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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATCCTTCACCGAATGTTCTCATTCCTGCTCTTCGTACGGTGGGAAACATTGTGACTGGTGACGATGTCCAAACGCAGgtaaacttgaaacggaacatcctagatatttcttacgcctgtctttaaatttatttccag

Basic information

species Selaginella moellendorffii
transcript EFJ31557
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ31557 (Selaginella moellendorffii), 5'ss of exon 7
lower sequence: GLYMA17G03430.1 (Glycine max), 5'ss of exon 7
GTATCCTTCACCGAATGTTCTCATTCCTGCTCTTCGTACGGTGGGAAACATTGTGACTGGTGACGATGTCCAAACGCAGgtaa--acttg-----aaacggaaca--tcctagatatttcttacg---------cctgtctttaaa-tttatttccag---------------------
  | || || ||    || || ||||||||||||||||| |||||||| ||||||||||| || ||| | || || |||||||  | |||     |   | |  |  | || ||||||  |              | || || ||  || |||| | |                     
ACACCCATCTCCCTCAGTGCTGATTCCTGCTCTTCGTACAGTGGGAAATATTGTGACTGGAGATGATATGCAGACTCAGgtaatgaattgtccacagttgtagtaatttcttgatattattggaaggaacagaagcagttttcaatcttcattttctgtcccagttgttccacgtattt

upper sequence: EFJ31557 (Selaginella moellendorffii), 5'ss of exon 7
lower sequence: GLYMA07G37180.1 (Glycine max), 5'ss of exon 8
GTATCCTTCACCGAATGTTCTCATTCCTGCTCTTCGTACGGTGGGAAACATTGTGACTGGTGACGATGTCCAAACGCAGgtaa--acttga-aacgg-----aacatcctagatatttcttacgcctgtctttaa-----atttatttccag---------------------------
| | || || ||    || || ||||||||||||||||| |||||||| ||||||||||| || ||  | || || |||||||  |||||  ||| |      |||   | |  |          | || || ||     |||| |||||                             
GCACCCATCTCCCTCGGTGCTGATTCCTGCTCTTCGTACAGTGGGAAATATTGTGACTGGAGATGACATGCAGACTCAGgtaataacttgtcaacagttcttgacactattggaaggaacagaagcagttttcaatcttcatttttttcccagttgtttcacatatttacctattcaac

upper sequence: EFJ31557 (Selaginella moellendorffii), 5'ss of exon 7
lower sequence: Vv14s0060g01510.t01 (Vitis vinifera), 5'ss of exon 7
GTATCCTTCACCGAATGTTCTCATTCCTGCTCTTCGTACGGTGGGAAACATTGTGACTGGTGACGATGTCCAAACGCAGgtaaacttga--aacggaacatcc-tagatatttcttacgcctgtctttaaa---tttatttccag----------------------------------
  | || || ||   ||||||||||||||| ||||| ||||| ||||||||||| ||||| || ||| | ||||| ||||||      |   |   ||||||  || ||||||    | ||||  | |||    ||||||   |                                   
TCACCCATCTCCTTCTGTTCTCATTCCTGCACTTCGCACGGTTGGAAACATTGTCACTGGAGATGATATGCAAACCCAGgtattgcccacttaaaaaacatctgtaaatattttggtctcctgcatgtaatccttttattcttaaaaatataaaaggtcaactaagttactaacagcta

upper sequence: EFJ31557 (Selaginella moellendorffii), 5'ss of exon 7
lower sequence: Vv05s0077g01430.t01 (Vitis vinifera), 5'ss of exon 7
GTATCCTTCACCGAATGTTCTCATTCCTGCTCTTCGTACGGTGGGAAACATTGTGACTGGTGACGATGTCCAAACGCAGgtaaac----ttgaaacggaa-----catcctagatatttcttacgcctgtctttaaatttatt-tccag------------------------------
  |||| || ||    || ||||||||||| ||||| || || |||||||||||||| || |||||| |||| || ||||||       |||||| | |      |  || |    ||| ||||  || |   |   |||||  | ||                               
TCATCCATCTCCATCAGTGCTCATTCCTGCCCTTCGCACAGTTGGAAACATTGTGACAGGAGACGATATCCAGACTCAGgtatgtgcttttgaaaagcattttttccccccaatggttttttacatcttttcctttttttatggtacaataatatttactgccaatctggcaagcctat

upper sequence: EFJ31557 (Selaginella moellendorffii), 5'ss of exon 7
lower sequence: PP1S43_141V6.1 (Physcomitrella patens), 5'ss of exon 8
GTATCCTTCACCGAATGTTCTCATTCCTGCTCTTCGTACGGTGGGAAACATTGTGACTGGTGACGATGTCCAAACGCAGgtaaac-----ttgaaacggaacatcctagatatttcttacgcctgtctttaaatttatttccag-----------------------------------
  |||| |||||   ||||||||||||||| || || || || || || ||||| |||||||||||| |||| |||||||||  |     ||||   |     | |  |||  ||        |      ||  | || |||                                     
CCATCCATCACCCTCTGTTCTCATTCCTGCACTGCGCACTGTCGGCAATATTGTTACTGGTGACGATCTCCAGACGCAGgtatgcatgctttgatttgacttctacgggattatttcggtttttagtacgaagatcatatcctttcaggagtgggctgacagcaccctcccagtaagaa

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|169031969|gb|FE440669.1|FE440669
EST:     CTCTTCGTACGGTGGGAAACATTGTGACTGGTGACGATGTCCAAACGCAG                         TTTATCANTAA-CAATGGAGCGCTGCCATATTT
genomic: CTCTTCGTACGGTGGGAAACATTGTGACTGGTGACGATGTCCAAACGCAGgtaaacttga ... ttatttccagTTTATCA-TAAACAATGGAGCGCTGCCATATTT
EST: gi|169030898|gb|FE438166.1|FE438166
EST:     CTCTTCGTACGGTGGGAAACATTGTGACTGGTGACGATGTCCAAACGCAG                         TTTATCATANACAATGGAGCGCTGCCATATTTGTTACATCTTCTTACCAAT
genomic: CTCTTCGTACGGTGGGAAACATTGTGACTGGTGACGATGTCCAAACGCAGgtaaacttga ... ttatttccagTTTATCATAAACAATGGAGCGCTGCCATATTTGTTACATCTTCTTACCAAT
EST: gi|169072117|gb|FE478729.1|FE478729
EST:     CTCTTCGTACGGTGGGAAACATTGTGACTGGTGACGATGTCCAAACGCAG                         TTCATCATAAACAATGGAGCGCTGCCATATTTGTTACATCTTCTCACCAAT
genomic: CTCTTCGTACGGTGGGAAACATTGTGACTGGTGACGATGTCCAAACGCAGgtaaacttga ... ttatttccagTTTATCATAAACAATGGAGCGCTGCCATATTTGTTACATCTTCTTACCAAT
EST: gi|169067353|gb|FE473106.1|FE473106
EST:     CTCTTCGTACGGTGGGAAACATTGTGACTGGTGACGATGTCCAAACGCAG                         TTTATCATAAACAATGGAGCGCTGCCATATTTGTTACATCTTCTTACCAAT
genomic: CTCTTCGTACGGTGGGAAACATTGTGACTGGTGACGATGTCCAAACGCAGgtaaacttga ... ttatttccagTTTATCATAAACAATGGAGCGCTGCCATATTTGTTACATCTTCTTACCAAT
EST: gi|169102471|gb|FE508021.1|FE508021
EST:     CTCTTCGTACGGTGGGAAACATTGTGACTGGTGACGATGTCCAAACGCAG                         TTCATCATAAAC
genomic: CTCTTCGTACGGTGGGAAACATTGTGACTGGTGACGATGTCCAAACGCAGgtaaacttga ... ttatttccagTTTATCATAAAC
EST: gi|169049984|gb|FE458076.1|FE458076
EST:     CTCTTCGTACGGTGGGAAACATTGTGACTGGTGACGATGTCCAAACGCAG                         TTCATCATAAACAATGGAGCGCTGCCATATTTGTTACATCTTCT
genomic: CTCTTCGTACGGTGGGAAACATTGTGACTGGTGACGATGTCCAAACGCAGgtaaacttga ... ttatttccagTTTATCATAAACAATGGAGCGCTGCCATATTTGTTACATCTTCT
EST: gi|169020321|gb|FE428305.1|FE428305
EST:     CTCTTCGTACGGTGGGAAACATTGTGACTGGTGACGATGTCCAAACGCAG                         TTCATCATAAACAATGGAGCGCTGCCATATTTGTTACATCTTCTCACCAAT
genomic: CTCTTCGTACGGTGGGAAACATTGTGACTGGTGACGATGTCCAAACGCAGgtaaacttga ... ttatttccagTTTATCATAAACAATGGAGCGCTGCCATATTTGTTACATCTTCTTACCAAT

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), 27 (downstream exon)
Score: 36

GTATCCTTCACCGAATGTTCTCATTCCTGCTCTTCGTACGGTGGGAAACATTGTGACTGGTGACGATGTCCAAACGCAGgtaaacttga ... ttatttccagTTTATCATAAACAATGGAGCGCTGCCATATTTGTTACATCTTCTTACCAATGTTTACAAGAAGAGCATAAAAAAGGAGGCTTGCTGGACAATCTCGAACA




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