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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgacgatcattctccttttttgtgcctgtgatctctcatctcttttttctccattgtctccagGTGGATTGGATTGGCCAGAAAAATCAAATTGATGCTG

Basic information

species Selaginella moellendorffii
transcript EFJ06085
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ06085 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os05g01970.1 (Oryza sativa), 3'ss of exon 2
-----------------gtatgacgatcattctcctttt----ttgtgcc------tgtgatctctcatctct-tttttctccattgtctccagGTGGATTGGATTGGCCAGAAAAATCAAATTGATGCTG
                 || | ||   |||| ||  | |    |||||||      ||  ||   |  | |||  | ||  | | | | |  |||||||||||||||||||||  |||||||| |||||||
gtgattaaatgtattttgtgtcactcacattttctgtatcaacttgtgccttcatttgaaattgatgttttctgctatttgctactctttgaagGTGGATTGGATTGGCCAGAGGAATCAAATAGATGCTG

upper sequence: EFJ06085 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G047219_T03 (Zea mays), 3'ss of exon 2
------------------------------------------------------------------------gtatgacgatcattctcct-tttttgtgcctgtgatctctcatctcttttttctccattgtctccagGTGGATTGGATTGGCCAGAAAAATCAAATTGATGCTG
                                                                        |||||  |   |||| |   ||| | ||    |||| |   || |  ||| ||||   ||| || ||||||||||||||||||| || ||||||||||||||||
gtgcctgaaattattcgatatacagtgctcttacagtatttatctaaaatacgtggtgctcttacggtagctgtatg-tgtcaattcccaaatttgtttggaattgatgttctatgttgtttgtctc---tgtttcaagGTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTG
















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|169100256|gb|FE501911.1|FE501911
EST:     CCGGTGGAAGGCCCGAGTTCTACTTCGAAGAGGGAGGCACGCCGGAAGAG                         GTGGATTGGATTGGCCAGAAAAATCAAATTGATGCTG
genomic: CCGGTGGAAGGCCCGAGTTCTACTTCGAAGAGGGAGGCACGCCGGAAGAGgtatgacgat ... ttgtctccagGTGGATTGGATTGGCCAGAAAAATCAAATTGATGCTG
EST: gi|169053684|gb|FE461503.1|FE461503
EST:     CCGGTGGAAGGCCCGAGTTCTACTTCGAAGAGGGAGGCACGCCGGAAGAG                         GTGGATTGGATTGGCCAGAAAAATCAAATTGATGCTG
genomic: CCGGTGGAAGGCCCGAGTTCTACTTCGAAGAGGGAGGCACGCCGGAAGAGgtatgacgat ... ttgtctccagGTGGATTGGATTGGCCAGAAAAATCAAATTGATGCTG
EST: gi|169104736|gb|FE508984.1|FE508984
EST:     CCGGTGGAAGGCCCGAGTTCTACTTCGAAGAGGGAGGCACGCCGGAAGAG                         GTGGATTGGATTGGCCAGAAAAATCAAATTGATGCTG
genomic: CCGGTGGAAGGCCCGAGTTCTACTTCGAAGAGGGAGGCACGCCGGAAGAGgtatgacgat ... ttgtctccagGTGGATTGGATTGGCCAGAAAAATCAAATTGATGCTG
EST: gi|169100257|gb|FE501912.1|FE501912
EST:     CCGGTGGAAGGCCCGAGTTCTACTTCGAAGAGGGAGGCACGCCGGAAGAG                         GTGGATTGGATTGGCCAGAAAAATCAAATTGATGCTG
genomic: CCGGTGGAAGGCCCGAGTTCTACTTCGAAGAGGGAGGCACGCCGGAAGAGgtatgacgat ... ttgtctccagGTGGATTGGATTGGCCAGAAAAATCAAATTGATGCTG
EST: gi|169104735|gb|FE508983.1|FE508983
EST:     CCGGTGGAAGGCCCGAGTTCTACTTCGAAGAGGGAGGCACGCCGGAAGAG                         GTGGATTGGATTGGCCAGAAAAATCAAATTGATGCTG
genomic: CCGGTGGAAGGCCCGAGTTCTACTTCGAAGAGGGAGGCACGCCGGAAGAGgtatgacgat ... ttgtctccagGTGGATTGGATTGGCCAGAAAAATCAAATTGATGCTG
EST: gi|169053685|gb|FE461504.1|FE461504
EST:     CCGGTGGAAGGCCCGAGTTCTACTTCGAAGAGGGAGGCACGCCGGAAGAG                         GTGGATTGGATTGGCCAGAAAAATCAAATTGATGCTG
genomic: CCGGTGGAAGGCCCGAGTTCTACTTCGAAGAGGGAGGCACGCCGGAAGAGgtatgacgat ... ttgtctccagGTGGATTGGATTGGCCAGAAAAATCAAATTGATGCTG
EST: gi|169113971|gb|FE516442.1|FE516442
EST:     CCGGTGGAAGGCCCGAGTTCTACTTCGAAGAGGGAGGCACGCCGGAAGAG                         GTGGATTGGATTGGCCAGAAAAATCAAATTGATGCTG
genomic: CCGGTGGAAGGCCCGAGTTCTACTTCGAAGAGGGAGGCACGCCGGAAGAGgtatgacgat ... ttgtctccagGTGGATTGGATTGGCCAGAAAAATCAAATTGATGCTG
EST: gi|70671101|gb|DN839678.1|DN839678
EST:     CCGGTGGAAGGCCCGAGTTCTACTTCGAAGAGGGAGGCACGCCGGAAGAG                         GTGGATTGGATTGGCCAGAAAAATCAAATTGATGCTG
genomic: CCGGTGGAAGGCCCGAGTTCTACTTCGAAGAGGGAGGCACGCCGGAAGAGgtatgacgat ... ttgtctccagGTGGATTGGATTGGCCAGAAAAATCAAATTGATGCTG
EST: gi|169052926|gb|FE460641.1|FE460641
EST:     CCGGTGGAAGGCCCGAGTTCTACTTCGAAGAGGGAGGCACGCCGGAAGAG                         GTGGATTGGATTGGCCAGAAAAATCAAATTGATGCTG
genomic: CCGGTGGAAGGCCCGAGTTCTACTTCGAAGAGGGAGGCACGCCGGAAGAGgtatgacgat ... ttgtctccagGTGGATTGGATTGGCCAGAAAAATCAAATTGATGCTG
EST: gi|169106432|gb|FE507444.1|FE507444
EST:     CCGGTGGAAGGCCCGAGTTCTACTTCGAAGAGGGAGGCACGCCGGAAGAG                         GTGGATTGGATTGGCCAGAAAAATCAAATTGATGCTG
genomic: CCGGTGGAAGGCCCGAGTTCTACTTCGAAGAGGGAGGCACGCCGGAAGAGgtatgacgat ... ttgtctccagGTGGATTGGATTGGCCAGAAAAATCAAATTGATGCTG
EST: gi|70670502|gb|DN839079.1|DN839079
EST:     CCGGTGGAAGGCCCGAGTTCTACTTCGAAGAGGGAGGCACGCCGGAAGAG                         GTGGATTGGATTGGCCAGAAAAATCAAATTGATGCTG
genomic: CCGGTGGAAGGCCCGAGTTCTACTTCGAAGAGGGAGGCACGCCGGAAGAGgtatgacgat ... ttgtctccagGTGGATTGGATTGGCCAGAAAAATCAAATTGATGCTG
EST: gi|169052925|gb|FE460640.1|FE460640
EST:     CCGGTGGAAGGCCCGAGTTCTACTTCGAAGAGGGAGGCACGCCGGAAGAG                         GTGGATTGGATTGGCCAGAAAAATCAAATTGATGCTG
genomic: CCGGTGGAAGGCCCGAGTTCTACTTCGAAGAGGGAGGCACGCCGGAAGAGgtatgacgat ... ttgtctccagGTGGATTGGATTGGCCAGAAAAATCAAATTGATGCTG

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: 35 (upstream exon), 35 (downstream exon)
Score: 118

CATCCTCACCAGCGCTGTGCCGAAGATGAAGCCGGGATTCAATCCAGCGTCCGGTGGAAGGCCCGAGTTCTACTTCGAAGAGGGAGGCACGCCGGAAGAGgtatgacgat ... ttgtctccagGTGGATTGGATTGGCCAGAAAAATCAAATTGATGCTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attctccttttttgtgcctgtgatctctcatctcttttttctccattgtctccagGTGGATTGGATTGGCCAGAAAAATCAAATTGATGCTG
                       tctctcatctcttttt  CT-rich tract
       ttttttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgacgatcattctccttttttgtgcctgtgatctctcatctcttttttctccattgtctccagGTGGATTGGATTGGCCAGAAAAATCAAATTGATGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG