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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGCTTCAAACTCCTGGTGCAACAAGTTACATGGGTTGCATTGGAAAGGATAAGTTTGGTGAGGAGATGAAGAAGAATGCCCAAGCTGCTGGTGTTACTgttagttctaaatctctctctctctctctctctttttcatggcatctgatgcaataatatcctacagtggcttgtcaactaactaaggtggtcttgctcttgacacacgctcggttag

Basic information

species Oryza sativa
transcript LOC_Os02g41590.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g41590.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G135132_T01 (Zea mays), 5'ss of exon 5
GATGCTTCAAACTCCTGGTGCAACAAGTTACATGGGTTGCATTGGAAAGGATAAGTTTGGTGAGGAGATGAAGAAGAATGCCCAAGCTGCTGGTGTTACTgttagttctaaatctctctctctctctctctctttttcatggcatctgatgcaataatatcctacagtggcttgtcaactaactaaggtggtcttgctcttgacacacgctcggttag
|||||||||||||||||||||||||||||||||||| |||||||| ||||| ||||||||||||||||||||||| ||||| |||||||| || ||||||||||||| |||       ||||        |||| ||||||  |  | |  || |||| | ||  | |   | |  || | ||||| |||| |||| | ||| | |   |    | ||
GATGCTTCAAACTCCTGGTGCAACAAGTTACATGGGATGCATTGGGAAGGACAAGTTTGGTGAGGAGATGAAGAAAAATGCTCAAGCTGCAGGAGTTACTgttagttttaa-------tctc-------atcttcttcatgctactttagacagtaatgttctg-atttattggctaattgactaatgtggccttgatgttggcgcttacctactcag

upper sequence: LOC_Os02g41590.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G540538_T02 (Zea mays), 5'ss of exon 5
GATGCTTCAAACTCCTGGTGCAACAAGTTACATGGGTTGCATTGGAAAGGATAAGTTTGGTGAGGAGATGAAGAAGAATGCCCAAGCTGCTGGTGTTACTgttagttctaaatctctctctctctctctctctttttcatggcatctgatgcaataatatcctacagtggcttgtcaactaactaaggtggtcttgctcttgacacacgctcggttag
|||||||||||||||||||||||||||||||||||| |||||||||||||| |||||||||||||| |||||||| || || |||||||| || ||||||||||||| | ||||||  | |||             |||||  |  | |  || |  | |   | | |   | || || | ||| |  ||| |||| | | | | ||  ||| |    
GATGCTTCAAACTCCTGGTGCAACAAGTTACATGGGATGCATTGGAAAGGACAAGTTTGGTGAGGAAATGAAGAAAAACGCTCAAGCTGCAGGAGTTACTgttagtttttaatctcattgtct-------------tcatgttactttagacagttttgttgca-atttattggttaattcactcatatggccttgatgtcgtcgcatactcag----

upper sequence: LOC_Os02g41590.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA13G20780.1 (Glycine max), 5'ss of exon 5
GATGCTTCAAACTCCTGGTGCAACAAGTTACATGGGTTGCATTGGAAAGGATAAGTTTGGTGAGGAGATGAAGAAGAATGCCCAAGCTGCTGGTGTTACTgttagttctaaatctctctctctctctctctctttttcatggcatctgatgcaataa-tatcctacagtggcttgtcaactaactaaggtggtcttgctcttgacacacgctcggttag
|||||||||| | || ||||| ||||||||||| |||||||| |||||||| || ||||| |||||||||||||||||      |  || |||||| |  || |||| |||   | |   |     ||||  || ||  ||  |    |  |  |   |  |||  ||     |  ||  |  || |  | | |||  |     || ||  || |    
GATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAGGACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTTGATGGTGTAAAGgtaagtt-taatcttgtgatttggcttctcctttctttgtgataagctactctgtgcctgacctttagaa---taccattt--ctgaaattgactttattcattca-acaatcag----

upper sequence: LOC_Os02g41590.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA19G36630.1 (Glycine max), 5'ss of exon 5
GATGCTTCAAACTCCTGGTGCAACAAGTTACATGGGTTGCATTGGAAAGGATAAGTTTGGTGAGGAGATGAAGAAGAATGCCCAAGCTGCTGGTGTTACTgttagttctaaatctctctctctctctctctctttttcatggcatctgatgcaataatatcctacagtggcttgtcaactaactaaggtggtcttgctcttgacacacgctcggttag
|||||| |||  ||||||||||||||||||||||||| |||| ||||||||||||||||| || ||||||||||||||  |  |   ||||||||| | |||  |||   |||||     | | ||| |||| |||   || ||| || | |          |  | |||||  |  |  || | |  |  | ||  || |    ||           
GATGCTCCAAGTTCCTGGTGCAACAAGTTACATGGGTGGCATAGGAAAGGATAAGTTTGGGGAAGAGATGAAGAAGAACTCAAAGCTTGCTGGTGTAAATgtaggttt--aatcttatgatatatct-tctcctttcattgtcatgtgcttc--------tttgtactggctgttttagaaatttaacttat-ttattcatccatcag----------

upper sequence: LOC_Os02g41590.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA10G06580.1 (Glycine max), 5'ss of exon 5
GATGCTTCAAACTCCTGGTGCAACAAGTTACATGGGTTGCATTGGAAAGGATAAGTTTGGTGAGGAGATGAAGAAGAATGCCCAAGCTGCTGGTGTTACTgttagttctaaatctctctctctctctctctctttttcatggcatctgatgcaataatatcctacagtggcttgtcaactaactaaggtggtcttgctcttgacacacgctcggttag
|||||||||| | || ||||| |||||||| || |||||||| |||||||| || ||||| |||||||||||||||||      |   | |||||| |  || ||||   |||||     | | |||| ||| |||   ||  ||  | | |  |  |  |  ||    |  |  ||  |  || |  | | |||  |     || |     |     
GATGCTTCAAGCACCAGGTGCCACAAGTTATATAGGTTGCATAGGAAAGGACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTAGATGGTGTAAAGgtaagttt--aatcttgtgatttgtctc-ctcctttctttgtgataagctactttg-tgcctgacctaagaataccattt--ctgaaattgactttattcattcaaaaatcag-----

upper sequence: LOC_Os02g41590.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA03G33910.3 (Glycine max), 5'ss of exon 2
GATGCTTCAAACTCCTGGTGCAACAAGTTACATGGGTTGCATTGGAAAGGATAAGTTTGGTGAGGAGATGAAGAAGAATGCCCAAGCTGCTGGTGTTACTgttagttctaaatctctctctctctctctctctttttcatggcatctgatgcaataatatcctacagtggcttgtcaactaactaaggtggtcttgctcttgacacacgctcggttag
|||||| |||  ||||||||||||||||||||||||| |||| ||||||||||||||||| || ||||||||||||||  |      ||||||||| | |||  |||| |  |     | | |||   |||| |||   || ||| || | |  |  || |   | ||   | |  || ||||| |  |  || | |    |                
GATGCTCCAAGTTCCTGGTGCAACAAGTTACATGGGTGGCATAGGAAAGGATAAGTTTGGGGAAGAGATGAAGAAGAACTCAAGGCTTGCTGGTGTAAATgtaggttcaatgttatgatttatct---tctcctttcattgtcatgtgcttctgtg-ta-ctggctgtt-ttagaaaattaacttatttactcatccatcag----------------

upper sequence: LOC_Os02g41590.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv13s0019g04480.t01 (Vitis vinifera), 5'ss of exon 5
GATGCTTCAAACTCCTGGTGCAACAAGTTACATGGGTTGCATTGGAAAGGATAAGTTTGGTGAGGAGATGAAGAAGAATGCCCAAGCTGCTGGTGTTACTgttagttctaa-atctctctctctctctctct-ctttttcatggcatctgatgcaataatatcctacagtggcttgtcaactaactaaggtggtcttgctcttgacacacgctcggttag
|||||||||||  ||||| |||||||| || ||||| |||||||||||||| |||||||| ||||| |||||||| ||  |  ||  ||||||||||| ||| |||| |   |  ||| |   ||| |  |  ||||| |||||      ||        ||  || | | | ||||    | ||| ||         ||||| ||| |  |  | | ||
GATGCTTCAAATCCCTGGAGCAACAAGCTATATGGGATGCATTGGAAAGGACAAGTTTGGGGAGGAAATGAAGAAAAACTCAAAACTTGCTGGTGTTAATgtaagttttttcacttctttacatcttttgcagcttttccatggttatccatct--ctccattttagattag-ttgttttgttactgagac-------ctcttaaca-atccatgatcag

upper sequence: LOC_Os02g41590.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv13s0019g04470.t01 (Vitis vinifera), 5'ss of exon 5
GATGCTTCAAACTCCTGGTGCAACAAGTTACATGGGTTGCATTGGAAAGGATAAGTTTGGTGAGGAGATGAAGAAGAATGCCCAAGCTGCTGGTGTTACTgttagttctaa-atctctctctctctctctct-ctttttcatggcatctgatgcaataatatcctacagtggcttgtcaactaactaaggtggtcttgctcttgacacacgctcggttag
|||||||||||  ||||| |||||||| || ||||| |||||||||||||| |||||||| ||||| |||||||| ||  |  ||  |||||||||||  || |||| |   || ||| |   ||| |  |  ||||| |||||      ||        ||  || | | | ||||    | ||| ||         ||||| ||| |  |  | | ||
GATGCTTCAAATCCCTGGAGCAACAAGCTATATGGGATGCATTGGAAAGGACAAGTTTGGGGAGGAAATGAAGAAAAACTCAAAACTTGCTGGTGTTAACgtaagttttttcatttctttacatcttttacagcttttccatggttatccatct--ctccattttagatttg-ttgttttgttactgagac-------ctcttaaca-atccatgatcag

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|84117280|gb|CD151047.1|CD151047
EST:     ATAAGTTTGGTGAGGAGATGAAGAAGAATGCCCAAGCTGCTGGTGTTACT                         GCTCATTACTACGAGGATGAGGCTGCTCCCACGGGCACATGTGCTGTCTGT
genomic: ATAAGTTTGGTGAGGAGATGAAGAAGAATGCCCAAGCTGCTGGTGTTACTgttagttcta ... gctcggttagGCTCATTACTACGAGGATGAGGCTGCTCCCACGGGCACATGTGCTGTCTGT
EST: gi|27576661|gb|CA999355.1|CA999355
EST:     ATAAGTTTGGTGAGGAGATGAAGAAGAATGCCCAAGCTGCTGGTGTTACT                         GCTCATTACTACGAGGATGAGGCTGCTCCCACGGGCACATGTGCTGTCTGT
genomic: ATAAGTTTGGTGAGGAGATGAAGAAGAATGCCCAAGCTGCTGGTGTTACTgttagttcta ... gctcggttagGCTCATTACTACGAGGATGAGGCTGCTCCCACGGGCACATGTGCTGTCTGT
EST: gi|58598930|gb|CK009458.1|CK009458
EST:     ATAAGTTTGGTGAGGAGATGAAGAAGAATGCCCAAGCTGCTGGTGTTACT                         GCTCATTACTACGAGGATGAGGCTGCTCCCACGGGCACATGTGCTGTCTGT
genomic: ATAAGTTTGGTGAGGAGATGAAGAAGAATGCCCAAGCTGCTGGTGTTACTgttagttcta ... gctcggttagGCTCATTACTACGAGGATGAGGCTGCTCCCACGGGCACATGTGCTGTCTGT
EST: gi|300215864|gb|HO088490.1|HO088490
EST:     AAGTTTGGTGAGGAGATGAAGAAGAATGCCCAAGCTGCTGGTGTTACT                         GCTCATTACTACGAGGATGAGGCTGCTCCCACGGGCACATGTGCTGTCTGT
genomic: AAGTTTGGTGAGGAGATGAAGAAGAATGCCCAAGCTGCTGGTGTTACTgttagttcta ... gctcggttagGCTCATTACTACGAGGATGAGGCTGCTCCCACGGGCACATGTGCTGTCTGT
EST: gi|163918496|gb|EG710298.1|EG710298
EST:     ATAAGTTTGGTGAGGAGATGAAGAAGAATGCCCAAGCTGCTGGTGTTACT                         GCTCATTACTACGAGGATGAGGCTGCTCCCACGGGCACATGTGCTGTCTGT
genomic: ATAAGTTTGGTGAGGAGATGAAGAAGAATGCCCAAGCTGCTGGTGTTACTgttagttcta ... gctcggttagGCTCATTACTACGAGGATGAGGCTGCTCCCACGGGCACATGTGCTGTCTGT
EST: gi|428228|gb|D24376.1|D24376
EST:     ATAAGTTTGGTGAGGAGATGAAGAAGAATGCCCAAGCTGCTGGTGTTACT                         GCTCATTACTACG
genomic: ATAAGTTTGGTGAGGAGATGAAGAAGAATGCCCAAGCTGCTGGTGTTACTgttagttcta ... gctcggttagGCTCATTACTACG
EST: gi|38470488|gb|CF954619.1|CF954619
EST:     GCTGGTGTTACT                         GCTCATTACTACGAGGATGAGGCTGCTCCCACGGGCACATGTGCTGTCTGT
genomic: GCTGGTGTTACTgttagttcta ... gctcggttagGCTCATTACTACGAGGATGAGGCTGCTCCCACGGGCACATGTGCTGTCTGT
EST: gi|88719065|gb|CI742575.1|CI742575
EST:     ATAAGTTTGGTGAGGAGATGAAGAAGAATGCCCAAGCTGCTGGTGTTACT                         GCTCATTACTACGAGGATGAGGCTGCTCCCACGGGCACATGTGCTGTCTGT
genomic: ATAAGTTTGGTGAGGAGATGAAGAAGAATGCCCAAGCTGCTGGTGTTACTgttagttcta ... gctcggttagGCTCATTACTACGAGGATGAGGCTGCTCCCACGGGCACATGTGCTGTCTGT
EST: gi|88394239|gb|CI603428.1|CI603428
EST:     ATAAGTTTGGTGAGGAGATGAAGAAGAATGCCCAAGCTGCTGGTGTTACT                         GCTCATTACTACGAGGATGAGGCTGCTCCCACG
genomic: ATAAGTTTGGTGAGGAGATGAAGAAGAATGCCCAAGCTGCTGGTGTTACTgttagttcta ... gctcggttagGCTCATTACTACGAGGATGAGGCTGCTCCCACG
EST: gi|88694901|gb|CI738939.1|CI738939
EST:     ATAAGTTTGGTGAGGAGATGAAGAAGAATGCCCAAGCTGCTGGTGTTACT                         GCTCATTACTACGAGGATGAGGCTGCTCCCACGGGCACATGTGCTGTCTGT
genomic: ATAAGTTTGGTGAGGAGATGAAGAAGAATGCCCAAGCTGCTGGTGTTACTgttagttcta ... gctcggttagGCTCATTACTACGAGGATGAGGCTGCTCCCACGGGCACATGTGCTGTCTGT
EST: gi|66922324|gb|CX109172.1|CX109172
EST:     ATAAGTTTGGTGAGGAGATGAAGAAGAATGCCCAAGCTGCTGGTGTTACT                         GCTCATTACTACGAGGATGAGGCTGCTCCCACGGGCACATGTGCTGTCTGT
genomic: ATAAGTTTGGTGAGGAGATGAAGAAGAATGCCCAAGCTGCTGGTGTTACTgttagttcta ... gctcggttagGCTCATTACTACGAGGATGAGGCTGCTCCCACGGGCACATGTGCTGTCTGT
EST: gi|55410432|gb|CV722808.1|CV722808
EST:     ATAAGTTTGGTGAGGAGATGAAGAAGAATGCCCAAGCTGCTGGTGTTACT                         GCTCATTACTACGAGGATGAGGCTGCTCCCACGGGCACATGTGCTGTCTGT
genomic: ATAAGTTTGGTGAGGAGATGAAGAAGAATGCCCAAGCTGCTGGTGTTACTgttagttcta ... gctcggttagGCTCATTACTACGAGGATGAGGCTGCTCCCACGGGCACATGTGCTGTCTGT
EST: gi|58657974|gb|CK046654.1|CK046654
EST:     ATAAGTTTGGTGAGGAGATGAAGAAGAATGCCCAAGCTGCTGGTGTTACT                         GCTCATTACTACGAGGATGAGGCTGCTCCCACGGGCACATGTGCTGTCTGT
genomic: ATAAGTTTGGTGAGGAGATGAAGAAGAATGCCCAAGCTGCTGGTGTTACTgttagttcta ... gctcggttagGCTCATTACTACGAGGATGAGGCTGCTCCCACGGGCACATGTGCTGTCTGT
EST: gi|2311475|gb|C27630.1|C27630
EST:     ATAAGTTTGGTGAGGAGATGAAGAAGAATGCCCAAGCTGCTGGTGTTACT                         GCTCATTACTACGAGGATGAGGCTGCTCCCACGGGCACATGTGCTGTCTGT
genomic: ATAAGTTTGGTGAGGAGATGAAGAAGAATGCCCAAGCTGCTGGTGTTACTgttagttcta ... gctcggttagGCTCATTACTACGAGGATGAGGCTGCTCCCACGGGCACATGTGCTGTCTGT
EST: gi|88729190|gb|CI752700.1|CI752700
EST:     ATAAGTTTGGTGAGGAGATGAAGAAGAATGCCCAAGCTGCTGGTGTTACT                         GCTCATTACTACGAGGATGAGGCTGCTCCCACGGGCACATGTGCTGTCTGT
genomic: ATAAGTTTGGTGAGGAGATGAAGAAGAATGCCCAAGCTGCTGGTGTTACTgttagttcta ... gctcggttagGCTCATTACTACGAGGATGAGGCTGCTCCCACGGGCACATGTGCTGTCTGT

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), 75 (downstream exon)
Score: 155

GATGCTTCAAACTCCTGGTGCAACAAGTTACATGGGTTGCATTGGAAAGGATAAGTTTGGTGAGGAGATGAAGAAGAATGCCCAAGCTGCTGGTGTTACTgttagttcta ... gctcggttagGCTCATTACTACGAGGATGAGGCTGCTCCCACGGGCACATGTGCTGTCTGTGTTGTTGGTGGTGAAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGCTTCAAACTCCTGGTGCAACAAGTTACATGGGTTGCATTGGAAAGGATAAGTTTGGTGAGGAGATGAAGAAGAATGCCCAAGCTGCTGGTGTTACTgttagttctaaatctctctctctctctctctctttttcatggcatctgatgcaataatatcctacagtggcttgtcaactaactaaggtggtcttgctcttgacacacgctcggttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT