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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcggtggcgtttcctcttctttttttgcttatgctgattgtgttataacgctcgtttgcgcagGTTGCTCTCAAGTTCGAGCATAGGAGCAGCAAAGGTTGCAACTACGGGCCTCCTTACGAATGGCAGGTTTACGA

Basic information

species Selaginella moellendorffii
transcript EFJ13521
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ13521 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: LOC_Os01g54100.1 (Oryza sativa), 3'ss of exon 2
-----------------gtcggtggcgtttcctcttctttttttgcttatgctgattgtgtta------taacgctcgtttgc---gcagGTTGCTCTCAAGTTCGAGCATAGGAGCAGCAAAGGTTGCAACTACGGGCCTCCTTACGAATGGCAGGTTTACGA
                  |  ||     |     |       | | |  |  | |  ||   |      || ||  | || |    | |||| || || ||||| || ||||| | ||| ||||| |||||| | ||||||||||||||||||||||||||| |
gtatttagtgccagcctatttgtaaaactgtacttgtaaccgtggatggtattaacggttgaaaataaatatcgtgctttcgaatggtagGTGGCGCTAAAGTTTGAACATAGAACCAGTAAAGGATGCAACCATGGGCCTCCTTACGAATGGCAGGTTTACAA

upper sequence: EFJ13521 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 3
-------------------------------gtcgg-tggcgt-ttcctcttctttttttgc---ttatgctgattgtg-ttataacgctcgtttgcgcagGTTGCTCTCAAGTTCGAGCATAGGAGCAGCAAAGGTTGCAACTACGGGCCTCCTTACGAATGGCAGGTTTACGA
                               || |  ||  || ||  |   | | |  ||     ||   || || |  ||||        | |   |||||||| || ||||| ||||| || | |||||||||||||||||| ||||||||||| || ||||| || |||  
gtattattaaggattccagtttctcattaaggttgaatgaagtattaatgaacctatactgtatgatacattgttttttcttattttaactttgtttacagGTTGCACTTAAGTTTGAGCACAGAAACAGCAAAGGTTGCAACTATGGGCCTCCTTATGAGTGGCAAGTATACAG

upper sequence: EFJ13521 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 2
-----------------------------gtcggtggcgtttcctcttctttttttgcttatgctgattgtgttataacgctcgtttg--cgcagGTTGCTCTCAAGTTCGAGCATAGGAGCAGCAAAGGTTGCAACTACGGGCCTCCTTACGAATGGCAGGTTTACGA
                                |   | ||||  |       | |||  | ||    |  ||   ||  ||||  |||   | |||| ||  | || || |||||||| ||||||||||| ||||| || || ||||| || || |||||||||||| |
gtatggtgttagcgtgttgatatttggttaaagagtgtgtttgattgatgcatattggatttgtcattattgacgtattgctctattgattgtagGTAGCCTTAAAATTTGAGCATAGAAGCAGCAAAGGGTGCAATTATGGACCTCCATATGAGTGGCAGGTTTACAA

upper sequence: EFJ13521 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: AT3G13670.1 (Arabidopsis thaliana), 3'ss of exon 2
---------------------------------------gtcggtg-gcgtttcctcttctttttttgcttatgctgattgtgttataa-----cgctcgtttgcgcagGTTGCTCTCAAGTTCGAGCATAGGAGCAGCAAAGGTTGCAACTACGGGCCTCCTTACGAATGGCAGGTTTACGA
                                       |||        | || |  | ||   ||  ||||||| |  ||||   |      | ||   ||    |||||||||| ||||| ||||||||||||||||| ||||||||||| || |||||  | || |||||||||||| |
gtaatataactcagtctgcgtttactgctgtggaggattgtcaccataaatatcattctattagcttagttatgcttacagtgtctcacatcttcactttcttatatagGTTGCTCTAAAGTTTGAGCATAGGAGCAGCAAGGGTTGCAACTATGGTCCTCCACATGAGTGGCAGGTTTACAA

upper sequence: EFJ13521 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S131_16V6.1 (Physcomitrella patens), 3'ss of exon 2
------------------------------------------------------------------gtcggtggcgtt----tcctcttctttttttgcttatgctgattgtgtt---ataacgctcgtttgcgcagGTTGCTCTCAAGTTCGAGCATAGGAGCAGCAAAGGTTGCAACTACGGGCCTCCTTACGAATGGCAGGTTTACGA
                                                                  |    | || |     || | |  |||||    | ||     |||| ||   ||    |||||||| |||||||||  | |||||||||||| |||| || || || ||||| || || |||||||| || ||||||||||||  
gtattcaatttcttacaatttgttctgctctacttctttcgcagcagcatgtttggaagatactctgcatattgcatcgaggtcttgtgatttttaatgtaataagttttgtattcatattgaactcgtttgtgcagGTTGCGTTGAAGTTCGAGCATCGGAGTAGTAAGGGCTGCAATTATGGTCCTCCTTATGAGTGGCAGGTTTACAC

upper sequence: EFJ13521 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 2
---------------------------------------------------------------------gtcggtggcgtttcctcttctttttttgcttatgctgattgtgttataacgctcgtttgcgcagGTTGCTCTCAAGTTCGAGCATAGGAGCAGCAAAGGTTGCAACTACGGGCCTCCTTACGAATGGCAGGTTTACGA
                                                                      |  | |    |   |  | | | | ||    | |  | || ||  |     ||||   ||||||| ||| | ||||| || ||| |||||||||| |||||||| || || ||||||||||| ||||| |||||| |
gtactctttactctaattcgttgaggtccggtcgtgtcgtattccgtatagtgccgagggttgtgattatttagcgagtatctttgctttgtgtctggaagtacaaactgagtcttgtt-ttcgtgctcgcagGTAGCTTTAAAGTTTGAACATCGGAGCAGCAAGGGTTGCAATTATGGTCCTCCTTACGAGTGGCAAGTTTACAA

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|169060166|gb|FE468152.1|FE468152
EST:     AAGTTGGGGCCTGGTGATCTAACCGGTCCAAATGCTGTAGAG                         GTTGCTCTCAAGTTCGAGCATAGGAGCAGCAAAGGTTGCAACTATGGGCCT
genomic: AAGTTGGGGCCTGGTGATCTAACCGGTCCAAATGCTGTAGAGgtcggtggcg ... gtttgcgcagGTTGCTCTCAAGTTCGAGCATAGGAGCAGCAAAGGTTGCAACTACGGGCCT
EST: gi|169070416|gb|FE476781.1|FE476781
EST:     TGGGTCGGAAGTTGGGGCCTGGTGATCTAACCGGTCCAAATGCTGTAGAG                         GTTGCTCTCAAGTTCGAGCATAGGAGCAGCAAAGGTTGCAACTATGGGCCT
genomic: TGGGTCGGAAGTTGGGGCCTGGTGATCTAACCGGTCCAAATGCTGTAGAGgtcggtggcg ... gtttgcgcagGTTGCTCTCAAGTTCGAGCATAGGAGCAGCAAAGGTTGCAACTACGGGCCT
EST: gi|169071027|gb|FE476352.1|FE476352
EST:     TGGGTCGGAAGTTGGGGCCTGGTGATCTAACCGGTCCAAATGCTGTAGAG                         GTTGCTCTCAAGTTCGAGCATAGGAGCAGCAAAGGTTGCAACTATGGGCCT
genomic: TGGGTCGGAAGTTGGGGCCTGGTGATCTAACCGGTCCAAATGCTGTAGAGgtcggtggcg ... gtttgcgcagGTTGCTCTCAAGTTCGAGCATAGGAGCAGCAAAGGTTGCAACTACGGGCCT
EST: gi|169055838|gb|FE465079.1|FE465079
EST:     TGGGTCGGAAGTTGGGGCCTGGTGATCTAACCGGTCCAAATGCTGTAGAG                         GTTGCTCTCAAGTTCGAGCATAGGAGCAGCAAAGGTTGCAACTATGGGCCT
genomic: TGGGTCGGAAGTTGGGGCCTGGTGATCTAACCGGTCCAAATGCTGTAGAGgtcggtggcg ... gtttgcgcagGTTGCTCTCAAGTTCGAGCATAGGAGCAGCAAAGGTTGCAACTACGGGCCT
EST: gi|169034150|gb|FE444275.1|FE444275
EST:     TGGGTCGGAAGTTGGGGCCTGGTGATCTAACCGGTCCAAATGCTGTAGAG                         GTTGCTCTCAAGTTCGAGCATAGGAGCAGCAAAGGTTGCAACTATGGGCCT
genomic: TGGGTCGGAAGTTGGGGCCTGGTGATCTAACCGGTCCAAATGCTGTAGAGgtcggtggcg ... gtttgcgcagGTTGCTCTCAAGTTCGAGCATAGGAGCAGCAAAGGTTGCAACTACGGGCCT

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), 34 (downstream exon)
Score: 56

CTATAGGACGGATAGGAAGCTGGGGAAAGGAGGCTTTGGTCAAGTTTACGTGGGTCGGAAGTTGGGGCCTGGTGATCTAACCGGTCCAAATGCTGTAGAGgtcggtggcg ... gtttgcgcagGTTGCTCTCAAGTTCGAGCATAGGAGCAGCAAAGGTTGCAACTACGGGCCTCCTTACGAATGGCAGGTTTACGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttcctcttctttttttgcttatgctgattgtgttataacgctcgtttgcgcagGTTGCTCTCAAGTTCGAGCATAGGAGCAGCAAAGGTTGCAACTACGGGCCTCCTTACGAATGGCAGGTTTACGA
                                  ttataac  putative branch site (score: 56)
                                          ctcgttt  CT-rich tract
        ttcttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcggtggcgtttcctcttctttttttgcttatgctgattgtgttataacgctcgtttgcgcagGTTGCTCTCAAGTTCGAGCATAGGAGCAGCAAAGGTTGCAACTACGGGCCTCCTTACGAATGGCAGGTTTACGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG