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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTATCGACAGAATCGTCGCGGGAATGGAAGGAACTACGATGACCGACGGCAAAACTAAGAGCCTTGTTGCTTATCACGAAGTTGGACATGCTGTGTGCGGgtaagattgctcacttttgttcgtttctttggcatcaaatactgacgcaggcttttcctgtttaacaag

Basic information

species Selaginella moellendorffii
transcript EFJ19987
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ19987 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: PP1S118_166V6.1 (Physcomitrella patens), 5'ss of exon 2
CTATCGACAGAATCGTCGCGGGAATGGAAGGAACTACGATGACCGACGGCAAAACTAAGAGCCTTGTTGCTTATCACGAAGTTGGACATGCTGTGTGCGGgtaaga---ttgctcacttttgttcgtttc-tttggcatcaaat-actgacgcaggcttttcctgtttaacaag---------------------------------------------------------------------------------------------------------------
| || ||||||||||| || || |||||||| ||    ||||| |||||||| |  ||||| |||||||| || |||||||| || |||||| | |||||||||||   |||  || ||  |   ||  | | |||  |    | |   | ||||  |||| || | ||                                                                                                                    
CAATTGACAGAATCGTTGCCGGGATGGAAGGTACCGTCATGACGGACGGCAAGAGCAAGAGTCTTGTTGCATACCACGAAGTCGGCCATGCTATCTGCGGgtaagaaacttgtacaattcgggatgtaccgtatggtttttgttcatatatgcag-ttttttctatgtagtggtggcttttgctggttctttgtagttggaataactgtgaagtgatatcttcacttaggtcaaaaccatttgatttctgtttgctgaagtgtatgtactgtgtattctgtgcag
















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|169115717|gb|FE517303.1|FE517303
EST:     AAAACTAAGAGCCTTGTTGCTTATCACGAAGTTGGACATGCTGTGTGCGG                         GACTCTGACGCCAGGACATGACCCGGTACAGAAAGTTACGTTGATACCACG
genomic: AAAACTAAGAGCCTTGTTGCTTATCACGAAGTTGGACATGCTGTGTGCGGgtaagattgc ... gtttaacaagGACTCTGACGCCAGGACATGACCCGGTACAGAAAGTTACGTTGATACCACG
EST: gi|169108620|gb|FE510796.1|FE510796
EST:     AAAACTAAGAGCCTTGTTGCTTATCACGAAGTTGGACATGCTGTGTGCGG                         GACTCTGACGCCAGGACATGACCCGGTACAGAAAGTTACGTTGATACCACG
genomic: AAAACTAAGAGCCTTGTTGCTTATCACGAAGTTGGACATGCTGTGTGCGGgtaagattgc ... gtttaacaagGACTCTGACGCCAGGACATGACCCGGTACAGAAAGTTACGTTGATACCACG
EST: gi|169094535|gb|FE492433.1|FE492433
EST:     GCTTATCACGAAGTTGGACATGCTGTGTGCGG                         GACTCTGACGCCAGGACATGACCCGGTACAGAAAGTTACGTTGATACCACG
genomic: GCTTATCACGAAGTTGGACATGCTGTGTGCGGgtaagattgc ... gtttaacaagGACTCTGACGCCAGGACATGACCCGGTACAGAAAGTTACGTTGATACCACG
EST: gi|169092756|gb|FE493698.1|FE493698
EST:     AAAACTAAGAGCCTTGTTGCTTATCACGAAGTTGGACATGCTGTGTGCGG                         GACTCTGACGCCAGGACATGACCCGGTACAGAAAGTTACGTTGATACCACG
genomic: AAAACTAAGAGCCTTGTTGCTTATCACGAAGTTGGACATGCTGTGTGCGGgtaagattgc ... gtttaacaagGACTCTGACGCCAGGACATGACCCGGTACAGAAAGTTACGTTGATACCACG
EST: gi|169056847|gb|FE465424.1|FE465424
EST:     AGAGCCTTGTTGCTTATCACGAAGTTGGACATGCTGTGTGCGG                         GACTCTGACGCCAGGACATGACCCGGTACAGAAAGTTACGTTGATACCACG
genomic: AGAGCCTTGTTGCTTATCACGAAGTTGGACATGCTGTGTGCGGgtaagattgc ... gtttaacaagGACTCTGACGCCAGGACATGACCCGGTACAGAAAGTTACGTTGATACCACG
EST: gi|169018982|gb|FE427375.1|FE427375
EST:     AAAACTAAGAGCCTTGTTGCTTATCACGAAGTTGGACATGCTGTGTGCGG                         GACTCTGACGCCAGGACATGACCCGGTACAGAAAGTTACGTTGATACCACG
genomic: AAAACTAAGAGCCTTGTTGCTTATCACGAAGTTGGACATGCTGTGTGCGGgtaagattgc ... gtttaacaagGACTCTGACGCCAGGACATGACCCGGTACAGAAAGTTACGTTGATACCACG
EST: gi|169098458|gb|FE498514.1|FE498514
EST:     AAGAGCCTTGTTGCTTATCACGAAGTTGGACATGCTGTGTGCGG                         GACTCTGACGCCAGGACATGACCCGGTACAGAAAGTTACGTTGATACCACG
genomic: AAGAGCCTTGTTGCTTATCACGAAGTTGGACATGCTGTGTGCGGgtaagattgc ... gtttaacaagGACTCTGACGCCAGGACATGACCCGGTACAGAAAGTTACGTTGATACCACG
EST: gi|169023480|gb|FE430078.1|FE430078
EST:     AAAACTAAGAGCCTTGTTGCTTATCACGAAGTTGGACATGCTGTGTGCGG                         GACTCTGACGCCAGGACATGACCCGGTACAGAAAGTTACGTTGATACCACG
genomic: AAAACTAAGAGCCTTGTTGCTTATCACGAAGTTGGACATGCTGTGTGCGGgtaagattgc ... gtttaacaagGACTCTGACGCCAGGACATGACCCGGTACAGAAAGTTACGTTGATACCACG
EST: gi|169098459|gb|FE498515.1|FE498515
EST:     AAAACTAAGAGCCTTGTTGCTTATCACGAAGTTGGACATGCTGTGTGCGG                         GACTCTGACGCCAGGACATGACCCGGTACAGAAAGTTACGTTGATACCACG
genomic: AAAACTAAGAGCCTTGTTGCTTATCACGAAGTTGGACATGCTGTGTGCGGgtaagattgc ... gtttaacaagGACTCTGACGCCAGGACATGACCCGGTACAGAAAGTTACGTTGATACCACG
EST: gi|169101335|gb|FE501997.1|FE501997
EST:     AAAACTAAGAGCCTTGTTGCTTATCACGAAGTTGGACATGCTGTGTGCGG                         GACTCTGACGCCAGGACATGACCCGGTACAGAAAGTTACGTTGATACCACG
genomic: AAAACTAAGAGCCTTGTTGCTTATCACGAAGTTGGACATGCTGTGTGCGGgtaagattgc ... gtttaacaagGACTCTGACGCCAGGACATGACCCGGTACAGAAAGTTACGTTGATACCACG
EST: gi|169023479|gb|FE430077.1|FE430077
EST:     TAAGAGCCTTGTTGCTTATCACGAAGTTGGACATGCTGTGTGCGG                         GACTCTGACGCCAGGACATGACCCGGTACAGAAAGTTACGTTGATACCACG
genomic: TAAGAGCCTTGTTGCTTATCACGAAGTTGGACATGCTGTGTGCGGgtaagattgc ... gtttaacaagGACTCTGACGCCAGGACATGACCCGGTACAGAAAGTTACGTTGATACCACG
EST: gi|169092755|gb|FE493697.1|FE493697
EST:     AAAACTAAGAGCCTTGTTGCTTATCACGAAGTTGGACATGCTGTGTGCGG                         GACTCTGACGCCAGGACATGACCCGGTACAGAAAGTTACGTTGATACCACG
genomic: AAAACTAAGAGCCTTGTTGCTTATCACGAAGTTGGACATGCTGTGTGCGGgtaagattgc ... gtttaacaagGACTCTGACGCCAGGACATGACCCGGTACAGAAAGTTACGTTGATACCACG

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), 35 (downstream exon)
Score: 25

CTATCGACAGAATCGTCGCGGGAATGGAAGGAACTACGATGACCGACGGCAAAACTAAGAGCCTTGTTGCTTATCACGAAGTTGGACATGCTGTGTGCGGgtaagattgc ... gtttaacaagGACTCTGACGCCAGGACATGACCCGGTACAGAAAGTTACGTTGATACCACGAGGCCAGGCTCGGGGCCTTACATGGTTTCTTCCGGGAGAGGACCCCACT




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTATCGACAGAATCGTCGCGGGAATGGAAGGAACTACGATGACCGACGGCAAAACTAAGAGCCTTGTTGCTTATCACGAAGTTGGACATGCTGTGTGCGGgtaagattgctcacttttgttcgtttctttggcatcaaatactgacgcaggcttttcctgtttaacaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG