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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtttgtcatcagggcttgggaccattttgttgtttttctgaataataatatctccaaaaatatgggatagatacacttataggagtttgttatgctgcagGGTTGGAGATCCATTTAAAGACACGGCGGGGCCTTCCATCCATGTTCTTATTAAGATGCTCGCTACAATCACATTAGTGATGGCTCCAATATTCTTGTGA

Basic information

species Oryza sativa
transcript LOC_Os02g33490.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g33490.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G075900_T01 (Zea mays), 3'ss of exon 14
--gtttgtcatcagggcttgggacc--attttgttgtttttctgaataataatatctccaaaaatatgggatagatacacttataggagtttgt--tatgctgcagGGTTGGAGATCCATTTAAAGACACGGCGGGGCCTTCCATCCATGTTCTTATTAAGATGCTCGCTACAATCACATTAGTGATGGCTCCAATATTCTTGTGA
    ||   |||| ||| || |||   |||| |  || |   ||| |   |  |   |||||| | |    |  || |||||||| |||| |||  | ||||||||||||||||| ||||| |||||||| || || || ||  | || |||||||| ||||||||||| || |||||| | || |||||||| ||||||||||||
acagttccgatcatggcgtgtgactttatttcggagtctggatgattggcacaac--ccaaaagttt----tttatgcacttataagagtatgtgttgtgctgcagGGTTGGAGACCCATTCAAAGACACTGCAGGACCATCGCTGCACGTTCTTATCAAGATGCTCGCCACGATCACACTGGTCATGGCTCCCATATTCTTGTGA

upper sequence: LOC_Os02g33490.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G069410_T01 (Zea mays), 3'ss of exon 6
-gtttgtcatcagggcttgggacc-attttgttgtttttctgaataataatatctccaaaaatatgggatagatacacttataggagtttgttatgctgcagGGTTGGAGATCCATTTAAAGACACGGCGGGGCCTTCCATCCATGTTCTTATTAAGATGCTCGCTACAATCACATTAGTGATGGCTCCAATATTCTTGTGA
  |||    |   |   | |  |  ||  ||  || |  || | |  |      ||   |    ||| | |     |     |    |||||| ||||||||||||||||| ||||| |||||||| || || || ||  | ||||||||||| ||||||||||| ||||||||  | || |||||||| ||||||||||||
tttttcctgtagcgaaatagttctgatcatggcgtgtggcttatt--ttgcgattctggatgattggtacaatccgaaagccatatatttgttgtgctgcagGGTTGGAGACCCATTCAAAGACACTGCTGGACCGTCGCTGCATGTTCTTATCAAGATGCTCGCCACAATCACGCTGGTCATGGCTCCGATATTCTTGTGA

upper sequence: LOC_Os02g33490.1 (Oryza sativa), 3'ss of exon 14
lower sequence: PP1S105_42V6.2 (Physcomitrella patens), 3'ss of exon 15
--gtttgtcatcagggctt---gggaccattttgttgtttttctgaat--aataatatctccaaaaatatgggatagatacacttataggagtttgttatgctgcagGGTTGGAGATCCATTTAAAGACACGGCGGGGCCTTCCATCCATGTTCTTATTAAGATGCTCGCTACAATCACATTAGTGATGGCTCCAATATTCTTGTGA
   |||   ||      ||   |  || |  |  |     ||  ||    |||  |   ||   | | | |   |    ||| | ||       | ||    ||||| ||||||||||| |||||||| || || || |||||  ||||||| || || |||||||||||||| |||||| | || ||||| ||  | ||| ||   
tcatttagtatttaactttcacgaaacgaagtgatacaagtttcgagctgaatgtttcttctggagacaggaacttatcacattcat-------ttttggattgcagAGTTGGAGATCCTTTTAAAGATACTGCTGGACCTTCTCTCCATGTGCTAATCAAGATGCTCGCTACCATCACACTGGTCATGGCACCGCTCTTCCTGGAC

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|86869043|gb|CI335610.1|CI335610
EST:     CTTGGTGGCAAAGGCAGTGAGTCTCACAAGGCTGCAATTACTGGTGATAC                         GGTTGGAGATCCATTTAAAGACACGGCCGGGCCTTCCATCCATGTTCTTAT
genomic: CTTGGTGGCAAAGGCAGTGAGTCTCACAAGGCTGCAGTTACTGGTGATACgtaagtgttt ... tatgctgcagGGTTGGAGATCCATTTAAAGACACGGCGGGGCCTTCCATCCATGTTCTTAT
EST: gi|88969788|gb|CI383290.1|CI383290
EST:     CTTGGTGCCAAAGGCAGTGATTCTCACAAGGCTGCAGTTACTGGTGATAC                         GGTTGGAGATCCATTTAAAGACACGGCGGGGCCTTCCATCCATCTTCTTAT
genomic: CTTGGTGGCAAAGGCAGTGAGTCTCACAAGGCTGCAGTTACTGGTGATACgtaagtgttt ... tatgctgcagGGTTGGAGATCCATTTAAAGACACGGCGGGGCCTTCCATCCATGTTCTTAT
EST: gi|86482441|gb|CI125074.1|CI125074
EST:     CTTGGTGGCAAAGGCAGTGAGTCTCACAAGGCTGCAGTTACTGGTGATAC                         GGTTGGAGATCCATTTAAAGACACGGCGGGGCCTTCCATCCATGTTCTTAT
genomic: CTTGGTGGCAAAGGCAGTGAGTCTCACAAGGCTGCAGTTACTGGTGATACgtaagtgttt ... tatgctgcagGGTTGGAGATCCATTTAAAGACACGGCGGGGCCTTCCATCCATGTTCTTAT
EST: gi|88198741|gb|CI198591.1|CI198591
EST:     CTTGGTGGCAAAGGCAGTGAGTCTCACAAGGCTGCAGTTACTGGTGATAC                         GGTTGGAGATCCATTTAAAGACACGGCGGGGCCTTCCATCCATGTTCTTAT
genomic: CTTGGTGGCAAAGGCAGTGAGTCTCACAAGGCTGCAGTTACTGGTGATACgtaagtgttt ... tatgctgcagGGTTGGAGATCCATTTAAAGACACGGCGGGGCCTTCCATCCATGTTCTTAT
EST: gi|88964660|gb|CI070006.1|CI070006
EST:     CTTGGTGGCAAAGGCAGTGAGTCTCACAAGGCTGCAGTTACTGGTGATAC                         GGTTGGAGATCCATTTAAAGACACGGCGGGGCCTTCCATCCATGTTCTTAT
genomic: CTTGGTGGCAAAGGCAGTGAGTCTCACAAGGCTGCAGTTACTGGTGATACgtaagtgttt ... tatgctgcagGGTTGGAGATCCATTTAAAGACACGGCGGGGCCTTCCATCCATGTTCTTAT
EST: gi|88276030|gb|CI396634.1|CI396634
EST:     CACAAGGCTGCAGTTACTGGTGATAC                         -GTTGGAGATCCATTTGAAGACACGGCGGGGCCTTCCATCCATGTTCTTAT
genomic: CACAAGGCTGCAGTTACTGGTGATACgtaagtgttt ... tatgctgcagGGTTGGAGATCCATTTAAAGACACGGCGGGGCCTTCCATCCATGTTCTTAT
EST: gi|86479841|gb|CI122474.1|CI122474
EST:     CTTGGTGGCAAAGGCAGTGAGTCTCACAAGGCTGCAGTTACTGGTGATGC                         GGTTGGAGATCCATTTAAAGACACGGCGGGGCCTTCCATCCATGTTCTTAT
genomic: CTTGGTGGCAAAGGCAGTGAGTCTCACAAGGCTGCAGTTACTGGTGATACgtaagtgttt ... tatgctgcagGGTTGGAGATCCATTTAAAGACACGGCGGGGCCTTCCATCCATGTTCTTAT
EST: gi|87039331|gb|CI193953.1|CI193953
EST:     CTTGGTGGCAAAGGCAGTGAGTCTCACAAGGCTGCAGTTACTGGTGATAC                         GGTTGGAGATCCATTTAAAGACACGGCGGGGCCTTCCATCCATGTTCTTAT
genomic: CTTGGTGGCAAAGGCAGTGAGTCTCACAAGGCTGCAGTTACTGGTGATACgtaagtgttt ... tatgctgcagGGTTGGAGATCCATTTAAAGACACGGCGGGGCCTTCCATCCATGTTCTTAT
EST: gi|88235891|gb|CI235093.1|CI235093
EST:     CTTGGTGGCAAAGGCAGTGAGTCTCACAAGGCTGCAGTTACTGGTGATAC                         GGTTGGAGATCCATTTAAAGACACGGCGGGGCCTTCCATCCATGTTCTTAT
genomic: CTTGGTGGCAAAGGCAGTGAGTCTCACAAGGCTGCAGTTACTGGTGATACgtaagtgttt ... tatgctgcagGGTTGGAGATCCATTTAAAGACACGGCGGGGCCTTCCATCCATGTTCTTAT
EST: gi|88484819|gb|CI422090.1|CI422090
EST:     CTTGGTGGCAAAGGCANTGAGTCTCACAAGGCTGCAGTTACTGGTGATAC                         GGTTGGAGATCCATTTAAAGACACGGCGGGGCCTTCCATCCATGTTCTTAT
genomic: CTTGGTGGCAAAGGCAGTGAGTCTCACAAGGCTGCAGTTACTGGTGATACgtaagtgttt ... tatgctgcagGGTTGGAGATCCATTTAAAGACACGGCGGGGCCTTCCATCCATGTTCTTAT
EST: gi|218504967|gb|FG957282.1|FG957282
EST:     CTTGGTGGCAAAGGCAGTGAGTCTCACAAGGCTGCAGTTACTGGTGATAC                         GGTTGGAGATCCATTTAAAGACACGGCGGGGCCTTCCATCCA
genomic: CTTGGTGGCAAAGGCAGTGAGTCTCACAAGGCTGCAGTTACTGGTGATACgtaagtgttt ... tatgctgcagGGTTGGAGATCCATTTAAAGACACGGCGGGGCCTTCCATCCA
EST: gi|87029760|gb|CI274441.1|CI274441
EST:     CTTGGTGGCAAAGGCAGTGAGTCTCACAAGGCTGCAGTTACTGGTGATAC                         GGTTGGAGATCCATTTAAAGACACGGCGGGGCCTTCCATCCATGTTCTTAT
genomic: CTTGGTGGCAAAGGCAGTGAGTCTCACAAGGCTGCAGTTACTGGTGATACgtaagtgttt ... tatgctgcagGGTTGGAGATCCATTTAAAGACACGGCGGGGCCTTCCATCCATGTTCTTAT
EST: gi|86429980|gb|CI082403.1|CI082403
EST:     CTTGGTGGCAAGGGCAGTGAGTCTCACAAGGCTGCAGTTACTGGTGATAC                         GGTTGGAGATCCATTTAAAGACACGGCGGGGCCTTCCATCCATGTTCTTAT
genomic: CTTGGTGGCAAAGGCAGTGAGTCTCACAAGGCTGCAGTTACTGGTGATACgtaagtgttt ... tatgctgcagGGTTGGAGATCCATTTAAAGACACGGCGGGGCCTTCCATCCATGTTCTTAT
EST: gi|88234284|gb|CI234133.1|CI234133
EST:     CTTGGTGGCAAAGGCAGTGAGTCTCACAAGGCTGCAGTTACTGGTGATAC                         GGTTGGAGATCCATTTAAAGACACGGCGGGGCCTTCCATCCATGTTCTTAT
genomic: CTTGGTGGCAAAGGCAGTGAGTCTCACAAGGCTGCAGTTACTGGTGATACgtaagtgttt ... tatgctgcagGGTTGGAGATCCATTTAAAGACACGGCGGGGCCTTCCATCCATGTTCTTAT
EST: gi|88263306|gb|CI367080.1|CI367080
EST:     CTTGGTGGCAAAGGCAGTGAGTCTCACAAGGCTGCAGTTACTGGTGATAC                         GGTTGGAGATCCATTTAAAGACACGGCGGGGCCTTCCATCCATGTTCTTAT
genomic: CTTGGTGGCAAAGGCAGTGAGTCTCACAAGGCTGCAGTTACTGGTGATACgtaagtgttt ... tatgctgcagGGTTGGAGATCCATTTAAAGACACGGCGGGGCCTTCCATCCATGTTCTTAT
EST: gi|86835449|gb|CI347906.1|CI347906
EST:     CTTGGTGGCAAAGGCAGTGAGTCTCACAAGGCTGCAGTTACTGGTGATAC                         GGTTGGAGATCCATTTAAAGACACGGCGGGGCCTTCCATCCATGTTCTTAT
genomic: CTTGGTGGCAAAGGCAGTGAGTCTCACAAGGCTGCAGTTACTGGTGATACgtaagtgttt ... tatgctgcagGGTTGGAGATCCATTTAAAGACACGGCGGGGCCTTCCATCCATGTTCTTAT
EST: gi|87017877|gb|CI273899.1|CI273899
EST:     CTTGGTGGCAAAGGGAGTGAGTCTCACAAGGCTGCAGTTACTGGTGATAC                         GGTTGGAGATCCATTTAAAGACACGGCGGGGCCTTCCATCCATGTTCTTAT
genomic: CTTGGTGGCAAAGGCAGTGAGTCTCACAAGGCTGCAGTTACTGGTGATACgtaagtgttt ... tatgctgcagGGTTGGAGATCCATTTAAAGACACGGCGGGGCCTTCCATCCATGTTCTTAT
EST: gi|88230400|gb|CI230276.1|CI230276
EST:     CTTGGTGGCAAAGGCAGTGAGTCTCACAAGGCTGCAGTTACTGGTGATAC                         GGTTGGAGATCCATTTAAAGACACGGCGGGGCCTTCCATCCATGTTCTTAT
genomic: CTTGGTGGCAAAGGCAGTGAGTCTCACAAGGCTGCAGTTACTGGTGATACgtaagtgttt ... tatgctgcagGGTTGGAGATCCATTTAAAGACACGGCGGGGCCTTCCATCCATGTTCTTAT
EST: gi|86481811|gb|CI124444.1|CI124444
EST:     CTTGGTGGCAAAGGCAGTGAGTCTCACAAGGCTGCAGTTACTGGTGATAC                         GGTTGGAGATCCATTTAAAGACACGGCGGGGCCTTCCATCCATGTTCTTAT
genomic: CTTGGTGGCAAAGGCAGTGAGTCTCACAAGGCTGCAGTTACTGGTGATACgtaagtgttt ... tatgctgcagGGTTGGAGATCCATTTAAAGACACGGCGGGGCCTTCCATCCATGTTCTTAT
EST: gi|86521014|gb|CI161220.1|CI161220
EST:     CTTGGTGGCAAAGGCAGTGAGTCTCACAAGGCTGCAGTTACTGGTGATAC                         GGTTGGAGATCCATTTAAAGACACGGCGGGGCCTTCCATCCATGTTCTTAT
genomic: CTTGGTGGCAAAGGCAGTGAGTCTCACAAGGCTGCAGTTACTGGTGATACgtaagtgttt ... tatgctgcagGGTTGGAGATCCATTTAAAGACACGGCGGGGCCTTCCATCCATGTTCTTAT
EST: gi|18388882|gb|BM422080.1|BM422080
EST:     CTTGGTGGCAAAGGCAGTGAGTCTCACAAGGCTGCAGTTACTGGTGATAC                         GGTTGGAGATCCATTTAAAGACACGGCGGGGCCTTCCATCCATGTTCTTAT
genomic: CTTGGTGGCAAAGGCAGTGAGTCTCACAAGGCTGCAGTTACTGGTGATACgtaagtgttt ... tatgctgcagGGTTGGAGATCCATTTAAAGACACGGCGGGGCCTTCCATCCATGTTCTTAT
EST: gi|87038030|gb|CI190654.1|CI190654
EST:     CTTGGTGGCAAAGGCAGTGAGTCTCACAAGGCTGCAGTTACTGGTGATAC                         GGTTGGAGATCCATTTAAAGACACGGCGGGGCCTTCCATCCATGTTCTTAT
genomic: CTTGGTGGCAAAGGCAGTGAGTCTCACAAGGCTGCAGTTACTGGTGATACgtaagtgttt ... tatgctgcagGGTTGGAGATCCATTTAAAGACACGGCGGGGCCTTCCATCCATGTTCTTAT
EST: gi|87038865|gb|CI193487.1|CI193487
EST:     CTTGGTGGCAAAGGCAGTGAGTCTCACAAGGCTGCAGTTACTGGTGATAC                         GGTTGGAGATCCATTTAAAGACACGGCGGGGCCTTCCATCCATGTTCTTAT
genomic: CTTGGTGGCAAAGGCAGTGAGTCTCACAAGGCTGCAGTTACTGGTGATACgtaagtgttt ... tatgctgcagGGTTGGAGATCCATTTAAAGACACGGCGGGGCCTTCCATCCATGTTCTTAT
EST: gi|86482488|gb|CI125121.1|CI125121
EST:     CTTGGTGGCAAAGGCAGTGAGTCTCACAAGGCTGCAGTTACTGGTGATAC                         GGTTGGAGATCCATTTAAAGACACGGCGGGGCCTTCCATCCATGTTCTTAT
genomic: CTTGGTGGCAAAGGCAGTGAGTCTCACAAGGCTGCAGTTACTGGTGATACgtaagtgttt ... tatgctgcagGGTTGGAGATCCATTTAAAGACACGGCGGGGCCTTCCATCCATGTTCTTAT
EST: gi|88837719|gb|CI079079.1|CI079079
EST:     CTTGGTGGCAAAGGCAGTGAGTCTCACAAGGCTGCAGTTACTGGTGATAC                         GGTTGGAGATCCATTTAAAGACACGGCGGGGCCTTCCATCCATGTTCTTAT
genomic: CTTGGTGGCAAAGGCAGTGAGTCTCACAAGGCTGCAGTTACTGGTGATACgtaagtgttt ... tatgctgcagGGTTGGAGATCCATTTAAAGACACGGCGGGGCCTTCCATCCATGTTCTTAT
EST: gi|88247939|gb|CI247788.1|CI247788
EST:     CTTGGTGGCAAAGGCAGTGAGTCTCACAAGGCTGCAGTTACTGGTGATAC                         GGTTGGAGATCCATTTAAAGACACGGCGGGGCCTTCCATCCATGTTCTTAT
genomic: CTTGGTGGCAAAGGCAGTGAGTCTCACAAGGCTGCAGTTACTGGTGATACgtaagtgttt ... tatgctgcagGGTTGGAGATCCATTTAAAGACACGGCGGGGCCTTCCATCCATGTTCTTAT

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: 67 (upstream exon), 48 (downstream exon)
Score: 10

CTGCTGGTGGTGCCTGGGATAATGCTAAGAAGTACATCGAGACTGGCGCTCTTGGTGGCAAAGGCAGTGAGTCTCACAAGGCTGCAGTTACTGGTGATACgtaagtgttt ... tatgctgcagGGTTGGAGATCCATTTAAAGACACGGCGGGGCCTTCCATCCATGTTCTTATTAAGATGCTCGCTACAATCACATTAGTGATGGCTCCAATATTCTTGTGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatatctccaaaaatatgggatagatacacttataggagtttgttatgctgcagGGTTGGAGATCCATTTAAAGACACGGCGGGGCCTTCCATCCATGTTCTTATTAAGATGCTCGCTACAATCACATTAGTGATGGCTCCAATATTCTTGTGA
          aaaaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtcatcagggcttgggaccattttgttgtttttctgaataataatatctccaaaaatatgggatagatacacttataggagtttgttatgctgcagGGTTGGAGATCCATTTAAAGACACGGCGGGGCCTTCCATCCATGTTCTTATTAAGATGCTCGCTACAATCACATTAGTGATGGCTCCAATATTCTTGTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - -gggcttg
- - - - - - - - - - - - - ttgttgt
- - - - - - - - - - - - - - - - - tttctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatacac