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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcttccactttcaagtaacctgtgattgaatctggcgtgtaaatccaagGTCGGGCCAAGGTTTTGTCTGAATCCCATCAAGATCTTCAGTGCTAGCATGGGTGGGAAGCCGCTGTACGAGAATCCCTTCTACACGGCTCCAAACATG

Basic information

species Selaginella moellendorffii
transcript EFJ12424
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ12424 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: AT1G52930.1 (Arabidopsis thaliana), 3'ss of exon 5
-------------------------gtaagtcttccactttcaa--gtaacctgtgattgaatctggcg---tgtaaatccaagGTCGGGCCAAGGTTTTGTCTGAATCCCATCAAGATCTTCAGTGCTAGCATGGGTGGGAAGCCGCTGTACGAGAATCCCTTCTACACGGCTCCAAACATG
                          | | |  |   ||||| |   |    | ||||||||   |      | |  |    |||| || |||||||||||||||||||| |||||||| |||   |  ||| | || ||     | || || ||||| || || |||    ||||||||  |
gtttgtggacaaagagttacaaacttttaataatagtctttcgaccatggtttttgattgaaatggatacactattgacaacagGTTGGTCCAAGGTTTTGTCTGAATCCAATCAAGATATTCGCGGGCAGCTTTGGAGGTCCTACTCTTTATGAGAACCCGTTATACGTATCTCCAAACCAG
















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|169061551|gb|FE469338.1|FE469338
EST:     ATTCAGACAAGCTCGACCGAGCGTCTGCCGAGAAGATGACTCTGATTGAG                         GTCGGGCCAAGGTTTTGTCTGAATCCCATCAAGATCTTCAGTGCTAGCATG
genomic: ATTCCGACAAGCTCGACCGAGCGTCTGCCGAGAAGATGACTCTGATTGAGgtaagtcttc ... taaatccaagGTCGGGCCAAGGTTTTGTCTGAATCCCATCAAGATCTTCAGTGCTAGCATG
EST: gi|169049031|gb|FE456109.1|FE456109
EST:     ATTCAGACAAGCTCGACCGAGCGTCTGCCGAGAAGATGACTCTGATTGAG                         GTCGGGCCAAGGTTTTGTCTGAATCCCATCAAGATCTTCAGTGCTAGCATG
genomic: ATTCCGACAAGCTCGACCGAGCGTCTGCCGAGAAGATGACTCTGATTGAGgtaagtcttc ... taaatccaagGTCGGGCCAAGGTTTTGTCTGAATCCCATCAAGATCTTCAGTGCTAGCATG
EST: gi|169060063|gb|FE468673.1|FE468673
EST:     ATTCAGACAAGCTCGACCGAGCGTCTGCCGAGAAGATGACTCTGATTGAN                         GTCGGGCCCAGGTTTTGTCTGAATCCCATCAAGATCTTCAGTGCTAGCATG
genomic: ATTCCGACAAGCTCGACCGAGCGTCTGCCGAGAAGATGACTCTGATTGAGgtaagtcttc ... taaatccaagGTCGGGCCAAGGTTTTGTCTGAATCCCATCAAGATCTTCAGTGCTAGCATG
EST: gi|169049030|gb|FE456108.1|FE456108
EST:     ATTCAGACAAGCTCGACCGAGCGTCTGCCGAGAAGATGACTTTGATTGAG                         GTCGGGCCAAGGTTTTGTTTGAATCCCATCAAGATTTTCAGTGCTAGCATG
genomic: ATTCCGACAAGCTCGACCGAGCGTCTGCCGAGAAGATGACTCTGATTGAGgtaagtcttc ... taaatccaagGTCGGGCCAAGGTTTTGTCTGAATCCCATCAAGATCTTCAGTGCTAGCATG
EST: gi|169071863|gb|FE477617.1|FE477617
EST:     ATTCAGACAAGCTCGACCGAGCGTCTGCCGAGAAGATGACTCTGATTGAG                         GTCGGGCCAAGGTTTTGTCTGAATCCCATCAAGATCTTCAGTGCTAGCATG
genomic: ATTCCGACAAGCTCGACCGAGCGTCTGCCGAGAAGATGACTCTGATTGAGgtaagtcttc ... taaatccaagGTCGGGCCAAGGTTTTGTCTGAATCCCATCAAGATCTTCAGTGCTAGCATG
EST: gi|169060062|gb|FE468672.1|FE468672
EST:     ATTCAGACAAGCTCGACCGAGCGTCTGCCGAGAAGATGACTCTGATTGAG                         GTCGGGCCAAGGTTTTGTCTGAATCCCATCAAGATCTTCAGTGCTAGCATG
genomic: ATTCCGACAAGCTCGACCGAGCGTCTGCCGAGAAGATGACTCTGATTGAGgtaagtcttc ... taaatccaagGTCGGGCCAAGGTTTTGTCTGAATCCCATCAAGATCTTCAGTGCTAGCATG
EST: gi|169099356|gb|FE502129.1|FE502129
EST:     ATTCAGACAAGCTCGACCGAGCGTCTGCCGAGAAGATGACTCTGATTGAG                         GTCGGGCCAAGGTTTTGTCTGAATCCCATCAAGATCTTCAGTGCTAGCATG
genomic: ATTCCGACAAGCTCGACCGAGCGTCTGCCGAGAAGATGACTCTGATTGAGgtaagtcttc ... taaatccaagGTCGGGCCAAGGTTTTGTCTGAATCCCATCAAGATCTTCAGTGCTAGCATG
EST: gi|169071864|gb|FE477618.1|FE477618
EST:     ATTCAGACAAGCTCGACCGAGCGTCTGCCGAGAAGATGACTCTGATTGAG                         GTCGGGCCAAGGTTTTGTCTGAATCCCATCAAGATCTTCAGTGCTAGCATG
genomic: ATTCCGACAAGCTCGACCGAGCGTCTGCCGAGAAGATGACTCTGATTGAGgtaagtcttc ... taaatccaagGTCGGGCCAAGGTTTTGTCTGAATCCCATCAAGATCTTCAGTGCTAGCATG
EST: gi|169053952|gb|FE461251.1|FE461251
EST:     ATTCAGACAAGCTCGACCGAGCGTCTGCCGAGAAGATGACTCTGATTGAG                         GTCGGGCCAAGGTTTTGTCTGAATCCCATCAAGATCTTCAGTGCTAGCATG
genomic: ATTCCGACAAGCTCGACCGAGCGTCTGCCGAGAAGATGACTCTGATTGAGgtaagtcttc ... taaatccaagGTCGGGCCAAGGTTTTGTCTGAATCCCATCAAGATCTTCAGTGCTAGCATG
EST: gi|169099357|gb|FE502130.1|FE502130
EST:     ATTCAGACAAGCTCGACCGAGCGTCTGCCGAGAAGATGACTCTGATTGAG                         GTCGGGCCAAGGTTTTGTCTGAATCCCATNCA-GATCTTCAGTGCTAGCAT
genomic: ATTCCGACAAGCTCGACCGAGCGTCTGCCGAGAAGATGACTCTGATTGAGgtaagtcttc ... taaatccaagGTCGGGCCAAGGTTTTGTCTGAATCCCAT-CAAGATCTTCAGTGCTAGCAT

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: 29 (upstream exon), 30 (downstream exon)
Score: 9

ATATCTGTGCCACACCATGATTCCGACAAGCTCGACCGAGCGTCTGCCGAGAAGATGACTCTGATTGAGgtaagtcttc ... taaatccaagGTCGGGCCAAGGTTTTGTCTGAATCCCATCAAGATCTTCAGTGCTAGCATGGGTGGGAAGCCGCTGTACGAGAATCCCTTCTACACGGCTCCAAACATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaagtcttccactttcaagtaacctgtgattgaatctggcgtgtaaatccaagGTCGGGCCAAGGTTTTGTCTGAATCCCATCAAGATCTTCAGTGCTAGCATGGGTGGGAAGCCGCTGTACGAGAATCCCTTCTACACGGCTCCAAACATG
                  aagtaac  putative branch site (score: 9)
                               attgaat  TA-rich tract