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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctagaatgagttgtatttgcactatattttattttagcagttcagaattgggttatgatcttcatttaatggtgttcttttaactgacatattgtgcagTCACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTCCG

Basic information

species Oryza sativa
transcript LOC_Os01g50760.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g50760.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G098569_T01 (Zea mays), 3'ss of exon 5
-------------------------------------------------------------tctagaatgagttgtatt-tgcactat-attttat-tttagcagttcagaattgggttatgatcttcatttaatggtgttcttt-----taactgacatattgtgcagTCACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTCCG
                                                             | | |  |   ||  |   ||   ||| ||| | | |||||||  ||| | || || ||  |||||   ||  || |  | | |     | | |  ||| |||  ||||||||||||||| |||||||||||||||||||| || |||||||| ||||| 
gtaagtttatgtttcgctgtatcagtaacataattcacacgctttgtttcctttcatggtttattgtttagtttccagaatgagttattattatgtgtttagcacctcaaatttaggataaaatcttttatttgtgctaatttctctcaatgattttcattttgcacagTCACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCCT

upper sequence: LOC_Os01g50760.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G147721_T01 (Zea mays), 3'ss of exon 5
---------------------------------------------------tctagaatgagttgt---atttgcactat---attttat------tttagcagttcagaattgggttatgatcttcatttaatggtgttcttttaactga----catattgtgcagTCACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTCCG
                                                   |  |  ||   ||||    ||| ||  ||   |  ||||      |||||||  ||| | |||||  || ||||| |||        ||| | | |  ||    ||| |||  ||||| ||||| ||| |||||||||||||||||||| || ||||| || ||||| 
gtaagatcatgttcactgtatcagtaacataattcacacgctttgtttccttacatgatttattgtttagtttccagaatgagacattatcatgcgtttagcacctcaaatttgggacataatctttattcgtgttaattcctctcaacgattttcattttgcacagTCGCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCT

upper sequence: LOC_Os01g50760.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv19s0015g01010.t01 (Vitis vinifera), 3'ss of exon 6
tctagaatgagttgtatttgcacta--tattttattttagcagttcagaattgggttatgatcttcatttaatggtgttcttttaactgacatattgt-----------gcagTCACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTCCG
   ||   || ||  | | |   |   | ||||||||||         ||||  | |   || ||  |||  ||   ||||||||| |  ||  | ||           |||||||||||||||||||||||||||| || ||||| |||||||| || ||||| 
gtaagtgagaattcaaatagtgattcttgttttattttacttacaatcaattttgattccatttttttttcttgtgtttcttttaattatcaagtggttgtgtttccatgcagTCACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCCA

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|27576581|gb|CA999275.1|CA999275
EST:     ATTACTACTCATGAGGGAGAAAAGGATCTCACAAAGTACAACTTGACAGT                         TCACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTCC
genomic: ATTACTACTCATGAGGGAGAAAAGGATCTCACAAAGTACAACTTGACAGTgtaagttcat ... tattgtgcagTCACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTCC
EST: gi|88690724|gb|CI734803.1|CI734803
EST:     ATTACTACTCATGAGGGAGAAAAGGATCTCACAAAGTACAACTTGACAGT                         TCACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTCC
genomic: ATTACTACTCATGAGGGAGAAAAGGATCTCACAAAGTACAACTTGACAGTgtaagttcat ... tattgtgcagTCACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTCC
EST: gi|27577652|gb|CB000347.1|CB000347
EST:     ATTACTACTCATGAGGGAGAAAAGGATCTCACAAAGTACAACTTGACAGT                         TCACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTCC
genomic: ATTACTACTCATGAGGGAGAAAAGGATCTCACAAAGTACAACTTGACAGTgtaagttcat ... tattgtgcagTCACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTCC
EST: gi|27576092|gb|CA998786.1|CA998786
EST:     ATTACTACTCATGAGGGAGAAAAGGATCTCACAAAGTACAACTTGACAGT                         TCACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTCC
genomic: ATTACTACTCATGAGGGAGAAAAGGATCTCACAAAGTACAACTTGACAGTgtaagttcat ... tattgtgcagTCACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTCC
EST: gi|29620886|gb|CB625897.1|CB625897
EST:     ATTACTACTCATGAGGGAGAAAAGGATCTCGCAAAGTACAACTTGACAGT                         TCACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTCC
genomic: ATTACTACTCATGAGGGAGAAAAGGATCTCACAAAGTACAACTTGACAGTgtaagttcat ... tattgtgcagTCACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTCC
EST: gi|27576091|gb|CA998785.1|CA998785
EST:     ATTACGACTCATGAGGGAGAAAAGGATCTCACAAAGTACAACTTGACAGT                         TCACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTCC
genomic: ATTACTACTCATGAGGGAGAAAAGGATCTCACAAAGTACAACTTGACAGTgtaagttcat ... tattgtgcagTCACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTCC
EST: gi|29684521|gb|CB680796.1|CB680796
EST:     ATTACTACTCATGAGGGAGAAAAGGATCTCACAAAGTACAACTTGACAGT                         TCACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTCC
genomic: ATTACTACTCATGAGGGAGAAAAGGATCTCACAAAGTACAACTTGACAGTgtaagttcat ... tattgtgcagTCACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTCC
EST: gi|8856728|gb|AU094046.1|AU094046
EST:     CACAAAGTNCAACTTGACAGT                         TCACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTCC
genomic: CACAAAGTACAACTTGACAGTgtaagttcat ... tattgtgcagTCACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTCC
EST: gi|29688203|gb|CB684478.1|CB684478
EST:     ATTACTACTCATGAGGGAGAAAAGGATCTCACAAAGTACAACTTGACAGT                         TCACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTCC
genomic: ATTACTACTCATGAGGGAGAAAAGGATCTCACAAAGTACAACTTGACAGTgtaagttcat ... tattgtgcagTCACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTCC
EST: gi|27554346|gb|CA998246.1|CA998246
EST:     ATTACTACTCATGAGGGAGAAAAGGATCTCACAAAGTACAACTTGACAGT                         TCACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTCC
genomic: ATTACTACTCATGAGGGAGAAAAGGATCTCACAAAGTACAACTTGACAGTgtaagttcat ... tattgtgcagTCACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTCC
EST: gi|29684202|gb|CB680477.1|CB680477
EST:     ATTACTACTCATGAGGGAGAAAAGGATCTCACAAAGTACAACTTGACAGT                         TCACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTCC
genomic: ATTACTACTCATGAGGGAGAAAAGGATCTCACAAAGTACAACTTGACAGTgtaagttcat ... tattgtgcagTCACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTCC

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: 73 (upstream exon), 52 (downstream exon)
Score: 68

GTTGAGTTTAAGACTGCTTCAGGTCAATTGTTGGATCTTATTACTACTCATGAGGGAGAAAAGGATCTCACAAAGTACAACTTGACAGTgtaagttcat ... tattgtgcagTCACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTCCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaattgggttatgatcttcatttaatggtgttcttttaactgacatattgtgcagTCACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTCCG
                                     aactgac  putative branch site (score: 68)
                ttcatttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctagaatgagttgtatttgcactatattttattttagcagttcagaattgggttatgatcttcatttaatggtgttcttttaactgacatattgtgcagTCACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTCCG

- - - - - - - -atttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggtgtt