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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatgctatctacacttgaacaagacaagtgaattttttttttttataaacttttgacagGTCGAGGCAGCATTATCGGTTAGCCCGATGGTGGACAGCATCATGGTGCATGCTGATCCTTTCCACAGCTACTGCGTTGCGCTGGTTGTACCATCGCAGA

Basic information

species Selaginella moellendorffii
transcript EFJ27012
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ27012 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: LOC_Os12g07110.2 (Oryza sativa), 3'ss of exon 9
gtatgatgctatctacacttgaacaagacaagtgaattttttttttttataaacttttg-------acagGTCGAGGCAGCATTATCGGTTAGCCCGATGGTGGACAGCATCATGGTGCATGCTGATCCTTTCCACAGCTACTGCGTTGCGCTGGTTGTACCATCGCAGA
||       ||   |   |      |||| |||   | ||     ||  |||    |||       |||||| ||||| ||  |    || |||||    ||||| | ||||||| | |||||||||||||||||||| ||||| ||||| || || ||| |  | || |
gt-cagcaatagtcatgttctgttcagactagtagttgttagcccttcttaactgattggaccatcacagGTGGAGGCTGCTCTGATTGTGAGCCCATATGTGGAGAACATCATGATCCATGCTGATCCTTTCCACAGTTACTGTGTTGCACTTGTGGTAGCTGCACACA

upper sequence: EFJ27012 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: LOC_Os11g06880.1 (Oryza sativa), 3'ss of exon 5
-----gtatgatgctatctacacttgaacaag-acaagtgaattttttttttttataaacttttg----acagGTCGAGGCAGCATTATCGGTTAGCCCGATGGTGGACAGCATCATGGTGCATGCTGATCCTTTCCACAGCTACTGCGTTGCGCTGGTTGTACCATCGCAGA
      || | | |  | | ||    ||  ||    ||| |  | || |  | ||   | | |      |||||| ||||| || ||    ||  ||||    || |||| ||||||| | |||||||| || ||||||| |||||||||||| || ||||||    | || |
gtaagctaagcttccttttccagccaaattagcggcagtcagctattgtaatctaactattataaaaccacagGTGGAGGCTGCTTTGAGTGTGTGCCCATATGTTGACAACATCATGATCCATGCTGACCCCTTCCACAACTACTGCGTTGCACTTGTTGTAGTTGCACACA
















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|169099834|gb|FE500839.1|FE500839
EST:     AGAAGGACATTGTTAAGCTTCAACATGGCGAATACGTATCGCTGGGCAAG                         GTCGAGGCAGCATTATCGGTTAGCCCGATGGTGGACAGCATCATGGTGCAT
genomic: AGAAGGACATTGTTAAGCTTCAACATGGCGAATACGTATCGCTGGGCAAGgtatgatgct ... cttttgacagGTCGAGGCAGCATTATCGGTTAGCCCGATGGTGGACAGCATCATGGTGCAT
EST: gi|169020952|gb|FE429339.1|FE429339
EST:     AGAAGGACATTGTTAAGCTTCAACATGGCGAATACGTATCGCTGGGCAAG                         GTCGAGGCAGCATTATCGGTTAGCCCGATGGTGGACAGCATCATGGTGCAT
genomic: AGAAGGACATTGTTAAGCTTCAACATGGCGAATACGTATCGCTGGGCAAGgtatgatgct ... cttttgacagGTCGAGGCAGCATTATCGGTTAGCCCGATGGTGGACAGCATCATGGTGCAT
EST: gi|169114439|gb|FE516312.1|FE516312
EST:     AGAAGGACATTGTTAAGCTTCAACATGGCGAATACGTATCGCTGGGCAAG                         GTCGAGGCAGCATTATCGGTTAGCCCGATGGTGGACAGCATCATGGTGCAT
genomic: AGAAGGACATTGTTAAGCTTCAACATGGCGAATACGTATCGCTGGGCAAGgtatgatgct ... cttttgacagGTCGAGGCAGCATTATCGGTTAGCCCGATGGTGGACAGCATCATGGTGCAT
EST: gi|169092854|gb|FE494979.1|FE494979
EST:     AGAAGGACATTGTTAAGCTTCAACATGGCGAATACGTATCGCTGGGCAAG                         GTCGAGGCAGCATTATCGGTTAGCCCGATGGTGGACAGCATCATGGTGCAT
genomic: AGAAGGACATTGTTAAGCTTCAACATGGCGAATACGTATCGCTGGGCAAGgtatgatgct ... cttttgacagGTCGAGGCAGCATTATCGGTTAGCCCGATGGTGGACAGCATCATGGTGCAT
EST: gi|169114438|gb|FE516311.1|FE516311
EST:     AGAAGGACATTGTTAAGCTTCAACATGGCGAATACGTATCGCTGGGCAAG                         GTCGAGGCAGCATTATCGGTTAGCCCGATGGTGGACAGCATCATGGTGCAT
genomic: AGAAGGACATTGTTAAGCTTCAACATGGCGAATACGTATCGCTGGGCAAGgtatgatgct ... cttttgacagGTCGAGGCAGCATTATCGGTTAGCCCGATGGTGGACAGCATCATGGTGCAT
EST: gi|169020906|gb|FE431984.1|FE431984
EST:     AGAAGGACATTGTTAAGCTTCAACATGGCGAATACGTATCGCTGGGCAAG                         GTCGAGGCAGCATTATCGGTTAGCCCGATGGTGGACAGCATCATGGTGCAT
genomic: AGAAGGACATTGTTAAGCTTCAACATGGCGAATACGTATCGCTGGGCAAGgtatgatgct ... cttttgacagGTCGAGGCAGCATTATCGGTTAGCCCGATGGTGGACAGCATCATGGTGCAT
EST: gi|169053814|gb|FE462894.1|FE462894
EST:     AGAAGGACATTGTTAAGCTTCAACATGGCGAATACGTATCGCTGGGCAAG                         GTCGAGGCAGCATTATCGGTTAGCCCGATGGTGGACAGCATCATGGTGCAT
genomic: AGAAGGACATTGTTAAGCTTCAACATGGCGAATACGTATCGCTGGGCAAGgtatgatgct ... cttttgacagGTCGAGGCAGCATTATCGGTTAGCCCGATGGTGGACAGCATCATGGTGCAT
EST: gi|169068347|gb|FE479171.1|FE479171
EST:     AGAAGGACATTGTTAAGCTTCAACATGGCGAATACGTATCGCTGGGCAAG                         GTCGAGGCAGCATTATCGGTTAGCCCGATGGTGGACAGCATCATGGTGCAT
genomic: AGAAGGACATTGTTAAGCTTCAACATGGCGAATACGTATCGCTGGGCAAGgtatgatgct ... cttttgacagGTCGAGGCAGCATTATCGGTTAGCCCGATGGTGGACAGCATCATGGTGCAT
EST: gi|169071984|gb|FE478193.1|FE478193
EST:     AGAAGGACATTGTTAAGCTTCAACATGGCGAATACGTATCGCTGGGCAAG                         GTCGAGGCAGCATTATCGGGTAGCCCGATGGTGGACAGCATCATGGTGCAT
genomic: AGAAGGACATTGTTAAGCTTCAACATGGCGAATACGTATCGCTGGGCAAGgtatgatgct ... cttttgacagGTCGAGGCAGCATTATCGGTTAGCCCGATGGTGGACAGCATCATGGTGCAT
EST: gi|169092855|gb|FE494980.1|FE494980
EST:     AGAAGGACATTGTTAAGCTTCAACATGGCGAATACGTATCGCTGGGCAAG                         GTCGAGGCAGCATTATCGGTTAGCCCGATGGTGGACAGCATCATGGTGCAT
genomic: AGAAGGACATTGTTAAGCTTCAACATGGCGAATACGTATCGCTGGGCAAGgtatgatgct ... cttttgacagGTCGAGGCAGCATTATCGGTTAGCCCGATGGTGGACAGCATCATGGTGCAT
EST: gi|169071983|gb|FE478192.1|FE478192
EST:     AGAAGGACATTGTTAAGCTTCAACATGGCGAATACGTATCGCTGGGCAAG                         GTCGAGGCAGCATTATCGGTTAGCCCGATGGTGGACAGCATCATGGTGCAT
genomic: AGAAGGACATTGTTAAGCTTCAACATGGCGAATACGTATCGCTGGGCAAGgtatgatgct ... cttttgacagGTCGAGGCAGCATTATCGGTTAGCCCGATGGTGGACAGCATCATGGTGCAT

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: 33 (upstream exon), 35 (downstream exon)
Score: 38

TGACATTGGACAGTTCCATCCCGATGGTTGCCTGGAAATTGTAGACCGGAAGAAGGACATTGTTAAGCTTCAACATGGCGAATACGTATCGCTGGGCAAGgtatgatgct ... cttttgacagGTCGAGGCAGCATTATCGGTTAGCCCGATGGTGGACAGCATCATGGTGCATGCTGATCCTTTCCACAGCTACTGCGTTGCGCTGGTTGTACCATCGCAGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatctacacttgaacaagacaagtgaattttttttttttataaacttttgacagGTCGAGGCAGCATTATCGGTTAGCCCGATGGTGGACAGCATCATGGTGCATGCTGATCCTTTCCACAGCTACTGCGTTGCGCTGGTTGTACCATCGCAGA
                                             ctttt  CT-rich tract
                aagacaagtgaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgatgctatctacacttgaacaagacaagtgaattttttttttttataaacttttgacagGTCGAGGCAGCATTATCGGTTAGCCCGATGGTGGACAGCATCATGGTGCATGCTGATCCTTTCCACAGCTACTGCGTTGCGCTGGTTGTACCATCGCAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT