  || |       | | || |||  ||||| |  | || |    | ||   ||  |||      || ||| ||   | |       | | | ||||        
AGGACAAAGATGTTTGGGTTATGAATGTGGTGCCAGAAAATGGACCAAACACTCTCAAGATCATATATGACAGAGGGCTGTTAGGAACAGTTCACAACTGgtatgactcttattcttatctttacaaaagaaattatcttcggtaggctattaacagacaattcctgtttaatttattgcttcacttttttttaat-gctc--------

upper sequence: LOC_Os10g33720.1 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv07s0005g03630.t01 (Vitis vinifera), 5'ss of exon 6
AGGAAAAGGATGTATGGGTCATGAATGTTGTTCCACATGATGGACCAAGCACTCTCAAGATAATCTATGACAGAGGGCTTATAGGTTCTACTCATGACTGgtatgtgtcatttta-tataaagaaaattgtgcttggcatatcagtagttgagcattatgctagtttgttaggttaaggca-actcagtagctctctgccac
| || ||  |||| ||||| |||||||| ||| || | |||||||| | ||||||||||||||| ||||||||||| || |||||  ||| |||| ||||||||||   |||||| | ||||    | | |    |  |    || |    |  |||  |  |   | | | || ||  || |||||  | |    || || 
AAGACAAAAATGTGTGGGTGATGAATGTGGTTGCAGAAGATGGACCCAACACTCTCAAGATAATATATGACAGAGGCCTGATAGGCACTATTCATAACTGgtatgttcaattttaatttaaacgccagtattgaggaaaagaaagaaacgaaatattgaga-atcgtataacgtcaattcatactcaa-accatcatgacat

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|58688720|gb|CK077407.1|CK077407
EST:     ACTCTCAAGATAATCTATGACAGAGGGCTTATAGGTTCTACTCATGACTG                         GTGTGAAGCATTCTCAACCTATCCTCGAACATATGATCTTCTCCATGCATG
genomic: ACTCTCAAGATAATCTATGACAGAGGGCTTATAGGTTCTACTCATGACTGgtatgtgtca ... gtatatgcagGTGTGAAGCATTCTCAACCTATCCTCGAACATATGATCTTCTCCATGCATG
EST: gi|86827969|gb|CI274889.1|CI274889
EST:     TCTCAAGATAATCTATGACAGAGGGCTTATAGGTTCTACTCATGACTG                         GTGTGAAGCATTCTCAACCTATCCTCGAACATATGATCTTCTCCATGCATG
genomic: TCTCAAGATAATCTATGACAGAGGGCTTATAGGTTCTACTCATGACTGgtatgtgtca ... gtatatgcagGTGTGAAGCATTCTCAACCTATCCTCGAACATATGATCTTCTCCATGCATG
EST: gi|87039140|gb|CI193762.1|CI193762
EST:     ACTCTCAAGATAATCTATGACAGAGGGCTTATAGGTTCTACTCATGACTG                         GTGTGAAGCATTCTCAACCTATCCTCGAACATATGATCTTCTCCATGCATG
genomic: ACTCTCAAGATAATCTATGACAGAGGGCTTATAGGTTCTACTCATGACTGgtatgtgtca ... gtatatgcagGTGTGAAGCATTCTCAACCTATCCTCGAACATATGATCTTCTCCATGCATG
EST: gi|25802153|gb|CA758114.1|CA758114
EST:     ACTCTCAAGATAATCTATGACAGAGGGCTTATAGGTTCTACTCATGACTG                         GTGTGAAGCATTCTCAACCTATCCTCGAACATATGATCTTCTCNCATGCAT
genomic: ACTCTCAAGATAATCTATGACAGAGGGCTTATAGGTTCTACTCATGACTGgtatgtgtca ... gtatatgcagGTGTGAAGCATTCTCAACCTATCCTCGAACATATGATCTTCTC-CATGCAT
EST: gi|87039008|gb|CI193630.1|CI193630
EST:     CTTATAGGTTCTACTCATGACTG                         GTGTGAAGCATTCTCAACCTATCCTCGAACATATGATCTTCTCCATGCATG
genomic: CTTATAGGTTCTACTCATGACTGgtatgtgtca ... gtatatgcagGTGTGAAGCATTCTCAACCTATCCTCGAACATATGATCTTCTCCATGCATG
EST: gi|58694554|gb|CK083241.1|CK083241
EST:     ACTCTCAAGATAATCTATGACAGAGGGCTTATAGGTTCTACTCATGACTG                         GTGTGAAGCATTCTCAACCTATCCTCGAACATATGATCTTCTCCATGCATG
genomic: ACTCTCAAGATAATCTATGACAGAGGGCTTATAGGTTCTACTCATGACTGgtatgtgtca ... gtatatgcagGTGTGAAGCATTCTCAACCTATCCTCGAACATATGATCTTCTCCATGCATG
EST: gi|58696008|gb|CK084695.1|CK084695
EST:     TAATCTATGACAGAGGGCTTATAGGTTCTACTCATGACTG                         GTGTGAAGCATTCTCAACCTATCCTCGAACATATGATCTTCTCCATGCATG
genomic: TAATCTATGACAGAGGGCTTATAGGTTCTACTCATGACTGgtatgtgtca ... gtatatgcagGTGTGAAGCATTCTCAACCTATCCTCGAACATATGATCTTCTCCATGCATG
EST: gi|163921630|gb|EG714156.1|EG714156
EST:     ACTCTCAAGATAATCTATGACAGAGGGCTTATAGGTTCTACTCATGACTG                         GTGTGAAGCATTCTCAACCTATCCTCGAACATATGATCTTCTCCATGCATG
genomic: ACTCTCAAGATAATCTATGACAGAGGGCTTATAGGTTCTACTCATGACTGgtatgtgtca ... gtatatgcagGTGTGAAGCATTCTCAACCTATCCTCGAACATATGATCTTCTCCATGCATG

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: 71 (upstream exon), 45 (downstream exon)
Score: 23

AGGAAAAGGATGTATGGGTCATGAATGTTGTTCCACATGATGGACCAAGCACTCTCAAGATAATCTATGACAGAGGGCTTATAGGTTCTACTCATGACTGgtatgtgtca ... gtatatgcagGTGTGAAGCATTCTCAACCTATCCTCGAACATATGATCTTCTCCATGCATGGACAGTCTTCTCTGACCTTGACAAGAGAGGTTGCAGCGCAGAAGATCTC




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