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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcaggctgttttaatattttagttttattgttttacatgggcgcttttatagGGAGACAATAAAGGATTTCTGGTCTGCAAAAAGAAAATGGCCACGTCCCCGGAGATGTTGTGCTGTTTCTGCCCGCCTCCATTCAAGCAGTTTTTGGAAA

Basic information

species Selaginella moellendorffii
transcript EFJ31718
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 7
lower sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 10
--------------------------------gtcaggctgttttaatattttagttttattgttttacatgggcgcttttatagGGAGACAATAAAGGATTTCTGGTCTGCAAAAAGAAAATGGCCACGTCCCCGGAGATGTTGTGCTGTTTCTGCCCGCCTCCATTCAAGCAGTTTTTGGAAA
                                  ||   |   || | |||      || |  | || | ||     || |  |||| || |  ||  | || || || ||||| ||||||||||| || || ||||||||| |  |||||||||| || ||||||||||| |||||| | ||| 
gtatattttaatatgcctattaacttcatgataccaacttcagttcagattagccaattctaatgttgcttgcttaattatgcagGGTGATACCAAGAGTTTCCTTGTTTGCAAGAAGAAAATGGCTACTTCTCCGGAGATGCTAAGCTGTTTCTGTCCACCTCCATTCAAACAGTTTCTTGAAG

upper sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 7
lower sequence: GLYMA08G21570.1 (Glycine max), 3'ss of exon 9
-----------gtcaggctgttttaatattttagtttta---ttgttttacatgggcgcttttatagGGAGACAATAAAGGATTTCTGGTCTGCAAAAAGAAAATGGCCACGTCCCCGGAGATGTTGTGCTGTTTCTGCCCGCCTCCATTCAAGCAGTTTTTGGAAA
                 || ||||| | ||    |   |   ||| | |  |       |||| |||||||| || |||||||||||||| ||||| ||||||||||  || || || ||||   | ||||| ||  | || |  || || ||||||||| | ||| 
gttggacattaaaataactcttttattcttacgttcagaaggttggtctctaacattatttttttagGGAGAAAACAAAGGATTTCTGGTTTGCAAGAAGAAAATGGGAACATCTCCTGAGACCCTATGCTGCTTTAGTCCCCTCCCTTTTAAGCAGTTTGTTGAAC

upper sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 7
lower sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 10
-----------------------------------------------------------------------gtcaggctgttttaatattttagttttattgttttacatgggcgcttttatagGGAGACAATAAAGGATTTCTGGTCTGCAAAAAGAAAATGGCCACGTCCCCGGAGATGTTGTGCTGTTTCTGCCCGCCTCCATTCAAGCAGTTTTTGGAAA
                                                                        |     | ||||  |||   | |||     || |   ||| |   | || |||| ||||||||| | ||||| || || || |||||||||||||| ||||||||| || ||||||| ||    ||  ||||||| ||||||||| | ||| 
gtatttttgtagcatcttgttttatattgattccttttttttttaacaggttttatagtgattcttgcttcttagaaatttttttttatgacaatttctcccttcttt-tggccatatctacagGGTGACAATAAAAGTTTTCTTGTTTGTAAGAAGAAAATGGCCACTTCCCCGGAGTTGATGTGCTGCTTTGTTCCTGCTCCATTTAAGCAGTTTCTTGAAG

upper sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 7
lower sequence: GLYMA04G09070.1 (Glycine max), 3'ss of exon 9
-----------------------gtcaggctgttttaatattttagttttattgtt-ttacatgggcgctt-ttatagGGAGACAATAAAGGATTTCTGGTCTGCAAAAAGAAAATGGCCACGTCCCCGGAGATGTTGTGCTGTTTCTGCCCGCCTCCATTCAAGCAGTTTTTGGAAA
                        |   |   |  |  ||  | |    |||  || |||   |     || ||| ||||||| |||||||||||||| |||||||| || || |||||||| || || || |  ||||| || || || || |  |||||   ||| ||| | ||| 
gttattattgtctcaaatagtcatttgagtactaatggtaagtcaaaaatatgattcttatgagattttttgttacagGGAGAAAATAAAGGATTTCTTGTCTGCAAGAAAAAGATGGCCACTTCTCCTGAAACTTTGTGTTGCTTGTGTCCTCAACCATTTCGGCAATTTGTTGAAT

upper sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 7
lower sequence: GLYMA06G09190.1 (Glycine max), 3'ss of exon 9
------------------------gtcag-gctgttttaatattttagttttattgttttacatgggcgcttttatagGGAGACAATAAAGGATTTCTGGTCTGCAAAAAGAAAATGGCCACGTCCCCGGAGATGTTGTGCTGTTTCTGCCCGCCTCCATTCAAGCAGTTTTTGGAAA
                         | ||  ||  ||  | ||   | | | | | || |  |       | ||| ||||||| |||||||| ||||| |||||||| || || ||||||||||| || || |  ||||| || || || || |  |||||   ||| ||| ||||| 
gttattattgtttcaaatagtcattttagtactaattgtaaatgaaaatatgactcttatgaa-actttttgttacagGGAGAAAATAAAGGGTTTCTTGTCTGCAAGAAAAAGATGGCCACGTCTCCAGAAACTTTGTGTTGCTTTTGTCCCCAACCATTTCGGCAATTTGTGGAAT

upper sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 7
lower sequence: PP1S131_16V6.1 (Physcomitrella patens), 3'ss of exon 9
---------------------------------------------------------------------------------------------------------------------------gtcaggctgttttaatatttta-gttttattgttttacatgggcgcttttatagGGAGACAATAAAGGATTTCTGGTCTGCAAAAAGAAAATGGCCACGTCCCCGGAGATGTTGTGCTGTTTCTGCCCGCCTCCATTCAAGCAGTTTTTGGAAA
                                                                                                                                    | | | ||||||   |||    ||  || ||    | |||| ||||| ||||| ||||| |||||||| || || ||||||||||| || || || || ||| |||||||||||||||||  ||| || || ||||||||||| |
gtactgattaactttgtggctagtagctaacgaggaagtgatcaatgtgaaatttttcttttcttcccacatcccacatcccactttttttgtattttgtttgttttgttttgttttgttttttctttttcctctcactatttttcatttggacgtgctatatatttggttttgtagGGCGACAACAAAGGTTTTCTGGTGTGTAAGAAGAAAATGGCAACTTCTCCCGAAATGCTGTGCTGTTTCTGCCCGGTTCCGTTTAAACAGTTTTTGGAGA

upper sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 7
lower sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 9
-------------------------------------------------------------------------gtcaggctgttttaatatt-ttagttttattgttt---tacatgggc-gcttttatagGGAGACAATAAAGGATTTCTGGTCTGCAAAAAGAAAATGGCCACGTCCCCGGAGATGTTGTGCTGTTTCTGCCCGCCTCCATTCAAGCAGTTTTTGGAAA
                                                                         | |   ||  ||    |   |  ||||   |   |   |  |||||  |  || | |||| ||||| || || ||| |||| ||||| ||||||||| | || || || || |||||||||||||| || |||| |||||||| |||||||||||| |
gtatgactctcttttgtgacttgaggtggaataactgtagttctttgtaagtgcggcattttctctgtataatgcctttcttattggccaccatctgtttctctaactagatggatgggttgggttaacagGGTGACAACAAGGGGTTTTTGGTATGCAAGAAGAAAATGTCAACTTCTCCAGAAATGTTGTGCTGTTTTTGTCCGCTTCCATTCAGGCAGTTTTTGGAGA

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|169114703|gb|FE516900.1|FE516900
EST:     ACACGCTAGTGTTTCTCCTTCGTGGTCGGCTTCCTTGGCAAGGATACCAG                         GGAGACAATAAAGGATTTCTGGTCTGCAAAAAGAAAATGGCCACGTCCCCG
genomic: ACACGCTAGTGTTTCTCCTTCGTGGTCGGCTTCCTTGGCAAGGATACCAGgtcaggctgt ... gcttttatagGGAGACAATAAAGGATTTCTGGTCTGCAAAAAGAAAATGGCCACGTCCCCG
EST: gi|169104490|gb|FE503774.1|FE503774
EST:     ACACGCTGGTGTTTCTCCTTCGTGGTCGGCTTCCTTGGCAAGGATACCAG                         GGAGACAATAAAGGATTTCTGGTCTGCAAAAAGAAAATGGCCACATCCCC
genomic: ACACGCTAGTGTTTCTCCTTCGTGGTCGGCTTCCTTGGCAAGGATACCAGgtcaggctgt ... gcttttatagGGAGACAATAAAGGATTTCTGGTCTGCAAAAAGAAAATGGCCACGTCCCC
EST: gi|169066653|gb|FE475435.1|FE475435
EST:     ACACGCTAGTGTTTCTCCTTCGTGGTCGGCTTCCTTGGCAAGGATACCAG                         GGAGACAATAAAGGATTTCTGGTCTGCAAAAAGAAAATGGCCACGTCCCCG
genomic: ACACGCTAGTGTTTCTCCTTCGTGGTCGGCTTCCTTGGCAAGGATACCAGgtcaggctgt ... gcttttatagGGAGACAATAAAGGATTTCTGGTCTGCAAAAAGAAAATGGCCACGTCCCCG
EST: gi|169094739|gb|FE491577.1|FE491577
EST:     ACACGCTAGTGTTTCTCCTTCGTGGTCGGCTTCCTTGGCAAGGATACCAG                         GGAGACAATAAAGGATTTCTGGTCTGCAAAAAGAAAATGGCCACGTCCCCG
genomic: ACACGCTAGTGTTTCTCCTTCGTGGTCGGCTTCCTTGGCAAGGATACCAGgtcaggctgt ... gcttttatagGGAGACAATAAAGGATTTCTGGTCTGCAAAAAGAAAATGGCCACGTCCCCG

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: 34 (upstream exon), 35 (downstream exon)
Score: 24

ACATTTGGGTCGCACTGGCAGTAGACGAGATGATCTGGAATCGCTTGGATACACGCTAGTGTTTCTCCTTCGTGGTCGGCTTCCTTGGCAAGGATACCAGgtcaggctgt ... gcttttatagGGAGACAATAAAGGATTTCTGGTCTGCAAAAAGAAAATGGCCACGTCCCCGGAGATGTTGTGCTGTTTCTGCCCGCCTCCATTCAAGCAGTTTTTGGAAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcaggctgttttaatattttagttttattgttttacatgggcgcttttatagGGAGACAATAAAGGATTTCTGGTCTGCAAAAAGAAAATGGCCACGTCCCCGGAGATGTTGTGCTGTTTCTGCCCGCCTCCATTCAAGCAGTTTTTGGAAA
           ttttaat  putative branch site (score: 24)
                                            cgctttt  putative PPT
         tgttttaatattttag  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcaggctgttttaatattttagttttattgttttacatgggcgcttttatagGGAGACAATAAAGGATTTCTGGTCTGCAAAAAGAAAATGGCCACGTCCCCGGAGATGTTGTGCTGTTTCTGCCCGCCTCCATTCAAGCAGTTTTTGGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT