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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATTTTGGATGCGCTGTTTCCTTCCGTGCTGGGGGGAACGTGTGCTATTCCGGGAGCATTTGGCTGTGGAAAGACCGTTATTAGTCAGGCGCTTTCGAAGgtatttggagttcttttgtaatgcgtgactaactttgtcatgaaacag

Basic information

species Selaginella moellendorffii
transcript EFJ30330
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ30330 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: LOC_Os06g45120.1 (Oryza sativa), 5'ss of exon 10
CATTTTGGATGCGCTGTTTCCTTCCGTGCTGGGGGGAACGTGTGCTATTCCGGGAGCATTTGGCTGTGGAAAGACCGTTATTAGTCAGGCGCTTTCGAAGgtatttgga--gttcttttgtaatgcgtgac---taactttgtcatgaaacag---------------------------------------------------------
  |  | ||||| || ||||| || || || || ||||| ||||||||||| ||||||||||| |||||||| || || ||||||||||| ||||| |||||||||  |   ||| | | || |   | ||   || | ||| |      ||                                                          
TGTACTTGATGCACTATTTCCCTCAGTTCTTGGAGGAACTTGTGCTATTCCTGGAGCATTTGGTTGTGGAAAAACTGTCATTAGTCAGGCACTTTCAAAGgtattttcactattcctctctatttgataactgctagcattgcccatgggcattagccttttaaaatgactgaattctgtgcctttcctgactgaaaatatcttatgcag

upper sequence: EFJ30330 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: LOC_Os02g07870.1 (Oryza sativa), 5'ss of exon 10
CATTTTGGATGCGCTGTTTCCTTCCGTGCTGGGGGGAACGTGTGCTATTCCGGGAGCATTTGGCTGTGGAAAGACCGTTATTAGTCAGGCGCTTTCGAAGgtatttggagttcttttgtaatgcgtgacta---actttgtcatgaaacag-----------------------------------------------------------------
  |  | |||||  |||| || || || || || ||||| ||||| ||||| ||||| ||||| ||||||||||| || ||||||||||| ||||| |||||  |     || || | |    | |  | |   | | | |   |||||                                                                   
TGTACTTGATGCATTGTTCCCCTCAGTTCTTGGAGGAACATGTGCCATTCCTGGAGCTTTTGGTTGTGGAAAGACTGTCATTAGTCAGGCACTTTCCAAGgtgatcactatttttctattcctcattgccatgtagtatctatagaaactatactctctttttgttgccttgatcacatctttgtactgagatgaatagcctctcaaactctgcag

upper sequence: EFJ30330 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: GRMZM2G421857_T03 (Zea mays), 5'ss of exon 10
CATTTTGGATGCGCTGTTTCCTTCCGTGCTGGGGGGAACGTGTGCTATTCCGGGAGCATTTGGCTGTGGAAAGACCGTTATTAGTCAGGCGCTTTCGAAGgtatttggagttc---ttttgtaatgcgtgactaactttgtcatgaaacag----------------------------------------------------------------
  |  ||||||| || || || || || ||||| || || ||||||||||| ||||||||||||||||| || || || ||||||||||| ||||| |||||  ||     ||    |||   |  | |      | || |  || | | |                                                                
TGTACTGGATGCACTATTCCCCTCGGTTCTGGGAGGCACTTGTGCTATTCCAGGAGCATTTGGCTGTGGTAAAACTGTCATTAGTCAGGCACTTTCCAAGgtgattttccctcaccctttactactcctactcccccttctgttgtagctgtacatattttttcttcattgtcttgatgatatcatctttaaactttgcctaatgttatctgcag

upper sequence: EFJ30330 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: GRMZM2G128877_T03 (Zea mays), 5'ss of exon 7
CATTTTGGATGCGCTGTTTCCTTCCGTGCTGGGGGGAACGTGTGCTATTCCGGGAGCATTTGGCTGTGGAAAGACCGTTATTAGTCAGGCGCTTTCGAAGgt-atttggagttcttttgtaatgc-gtgactaactttgtcatgaaacag-----------------------------------------------------------
  |  ||||||| || || || || || ||||| || || ||||||||||| || |||||||| ||||| || || || ||||||||||| ||||| ||||| ||||    |     | || | | |   |  |  ||||      |||                                                            
TGTACTGGATGCACTATTCCCCTCAGTTCTGGGAGGCACTTGTGCTATTCCAGGGGCATTTGGTTGTGGTAAAACTGTCATTAGTCAGGCACTTTCCAAGgtgatttctcctcaccctttactactgctccatatgttgtagctgtacatattttttcttttttattgtcctgatggtctcatctagcttcccctaatgttatctgcag

upper sequence: EFJ30330 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: AT1G78900.2 (Arabidopsis thaliana), 5'ss of exon 10
CATTTTGGATGCGCTGTTTCCTTCCGTGCTGGGGGGAACGTGTGCTATTCCGGGAGCATTTGGCTGTGGAAAGACCGTTATTAGTCAGGCGCTTTCGAAGgtatttggagttcttttgtaatgcgtgactaactttgtcatgaaacag--------------------------------------
  || | ||||| || || ||||| || || || ||||| ||||| ||||| || || ||||||||||| || || ||||| |||||||| ||||| ||||||  | | |    | | |  |   ||    | ||  | |    | ||                                      
TGTTCTTGATGCCCTTTTCCCTTCTGTTCTTGGTGGAACCTGTGCCATTCCTGGTGCTTTTGGCTGTGGGAAAACTGTTATCAGTCAGGCACTTTCCAAGgtaccttgtgacactctctggttt-tgttccatttaattactggatagattgaatttccaaagctaactttttcttatttacatag

upper sequence: EFJ30330 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: PP1S44_102V6.1 (Physcomitrella patens), 5'ss of exon 10
CATTTTGGATGCGCTGTTTCCTTCCGTGCTGGGGGGAACGTGTGCTATTCCGGGAGCATTTGGCTGTGGAAAGACCGTTATTAGTCAGGCGCTTTCGAAGgtatttggagttcttttgtaatgcgtgactaactttgtcatgaaacag--------------------------------------------------------------------------------------------------------------------
 ||  ||||||| || || ||||| || || || || || || || ||||| || |||||||| ||||||||||| || |||||||| ||||| || |||||| ||||     | |  |      |  | || ||  |   | | ||                                                                                                                     
TATACTGGATGCTCTATTCCCTTCTGTTCTTGGAGGTACTTGCGCCATTCCTGGTGCATTTGGATGTGGAAAGACTGTCATTAGTCAAGCGCTCTCTAAGgtagttggttacatctgtttggatttttcgaagttcatttcgcatcatacattttttctttttcttttctttggttgtgtatttaagctgcagaaactattgtttgaagtttgtatgaaagttctggaacgaggcttattttttgcaaatttgtttgtgtgcag

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|169055455|gb|FE465853.1|FE465853
EST:     CGGGAGCATTTGGCTGTGGAAAGACCGTTATTAGTCAGGCGCTTTCGAAG                         TTTTCGAACTCTGACGCTGTCATTTACGTGGGATGTGGCGAGCGAGGAAAC
genomic: CGGGAGCATTTGGCTGTGGAAAGACCGTTATTAGTCAGGCGCTTTCGAAGgtatttggag ... catgaaacagTTTTCGAACTCTGACGCTGTCATTTACGTGGGATGTGGCGAGCGAGGAAAC
EST: gi|169098593|gb|FE497219.1|FE497219
EST:     CGGGAGCATTTGGCTGTGGAAAGACCGTTATTAGTCAGGCGCTTTCGAAG                         TTTTCGAACTCTGACGCTGTCATTTACGTGGGATGTGGCGAGCGAGGAAAC
genomic: CGGGAGCATTTGGCTGTGGAAAGACCGTTATTAGTCAGGCGCTTTCGAAGgtatttggag ... catgaaacagTTTTCGAACTCTGACGCTGTCATTTACGTGGGATGTGGCGAGCGAGGAAAC
EST: gi|169081165|gb|FE489259.1|FE489259
EST:     CGGGAGCATTTGGCTGTGGAAAGACCGTTATTAGTCAGGCGCTTTCGAAG                         TTTTCGAACTCTGACGCTGTCATTTACGTGGGATGTGGCGAGCGAGGAAAC
genomic: CGGGAGCATTTGGCTGTGGAAAGACCGTTATTAGTCAGGCGCTTTCGAAGgtatttggag ... catgaaacagTTTTCGAACTCTGACGCTGTCATTTACGTGGGATGTGGCGAGCGAGGAAAC
EST: gi|169074666|gb|FE480896.1|FE480896
EST:     CGGGAGCATTTGGCTGTGGAAAGACCGTTATTAGTCAGGCGCTTTCGAAG                         TTTTCGAACTCTGACGCTGTCATTTACGTGGGATGTGGCGAACGAGGAAAC
genomic: CGGGAGCATTTGGCTGTGGAAAGACCGTTATTAGTCAGGCGCTTTCGAAGgtatttggag ... catgaaacagTTTTCGAACTCTGACGCTGTCATTTACGTGGGATGTGGCGAGCGAGGAAAC
EST: gi|169075918|gb|FE482837.1|FE482837
EST:     CGGGAGCATTTGGCTGTGGAAAGACCGTTATTAGTCAGGCGCTTTCGAAG                         TTTTCGAACTCTGACGCTGTCATTTACGTGGGATGTGGCGAACGAGGAAAC
genomic: CGGGAGCATTTGGCTGTGGAAAGACCGTTATTAGTCAGGCGCTTTCGAAGgtatttggag ... catgaaacagTTTTCGAACTCTGACGCTGTCATTTACGTGGGATGTGGCGAGCGAGGAAAC
EST: gi|169096021|gb|FE500012.1|FE500012
EST:     CGGGAGCATTTGGCTGTGGAAAGACCGTTATTAGTCAGGCGCTTTCGAAG                         TTTTCGAACTCTGACGCTGTCATTTACGTGGGATGTGGCGA
genomic: CGGGAGCATTTGGCTGTGGAAAGACCGTTATTAGTCAGGCGCTTTCGAAGgtatttggag ... catgaaacagTTTTCGAACTCTGACGCTGTCATTTACGTGGGATGTGGCGA
EST: gi|169067638|gb|FE475315.1|FE475315
EST:     CGGGAGCATTTGGCTGTGGAAAGACCGTTATTAGTCAGGCGCTTTCGAAG                         TTTTCGAACTCTGACGCTGTCATTTACGTGGGATGTGGCGAGCGAGGAAAC
genomic: CGGGAGCATTTGGCTGTGGAAAGACCGTTATTAGTCAGGCGCTTTCGAAGgtatttggag ... catgaaacagTTTTCGAACTCTGACGCTGTCATTTACGTGGGATGTGGCGAGCGAGGAAAC
EST: gi|169077659|gb|FE484921.1|FE484921
EST:     CGGGAGCATTTGGCTGTGGAAAGACCGTTATTAGTCAGGCGCTTTCGAAG                         TTTTCGAACTCTGACGCTGTCATTTACGTGGGATGTGGCGAACGAGGAAAC
genomic: CGGGAGCATTTGGCTGTGGAAAGACCGTTATTAGTCAGGCGCTTTCGAAGgtatttggag ... catgaaacagTTTTCGAACTCTGACGCTGTCATTTACGTGGGATGTGGCGAGCGAGGAAAC
EST: gi|169047687|gb|FE454855.1|FE454855
EST:     CGGGAGCATTTGGCTGTGGAAAGACCGTTATTAGTCAGGCGCTTTCGAAG                         TTTTCGAACTCTGACGCTGTCATTTACGTGGGATGTGGCGA
genomic: CGGGAGCATTTGGCTGTGGAAAGACCGTTATTAGTCAGGCGCTTTCGAAGgtatttggag ... catgaaacagTTTTCGAACTCTGACGCTGTCATTTACGTGGGATGTGGCGA
EST: gi|169058961|gb|FE467729.1|FE467729
EST:     CGGGAGCATTTGGCTGTGGAAAGACCGTTATTAGTCAGGCGCTTTCGAAG                         TTTTCGAACTCTGACGCTGTCATTTACGTGGGATGTGGCGAACGAGGAAAC
genomic: CGGGAGCATTTGGCTGTGGAAAGACCGTTATTAGTCAGGCGCTTTCGAAGgtatttggag ... catgaaacagTTTTCGAACTCTGACGCTGTCATTTACGTGGGATGTGGCGAGCGAGGAAAC
EST: gi|169045569|gb|FE452530.1|FE452530
EST:     CGGGAGCATTTGGCTGTGGAAAGACCGTTATTAGTCAGGCGCTTTCGAAG                         TTTTCGAACTCTGACGCTGTCATTTACGTGGGATGTGGCGAGCGAGGAAAC
genomic: CGGGAGCATTTGGCTGTGGAAAGACCGTTATTAGTCAGGCGCTTTCGAAGgtatttggag ... catgaaacagTTTTCGAACTCTGACGCTGTCATTTACGTGGGATGTGGCGAGCGAGGAAAC
EST: gi|169094897|gb|FE491631.1|FE491631
EST:     CGGGAGCATTTGGCTGTGGAAAGACTGTTATTAGTCAGGCGCTTTCGAAG                         TTTTCGAACTCTGACGCTGTCATTTACGTGGGATGTGGCGAACGAGGAAAC
genomic: CGGGAGCATTTGGCTGTGGAAAGACCGTTATTAGTCAGGCGCTTTCGAAGgtatttggag ... catgaaacagTTTTCGAACTCTGACGCTGTCATTTACGTGGGATGTGGCGAGCGAGGAAAC
EST: gi|169026426|gb|FE435779.1|FE435779
EST:     CGGGAGCATTTGGCTGTGGAAAGACCGTTATTAGTCAGGCGCTTTCGAAG                         TTTTCGAACTCTGACGCTGTCATTTACGTGGGATGTGGCGAGCGAGGAAAC
genomic: CGGGAGCATTTGGCTGTGGAAAGACCGTTATTAGTCAGGCGCTTTCGAAGgtatttggag ... catgaaacagTTTTCGAACTCTGACGCTGTCATTTACGTGGGATGTGGCGAGCGAGGAAAC

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: 22

CATTTTGGATGCGCTGTTTCCTTCCGTGCTGGGGGGAACGTGTGCTATTCCGGGAGCATTTGGCTGTGGAAAGACCGTTATTAGTCAGGCGCTTTCGAAGgtatttggag ... catgaaacagTTTTCGAACTCTGACGCTGTCATTTACGTGGGATGTGGCGAGCGAGGAAACGAAATGGCTGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATTTTGGATGCGCTGTTTCCTTCCGTGCTGGGGGGAACGTGTGCTATTCCGGGAGCATTTGGCTGTGGAAAGACCGTTATTAGTCAGGCGCTTTCGAAGgtatttggagttcttttgtaatgcgtgactaactttgtcatgaaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA