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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcgtgtctttagctgtgacttttaactgggctgacgttcctggttccagGTATCCTTCACCGAATGTTCTCATTCCTGCTCTTCGTACGGTGGGAAACATTGTGACTGGTGACGATGTCCAAACGCAG

Basic information

species Selaginella moellendorffii
transcript EFJ31557
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ31557 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GLYMA17G03430.1 (Glycine max), 3'ss of exon 6
--------------------------gtaagtcgtgtctttagctgtgacttttaactgggctgacgttcctgg------ttccagGTATCCTTCACCGAATGTTCTCATTCCTGCTCTTCGTACGGTGGGAAACATTGTGACTGGTGACGATGTCCAAACGCAG
                            || | |  ||| | | | | | | |||||||   | || ||    |      || |||  | || || ||    || || ||||||||||||||||| |||||||| ||||||||||| || ||| | || || |||
gtgagtattagttctgctatacctattgaaatagattctgttgttttaattgttaactgtcttaactttgtatgcatgcttttcagACACCCATCTCCCTCAGTGCTGATTCCTGCTCTTCGTACAGTGGGAAATATTGTGACTGGAGATGATATGCAGACTCAG

upper sequence: EFJ31557 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GLYMA07G37180.1 (Glycine max), 3'ss of exon 7
--------------------------gtaagtcgtgtctttagctgtgacttttaactgggctgacgttcctgg------ttccagGTATCCTTCACCGAATGTTCTCATTCCTGCTCTTCGTACGGTGGGAAACATTGTGACTGGTGACGATGTCCAAACGCAG
                            || | |  ||| | | | | | | |||||||   | || ||    |      || |||| | || || ||    || || ||||||||||||||||| |||||||| ||||||||||| || ||  | || || |||
gtgagtattagttctactatacctattgaaatagattctgttgttttaattgttaactgtcttaactttgtatgaatgcttttcagGCACCCATCTCCCTCGGTGCTGATTCCTGCTCTTCGTACAGTGGGAAATATTGTGACTGGAGATGACATGCAGACTCAG

upper sequence: EFJ31557 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: Vv14s0060g01510.t01 (Vitis vinifera), 3'ss of exon 6
---------------------------------------------gtaagtcgtgtctttagctgtgacttttaact--gggctgacgttcctggtt---------ccagGTATCCTTCACCGAATGTTCTCATTCCTGCTCTTCGTACGGTGGGAAACATTGTGACTGGTGACGATGTCCAAACGCAG
                                             ||  |  ||||  ||  |  | | || || ||  || ||||  ||| |  ||          |||  | || || ||   ||||||||||||||| ||||| ||||| ||||||||||| ||||| || ||| | ||||| |||
gtgagtttttagaaattttgagttagttctggacttcttttggctgtgggatgtgttgtttccattaatttgtacctcgggcctgaacttctttcttggactttggtcagTCACCCATCTCCTTCTGTTCTCATTCCTGCACTTCGCACGGTTGGAAACATTGTCACTGGAGATGATATGCAAACCCAG

upper sequence: EFJ31557 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: Vv05s0077g01430.t01 (Vitis vinifera), 3'ss of exon 6
------------------------------------------gtaagtcgtgtctt---tagctgtgactttt-aactgggctgacgttcctg--gttccagGTATCCTTCACCGAATGTTCTCATTCCTGCTCTTCGTACGGTGGGAAACATTGTGACTGGTGACGATGTCCAAACGCAG
                                           ||  |    ||||    |  |  |||     |||| |    |||    ||  |||||||  |||| || ||    || ||||||||||| ||||| || || |||||||||||||| || |||||| |||| || |||
gtaagtgttacattttattactcactttgtcagacagctcctttatattccatcttatgcatttaagacccaagaacttgaaacacgcatgtgttgttccagTCATCCATCTCCATCAGTGCTCATTCCTGCCCTTCGCACAGTTGGAAACATTGTGACAGGAGACGATATCCAGACTCAG

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:     CAAGCTGTCATTGAGGCCGGTGTGTGTCCACGTCTTGTGAGTCTACTCAT                         GTATCCTTCACCGAATGTTCTCATTCCTGCTCTTCGTACGGTGGGAAACAT
genomic: CAAGCTGTCATTGAGGCCGGTGTGTGTCCACGTCTTGTGAGTCTACTCATgtaagtcgtg ... ctggttccagGTATCCTTCACCGAATGTTCTCATTCCTGCTCTTCGTACGGTGGGAAACAT
EST: gi|169030898|gb|FE438166.1|FE438166
EST:     CAAGCTGTCATTGAGGCCGGTGTGTGTCCACGTCTTGTGAGTCTACTCAT                         GTATCCTTCACCGAATGTTCTCATTCCTGCTCTTCGTACGGTGGGAAACAT
genomic: CAAGCTGTCATTGAGGCCGGTGTGTGTCCACGTCTTGTGAGTCTACTCATgtaagtcgtg ... ctggttccagGTATCCTTCACCGAATGTTCTCATTCCTGCTCTTCGTACGGTGGGAAACAT
EST: gi|169072117|gb|FE478729.1|FE478729
EST:     CAAGCTGTCATTGAGGCCGGTGTGTGTCCACGTCTTGTGAGTCTACTCAT                         GTATCCTTCACCGAATGTTCTTATTCCTGCTCTTCGTACGGTGGGAAACAT
genomic: CAAGCTGTCATTGAGGCCGGTGTGTGTCCACGTCTTGTGAGTCTACTCATgtaagtcgtg ... ctggttccagGTATCCTTCACCGAATGTTCTCATTCCTGCTCTTCGTACGGTGGGAAACAT
EST: gi|169067353|gb|FE473106.1|FE473106
EST:     CAAGCTGTCATTGAGGCCGGTGTGTGTCCACGTCTTGTGAGTCTACTCAT                         GTATCCTTCACCGAATGTTCTCATTCCTGCTCTTCGTACGGTGGGAAACAT
genomic: CAAGCTGTCATTGAGGCCGGTGTGTGTCCACGTCTTGTGAGTCTACTCATgtaagtcgtg ... ctggttccagGTATCCTTCACCGAATGTTCTCATTCCTGCTCTTCGTACGGTGGGAAACAT
EST: gi|169045304|gb|FE453617.1|FE453617
EST:     CAAGCTGTCATTGAGGCCGGTGTGTGTCCACGTCTTGTGAGTCTACTCAT                         GTATCCTTCACCGAATGTTCTTATTCCTGCTCTT
genomic: CAAGCTGTCATTGAGGCCGGTGTGTGTCCACGTCTTGTGAGTCTACTCATgtaagtcgtg ... ctggttccagGTATCCTTCACCGAATGTTCTCATTCCTGCTCTT
EST: gi|169076232|gb|FE485262.1|FE485262
EST:     CAAGCTGTCATTGAGGCCGGTGTGTGTCCACGTCTTGTGAGTCTACTCAT                         GTATCCTTCACCGAATGTTCTCATTCCTGCTCTT
genomic: CAAGCTGTCATTGAGGCCGGTGTGTGTCCACGTCTTGTGAGTCTACTCATgtaagtcgtg ... ctggttccagGTATCCTTCACCGAATGTTCTCATTCCTGCTCTT
EST: gi|169102471|gb|FE508021.1|FE508021
EST:     CAAGCTGTCATTGAGGCCGGTGTGTGTCCACGTCTTGTGAGTCTACTCAT                         GTATCCTTCACCGAATGTTCTTATTCCTGCTCTTCGTACGGTGGGAAACAT
genomic: CAAGCTGTCATTGAGGCCGGTGTGTGTCCACGTCTTGTGAGTCTACTCATgtaagtcgtg ... ctggttccagGTATCCTTCACCGAATGTTCTCATTCCTGCTCTTCGTACGGTGGGAAACAT
EST: gi|169049984|gb|FE458076.1|FE458076
EST:     CAAGCTGTCATTGAGGCCGGTGTGTGTCCACGTCTTGTGAGTCTACTCAT                         GTATCCTTCACCGAATGTTCTTATTCCTGCTCTTCGTACGGTGGGAAACAT
genomic: CAAGCTGTCATTGAGGCCGGTGTGTGTCCACGTCTTGTGAGTCTACTCATgtaagtcgtg ... ctggttccagGTATCCTTCACCGAATGTTCTCATTCCTGCTCTTCGTACGGTGGGAAACAT
EST: gi|169028583|gb|FE440440.1|FE440440
EST:     CAAGCTGTCATTGAGGCCGGTGTGTGTCCACGTCTTGTGAGTCTACTCAT                         GTATCCTTCACCGAAATGT-CTTATTCCTGCTCTT
genomic: CAAGCTGTCATTGAGGCCGGTGTGTGTCCACGTCTTGTGAGTCTACTCATgtaagtcgtg ... ctggttccagGTATCCTTCACCGAA-TGTTCTCATTCCTGCTCTT
EST: gi|169020321|gb|FE428305.1|FE428305
EST:     CAAGCTGTCATTGAGGCCGGTGTGTGTCCACGTCTTGTGAGTCTACTCAT                         GTATCCTTCACCGAATGTTCTTATTCCTGCTCTTCGTACGGTGGGAAACAT
genomic: CAAGCTGTCATTGAGGCCGGTGTGTGTCCACGTCTTGTGAGTCTACTCATgtaagtcgtg ... ctggttccagGTATCCTTCACCGAATGTTCTCATTCCTGCTCTTCGTACGGTGGGAAACAT

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: 24

ATGCATGCTGGGCTTTGTCATACATATCCGATGGTACAAACGATAAGATTCAAGCTGTCATTGAGGCCGGTGTGTGTCCACGTCTTGTGAGTCTACTCATgtaagtcgtg ... ctggttccagGTATCCTTCACCGAATGTTCTCATTCCTGCTCTTCGTACGGTGGGAAACATTGTGACTGGTGACGATGTCCAAACGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaagtcgtgtctttagctgtgacttttaactgggctgacgttcctggttccagGTATCCTTCACCGAATGTTCTCATTCCTGCTCTTCGTACGGTGGGAAACATTGTGACTGGTGACGATGTCCAAACGCAG
                                        cgttcct  CT-rich tract
                       acttttaa  TA-rich tract