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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgacttctctcctgtaattgagaatagaccactgacttttgccgtcatgaaggaaattattctcatcacttttaaattctatttattccttatttgttagGTTCCTGGAGCCGAAGGTCTTGTGGTTAGAGTTGTTTCATCAGTGGACAAGAAGCTGGAAGTAAAACCACGTTTTTTGGAAATTTTTCAAGAAGATAACT

Basic information

species Oryza sativa
transcript LOC_Os02g04490.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g04490.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G470556_T01 (Zea mays), 3'ss of exon 7
tgacttctctcctgtaattgagaatag-accactgacttt---tgccgtcatgaaggaaattattctcatcacttttaaattctatttattccttatttgttagGTTCCTGGAGCCGAAGGTCTTGTGGTTAGAGTTGTTTCATCAGTGGACAAGAAGCTGGAAGTAAAACCACGTTTTTTGGAAATTTTTCAAGAAGATAACT
       | | ||| | ||     |    |||   | |||   | | |  |||| |    ||     |||||  |  |  ||||| |||| ||||| ||| ||| |||||||||| ||||| |||||||| |||||||||||||||||||| || |||||||| || |||||||||||||||||||||||||||||||| ||||
---gcattatgctgcacttattctttttgccatcaaatttgattcctggtatgatgtcctttcactccatcaagtccac-ttctaattatgccttacttggtagATTCCTGGAGCGGAAGGACTTGTGGTCAGAGTTGTTTCATCAGTGGATAAAAAGCTGGAGGTTAAACCACGTTTTTTGGAAATTTTTCAAGAAGACAACT

upper sequence: LOC_Os02g04490.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G139977_T02 (Zea mays), 3'ss of exon 1
------tgacttctctcctgtaattgagaatagaccactgacttttgccgtcatgaaggaaattattctcatcacttttaaattctatttattccttatttgttagGTTCCTGGAGCCGAAGGTCTTGTGGTTAGAGTTGTTTCATCAGTGGACAAGAAGCTGGAAGTAAAACCACGTTTTTTGGAAATTTTTCAAGAAGATAACT
      || |     |  | |  |||  |  |      |||||  ||     |||| |    ||     |||||  ||||  ||||| |||| | ||||||||||| |||||||||| ||||| ||||| || |||||||||||||||||||| ||||||||||| || |||||||||||||| ||||||||||||||||| ||||
gcattatggcgcacttattctttttgccatcaagt--ttgactcctggt---atgatgtcctttcactccatcaagtttac-ttctaattatgctttatttgttagATTCCTGGAGCGGAAGGACTTGTTGTCAGAGTTGTTTCATCAGTGGATAAGAAGCTGGAGGTTAAACCACGTTTTTTAGAAATTTTTCAAGAAGACAACT

upper sequence: LOC_Os02g04490.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT1G16710.1 (Arabidopsis thaliana), 3'ss of exon 8
--------------------------------------------------tgacttctctcctgtaattgagaatagaccactgactt--ttgccgtcatgaaggaaattattctcatcacttttaaattct---atttattccttatttgt-----tagGTTCCTGGAGCCGAAGGTCTTGTGGTTAGAGTTGTTTCATCAGTGGACAAGAAGCTGGAAGTAAAACCACGTTTTTTGGAAATTTTTCAAGAAGATAACT
                                                  ||| | || || | || |      |  |   ||   |   | |     ||  |   ||   | ||  |   |     ||| |   |||| |   ||| | |       || ||||    |  |||   ||||||||||||||||||||||| || ||||||||||| ||||| ||| | || ||| | ||||||||||  || ||||| |
gtaatctggcggtggaatacagggttttaaagtctcatgtgattttgcattgagtcctatcttctattgtttgttgaagtgctacttcactggaaacaatagattgaagcttactggttggtcactgattgtttaatttttcttttactggcactaacagATTCCAACTGTTGAATCCCTTGTGGTTAGAGTTGTTTCATCTGTTGACAAGAAGCTAGAAGTTAAATCTCGATTTCTTGAAATTTTTCGGGAGGATAATT

upper sequence: LOC_Os02g04490.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT1G79000.2 (Arabidopsis thaliana), 3'ss of exon 9
----------------------------------------------------------------tgacttctctcctgtaattgagaatagaccactgacttttgccgtcatgaaggaaattattctcatcacttttaaattctatttattccttatttgttagGTTCCTGGAGCCGAAGGTCTTGTGGTTAGAGTTGTTTCATCAGTGGACAAGAAGCTGGAAGTAAAACCACGTTTTTTGGAAATTTTTCAAGAAGATAACT
                                                                | | || | |  |   |||  |  |   | | ||| | ||   || | |||  |   ||||         |||   || | |||              || ||||    |||||    |||||| |||||||||||||||| || ||||||||||||||||| ||||| || ||| | ||||||||||  || ||||  |
gtaatttaatggtggagtttgttaacgtttatttctttcatttattttcacatctgcaagctctttatttttatttttctattt-gtttgatctagtgattctt--tgtta-gaaacagtatattgaagctgactttgttttttctttgacttgatacgaacagATTCCCACTGCCGAGTCCCTTGTGATTAGAGTTGTTTCATCTGTTGACAAGAAGCTGGAAGTCAAACCTCGATTTCTTGAAATTTTTCGGGAGGATAGTT

upper sequence: LOC_Os02g04490.1 (Oryza sativa), 3'ss of exon 8
lower sequence: PP1S462_17V6.1 (Physcomitrella patens), 3'ss of exon 3
-----------------------------------------------------------------------------------------tgacttctctcctgtaattgagaatagaccactgacttttgccgtcatgaaggaaattattctcatcacttttaaattctatttattcct-------tatttgt-tagGTTCCTGGAGCCGAAGGTCTTGTGGTTAGAGTTGTTTCATCAGTGGACAAGAAGCTGGAAGTAAAACCACGTTTTTTGGAAATTTTTCAAGAAGATAACT
                                                                                         | | |  |  |    ||   | || | |  |   |    ||| | |     |  |    |  |    |   || |||||||   | || |       |||   | |||||| |  | || || | | | |||||||||||||| || || |||||||||||||||||||| || | ||| || |||||| ||||||||| |||| |  
gtacttgcatgtgcttttccagttactgtagttattctataattttttgtttcaagttttgtaatcgaattcttaagttttattcaaccttattcatgactatgaaaaaataaaaaataaaaaaacaatgctgcctctctgacagcgctcttttgtatgctttaattctaacaagtcatatgacactatgaatgtagGTTGCCAGTGCAGAGGCTTTGGTGGTTAGAGTTGTATCCTCCGTGGACAAGAAGCTGGAAGTGAAGCAACGGTTCTTGGAAGTTTTTCAAGGAGATTATC

upper sequence: LOC_Os02g04490.1 (Oryza sativa), 3'ss of exon 8
lower sequence: PP1S404_36V6.1 (Physcomitrella patens), 3'ss of exon 1
------------------------------------------------------------------------------------tgacttctctcctg--taattgagaat-agaccactgacttttgccgtcatgaaggaaattattctcatcacttttaaatt--ctatttattccttatt-tgt---tagGTTCCTGGAGCCGAAGGTCTTGTGGTTAGAGTTGTTTCATCAGTGGACAAGAAGCTGGAAGTAAAACCACGTTTTTTGGAAATTTTTCAAGAAGATAACT--------
                                                                                      || ||  || ||  |||   | ||| |||  |   | |  ||||    |||  |  ||   |   ||  |||| |   |  | | | ||    || | ||    |||||  |  | || || | | | |||||||||||||| || || |||||||||||||||||||| |||| ||| || |||||||||||||||| |||| |          
gtacttgcatgtggttttccagttactgtggctattctaaaaatttttgtttcaagttttgtaatcgaattcttaagttttattcaacctcattcatgactaagaaaaaatcagaaaaagcaatgctgcctgtctgacagcgatcgattgtat-gctttaacgctaacaagtcatatgatactatgaatgtaggtggccagTGCAGAGGCTTTGGTGGTTAGAGTTGTATCCTCCGTGGACAAGAAGCTGGAAGTCAAACAACGGTTCTTGGAAATTTTTCAAGGAGATTATCCAACTGAG

upper sequence: LOC_Os02g04490.1 (Oryza sativa), 3'ss of exon 8
lower sequence: PP1S193_70V6.1 (Physcomitrella patens), 3'ss of exon 9
--------------------------------------------------------------------------------------------tgacttctctcctgt---aattgagaatagaccactgacttttgccgtcatgaaggaaattattctcatcacttttaaatt-ctatttattccttatttgttagGTTCCTGGAGCCGAAGGTCTTGTGGTTAGAGTTGTTTCATCAGTGGACAAGAAGCTGGAAGTAAAACCACGTTTTTTGGAAATTTTTCAAGAAGATAACT
                                                                                            |   ||   |   |    |||||  ||   |   ||| || ||||       |     |||  | | || | |  | | || || | |  | ||      ||||||| |  | || || |   | ||||| |||||||| || || |||||||||||||||||||| || | ||| |||||||||||||||||||||||  |||
gtacttgcacgtgcttttatttagttactgtagttattcttggatttgatctttcgagctgtcatgtttcaatcctatgtctttcacgaccttagttttaatttcgacagaattgcaaaagcaatgctgtctcttgctac----atctccattgct-tgattagtgctgacttgctgtatgatactatgagtttagGTTGCCAGTGCAGAGGCCTTAGTGGTCAGAGTTGTGTCCTCTGTGGACAAGAAGCTGGAAGTCAAGCAACGGTTTTTGGAAATTTTTCAAGAAGAAGACT

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|88301912|gb|CI667758.1|CI667758
EST:     AGCAGGAGAGACAGGATAGGGCAGCTCAGGAGAGGAAAAGCATTGAGGAG                         GTTCCTGGAGCCGAAGGTCTTGTGGTTAGAGTTGTTTCATCAGTGGACAAG
genomic: AGCAGGAGAGACAGGATAGGGCAGCTCAGGAGAGGAAAAGCATTGAGGAGgttagttaaa ... tatttgttagGTTCCTGGAGCCGAAGGTCTTGTGGTTAGAGTTGTTTCATCAGTGGACAAG
EST: gi|88306088|gb|CI635094.1|CI635094
EST:     AGCAGGAGAGACAGGATAGGGCAGCTCAGGAGAGGAAAAGCATTGAGGAG                         GTTCCTGGAGCCGAAGGTCTTGTGGTTAGAGTTGTTTCATCAGTGGACAAG
genomic: AGCAGGAGAGACAGGATAGGGCAGCTCAGGAGAGGAAAAGCATTGAGGAGgttagttaaa ... tatttgttagGTTCCTGGAGCCGAAGGTCTTGTGGTTAGAGTTGTTTCATCAGTGGACAAG
EST: gi|58653969|gb|CK042649.1|CK042649
EST:     AGCAGGAGAGACAGGATAGGGCAGCTCAGGAGAGGAAAAGCATTGAGGAG                         GTTCCTGGAGCCGAAGGTCTTGTGGTTAGAGTTGTTTCATCAGTGGACAAG
genomic: AGCAGGAGAGACAGGATAGGGCAGCTCAGGAGAGGAAAAGCATTGAGGAGgttagttaaa ... tatttgttagGTTCCTGGAGCCGAAGGTCTTGTGGTTAGAGTTGTTTCATCAGTGGACAAG
EST: gi|29635246|gb|CB640255.1|CB640255
EST:     AAAAGCATTGAGGAG                         GTTCCTGGAGCCGAAGGTCTTGTGGTTAGAGTTGTTTCATCAGTGGACAAG
genomic: AAAAGCATTGAGGAGgttagttaaa ... tatttgttagGTTCCTGGAGCCGAAGGTCTTGTGGTTAGAGTTGTTTCATCAGTGGACAAG
EST: gi|58692816|gb|CK081503.1|CK081503
EST:     AGCAGGAGAGACAGGATAGGGCAGCTCAGGAGAGGAAAAGCATTGAGGAG                         GTTCCTGGAGCCGAAGGTCTTGTGGTTAGAGTTGTTTCATCAGTGGACAAG
genomic: AGCAGGAGAGACAGGATAGGGCAGCTCAGGAGAGGAAAAGCATTGAGGAGgttagttaaa ... tatttgttagGTTCCTGGAGCCGAAGGTCTTGTGGTTAGAGTTGTTTCATCAGTGGACAAG
EST: gi|29622743|gb|CB627754.1|CB627754
EST:     AGGGCAGCTCAGGAGAGGAAAAGCATTGAGGAG                         GTTCCTGGAGCCGAAGGTCTTGTGGTTAGAGTTGTTTCATCAGTGGACAAG
genomic: AGGGCAGCTCAGGAGAGGAAAAGCATTGAGGAGgttagttaaa ... tatttgttagGTTCCTGGAGCCGAAGGTCTTGTGGTTAGAGTTGTTTCATCAGTGGACAAG
EST: gi|88570132|gb|CI661307.1|CI661307
EST:     AGCAGGAGAGACAGGATAGGGCAGCTCAGGAGAGGAAAAGCATTGAGGAG                         GTTCCTGGAGCCGAAGGTCTTGTGGTTAGAGTTGTTTCATCAGTGGACAAG
genomic: AGCAGGAGAGACAGGATAGGGCAGCTCAGGAGAGGAAAAGCATTGAGGAGgttagttaaa ... tatttgttagGTTCCTGGAGCCGAAGGTCTTGTGGTTAGAGTTGTTTCATCAGTGGACAAG

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: 69 (upstream exon), 71 (downstream exon)
Score: 10

TAGAACTGTACTAAGCGATCATATTGAAGATCGGCTTTTTAAACGGTTGAAGCAGGAGAGACAGGATAGGGCAGCTCAGGAGAGGAAAAGCATTGAGGAGgttagttaaa ... tatttgttagGTTCCTGGAGCCGAAGGTCTTGTGGTTAGAGTTGTTTCATCAGTGGACAAGAAGCTGGAAGTAAAACCACGTTTTTTGGAAATTTTTCAAGAAGATAACT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgaaggaaattattctcatcacttttaaattctatttattccttatttgttagGTTCCTGGAGCCGAAGGTCTTGTGGTTAGAGTTGTTTCATCAGTGGACAAGAAGCTGGAAGTAAAACCACGTTTTTTGGAAATTTTTCAAGAAGATAACT
                               ttctatttattcctt  CT-rich tract
        aaattattctcatcac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgacttctctcctgtaattgagaatagaccactgacttttgccgtcatgaaggaaattattctcatcacttttaaattctatttattccttatttgttagGTTCCTGGAGCCGAAGGTCTTGTGGTTAGAGTTGTTTCATCAGTGGACAAGAAGCTGGAAGTAAAACCACGTTTTTTGGAAATTTTTCAAGAAGATAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - ctcctgt
- - - - - - - - - - agaataga
- - - - - - - - - - - - - - - - - -cttttgc
- - - - - - - - - - - - - - - - - - - - - - -catgaag