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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACTACTACTTCATGAAGACCAAGATGTCCGGGTTTTTCCAAACGAGTTTCTACTTCGGCTACACTCTGATGCTCTGCGTTGGACTGGGGAGCCTCTGTGgtgagtaccatacactccgattgttttcttggtcggatggattgatgactttgatggttttgatgcgcag

Basic information

species Selaginella moellendorffii
transcript EFJ37593
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ37593 (Selaginella moellendorffii), 5'ss of exon 12
lower sequence: LOC_Os02g34690.1 (Oryza sativa), 5'ss of exon 11
TACTACTACTTCATGAAGACCAAGATGTCCGGGTTTTTCCAAACGAGTTTCTACTTCGGCTACACTCTGATGCTCTGCGTTGGACTGGGGAGCCTCTGTGgtgagtaccatacactccgattgttttcttggtcggatggatt-gatgactttga-tggttttgatgcgcag----------
|| || |||    |||||||||||||||| || || || || || ||||||||||||||||||||||| ||| ||||| | ||  | || |  ||||| ||| ||  |  |  || ||| | |  | |||   |  | | ||| ||||  ||  | || |   | | || |           
TATTATTACCATGTGAAGACCAAGATGTCAGGATTCTTTCAGACAAGTTTCTACTTCGGCTACACTCTTATGTTCTGCCTAGGTTTAGGAACACTCTGCGgtaagctct-tctacaccggtagcatgcttaaacccaagaatttgatggtttcaactgataccggttcgaattttggtccag

upper sequence: EFJ37593 (Selaginella moellendorffii), 5'ss of exon 12
lower sequence: LOC_Os12g07670.1 (Oryza sativa), 5'ss of exon 11
TACTACTACTTCATGAAGACCAAGATGTCCGGGTTTTTCCAAACGAGTTTCTACTTCGGCTACACTCTGATGCTCTGCGTTGGACTGGGGAGCCTCTGTGgtgag-taccatacactccgattgttttcttggtcggatggattgatgactttgatggttttgatgcgcag------------------
||||||||     | ||||| |||||||| || |||||||| ||||||||||||||||| |||||  ||||| ||||| |||| || || |  || |||||| || |   |    || | | |   || |    ||      || || | | ||||| ||||| |  |                     
TACTACTATCATGTAAAGACAAAGATGTCAGGTTTTTTCCAGACGAGTTTCTACTTCGGTTACACATTGATGTTCTGCCTTGGTCTAGGCATACTTTGTGgtaagatcttaatttctactagtaccttttaatccgtgacactttatcattatgatgtttttgttttgacatctgttttggcgattcag

upper sequence: EFJ37593 (Selaginella moellendorffii), 5'ss of exon 12
lower sequence: GRMZM2G420310_T01 (Zea mays), 5'ss of exon 11
TACTACTACTTCATGAAGACCAAGATGTCCGGGTTTTTCCAAACGAGTTTCTACTTCGGCTACACTCTGATGCTCTGCGTTGGACTGGGGAGCCTCTGTGgtgag--taccatacactccgat-tgttttcttggtcggatggattgatgactttgatggttttgatgcgcag---------------------
|||||||||    ||||||| |||||||| || || ||||| || |||||||| ||||||||||| |||||| ||||| |||| || || |  || |||||| ||    || | ||  |  |  |  |  |||||    |    |   ||  |||| |   | |||   |  |                     
TACTACTACCATGTGAAGACAAAGATGTCAGGCTTCTTCCAGACAAGTTTCTATTTCGGCTACACGCTGATGTTCTGCCTTGGCCTAGGCATACTTTGTGgtaagatcgcctttcaaccaaagatcatgccttggcaatagatgtgactgtttttggt--ctctgacctgtcgtcttttgtttggtgattccag

upper sequence: EFJ37593 (Selaginella moellendorffii), 5'ss of exon 12
lower sequence: GRMZM2G026231_T01 (Zea mays), 5'ss of exon 11
TACTACTACTTCATGAAGACCAAGATGTCCGGGTTTTTCCAAACGAGTTTCTACTTCGGCTACACTCTGATGCTCTGCGTTGGACTGGGGAGCCTCTGTGgtgagt--accatacactccgattgttttcttggtcggatggattgatgactttgatggtt-ttgatg-cgcag
|||||||||    ||||||| |||||||| || || ||||| || ||||||||||| || ||||| |||||| ||||| |||| || || |  || |||||| ||   |   |   |  |     | |   ||       || ||     || ||||  || ||| ||   |||
TACTACTACCATGTGAAGACAAAGATGTCAGGCTTCTTCCAGACAAGTTTCTACTTTGGTTACACACTGATGTTCTGCCTTGGTCTAGGCATACTTTGTGgtaagctaatattgtgcctctgcaatatatgtgacttttcggtttttgacctgtgatttttgttggtgattcag

upper sequence: EFJ37593 (Selaginella moellendorffii), 5'ss of exon 12
lower sequence: Vv12s0035g00280.t01 (Vitis vinifera), 5'ss of exon 11
TACTACTACTTCATGAAGACCAAGATGTCCGGGTTTTTCCAAACGAGTTTCTACTTCGGCTACACTCTGATGCTCTGCGTTGGACTGGGGAGCCTCTGTGgtgagtacca--tacactccgattgttttcttggtcggatggattgatgacttt----------gatggttttgatgcgcag------------------
|| |||||||   ||||||| |||||||| || || |||||||| || ||||||||||| ||||| |||||| | ||| ||||  | || | ||||||||||||||  |        || ||||  ||| ||  |    ||  |   | | |||            || |||| ||  | |                   
TATTACTACTATGTGAAGACTAAGATGTCAGGCTTCTTCCAAACCAGCTTCTACTTCGGATACACCCTGATGTTTTGCCTTGGTTTAGGAATCCTCTGTGgtgagtttctacggtgttctgattcctttttttataatttgtgtaccttatttttcacatattcattgatttttatatgaaatttcattttctaaaaaag

upper sequence: EFJ37593 (Selaginella moellendorffii), 5'ss of exon 12
lower sequence: PP1S438_29V6.1 (Physcomitrella patens), 5'ss of exon 4
TACTACTACTTCATGAAGACCAAGATGTCCGGGTTTTTCCAAACGAGTTTCTACTTCGGCTACACTCTGATGCTCTGCGTTGGACTGGGGAGCCTCTGTGgtgagt---accataca--ctccgattgttttcttg--gtcggatggattgatgactttgatggttttgatgcgcag------------------------------------------------
||||||| || ||||||||| |||||||||||||||||||| |  |||||||||||||| ||||| |||||| ||||| | ||  |||| |   |||||||| |||   ||    ||  |   | | | | || ||  || |   | | |  |   ||    |||| ||| |||                                                   
TACTACTTCTACATGAAGACGAAGATGTCCGGGTTTTTCCAGATCAGTTTCTACTTCGGGTACACGCTGATGTTCTGCCTGGGGTTGGGCATATTCTGTGgtaagtgggactgggcaggcgtgggtgggtatcctggggtagtgcgtaatatttggttgatgggttgtgaggcggttgagtggagtggagggtctgacgggtgtgctgtttgtggcggctggcag

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|169114580|gb|FE515529.1|FE515529
EST:     CTACTTCGGCTACACTCTGATGCTCTGCGTTGGACTGGGGAGCCTCTGTG                         GTGCGGTGGGCTACTTGGGCTCGAGCGTGTTTGTTCGGAGGATCTATAGGA
genomic: CTACTTCGGCTACACTCTGATGCTCTGCGTTGGACTGGGGAGCCTCTGTGgtgagtacca ... tgatgcgcagGTGCGGTGGGCTACTTGGGCTCGAGCGTGTTTGTTCGGAGGATCTATAGGA
EST: gi|169088031|gb|FE492594.1|FE492594
EST:     CTACTTCGGCTACACTCTGATGCTCTGCGTTGGACTGGGGAGCCTCTGTG                         GTGCGGTGGGCTACTTGGGCTCGAGCGTGTTTGTTCGGAGGATCTATAGGA
genomic: CTACTTCGGCTACACTCTGATGCTCTGCGTTGGACTGGGGAGCCTCTGTGgtgagtacca ... tgatgcgcagGTGCGGTGGGCTACTTGGGCTCGAGCGTGTTTGTTCGGAGGATCTATAGGA
EST: gi|169087208|gb|FE493116.1|FE493116
EST:     CTACTTCGGCTACACTCTGATGCTCTGCGTTGGACTGGGGAGCCTCTGTG                         GTGCGGTGGGCTACTTGGGCTCGAGCGTGTTTGTTCGGAGGATCTATAGGA
genomic: CTACTTCGGCTACACTCTGATGCTCTGCGTTGGACTGGGGAGCCTCTGTGgtgagtacca ... tgatgcgcagGTGCGGTGGGCTACTTGGGCTCGAGCGTGTTTGTTCGGAGGATCTATAGGA
EST: gi|169044496|gb|FE451094.1|FE451094
EST:     CTACTTCGGCTACACTCTGATGCTCTGCGTTGGACTGGGGAGCCTCTGTG                         GTGCGGTGGGCTACTTGGGCTCGAGCGTGTTTGTTCGGAGGATCTATAGGA
genomic: CTACTTCGGCTACACTCTGATGCTCTGCGTTGGACTGGGGAGCCTCTGTGgtgagtacca ... tgatgcgcagGTGCGGTGGGCTACTTGGGCTCGAGCGTGTTTGTTCGGAGGATCTATAGGA
EST: gi|169095560|gb|FE498836.1|FE498836
EST:     CTACTTCGGCTACACTCTGATGCTCTGCGTTGGACTGGGGAGCCTCTGTG                         GTGCGGTGGGCTACTTGGGCTCGAGCGTGTTTGTTCGGAGGATCTATAGGA
genomic: CTACTTCGGCTACACTCTGATGCTCTGCGTTGGACTGGGGAGCCTCTGTGgtgagtacca ... tgatgcgcagGTGCGGTGGGCTACTTGGGCTCGAGCGTGTTTGTTCGGAGGATCTATAGGA
EST: gi|169114581|gb|FE515530.1|FE515530
EST:     CTACTTCGGCTACACTCTGATGCTCTGCGTTGGACTGGGGAGCCTCTGTG                         GTGCGGTGGGCTACTTGGGCTCGAGCGTGTTTGTTCGGAGGATCTATAGGA
genomic: CTACTTCGGCTACACTCTGATGCTCTGCGTTGGACTGGGGAGCCTCTGTGgtgagtacca ... tgatgcgcagGTGCGGTGGGCTACTTGGGCTCGAGCGTGTTTGTTCGGAGGATCTATAGGA

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: 30

TACTACTACTTCATGAAGACCAAGATGTCCGGGTTTTTCCAAACGAGTTTCTACTTCGGCTACACTCTGATGCTCTGCGTTGGACTGGGGAGCCTCTGTGgtgagtacca ... tgatgcgcagGTGCGGTGGGCTACTTGGGCTCGAGCGTGTTTGTTCGGAGGATCTATAGGAACATTAAGTGCGACTAAATCACCATTTCCCACATCCATTTGTTGCTGAC




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