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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgagaagattgatgtttttatttcctctttgatcaccctcagcgtttttgtagATTTTGAAGACATGAGCTGTGAGATGATCTATGGGCTCCAGCCAACCTCTCTTGAAGAAGATCCTGCATTGAAGCAACCATGCCTCCAGCTAT

Basic information

species Selaginella moellendorffii
transcript EFJ25335
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ25335 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: AT1G64680.1 (Arabidopsis thaliana), 3'ss of exon 2
-------------------------gtacgagaagattgatgtttttatttcctctttgatcaccctcagcgtttttgtagATTTTGAAGACATGAGCTGTGAGATGATCTATGGGCTCCAGCCAACCTCTCTTGAAGAAGATCCTGCATTGAAGCAACCATGCCTC-CAGCTAT--
                          | |    | |||| ||||| | |||| |     ||| | |        |||||||||| ||||||||||||||| |||||||| || ||||     ||  |  |  |||| || |||   ||    |||||||| || ||  ||| |||  
gtatgtaacatatctccttttgaccatccttatacattggtgtttgt-tttcattagccatctctccattttggtttgtagATTATGAAGACATGAGCTGCGAGATGATATACGGGCAAGCACCTCCGGCCTTTGAGGAGGATGTAGCCACCAAGCAACCTTGTCTAGCAGATATAT
















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|169068945|gb|FE476662.1|FE476662
EST:     CCAGGATTTCTTCACAAATGACTTTGGGTTGCCTCTCACCATGACACCAA                         ATTTTGAAGACATGAGCTGTGAGATGATCTATGGGCTCCAGCCAACCTCTC
genomic: CCAGGATTTCTTCACAAATGACTTTGGGTTGCCTCTCACCATGACACCAAgtacgagaag ... gtttttgtagATTTTGAAGACATGAGCTGTGAGATGATCTATGGGCTCCAGCCAACCTCTC
EST: gi|169077052|gb|FE485367.1|FE485367
EST:     CCAGGATTTCTTCACAAATGACTTTGGGTTGCCTCTCACCATGACACCAA                         ATTTTGAAGACATGAGCTGTGAGATGATCTATGGGCTCCAGCCAACCTCTC
genomic: CCAGGATTTCTTCACAAATGACTTTGGGTTGCCTCTCACCATGACACCAAgtacgagaag ... gtttttgtagATTTTGAAGACATGAGCTGTGAGATGATCTATGGGCTCCAGCCAACCTCTC
EST: gi|169101826|gb|FE500772.1|FE500772
EST:     CCAGGATTTCTTCACAAATGACTTTGGGTTGCCTCTCACCATGACACCAA                         ATTTTGAAGACATGAGCTGTGAGATGATCTATGGGCTCCAGCCAACCTCTC
genomic: CCAGGATTTCTTCACAAATGACTTTGGGTTGCCTCTCACCATGACACCAAgtacgagaag ... gtttttgtagATTTTGAAGACATGAGCTGTGAGATGATCTATGGGCTCCAGCCAACCTCTC
EST: gi|169046384|gb|FE457388.1|FE457388
EST:     CCAGGATTTCTTCACAAATGACTTTGGGTTGCCTCTCACCATGACACCAA                         ATTTTGAAGACATGAGCTGTGAGATGATCTATGGGCTCCAGCCAACCTCTC
genomic: CCAGGATTTCTTCACAAATGACTTTGGGTTGCCTCTCACCATGACACCAAgtacgagaag ... gtttttgtagATTTTGAAGACATGAGCTGTGAGATGATCTATGGGCTCCAGCCAACCTCTC
EST: gi|169101827|gb|FE500773.1|FE500773
EST:     CCAGGATTTCTTCACAAATGACTTTGGGTTGCCTCTCACCATGACACCAA                         ATTTTGAAGACATGAGCTGTGAGATGATCTATGGGCTCCAGCCAACCTCTC
genomic: CCAGGATTTCTTCACAAATGACTTTGGGTTGCCTCTCACCATGACACCAAgtacgagaag ... gtttttgtagATTTTGAAGACATGAGCTGTGAGATGATCTATGGGCTCCAGCCAACCTCTC
EST: gi|169068806|gb|FE478499.1|FE478499
EST:     CCAGGATTTCTTCACAAATGACTTTGGGTTGCCTCTCACCATGACACCAA                         ATTTTGAAGACATGAGCTGTGAGATGATCTATGGGCTCCAGCCAACCTCTC
genomic: CCAGGATTTCTTCACAAATGACTTTGGGTTGCCTCTCACCATGACACCAAgtacgagaag ... gtttttgtagATTTTGAAGACATGAGCTGTGAGATGATCTATGGGCTCCAGCCAACCTCTC
EST: gi|169068944|gb|FE476661.1|FE476661
EST:     CCAGGATTTCTTCACAAATGACTTTGGGTTGCCTCTCACCATGACACCAA                         ATTTTGAAGACATGAGCTGTGAGATGATCTATGGGCTCCAGCCAACCTCTC
genomic: CCAGGATTTCTTCACAAATGACTTTGGGTTGCCTCTCACCATGACACCAAgtacgagaag ... gtttttgtagATTTTGAAGACATGAGCTGTGAGATGATCTATGGGCTCCAGCCAACCTCTC
EST: gi|169046385|gb|FE457389.1|FE457389
EST:     CCAGGATTTCTTCACAAATGACTTTGGGTTGCCTCTCACCATGACACCAA                         ATTTTGAAGACATGAGCTGTGAGATGATCTATGGGCTCCAGCCAACCTCTC
genomic: CCAGGATTTCTTCACAAATGACTTTGGGTTGCCTCTCACCATGACACCAAgtacgagaag ... gtttttgtagATTTTGAAGACATGAGCTGTGAGATGATCTATGGGCTCCAGCCAACCTCTC
EST: gi|169107502|gb|FE511667.1|FE511667
EST:     CCAGGATTTCTTCACAAATGACTTTGGGTTGCCTCTCACCATGACACCAA                         ATTTTGAAGACATGAGCTGTGAGATGATCTATGGGCTCCAGCCAACCTCTC
genomic: CCAGGATTTCTTCACAAATGACTTTGGGTTGCCTCTCACCATGACACCAAgtacgagaag ... gtttttgtagATTTTGAAGACATGAGCTGTGAGATGATCTATGGGCTCCAGCCAACCTCTC

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), 28 (downstream exon)
Score: 7

GAGAACAGCAATTGTGTTGGAATGTGCGTAAATATGTGTAAAATTCCCACCCAGGATTTCTTCACAAATGACTTTGGGTTGCCTCTCACCATGACACCAAgtacgagaag ... gtttttgtagATTTTGAAGACATGAGCTGTGAGATGATCTATGGGCTCCAGCCAACCTCTCTTGAAGAAGATCCTGCATTGAAGCAACCATGCCTCCAGCTAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacgagaagattgatgtttttatttcctctttgatcaccctcagcgtttttgtagATTTTGAAGACATGAGCTGTGAGATGATCTATGGGCTCCAGCCAACCTCTCTTGAAGAAGATCCTGCATTGAAGCAACCATGCCTCCAGCTAT
                                            cgttttt  CT-rich tract
         attgatgtttttattt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgagaagattgatgtttttatttcctctttgatcaccctcagcgtttttgtagATTTTGAAGACATGAGCTGTGAGATGATCTATGGGCTCCAGCCAACCTCTCTTGAAGAAGATCCTGCATTGAAGCAACCATGCCTCCAGCTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA