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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtggctactggctagtcaaatttggatatcgttctttagttagtgttttaccacttatctcgtggttaattttcaattgcattctcatttgtgcgcagGATTTGGATACTGAAGTCATAGTTGCAACAGCAAGAACTCCTGATGCTACAGCAGTATCGGCTAATGTTGTCGTTGACGAGAGACAGATGAATGCATTGT

Basic information

species Oryza sativa
transcript LOC_Os07g12530.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g12530.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G031780_T02 (Zea mays), 3'ss of exon 7
ttgtggctactggctagtcaaatttggatatcgttcttta-gttagtgttttaccacttatctcgtggttaattttcaattgcattctcatttgt-gcgcagGATTTGGATACTGAAGTCATAGTTGCAACAGCAAGAACTCCTGATGCTACAGCAGTATCGGCTAATGTTGTCGTTGACGAGAGACAGATGAATGCATTGT
       | ||    |   |||| ||  ||| |        |||   ||   | ||    |         |||   | | ||  |||||||||||   ||||||  ||||||||||| ||||||| ||||||||||| || |||||||||||||||||||| |||||||||||| |||| ||||| |||||||||||  | |
--cctttttcttatcatgtaaatctgtgtattggaggacgtgttgaagtcaaaacaacagtacacaaaaaaatgcgctaatgttttctcatttgttaagcagGACCTGGATACTGAAATCATAGTGGCAACAGCAAGGACCCCTGATGCTACAGCAGTATCTGCTAATGTTGTCCTTGATGAGAGGCAGATGAATGCTCTTT
















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|86501461|gb|CI144094.1|CI144094
EST:     ATGTTAATGAATTTGCAAAGGACTTGGAAAAAATATTCTCATCAATACAG                         GATTTGGATACTGAAGTCATAGTTGCAACAGCAAGAACTCCTGATGCTACA
genomic: ATGTTAATGAATTTGCAAAGGACTTGGAAAAAATATTCTCATCAATACAGgtaatatttc ... ttgtgcgcagGATTTGGATACTGAAGTCATAGTTGCAACAGCAAGAACTCCTGATGCTACA
EST: gi|29615294|gb|CB620306.1|CB620306
EST:     ATGTTAATGAATTTGCAAAGGACTTGGAAAAAATATTCTCATCAATACAG                         GATTTGGATACTGAAGTCATAGTTGCAACAGCAAGAACTCCTGATGCTACA
genomic: ATGTTAATGAATTTGCAAAGGACTTGGAAAAAATATTCTCATCAATACAGgtaatatttc ... ttgtgcgcagGATTTGGATACTGAAGTCATAGTTGCAACAGCAAGAACTCCTGATGCTACA
EST: gi|29615506|gb|CB620518.1|CB620518
EST:     ATGTTAATGAATTTGCAAAGGACTTGGAAAAAATATTCTCATCAATACAG                         GATTTGGATACTGAAGTCATAGTTGCAACAGCAAGAACTCCTGATGCTACA
genomic: ATGTTAATGAATTTGCAAAGGACTTGGAAAAAATATTCTCATCAATACAGgtaatatttc ... ttgtgcgcagGATTTGGATACTGAAGTCATAGTTGCAACAGCAAGAACTCCTGATGCTACA
EST: gi|29615267|gb|CB620279.1|CB620279
EST:     ATGTTAATGAATTTGCAAAGGACTTGGAAAAAATATTCTCATCAATACAG                         GATTTGGATACTGAAGTCATAGTTGCAACAGCAAGAACTCCTGATGCTACA
genomic: ATGTTAATGAATTTGCAAAGGACTTGGAAAAAATATTCTCATCAATACAGgtaatatttc ... ttgtgcgcagGATTTGGATACTGAAGTCATAGTTGCAACAGCAAGAACTCCTGATGCTACA
EST: gi|29615259|gb|CB620271.1|CB620271
EST:     ATGTTAATGAATTTGCAAAGGACTGGGAAAAAATATTGTCATCAATACAG                         GATTTGGATACTGAAGTCATAGTTGCAACAGCAAGAACTCCGGATGGTACA
genomic: ATGTTAATGAATTTGCAAAGGACTTGGAAAAAATATTCTCATCAATACAGgtaatatttc ... ttgtgcgcagGATTTGGATACTGAAGTCATAGTTGCAACAGCAAGAACTCCTGATGCTACA
EST: gi|29615076|gb|CB620089.1|CB620089
EST:     ATGTTAATGAATTTGCAAAGGACTTGGAAAAAATATTCTCATCAATACAG                         GATTTGGATACTGAAGTCATAGTTGCAACAGCAAGAACTCCTGATGCTACA
genomic: ATGTTAATGAATTTGCAAAGGACTTGGAAAAAATATTCTCATCAATACAGgtaatatttc ... ttgtgcgcagGATTTGGATACTGAAGTCATAGTTGCAACAGCAAGAACTCCTGATGCTACA
EST: gi|86888115|gb|CI300015.1|CI300015
EST:     ATGTTAATGAATTTGCAAAGGACTTGGAAAAAATATTCTCATCAATACAG                         GATTTGGATACTGAAGTCATAGTTGCAACAGCAAGAACTCCTGATGCTACA
genomic: ATGTTAATGAATTTGCAAAGGACTTGGAAAAAATATTCTCATCAATACAGgtaatatttc ... ttgtgcgcagGATTTGGATACTGAAGTCATAGTTGCAACAGCAAGAACTCCTGATGCTACA
EST: gi|29619071|gb|CB624083.1|CB624083
EST:     ATGTTAATGAATTTGCAAAGGACTTGGAAAAAATATTCTCATCAATACAG                         GATTTGGATACTGAAGTCATAGTTGCAACAGCAAGAACTCCTGATGCTACA
genomic: ATGTTAATGAATTTGCAAAGGACTTGGAAAAAATATTCTCATCAATACAGgtaatatttc ... ttgtgcgcagGATTTGGATACTGAAGTCATAGTTGCAACAGCAAGAACTCCTGATGCTACA
EST: gi|88530343|gb|CI458730.1|CI458730
EST:     ATATTGTCATCGATACAG                         GATGGGGATACTGGAAGTCATAGTTGCAACAGCAAGAACTCCTGATGCTAC
genomic: ATATTCTCATCAATACAGgtaatatttc ... ttgtgcgcagGATTTGGATACT-GAAGTCATAGTTGCAACAGCAAGAACTCCTGATGCTAC
EST: gi|29615292|gb|CB620304.1|CB620304
EST:     ATGTTAATGAATTTGCAAAGGACTTGGAAAAAATATTCTCATCAATACAG                         GATTTGGATACTGAAGTCATAGTTGCAACAGCAAGAACTCCTGATGCTACA
genomic: ATGTTAATGAATTTGCAAAGGACTTGGAAAAAATATTCTCATCAATACAGgtaatatttc ... ttgtgcgcagGATTTGGATACTGAAGTCATAGTTGCAACAGCAAGAACTCCTGATGCTACA
EST: gi|86254363|gb|CI059090.1|CI059090
EST:     ATGTTAATGAATTTGCAAAGGACTTGGAAAAAATATTCTCATCAATACAG                         GATTTGGATACTGAAGTCATAGTTGCAACAGCAAGAACTCCTGATGCTACA
genomic: ATGTTAATGAATTTGCAAAGGACTTGGAAAAAATATTCTCATCAATACAGgtaatatttc ... ttgtgcgcagGATTTGGATACTGAAGTCATAGTTGCAACAGCAAGAACTCCTGATGCTACA
EST: gi|88998076|gb|CI037961.1|CI037961
EST:     TGTTAATGAATTTTGCAAAGGACTTGGAAAAAATATTCTCATCAATACAG                         GATTTGGATACTGAAGTCATAGTTGCAACAGCAAGAACTCCTGATGCTACA
genomic: TGTTAATGAA-TTTGCAAAGGACTTGGAAAAAATATTCTCATCAATACAGgtaatatttc ... ttgtgcgcagGATTTGGATACTGAAGTCATAGTTGCAACAGCAAGAACTCCTGATGCTACA
EST: gi|33796723|gb|CF324229.1|CF324229
EST:     ATGTTAATGAATTTGCAAAGGACTTGGAAAAAATATTCTCATCAATACAG                         GATTTGGATACTGAAGTCATAGTTGCAACAGCAAGAACTCCTGATGCTACA
genomic: ATGTTAATGAATTTGCAAAGGACTTGGAAAAAATATTCTCATCAATACAGgtaatatttc ... ttgtgcgcagGATTTGGATACTGAAGTCATAGTTGCAACAGCAAGAACTCCTGATGCTACA
EST: gi|29615297|gb|CB620309.1|CB620309
EST:     ATGTTAATGAATTTGCAAAGGACTTGGAAAAAATATTCTCATCAATACAG                         GATTTGGATACTGAAGTCATAGTTGCAACAGCAAGAACTCCTGATGCTACA
genomic: ATGTTAATGAATTTGCAAAGGACTTGGAAAAAATATTCTCATCAATACAGgtaatatttc ... ttgtgcgcagGATTTGGATACTGAAGTCATAGTTGCAACAGCAAGAACTCCTGATGCTACA
EST: gi|29615223|gb|CB620236.1|CB620236
EST:     ATGTTAATGAATTTGCAAAGGACTTGGAAAAAATATTCTCATCAATACAG                         GATTTGGATACTGAAGTCATAGTTGCAACAGCAAGAACTCCTGATGCTACA
genomic: ATGTTAATGAATTTGCAAAGGACTTGGAAAAAATATTCTCATCAATACAGgtaatatttc ... ttgtgcgcagGATTTGGATACTGAAGTCATAGTTGCAACAGCAAGAACTCCTGATGCTACA
EST: gi|86493802|gb|CI136435.1|CI136435
EST:     ATGTTAATGAATTTGCAAAGGACTTGGAAAAAATATTCTCATCAATACAG                         GATTTGGATACTGAAGTCATAGTTGCAACAGCAAGAACTCCTGATGCTACA
genomic: ATGTTAATGAATTTGCAAAGGACTTGGAAAAAATATTCTCATCAATACAGgtaatatttc ... ttgtgcgcagGATTTGGATACTGAAGTCATAGTTGCAACAGCAAGAACTCCTGATGCTACA
EST: gi|113931013|gb|DQ884108.1|DQ884108
EST:     AATTTGCAAAGGACTTGGAAAAAATATTCTCATCAATACAG                         GATTTGGATACTGAAGTCATAGTTGCAACAGCAAGAACTCCTGATGCTACA
genomic: AATTTGCAAAGGACTTGGAAAAAATATTCTCATCAATACAGgtaatatttc ... ttgtgcgcagGATTTGGATACTGAAGTCATAGTTGCAACAGCAAGAACTCCTGATGCTACA
EST: gi|88964216|gb|CI045409.1|CI045409
EST:     ATGTTAATGAATTTGCAAAGGACTTGGAAAAAATATTCTCATCAATACAG                         GATTTGGATACTGAAGTCATAGTTGCAACAGCAAGAACTCCTGATGCTACA
genomic: ATGTTAATGAATTTGCAAAGGACTTGGAAAAAATATTCTCATCAATACAGgtaatatttc ... ttgtgcgcagGATTTGGATACTGAAGTCATAGTTGCAACAGCAAGAACTCCTGATGCTACA

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), 61 (downstream exon)
Score: 27

TGCTATGGCATCAGCCCTTTCTGAAATGGGTGCTACAGGGAATGATATAAATGTTAATGAATTTGCAAAGGACTTGGAAAAAATATTCTCATCAATACAGgtaatatttc ... ttgtgcgcagGATTTGGATACTGAAGTCATAGTTGCAACAGCAAGAACTCCTGATGCTACAGCAGTATCGGCTAATGTTGTCGTTGACGAGAGACAGATGAATGCATTGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttttaccacttatctcgtggttaattttcaattgcattctcatttgtgcgcagGATTTGGATACTGAAGTCATAGTTGCAACAGCAAGAACTCCTGATGCTACAGCAGTATCGGCTAATGTTGTCGTTGACGAGAGACAGATGAATGCATTGT
                    ggttaat  putative branch site (score: 27)
                                      ttctcattt  putative PPT
                      ttaattttcaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtggctactggctagtcaaatttggatatcgttctttagttagtgttttaccacttatctcgtggttaattttcaattgcattctcatttgtgcgcagGATTTGGATACTGAAGTCATAGTTGCAACAGCAAGAACTCCTGATGCTACAGCAGTATCGGCTAATGTTGTCGTTGACGAGAGACAGATGAATGCATTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG