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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttcaacagcgtgttgatgaaactttttcccttcgtctgttatgtcacatctgtctgaaataaacactgagtaagcttcctgttttcgtgatacttgcagGATATCAATGAGGAATGGATATCTGACAAAACACGGTTTTGTTATGATGGTCTGAAGAGGCAAAGACTAAACGACCCCATGATCCGTGGTACTGATGGCA

Basic information

species Oryza sativa
transcript LOC_Os03g50540.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g50540.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G126038_T01 (Zea mays), 3'ss of exon 3
-----------------------------------------------------------------------------gttcaacagcgtgttgatgaaacttttt-------cccttcgtctgttatgtcacatctgtc-tgaaataaacactg--agtaagctt--------cctgttttcgtgatacttgcagGATATCAATGAGGAATGGATATCTGACAAAACACGGTTTTGTTATGATGGTCTGAAGAGGCAAAGACTAAACGACCCCATGATCCGTGGTACTGATGGCA
                                                                             | |     | || |   |||     |||         ||   ||| | ||   |    | |  | | |||||   ||  | || | ||        ||  ||| | || |  |||||||| || ||||||||||||||||| || || ||||| ||||||||||||||| ||||||||||||||||||| ||||| |||||||||||| |||||||||
gttggtttattctccatttctgttacaattttgacttttgtgtttgttttgttggtggggtattcatgtgtcctaatgcttcgtggtgtatcattgacttcatttagtccgcttctatatctttgataaaaaggttattatcatataaattatgtcaatatgtttagttaacaccactttccctgttcattgcagGACATTAATGAGGAATGGATATCGGATAAGACACGATTTTGTTATGATGGTTTGAAGAGGCAAAGACTAAATGACCCTATGATCCGTGGTCCTGATGGCA

upper sequence: LOC_Os03g50540.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G145854_T01 (Zea mays), 3'ss of exon 3
-------------------------------------------------------------gttcaacagcgtgttgatgaaactttttcccttcgtct-gttatgtcacatctgtctgaaataaa-----------------cactgagtaagc-----ttcctgttttcgtgatacttgcagGATATCAATGAGGAATGGATATCTGACAAAACACGGTTTTGTTATGATGGTCTGAAGAGGCAAAGACTAAACGACCCCATGATCCGTGGTACTGATGGCA
                                                             |  | || || |    ||| | | ||    | || | | | |||   | |||| |  ||||  ||                    | ||| | |     ||    ||||  |  | ||||||||| || |||||||||||||| || ||||||||||||||||||||||||||||||||||||||||||||||| ||||| |||||||||||| |||||||||
gtttgtttattctccatttattttacaatttggatttttgtgtttttttttgtattcatgtgacctactgcttcgctatgtatcattagttcatcattttgctattctatatctttgagaaaccaaagattattatgttaatatgtttagtgaacatcacttttcctttttcttttccttgcagGACATTAATGAGGAATGGATTTCGGACAAAACACGGTTTTGTTATGATGGTCTGAAGAGGCAAAGACTAAATGACCCTATGATCCGTGGTCCTGATGGCA

upper sequence: LOC_Os03g50540.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA18G04730.1 (Glycine max), 3'ss of exon 3
-gttcaacagcgtgttgatgaaactttttcccttcgtctgttatgtcacatctgtctgaaataaacactgagtaagcttcctgttttcgtgatacttgcagGATATCAATGAGGAATGGATATCTGACAAAACACGGTTTTGTTATGATGGTCTGAAGAGGCAAAGACTAAACGACCCCATGATCCGTGGTACTGATGGCA-
  ||    |    |   |  |||||| ||          |   | |  | ||| ||   | |   |  |   |||   |  | | | | ||    |||||||| || ||||| |||||||| || || ||||| || ||||||||||||||| |||| ||||||||  |||| || |||||||| |||||| |||||||   
tttttccaaaaaagaaaaaaaaacttcttagggatagaagaggt-tggcttctttccatagtttgctatttttaaagcttgt-tctgcttgcccattgcaggAGATAAATGAAGAATGGATTTCGGATAAAACCCGCTTTTGTTATGATGGTTTGAAAAGGCAAAGGTTAAATGATCCCATGATACGTGGTTCTGATGGACG

upper sequence: LOC_Os03g50540.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA11G33480.1 (Glycine max), 3'ss of exon 3
gttcaacagcgtgttgatgaaactttttcccttcgtctgttatgtca-catctgtctgaaataaacactgagtaagcttcctgttttcgtgatacttgcagGATATCAATGAGGAATGGATATCTGACAAAACACGGTTTTGTTATGATGGTCTGAAGAGGCAAAGACTAAACGACCCCATGATCCGTGGTACTGATGGCA
  | || ||       |  ||| | ||       |      | ||   | ||| ||   | |   |  |   |||   |  | | | | ||    |||||||| || ||||| |||||||| || |||||||| || ||||||||||||||| |||| ||||| ||  |||| ||||||||||| |||||| |||||||  
tctaaaaagaaaagaaaaaaaaatcttcttagggggagaagaggttggcttctttccatagtttgctatttttaaagcttgt-tctgcttgcccattgcagGACATAAATGAAGAATGGATTTCAGACAAAACCCGCTTTTGTTATGATGGTTTGAAAAGGCAGAGGTTAAATGACCCCATGATTCGTGGTTCTGATGGAC

upper sequence: LOC_Os03g50540.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT5G37510.2 (Arabidopsis thaliana), 3'ss of exon 3
gttcaacagcgtgttgatgaaactttttcccttcgtctgttatgtcacatctgtctgaaataaac-actgagtaagcttcctgttttcgtgatacttgcagGATATCAATGAGGAATGGATATCTGACAAAACACGGTTTTGTTATGATGGTCTGAAGAGGCAAAGACTAAACGACCCCATGATCCGTGGTACTGATGGCA
                     |  |  | | || ||     |   |||   | |   || ||     |||  |      | |||    ||  |  || |||||||| || || |||||||||||||||||||| || || |||||||| || ||||| || ||||| || | |||||| |||||||| | | | |||||  
-------------------gtatgtaatgcttttgttca--aaaacactatttttaaaagtattttgctggatgttgaacttgtgaatgttcttatt-cagGATATAAACGAAGAATGGATATCTGACAAAACCCGATTCTGTTATGACGGCCTGAAAAGACAAAGGCTGAGCGACCCTATGATCCGAGATTCCGATGGAC

upper sequence: LOC_Os03g50540.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv14s0006g02020.t01 (Vitis vinifera), 3'ss of exon 3
gttcaacagcgtgttgatgaaactttttcccttcgtctgttatgtcacatctgtctgaaataaacactgagtaagcttc-ctgttttcgtgatact--tgcagGATATCAATGAGGAATGGATATCTGACAAAACACGGTTTTGTTATGATGGTCTGAAGAGGCAAAGACTAAACGACCCCATGATCCGTGGTACTGATGGCA
|   | |   |||||  |  ||||| |||   | |||| |||   ||  | |  |||||||  |   | |  ||  |   |||  || |    |||  ||||||| || ||||||||||||||||| ||||||||||| || ||||||||||||||||||||||| ||  |||| || || ||||| |||||| |||||||  
gaggatctttgtgtttttttaacttgttcagat-gtcttttag--catcttttactgaaatgtaagatcatcaatttcagctggctttgctgaactgttgcagGACATAAATGAGGAATGGATATCAGACAAAACACGTTTCTGTTATGATGGTCTGAAGAGGCAGAGGTTAAATGATCCTATGATTCGTGGTGCTGATGGAC

upper sequence: LOC_Os03g50540.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ11043 (Selaginella moellendorffii), 3'ss of exon 3
gttcaacagcgtgttgatgaaactttttcccttcgtctgttatgtcacatctgtctgaaataaacactgagtaagcttcctgttttcgtgatacttgcagGATATCAATGAGGAATGGATATCTGACAAAACACGGTTTTGTTATGATGGTCTGAAGAGGCAAAGACTAAACGACCCCATGATCCGTGGTACTGATGGCA
                                                      |   |  |||  ||  |     ||  ||     |  |   |  |||||| | ||||||||||||||||| |||||  | ||||||||||| |||||| | ||  | ||  | || ||||| || ||| | ||||||    |||| |
-------------------------------------------------gtaaaccccagcaaaagctatgcttttttgttgaacgtgctactttgacagGATGTGAATGAGGAATGGATATCGGACAAGGCTCGGTTTTGTTACGATGGTTTAAAACGCCAGCGTCTCAACGAGCCAATGCTGCGTGGTGAAAATGGGA

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|33796628|gb|CF324182.1|CF324182
EST:     TTGACAGCAGAGGTCCTGAAGTTATGCGTATCGTTCCACGTCTCAATGAG                         GATATCAATGAGGAATGGATATCTGACAAAACACGGTTTTGTTATGATGGT
genomic: TTGACAGCAGAGGTCCTGAAGTTATGCGTATCGTTCCACGTCTCAATGAGgttcgcttat ... atacttgcagGATATCAATGAGGAATGGATATCTGACAAAACACGGTTTTGTTATGATGGT
EST: gi|33677788|gb|CF306027.1|CF306027
EST:     TGACAGCAGAGGTCCTGAAGTT-GGCTTAAT-GTTCCACGTCTCAATGAG                         GATATCAATGAGGAATGTTTATTTGACAAAACACGGTTTTGTTATGATGGT
genomic: TGACAGCAGAGGTCCTGAAGTTATGCGT-ATCGTTCCACGTCTCAATGAGgttcgcttat ... atacttgcagGATATCAATGAGGAATGGATATCTGACAAAACACGGTTTTGTTATGATGGT
EST: gi|33675255|gb|CF303494.1|CF303494
EST:     GTTCCACGTCTCAATGAG                         GATATCAATGAGGAATGGATATCTGACAAAACACGGTTTTGTTATGATGGT
genomic: GTTCCACGTCTCAATGAGgttcgcttat ... atacttgcagGATATCAATGAGGAATGGATATCTGACAAAACACGGTTTTGTTATGATGGT
EST: gi|58606090|gb|CK034123.1|CK034123
EST:     TGACAGCAGAGGTCCGTGAAGTTATGCGTATCGTTCCACGTCTCAATGAG                         GATATCAATGAGGAATGGATATCTGACAAAACACGGTTTTGTTATGATGGT
genomic: TGACAGCAGAGGTCC-TGAAGTTATGCGTATCGTTCCACGTCTCAATGAGgttcgcttat ... atacttgcagGATATCAATGAGGAATGGATATCTGACAAAACACGGTTTTGTTATGATGGT
EST: gi|29633070|gb|CB638079.1|CB638079
EST:     TTGACAGCAGAGGTCCTGAAGTTATGCGTATCGTTCCACGTCTCAATGAG                         GATATCAATGAGGAATGGATATCTGACAAAACACGGTTTTGTTATGATGGT
genomic: TTGACAGCAGAGGTCCTGAAGTTATGCGTATCGTTCCACGTCTCAATGAGgttcgcttat ... atacttgcagGATATCAATGAGGAATGGATATCTGACAAAACACGGTTTTGTTATGATGGT
EST: gi|29628500|gb|CB633511.1|CB633511
EST:     TTGACAGCAGAGGTCCTGAAGTTATGCGTATCGTTCCACGTCTCAATGAA                         GATATCAATGAGGAATGGATATCTG
genomic: TTGACAGCAGAGGTCCTGAAGTTATGCGTATCGTTCCACGTCTCAATGAGgttcgcttat ... atacttgcagGATATCAATGAGGAATGGATATCTG
EST: gi|58612327|gb|CK040039.1|CK040039
EST:     GTCTCAATGAG                         GATATCAATGAGGAATGGATATCTGACAAAACACGGTTTTGTTATGATGGT
genomic: GTCTCAATGAGgttcgcttat ... atacttgcagGATATCAATGAGGAATGGATATCTGACAAAACACGGTTTTGTTATGATGGT

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), 72 (downstream exon)
Score: 37

GGGCACTGAAACTATTGATGTTACTGATGCAGTAGGTTCAAACATTAGAGTTGACAGCAGAGGTCCTGAAGTTATGCGTATCGTTCCACGTCTCAATGAGgttcgcttat ... atacttgcagGATATCAATGAGGAATGGATATCTGACAAAACACGGTTTTGTTATGATGGTCTGAAGAGGCAAAGACTAAACGACCCCATGATCCGTGGTACTGATGGCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacatctgtctgaaataaacactgagtaagcttcctgttttcgtgatacttgcagGATATCAATGAGGAATGGATATCTGACAAAACACGGTTTTGTTATGATGGTCTGAAGAGGCAAAGACTAAACGACCCCATGATCCGTGGTACTGATGGCA
          tgaaataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcaacagcgtgttgatgaaactttttcccttcgtctgttatgtcacatctgtctgaaataaacactgagtaagcttcctgttttcgtgatacttgcagGATATCAATGAGGAATGGATATCTGACAAAACACGGTTTTGTTATGATGGTCTGAAGAGGCAAAGACTAAACGACCCCATGATCCGTGGTACTGATGGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- -caacagc
- - - - - - gttgatg
- - - - - - - - - - - - - - - - - - -tgttatg
- - - - - - - - - - - - - - - - - - - - - - - - - ctgtctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaataaa