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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgagtcaagtaggctttgtaagatcatagttgattgcattcaacaattcagcatgccatcatgttgtaagaaaagtttctaattaactttcttatcgcagAATGGTGATCCTCGTCTATCATGCTTTGGTTTGATGAAAAACAGCAGGGATGGGAAAAGTTATAGTACAAACCTGGCATATACACCTCCAGAATATCTGA

Basic information

species Oryza sativa
transcript LOC_Os10g39670.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g39670.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G026767_T01 (Zea mays), 3'ss of exon 3
tgagtcaagtaggctttgtaagatcatagttgattgcattcaacaattcagcatgccatcatgttgtaagaaaagtttctaatta------actttcttatcgcagAATGGTGATCCTCGTCTATCATGCTTTGGTTTGATGAAAAACAGCAGGGATGGGAAAAGTTATAGTACAAACCTGGCATATACACCTCCAGAATATCTGA
| ||| | || | | | ||| ||||| ||| || ||| | | | || || || |||| | |||| ||| ||||||| | |||||||||||| ||||| || |||||||||||| |||||||||||||||||||||| ||||| ||||| || ||||| |||||||||||||||||||||||||
taagttga-tactcctaattgcatc-cagttg-ttgaat---gtcattttgtactgtcttattttcaaacaaaaatgtctagttataatgaactttctggttgcagAATGGTGACCCTCGGCTGTCATGCTTTGGTCTGATGAAAAACAGCAGGGATGGAAAAAGCTATAGCACGAACCTAGCATATACACCTCCAGAATATCTGA

upper sequence: LOC_Os10g39670.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT4G35230.1 (Arabidopsis thaliana), 3'ss of exon 3
tgagtcaa-gtaggctttgtaagatcatagttgatt-gcattcaaca-attcagcatgccatcatgttgtaagaaaagtttctaattaactttcttatcgcagAATGGTGATCCTCGTCTATCATGCTTTGGTTTGATGAAAAACAGCAGGGATGGGAAAAGTTATAGTACAAACCTGGCATATACACCTCCAGAATATCTGA
| | | | ||| |||| || || || | || || | || | | | | | || | |||| | ||| | ||| | || |||||||||||||||| ||||| ||||| |||||||| ||||| |||||||| ||||||||||| ||||| | || |||||||| || |||||||| |
-gtattattattttcttctcaagagt-tatttatttcgtgtttaagagatgccctgtctcgttgcggtgcctaacaagtat---attggaatgaatatggtagGATGGTGATCCTCGTCTCTCATGTTTTGGCTTGATGAAGAACAGTAGGGATGGTAAAAGTTATAGCACAAATTTAGCTTATACACCACCTGAATATCTAA

upper sequence: LOC_Os10g39670.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv18s0001g00180.t01 (Vitis vinifera), 3'ss of exon 3
tgagtcaagtaggc-tttgtaagatcatagttgattgcattcaacaattcagcatgccatcatgtt-gtaagaaa-agtttctaattaactttcttatcgcagAATGGTGATCCTCGTCTATCATGCTTTGGTTTGATGAAAAACAGCAGGGATGGGAAAAGTTATAGTACAAACCTGGCATATACACCTCCAGAATATCTGA
| ||||| | ||| | | || | | | | | | | || | | | | || || || || ||| || || | ||||||||||||||| || || || ||||||||| |||||||||| ||||| ||||| |||||||| || ||||| || || ||||||||||| || ||||| |
--taaccagtagacattttcctggttgtattgaaataaaactatctggagaccaattagtagtaatagcaacaagtggtaacttattgg-ttggttttagcagAATGGTGATCCACGGCTTTCTTGCTTTGGTATGATGAAAAATAGCAGAGATGGAAAAAGTTACAGCACAAATCTTGCCTATACACCTCCTGAGTATCTAA

upper sequence: LOC_Os10g39670.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv03s0038g03270.t01 (Vitis vinifera), 3'ss of exon 3
-------------tgagtcaagtaggctttgtaagatcatagttgattgcattcaacaattcagcatgccatcatgttgtaagaaaagtttctaattaactttcttatcgcagAATGGTGATCCTCGTCTATCATGCTTTGGTTTGATGAAAAACAGCAGGGATGGGAAAAGTTATAGTACAAACCTGGCATATACACCTCCAGAATATCTGA
| | | ||| ||| | || | | || | | |||| | | || ||| || || | ||| || | || ||||||| || || || ||||| ||||| ||||||||||| || || ||||||||||||||||| ||||| || || || |||||||| |||||||| |
gtgctataatggattcttttctcaaaattttaaagtttattatctactgttatacataatttgatgtttagctaggtgataatctaatattttgattggacttt-----gtagGATGGTGACCCACGGCTTTCATGTTTTGGCTTGATGAAAAATAGTAGAGATGGGAAAAGTTATAGCACAAATCTTGCCTACACACCTCCGGAATATCTAA

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|88349676|gb|CI632811.1|CI632811
EST:     AAAGGCCTTTATATCACGACCTAAATGCATACAGAGTACTCTTTGATGAG                         AATGGTGATCCTCGTCTATCATGCTTTGGTTTGATGAAAAACAGCAGGGAT
genomic: AAAGGCCTTTATATCACGACCTAAATGCATACAGAGTACTCTTTGATGAGgtaagcgatc ... cttatcgcagAATGGTGATCCTCGTCTATCATGCTTTGGTTTGATGAAAAACAGCAGGGAT
EST: gi|29664957|gb|CB661232.1|CB661232
EST:     AAAGGCCTTTATATCACGACCTAAATGCATACAGAGTACTCTTTGATGAG                         AATGGTGATCCTCGTCTATCATGCTTTGGTTTGATGAAAAACAGCAGGGAT
genomic: AAAGGCCTTTATATCACGACCTAAATGCATACAGAGTACTCTTTGATGAGgtaagcgatc ... cttatcgcagAATGGTGATCCTCGTCTATCATGCTTTGGTTTGATGAAAAACAGCAGGGAT
EST: gi|33675246|gb|CF303485.1|CF303485
EST:     AAAGGCCTTTATATCACGACCTAAATGCATACAGAGTACTCTTTGATGAG                         AATGGTGATCCTCGTCTATCATGCTTTGGTTTGATGAAAAACAGCAGGGAT
genomic: AAAGGCCTTTATATCACGACCTAAATGCATACAGAGTACTCTTTGATGAGgtaagcgatc ... cttatcgcagAATGGTGATCCTCGTCTATCATGCTTTGGTTTGATGAAAAACAGCAGGGAT
EST: gi|88335903|gb|CI645504.1|CI645504
EST:     AAAGGCCTTTATATCACGACCTAAATGCATACAGAGTACTCTTTGATGAG                         AATGGTGATCCTCGTCTATCATGCTTTGGTTTGATGAAAAACAGCAGGG
genomic: AAAGGCCTTTATATCACGACCTAAATGCATACAGAGTACTCTTTGATGAGgtaagcgatc ... cttatcgcagAATGGTGATCCTCGTCTATCATGCTTTGGTTTGATGAAAAACAGCAGGG
EST: gi|29664958|gb|CB661233.1|CB661233
EST:     AAAGGCCTTTATATCACGACCTAAATGCATACAGAGTACTCTTTGATGAG                         AATGGTGATCCTCGTCTATCATGCTTTGGTTTGATGAAAAACAGCAGGGAT
genomic: AAAGGCCTTTATATCACGACCTAAATGCATACAGAGTACTCTTTGATGAGgtaagcgatc ... cttatcgcagAATGGTGATCCTCGTCTATCATGCTTTGGTTTGATGAAAAACAGCAGGGAT

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), 66 (downstream exon)
Score: 20

CAGAGTTGCATACAACATTGCTGAAGCATTGGAATATTGTAGCAATGAGGAAAGGCCTTTATATCACGACCTAAATGCATACAGAGTACTCTTTGATGAGgtaagcgatc ... cttatcgcagAATGGTGATCCTCGTCTATCATGCTTTGGTTTGATGAAAAACAGCAGGGATGGGAAAAGTTATAGTACAAACCTGGCATATACACCTCCAGAATATCTGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcagcatgccatcatgttgtaagaaaagtttctaattaactttcttatcgcagAATGGTGATCCTCGTCTATCATGCTTTGGTTTGATGAAAAACAGCAGGGATGGGAAAAGTTATAGTACAAACCTGGCATATACACCTCCAGAATATCTGA
                                   aattaac  putative branch site (score: 20)
 ctttcttatc  CT-rich tract
 aaaagtttctaattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgagtcaagtaggctttgtaagatcatagttgattgcattcaacaattcagcatgccatcatgttgtaagaaaagtttctaattaactttcttatcgcagAATGGTGATCCTCGTCTATCATGCTTTGGTTTGATGAAAAACAGCAGGGATGGGAAAAGTTATAGTACAAACCTGGCATATACACCTCCAGAATATCTGA

- - - - - - - - - - - - - - - - - tgcattc
- - - - - - - - - - - - - - - - - - - - - - - - -agcatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagaaaa