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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctggttctagcttcaaaggatggttttttacgagtctatttttacgtccagGGATACTGCTGGCCAGGAGCGCTTCCGGAGTTTGATTCCCAGCTACATACGGGATTCGTCCGTGGCAGTCGTCGTGTACGATGTAGCGA

Basic information

species Selaginella moellendorffii
transcript EFJ22994
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ30542 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S39_147V6.1 (Physcomitrella patens), 3'ss of exon 4
----------------------------------------------------------------------------------------------------------------------------gtatgctggttct--agcttcaaaggatggttttttacgagtctatttttacgtccagGGATACTGCTGGCCAGGAGCGCTTCCGGAGTTTGATTCCCAGCTACATACGGGATTCGTCCGTGGCAGTCGTCGTGTACGATGTAGCGA
                                                                                                                               |   ||||    | |      |  || ||| | |  | |      |   |  |||||| |||||||| |||||| | ||  |||||||||||||||||||||| |||||||||||||||||||| || || || |||||  | |
gtaaaggcgttcagacgtccatattgcatgacaattgagtttatttgcaccagtaaatcagttattctcttccttgcagggcaatttaagttgctgtttgtctttgttgtctgctttacattacaagtatcggtttagaaaccgtcgcgtttgatttatcagaatttggacgtgttgcgcagGGACACTGCTGGACAGGAGAGGTTTAGGAGTTTGATTCCCAGCTACATCCGGGATTCGTCCGTGGCAGTGGTTGTCTATGATGTTTCCA

upper sequence: EFJ30542 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S346_29V6.1 (Physcomitrella patens), 3'ss of exon 3
-------------------------------------gtatgctggttctagcttcaaaggatggttttt-------tacgagtctatttttacgtccagGGATACTGCTGGCCAGGAGCGCTTCCGGAGTTTGATTCCCAGCTACATACGGGATTCGTCCGTGGCAGTCGTCGTGTACGATGTAGCGA
                                     |    || ||| |||   | ||  |  |  |         |  | | || || | |  | ||||||||| ||||| |||||| | ||| ||||||| ||||| || ||||| |||||||||||||||||||| || |||||||||||  | |
attagataacgagatggaggttgtcttcttgtttcttgacgtcttgttgtagaaacgaaatactgaatccatcataatttggggctgttatgaaatgcagGGATACCGCTGGACAGGAGAGGTTCAGGAGTTTAATTCCTAGTTACATTCGGGATTCGTCCGTGGCAGTGGTTGTGTACGATGTTTCAA

upper sequence: EFJ30542 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S2_143V6.1 (Physcomitrella patens), 3'ss of exon 4
---------------------------------------------------------------------------------------------------------------gtatgctggttctagcttca-aaggatggttttttacga-gtctat---ttttacgtcc--agGGATACTGCTGGCCAGGAGCGCTTCCGGAGTTTGATTCCCAGCTACATACGGGATTCGTCCGTGGCAGTCGTCGTGTACGATGTAGCGA
                                                                                                                | |   |||||      || |   || | || ||     || | |   | ||| | ||  ||||| || ||||| || ||||| ||| ||||||||||||| |||||||| ||||| |||||||||||||| || ||||| |||       
gtaaagggcattgggacgtgcacgttaatatgcaattgagagcatttttgtcgttttgttctttgctgagcagtttaagttgctgtttgttgtgtttcttacgcgcccctcatttatcggttccgaaaacacatcaattgcttattgtagcgtttgtggctgttatgacctcagGGACACAGCTGGACAAGAGCGGTTCAGGAGTTTGATTCCTAGCTACATTCGGGACTCGTCCGTGGCAGTGGTTGTGTATGAT-------

upper sequence: EFJ30542 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S456_9V6.1 (Physcomitrella patens), 3'ss of exon 3
----------------------------------------gtatgctggttctagcttcaaaggatggtttttt----acgagtctatttttacgtccagGGATACTGCTGGCCAGGAGCGCTTCCGGAGTTTGATTCCCAGCTACATACGGGATTCGTCCGTGGCAGTCGTCGTGTACGATGTAGCGA
                                         |   || ||   |  | | |  ||   |  |      | | | || || | |  |  ||||| || ||||| || ||| | ||| ||||||| |||||||||||||| || || ||||| |||||||| || || ||||||||  |||
agtactccttgtgataatggttatcttttttgcacatgacattgccttgtggaaattcccattgaatttcatcagaaaatgggactgttatgaaatgtagGGACACAGCTGGACAAGAGAGGTTCAGGAGTTTAATTCCCAGCTACATTCGAGACTCGTCTGTGGCAGTAGTTGTTTACGATGTTTCGA

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|169042135|gb|FE454178.1|FE454178
EST:     TTATCCAAGACCATGTATCTGGAAGATCGCACAGTCCGCTTGCAGCTCTG                         GGATACTGCTGGCCAGGAGCGCTTCCGGAGTTTGATTCCCAGCTACATACG
genomic: TTATCCAAGACCATGTATCTGGAAGATCGCACAGTCCGCTTGCAGCTCTGgtatgctggt ... ttacgtccagGGATACTGCTGGCCAGGAGCGCTTCCGGAGTTTGATTCCCAGCTACATACG
EST: gi|169040414|gb|FE450299.1|FE450299
EST:     TTATCCAAGACCATGTATCTGGAAGATCGCACAGTCCGCTTGCAGCTCTG                         GGATACTGCTGGCCAGGAGCGCTTCCGGAGTTTGATTCCCAGCTACATACG
genomic: TTATCCAAGACCATGTATCTGGAAGATCGCACAGTCCGCTTGCAGCTCTGgtatgctggt ... ttacgtccagGGATACTGCTGGCCAGGAGCGCTTCCGGAGTTTGATTCCCAGCTACATACG
EST: gi|169033383|gb|FE441762.1|FE441762
EST:     TTATCCAAGACCATGTATCTGGAAGATCGCACAGTCCGCTTGCAGCTCTG                         GGATACTGCTGGCCAGGAGCGCTTCCGGAGTTTGATTCCCAGCTACATACG
genomic: TTATCCAAGACCATGTATCTGGAAGATCGCACAGTCCGCTTGCAGCTCTGgtatgctggt ... ttacgtccagGGATACTGCTGGCCAGGAGCGCTTCCGGAGTTTGATTCCCAGCTACATACG
EST: gi|169039199|gb|FE447795.1|FE447795
EST:     TTATCCAAGACCATGTATCTGGAAGATCGCACAGTCCGCTTGCAGCTCTG                         GGATACTGCTGGCCAGGAGCGCTTCCGGAGTTTGATTCCCAGCTACATACG
genomic: TTATCCAAGACCATGTATCTGGAAGATCGCACAGTCCGCTTGCAGCTCTGgtatgctggt ... ttacgtccagGGATACTGCTGGCCAGGAGCGCTTCCGGAGTTTGATTCCCAGCTACATACG
EST: gi|169047766|gb|FE454622.1|FE454622
EST:     TTATCCAAGACCATGTATCTGGAAGATCGCACAGTCCGCTTGCAGCTCTG                         GGATACTGCTGGCCAGGAGCGCTTCCGGAGTTTGATTCCCAGCTACATACG
genomic: TTATCCAAGACCATGTATCTGGAAGATCGCACAGTCCGCTTGCAGCTCTGgtatgctggt ... ttacgtccagGGATACTGCTGGCCAGGAGCGCTTCCGGAGTTTGATTCCCAGCTACATACG
EST: gi|169033384|gb|FE441763.1|FE441763
EST:     TTATCCAAGACCATGTATCTGGAAGATCGCACAGTCCGCTTGCAGCTCTG                         GGATACTGCTGGCCAGGAGCGCTTCCGGAGTTTGATTCCCAGCTACATACG
genomic: TTATCCAAGACCATGTATCTGGAAGATCGCACAGTCCGCTTGCAGCTCTGgtatgctggt ... ttacgtccagGGATACTGCTGGCCAGGAGCGCTTCCGGAGTTTGATTCCCAGCTACATACG
EST: gi|169101421|gb|FE502538.1|FE502538
EST:     TTATCCAAGACCATGTATCTGGAAGATCGCACAGTCCGCTTGCAGCTCTG                         GGATACTGCTGGCCAGGAGCGCTTCCGGAGTTTGATTCCCAGCTACATACG
genomic: TTATCCAAGACCATGTATCTGGAAGATCGCACAGTCCGCTTGCAGCTCTGgtatgctggt ... ttacgtccagGGATACTGCTGGCCAGGAGCGCTTCCGGAGTTTGATTCCCAGCTACATACG
EST: gi|169039198|gb|FE447794.1|FE447794
EST:     TTATCCAAGACCATGTATCTGGAAGATCGCACAGTCCGCTTGCAGCTCTG                         GGATACTGCTGGCCAGGAGCGCTTCCGGAGTTTGATTCCCAGCTACATACG
genomic: TTATCCAAGACCATGTATCTGGAAGATCGCACAGTCCGCTTGCAGCTCTGgtatgctggt ... ttacgtccagGGATACTGCTGGCCAGGAGCGCTTCCGGAGTTTGATTCCCAGCTACATACG
EST: gi|169101420|gb|FE502537.1|FE502537
EST:     TTATCCAAGACCATGTATCTGGAAGATCGCACAGTCCGCTTGCAGCTCTG                         GGATACTGCTGGCCAGGAGCGCTTCCGGAGTTTGATTCCCAGCTACATACG
genomic: TTATCCAAGACCATGTATCTGGAAGATCGCACAGTCCGCTTGCAGCTCTGgtatgctggt ... ttacgtccagGGATACTGCTGGCCAGGAGCGCTTCCGGAGTTTGATTCCCAGCTACATACG
EST: gi|169036631|gb|FE446555.1|FE446555
EST:     TTATCCAAGACCATGTATCTGGAAGATCGCACAGTCCGCTTGCAGCTCTG                         GGATACTGCTGGCCAGGAGCGCTTCCGGAGTTTGATTCCCAGCTACATACG
genomic: TTATCCAAGACCATGTATCTGGAAGATCGCACAGTCCGCTTGCAGCTCTGgtatgctggt ... ttacgtccagGGATACTGCTGGCCAGGAGCGCTTCCGGAGTTTGATTCCCAGCTACATACG
EST: gi|169104604|gb|FE508204.1|FE508204
EST:     TTATCCAAGACCATGTATCTGGAAGATCGCACAGTCCGCTTGCAGCTCTG                         GGATACTGCTGGCCAGGAGCGCTTCCGGAGTTTGATTCCCAGCTACATACG
genomic: TTATCCAAGACCATGTATCTGGAAGATCGCACAGTCCGCTTGCAGCTCTGgtatgctggt ... ttacgtccagGGATACTGCTGGCCAGGAGCGCTTCCGGAGTTTGATTCCCAGCTACATACG

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: 105

GCTACGATTGGGATCGATTTCTTATCCAAGACCATGTATCTGGAAGATCGCACAGTCCGCTTGCAGCTCTGgtatgctggt ... ttacgtccagGGATACTGCTGGCCAGGAGCGCTTCCGGAGTTTGATTCCCAGCTACATACGGGATTCGTCCGTGGCAGTCGTCGTGTACGATGTAGCGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgctggttctagcttcaaaggatggttttttacgagtctatttttacgtccagGGATACTGCTGGCCAGGAGCGCTTCCGGAGTTTGATTCCCAGCTACATACGGGATTCGTCCGTGGCAGTCGTCGTGTACGATGTAGCGA
                                      tctattttt  CT-rich tract
                                      tctattttta  TA-rich tract