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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttttttctataccagttttagtttagaacaatgttttccagGTTTGTGCGTACAAGGATGGAAAAGTTATCGTCGATACAGCGGCTGGTTACCTTGGAAAGTATGATCCTCGCCCGGTGCGTTGTGACAGTTTGTTTCTGG

Basic information

species Selaginella moellendorffii
transcript EFJ33842
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ33842 (Selaginella moellendorffii), 3'ss of exon 16
lower sequence: PP1S81_95V6.1 (Physcomitrella patens), 3'ss of exon 14
---------------------------------------------------gtaagttttttc---tataccagttttagtttagaacaatgttttccagGTTTGTGCGTACAAGGATGGAAAAGTTATCGTCGATACAGCGGCTGGTTACCTTGGAAAGTATGATCCTCGCCCGGTGCGTTGTGACAGTTTGTTTCTGG
                                                    |  | | || |    ||||  | |  |  |||  ||||   ||||||||||||||| || ||||||||||||||| |  | || || ||||  ||    |||||||||| ||||||  | || || |     || || |||||     
tctgtatgttttctgtgtttcttctcttattgaattcctcattctcagtagatgcgctcttgcgatcatacatgctcgacattaagacaaatgtttccagGTTTGTGCATATAAGGATGGAAAAGTTGTTCTTGACACTGCGGGCGGAGTACTTGGAAAGTTTGATCCAAGGCCAGTTCAACCAGATAGCTTGTTCTCTT
















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|169029830|gb|FE441037.1|FE441037
EST:     ATCAACTTTTACGTGAGATGCACAAGCAACAACGGATACTTGGTGTTCAA                         GTTTGTGCGTACAAGGATGGAAAAGTTATCGTCGATACAGCGGCTGGTTAC
genomic: ATCAACTTTTACGTGAGATGCACAAGCAACAACGGATACTTGGTGTTCAAgtaagttttt ... tgttttccagGTTTGTGCGTACAAGGATGGAAAAGTTATCGTCGATACAGCGGCTGGTTAC
EST: gi|169056743|gb|FE463916.1|FE463916
EST:     ATCAACTTTTACGTGAGATGCACAAGCAACAACGGATACTTGGTGTTCAA                         GTTTGTGCGTACAAGGATGGAAAAGTTATCGTCGATACAGCGGCTGGTTAC
genomic: ATCAACTTTTACGTGAGATGCACAAGCAACAACGGATACTTGGTGTTCAAgtaagttttt ... tgttttccagGTTTGTGCGTACAAGGATGGAAAAGTTATCGTCGATACAGCGGCTGGTTAC
EST: gi|169067871|gb|FE473416.1|FE473416
EST:     ATCAACTTTTACGTGAGATGCACAAGCAACAACGGATACTTGGTGTTCAA                         GTTTGTGCGTACAAGGATGGAAAAGTTATCGTCGATACAGCGGCTGGTTAC
genomic: ATCAACTTTTACGTGAGATGCACAAGCAACAACGGATACTTGGTGTTCAAgtaagttttt ... tgttttccagGTTTGTGCGTACAAGGATGGAAAAGTTATCGTCGATACAGCGGCTGGTTAC
EST: gi|169055550|gb|FE464583.1|FE464583
EST:     ATCAACTTTTACGTGAGATGCACAAGCAACAACGGATACTTGGTGTTCAA                         GTTTGTGCGTACAAGGATGGAAAAGTTATCGTCGATACAGCGGCTGGTTAC
genomic: ATCAACTTTTACGTGAGATGCACAAGCAACAACGGATACTTGGTGTTCAAgtaagttttt ... tgttttccagGTTTGTGCGTACAAGGATGGAAAAGTTATCGTCGATACAGCGGCTGGTTAC
EST: gi|169049893|gb|FE458609.1|FE458609
EST:     ATCAACTTTTACGTGAGATGCACAAGCAACAACGGATACTTGGTGTTCAA                         GTTTGTGCGTACAAGGATGGAAAAGTTATCGTCGATACAGCGGCTGGTTAC
genomic: ATCAACTTTTACGTGAGATGCACAAGCAACAACGGATACTTGGTGTTCAAgtaagttttt ... tgttttccagGTTTGTGCGTACAAGGATGGAAAAGTTATCGTCGATACAGCGGCTGGTTAC
EST: gi|169099786|gb|FE500791.1|FE500791
EST:     ATCAACTTTTACGTGAGATGCACAAGCAACAACCTTTACTTGGTGTTCAA                         GTTTGTGCGTACAAGGATGGAAAAGTTATCGTCGATACAGCGGCTGGTTAC
genomic: ATCAACTTTTACGTGAGATGCACAAGCAACAACGGATACTTGGTGTTCAAgtaagttttt ... tgttttccagGTTTGTGCGTACAAGGATGGAAAAGTTATCGTCGATACAGCGGCTGGTTAC
EST: gi|169099114|gb|FE502836.1|FE502836
EST:     ATCAACTTTTACGTGAGATGCACAAGCAACAACGGATACTTGGTGTTCAA                         GTTTGTGCGTACAAGGATGGAAAAGTTATCGTCGATACAGCGGCTGGTTAC
genomic: ATCAACTTTTACGTGAGATGCACAAGCAACAACGGATACTTGGTGTTCAAgtaagttttt ... tgttttccagGTTTGTGCGTACAAGGATGGAAAAGTTATCGTCGATACAGCGGCTGGTTAC
EST: gi|169068100|gb|FE477390.1|FE477390
EST:     ATCAACTTTTACGTGAGATGCACAAGCAACAACGGATACTTGGTGTTCAA                         GTTTGTGCGTACAAGGATGGAAAAGTTATCGTCGATACAGCGGCTGGTTAC
genomic: ATCAACTTTTACGTGAGATGCACAAGCAACAACGGATACTTGGTGTTCAAgtaagttttt ... tgttttccagGTTTGTGCGTACAAGGATGGAAAAGTTATCGTCGATACAGCGGCTGGTTAC
EST: gi|169038685|gb|FE450156.1|FE450156
EST:     ATCAACTTTTACGTGAGATGCACAAGCAACAACGGATACTTGGTGTTCAA                         GTTTGTGCGTACAAGGATGGAAAAGTTATCGTCGATACAGCGGCTGGTTAC
genomic: ATCAACTTTTACGTGAGATGCACAAGCAACAACGGATACTTGGTGTTCAAgtaagttttt ... tgttttccagGTTTGTGCGTACAAGGATGGAAAAGTTATCGTCGATACAGCGGCTGGTTAC
EST: gi|169019820|gb|FE426907.1|FE426907
EST:     ATCAACTTTTACGTGAGATGCACAAGCAACAACGGATACTTGGTGTTCAA                         GTTTGTGCGTACAAGGATGGAAAAGTTATCGTCGATACAGCGGCTGGTTAC
genomic: ATCAACTTTTACGTGAGATGCACAAGCAACAACGGATACTTGGTGTTCAAgtaagttttt ... tgttttccagGTTTGTGCGTACAAGGATGGAAAAGTTATCGTCGATACAGCGGCTGGTTAC
EST: gi|169031178|gb|FE440383.1|FE440383
EST:     ACAACGGATACTTGGTGTTCAA                         GTTTGTGCGTACAAGGATGGAAAAGTTATCGTCGATACAGCGGCTGGTTAC
genomic: ACAACGGATACTTGGTGTTCAAgtaagttttt ... tgttttccagGTTTGTGCGTACAAGGATGGAAAAGTTATCGTCGATACAGCGGCTGGTTAC
EST: gi|169082975|gb|FE488497.1|FE488497
EST:     ATCAACTTTTACGTGAGATGCACAAGCAACAACGGATACTTGGTGTTCAA                         GTTTGTGCGTACAAGGATGGGAAAGTTATCGTCGATACAGCGGCTGGTTAC
genomic: ATCAACTTTTACGTGAGATGCACAAGCAACAACGGATACTTGGTGTTCAAgtaagttttt ... tgttttccagGTTTGTGCGTACAAGGATGGAAAAGTTATCGTCGATACAGCGGCTGGTTAC
EST: gi|169102500|gb|FE503903.1|FE503903
EST:     ATCAACTTTTACGTGAGATGCACAAGCAACAACGGATACTTGGTGTTCAA                         GTTTGTGCGTACAAGGATGGAAAAGTTATCGTCGATACAGCGGCTGGTTAC
genomic: ATCAACTTTTACGTGAGATGCACAAGCAACAACGGATACTTGGTGTTCAAgtaagttttt ... tgttttccagGTTTGTGCGTACAAGGATGGAAAAGTTATCGTCGATACAGCGGCTGGTTAC

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: 33 (upstream exon), 34 (downstream exon)
Score: 13

ACTACCAATTTTTGATAGTCCATTGCATTCTCAGGCTGAGGTCAAGCTCCATCAACTTTTACGTGAGATGCACAAGCAACAACGGATACTTGGTGTTCAAgtaagttttt ... tgttttccagGTTTGTGCGTACAAGGATGGAAAAGTTATCGTCGATACAGCGGCTGGTTACCTTGGAAAGTATGATCCTCGCCCGGTGCGTTGTGACAGTTTGTTTCTGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaagttttttctataccagttttagtttagaacaatgttttccagGTTTGTGCGTACAAGGATGGAAAAGTTATCGTCGATACAGCGGCTGGTTACCTTGGAAAGTATGATCCTCGCCCGGTGCGTTGTGACAGTTTGTTTCTGG
                                                     tgttttcc  CT-rich tract
          taagttttttctata  TA-rich tract