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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataattcattcatcgcccctgatctccatccatctcctgtgctcttgtgctcttcagGTGATCCCCTGGGGCGACTTGGATTCCCTGGCAATGCTCCAGAGGCAGCTCGACGTTGACATCCTCATCACCGGGCACACGCACCAGTTCAAGGCGTACA

Basic information

species Selaginella moellendorffii
transcript EFJ29006
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ29006 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: LOC_Os02g16550.1 (Oryza sativa), 3'ss of exon 2
---------------------------------------gtataattcat--tcatcgcccctgatctccatccatctcctgtgctcttgtgctcttcagGTGATCCCCTGGGGCGACTTGGATTCCCTGGCAATGCTCCAGAGGCAGCTCGACGTTGACATCCTCATCACCGGGCACACGCACCAGTTCAAGGCGTACA
                                       ||  || |     |  |    |    | |||     | | || ||  | ||   || ||||||  | || |||||||| ||||| |||||||| ||||||||  ||||||| ||||| ||||||||| |||| |||||||| |||||||||||||||||||
ctttttgttagtacatgccaaagagtctgatcagtcagtgtcaaacttgagattgttttgcagtgtatcctaatcttttctctgaccatgcaatcatcagGTTGTTCCATGGGGCGATTTGGACTCCCTGGCGATGCTCCAACGGCAGCTGGACGTGGACATCCTCGTCACAGGGCACACCCACCAGTTCAAGGCGTACA

upper sequence: EFJ29006 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G068489_T02 (Zea mays), 3'ss of exon 1
---------------------------------------gtataattcattcatcgcccctga---tctccatccatctcctgtgctcttgtgctcttcagGTGATCCCCTGGGGCGACTTGGATTCCCTGGCAATGCTCCAGAGGCAGCTCGACGTTGACATCCTCATCACCGGGCACACGCACCAGTTCAAGGCGTACA
                                        | | |   ||   | |      |   | | ||   |    |||      |  |  |  |||||  | || ||||||||| |||| |||||||| ||||||||| ||||||| ||||| ||||||||  | |||||||||||||||||||||||||| || |
cacatgctaaatttgtgcgtgcggtcattgagactgactatctgacatatattttgtgttaaacatttttcactaaatctctgcatcgat-cgaacaccagGTTGTTCCATGGGGCGACCTGGACTCCCTGGCGATGCTCCAGCGGCAGCTGGACGTGGACATCCTGGTGACCGGGCACACGCACCAGTTCAAGGCATATA

upper sequence: EFJ29006 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G109315_T02 (Zea mays), 3'ss of exon 2
---------------------------------------gtataattcattcatcgcc---cctgatctccatccatctcctgtgctcttgtgctcttcagGTGATCCCCTGGGGCGACTTGGATTCCCTGGCAATGCTCCAGAGGCAGCTCGACGTTGACATCCTCATCACCGGGCACACGCACCAGTTCAAGGCGTACA
                                        | |    ||||    |       |  | | ||   |    |||   ||    |  | ||||||  | || ||||||||| |||| |||||||| ||||||||| ||||||| ||||| ||||||||  | ||||||||||  || ||||||||||| || |
gtttgtgcactttgtggctcttgaattccagtagactagctgtgccccattttctgttaagtatttttttcactaaatctctgca-tcaaccgaacatcagGTTGTTCCATGGGGCGACCTGGACTCCCTGGCGATGCTCCAGCGGCAGCTGGACGTGGACATCCTGGTGACCGGGCACAGCCATCAGTTCAAGGCATATA

upper sequence: EFJ29006 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA02G43610.3 (Glycine max), 3'ss of exon 4
-------------------------------------gtataattcattcatcgcccctgatctccatccatctcctgtg---ctcttgtgctcttca-gGTGATCCCCTGGGGCGACTTGGATTCCCTGGCAATGCTCCAGAGGCAGCTCGACGTTGACATCCTCATCACCGGGCACACGCACCAGTTCAAGGCGTACA
                                        |||    | |          ||    ||        | ||   || |  || |  | | ||| || || ||||| ||| | || || ||||||||||| |||||||||||||| || ||||||||  |||| |                           
ttttatatgaaactgttactggttctgtttagtcgaaacttaaactgtgctatattatgcattggtatatgatagttatgaatctttaatgattgtgaagGTTATTCCATGGGGAGACCTAGACTCACTGGCAATGCTACAGAGGCAGCTCGATGTAGACATCCTTGTCACAG---------------------------

upper sequence: EFJ29006 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA02G43610.2 (Glycine max), 3'ss of exon 4
-------------------------------------gtataattcattcatcgcccctgatctccatccatctcctgtg---ctcttgtg-ctcttcagGTGATCCCCTGGGGCGACTTGGATTCCCTGGCAATGCTCCAGAGGCAGCTCGACGTTGACATCCTCATCACCGGGCACACGCACCAGTTCAAGGCGTACA
                                        |||    | |          ||    ||        | ||   || |  ||  | |  |||| || || ||||| ||| | || || ||||||||||| |||||||||||||| || ||||||||  |||| || ||||| || || || |  || ||||
ttttatatgaaactgttactggttctgtttagtcgaaacttaaactgtgctatattatgcattggtatatgatagttatgaatctttaatgattgtgaagGTTATTCCATGGGGAGACCTAGACTCACTGGCAATGCTACAGAGGCAGCTCGATGTAGACATCCTTGTCACAGGTCACACCCATCAATTTACAGCTTACA

upper sequence: EFJ29006 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: Vv01s0026g01860.t01 (Vitis vinifera), 3'ss of exon 3
-------------------------------------------gtataattcattcatcgcccctgatctccatccatctcctgtgctcttgtgctcttcagGTGATCCCCTGGGGCGACTTGGATTCCCTGGCAATGCTCCAGAGGCAGCTCGACGTTGACATCCTCATCACCGGGCACACGCACCAGTTCAAGGCGTACA
                                            | | || |||| |||   | | |    |||  || |  | |  |       |||  |||| || || ||||| ||||||||||| ||||||||||| || |||||| | || || ||||||||  | || || ||||| || ||||||||||| ||||
gtgatgattgtgatagtaaaagatccttagttctcttcttcaattttgatacatttatctggcattaga--cattaattttttctttttaaacaatctgaagGTTATTCCATGGGGAGACTTGGATTCGCTGGCAATGCTACAAAGGCAGTTGGATGTGGACATCCTAGTGACTGGACACACCCATCAGTTCAAGGCCTACA

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|169033283|gb|FE441303.1|FE441303
EST:     AGCAGCTGAGCATCGGAAGCTTCAAGATCGGCCTGTGCCACGGCCACCAG                         GTGATCCCCTGGGGCGACTTGGATTCCCTGGCAATGCTCCAGAGGCAGCTC
genomic: AGCAGCTGAGCATCGGAAGCTTCAAGATCGGCCTGTGCCACGGCCACCAGgtataattca ... tgctcttcagGTGATCCCCTGGGGCGACTTGGATTCCCTGGCAATGCTCCAGAGGCAGCTC
EST: gi|70670089|gb|DN838666.1|DN838666
EST:     AGCAGCTGAGCATCGGAAGCTTCAAGATCGGCCTGTGCCACGGCCACCAG                         GTGATCCCCTGGGGCGACTTGGATTCCCTGGCAATGCTCCAGAGGCAGCTC
genomic: AGCAGCTGAGCATCGGAAGCTTCAAGATCGGCCTGTGCCACGGCCACCAGgtataattca ... tgctcttcagGTGATCCCCTGGGGCGACTTGGATTCCCTGGCAATGCTCCAGAGGCAGCTC
EST: gi|169101456|gb|FE501429.1|FE501429
EST:     AGCAGCTGAGCATCGGAAGCTTCAAGATCGGCCTGTGCCACGGCCACCAG                         GTGATCCCCTGGGGCGACTTGGATTCCCTGGCAATGCTCCAGAGGCAGCTC
genomic: AGCAGCTGAGCATCGGAAGCTTCAAGATCGGCCTGTGCCACGGCCACCAGgtataattca ... tgctcttcagGTGATCCCCTGGGGCGACTTGGATTCCCTGGCAATGCTCCAGAGGCAGCTC
EST: gi|169048614|gb|FE455796.1|FE455796
EST:     AGCAGCTGAGCATCGGAAGCTTCAAGATCGGCCTGTGCCACGGCCACCAG                         GTGATCCCCTGGGGCGACTTGGATTCCCTGGCAATGCTCCAGAGGCAGCTC
genomic: AGCAGCTGAGCATCGGAAGCTTCAAGATCGGCCTGTGCCACGGCCACCAGgtataattca ... tgctcttcagGTGATCCCCTGGGGCGACTTGGATTCCCTGGCAATGCTCCAGAGGCAGCTC
EST: gi|169115209|gb|FE515625.1|FE515625
EST:     AGCAGCTGAGCATCGGAAGCTTCAAGATCGGCCTGTGCCACGGCCACCAG                         GTGATCCCCTGGGGCGACTTGGATTCCCTGGCAATGCTCCAGAGGCAGCTC
genomic: AGCAGCTGAGCATCGGAAGCTTCAAGATCGGCCTGTGCCACGGCCACCAGgtataattca ... tgctcttcagGTGATCCCCTGGGGCGACTTGGATTCCCTGGCAATGCTCCAGAGGCAGCTC
EST: gi|169033282|gb|FE441302.1|FE441302
EST:     AGCAGCTGAGCATCGGAAGCTTCAAGATCGGCCTGTGCCACGGCCACCAG                         GTGATCCCCTGGGGCGACTTGGATTCCCTGGCAATGCTCCAGAGGCAGCTG
genomic: AGCAGCTGAGCATCGGAAGCTTCAAGATCGGCCTGTGCCACGGCCACCAGgtataattca ... tgctcttcagGTGATCCCCTGGGGCGACTTGGATTCCCTGGCAATGCTCCAGAGGCAGCTC
EST: gi|169115208|gb|FE515624.1|FE515624
EST:     AGCAGCTGAGCATCGGAAGCTTCAAGATCGGCCTGTGCCACGGCCACCAG                         GTGATCCCCTGGGGCGACTTGGATTCCCTGGCAATGCTCCAGAGGCAGCTC
genomic: AGCAGCTGAGCATCGGAAGCTTCAAGATCGGCCTGTGCCACGGCCACCAGgtataattca ... tgctcttcagGTGATCCCCTGGGGCGACTTGGATTCCCTGGCAATGCTCCAGAGGCAGCTC

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: 40

GCACATCGTGCGAGGTGAATACGACGAGGACAGTCGCTACCCAGAGACGAAGCAGCTGAGCATCGGAAGCTTCAAGATCGGCCTGTGCCACGGCCACCAGgtataattca ... tgctcttcagGTGATCCCCTGGGGCGACTTGGATTCCCTGGCAATGCTCCAGAGGCAGCTCGACGTTGACATCCTCATCACCGGGCACACGCACCAGTTCAAGGCGTACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattcattcatcgcccctgatctccatccatctcctgtgctcttgtgctcttcagGTGATCCCCTGGGGCGACTTGGATTCCCTGGCAATGCTCCAGAGGCAGCTCGACGTTGACATCCTCATCACCGGGCACACGCACCAGTTCAAGGCGTACA
              ccctgat  putative branch site (score: 40)
                                       ctcttgtgctcttc  putative PPT