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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttagcttagcatgttttggacgatgggcccctgaatgacgaatgtactgtgctttggcagCCGGACACAATCACCGGGGACATCATCTTCGTTTTGCAACAGAAGGAGCATCCCAAGTTCAAGAGGAAGGGCGACGATCTCTTTCTGGAGCACAGCCTCT

Basic information

species Selaginella moellendorffii
transcript EFJ24912
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ24912 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: PP1S100_36V6.1 (Physcomitrella patens), 3'ss of exon 5
-------------------------------------------------------gtaagttagcttagcatg-ttttggacgat---gggcccctgaat-gacgaa----tgtac-tgtgctttggcagCCGGACACAATCACCGGGGACATCATCTTCGTTTTGCAACAGAAGGAGCATCCCAAGTTCAAGAGGAAGGGCGACGATCTCTTTCTGGAGCACAGCCTCT
                                                       |||  ||    |    || || |    |||   |    |||||||  ||  |    |||    || ||   ||||||||| || || || || |||||| |||| || ||||||| |||||||||||| || ||||||||||| | ||||||||| ||| ||||||| |   |  
gtacgtttcccagaacaaccacgtcaatgattatttatagttttgggatgccttagtagattgcaatgttgtggttcttcgtgattcggtattcctgaattaacacacctttgtgtgcgtcctcgtgcagCCGGATACCATTACAGGTGACATCGTCTTTGTATTGCAACTGAAGGAGCATCCTAAATTCAAGAGGAAAGTCGACGATCTGTTTGTGGAGCATACTTTGA

upper sequence: EFJ24912 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: PP1S174_37V6.1 (Physcomitrella patens), 3'ss of exon 4
----------------------------------------------------------------------------------------------------------------gtaa-gttagcttagcatgttttggacgatgggcccctgaatgacgaatgtactgtgctt-tggcagCCGGACACAATCACCGGGGACATCATCTTCGTTTTGCAACAGAAGGAGCATCCCAAGTTCAAGAGGAAGGGCGACGATCTCTTTCTGGAGCACAGCCTCT
                                                                                                                 ||| ||||   | | |   |   |||| |  |        |   |       |||| || | |||||| |||||| | || || |||||  | ||||||||||||| ||||||||| || |||||||||||||| || || ||||| ||| ||||||| |   |  
gtgcgttactctccgtgcgttcaaggcgtgctcttctgacaacaaatttcgtagaagtttttgtgaacaggataacgcttggatgtgtatatggattgtctgatacgaaaagttaatgttattctggaaacatgctgacggttagattgcattttgtgtgatcgatgtgtttgttgcagCCCGACACAGTGACAGGAGACATTGTATTCGTTTTGCAACTGAAGGAGCACCCGAAGTTCAAGAGGAAAGGGGATGATCTGTTTGTGGAGCATACTTTGA

upper sequence: EFJ24912 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: PP1S174_97V6.1 (Physcomitrella patens), 3'ss of exon 4
-------------------------------------------------------------------------------------------------------------------------gtaagttagct-tagcatgttttggacgatgggcccctgaatgacgaatgtact--gtgctttgg---cagCCGGACACAATCACCGGGGACATCATCTTCGTTTTGCAACAGAAGGAGCATCCCAAGTTCAAGAGGAAGGGCGACGATCTCTTTCTGGAGCACAGCCTCT
                                                                                                                         |   |||||    |     ||  | || |||      |||     || |||  |   ||  ||||    |||   | | |   || |  ||  |  | |||||||| |||| ||||||||||||  ||||||| ||||| || ||||| || |||||||||| ||  ||  
gtatgtaatgctgtaggatgtatttgcggctatgtggggttgaatgtaatgtttgactctggagaaggtgggagtaagttatgttgatgggagttttatgtgtaggagaagttgacgatacgcgtgttaggggcattgcattgcgaac-atgcaatggtgacacgtgattgtctttgttgtgttggatatagCACAAGAAAGCAACAGAAGATGTTGTGTTCGTTTTACAACTGAAGGAGCATCCGGAGTTCAAAAGGAAAGGAGACGACCTGTTTCTGGAGCGCACACTGA

upper sequence: EFJ24912 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: PP1S17_208V6.1 (Physcomitrella patens), 3'ss of exon 4
-----------------------------------gtaagttagcttagcatgttttggacgatgggcccctgaatgacgaatgtac-tgtgctttg-gcagCCGGACACAATCACCGGGGACATCATCTTCGTTTTGCAACAGAAGGAGCATCCCAAGTTCAAGAGGAAGGGCGACGATCTCTTTCTGGAGCACAGCCTCT
                                    ||| ||| ||          ||   | |||   |  |  ||  |  |||   ||||  ||| |||||| ||||||   || || || ||| | ||||| ||||||  |||||||||||| |||||||||||||| || || ||| | ||| |||||||||   |  
atggacctttaagattggtatgttggtaggaattgataactta-ctggctgcacgctgagagttggattcg-gtttgctgtgtgtgtgtgtgtgttgagcagCCTGACACACAGACTGGAGATATCGTGTTCGTGTTGCAATTGAAGGAGCATCCTAAGTTCAAGAGGAAAGGGGATGATTTGTTTGTGGAGCACACATTGA

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|169047450|gb|FE455645.1|FE455645
EST:     GAATGTCTCACAATCAAAAGATTACTTTCCAAGGAGAGGCCGACGAAGCG                         CCGGACACAATCACCGGGGACATCATCTTCGTTTTGCAACAGAAGGAGCAT
genomic: GAATGTCTCACAATCAAAAGATTACTTTCCAAGGAGAGGCCGACGAAGCGgtaagttagc ... gctttggcagCCGGACACAATCACCGGGGACATCATCTTCGTTTTGCAACAGAAGGAGCAT
EST: gi|169113322|gb|FE515273.1|FE515273
EST:     GAATGTCTCACAATCAGAAGATTACCTTCCAAGGAGAGGCCGACGAAGCG                         CCGGACACAATCACCGGGGACATCATCTTCGTTTTGCAACAGAAGGAGCAT
genomic: GAATGTCTCACAATCAAAAGATTACTTTCCAAGGAGAGGCCGACGAAGCGgtaagttagc ... gctttggcagCCGGACACAATCACCGGGGACATCATCTTCGTTTTGCAACAGAAGGAGCAT
EST: gi|169050972|gb|FE458142.1|FE458142
EST:     GAATGTCTCACAATCAGAAGATTACCTTCCAAGGAGAGGCCGACGAAGCG                         CCGGACACAATCACCGGGGACATCATCTTCGTTTTGCAACAGAAGGAGCAT
genomic: GAATGTCTCACAATCAAAAGATTACTTTCCAAGGAGAGGCCGACGAAGCGgtaagttagc ... gctttggcagCCGGACACAATCACCGGGGACATCATCTTCGTTTTGCAACAGAAGGAGCAT
EST: gi|169104150|gb|FE507139.1|FE507139
EST:     GAATGTCTCACAATCAAAAGATTACTTTCCAAGGAGAGGCCGACGAAGCG                         CCGGACACAATCACCGGGGACATCATCTTCGTTTTGCAACAGAAGGAGCAT
genomic: GAATGTCTCACAATCAAAAGATTACTTTCCAAGGAGAGGCCGACGAAGCGgtaagttagc ... gctttggcagCCGGACACAATCACCGGGGACATCATCTTCGTTTTGCAACAGAAGGAGCAT
EST: gi|169050973|gb|FE458143.1|FE458143
EST:     GAATGTCTCACAATCAGAAGATTACCTTCCAAGGAGAGGCCGACGAAGCG                         CCGGACACAATCACCGGGGACATCATCTTCGTTTTGCAACAGAAGGAGCAT
genomic: GAATGTCTCACAATCAAAAGATTACTTTCCAAGGAGAGGCCGACGAAGCGgtaagttagc ... gctttggcagCCGGACACAATCACCGGGGACATCATCTTCGTTTTGCAACAGAAGGAGCAT
EST: gi|169087097|gb|FE496203.1|FE496203
EST:     GAATGTCTCACAATCAGAAGATTACCTTCCAAGGAGAGGCCGACGAAGCG                         CCGGACACAATCACCGGGGACATCATCTTCGTTTTGCAACAGAAGGAGCAT
genomic: GAATGTCTCACAATCAAAAGATTACTTTCCAAGGAGAGGCCGACGAAGCGgtaagttagc ... gctttggcagCCGGACACAATCACCGGGGACATCATCTTCGTTTTGCAACAGAAGGAGCAT
EST: gi|169104151|gb|FE507140.1|FE507140
EST:     GAATGTCTCACAATCAAAAGATTACTTTCCAAGGAGAGGCCGACGAAGCG                         CCGGACACAATCACCGGGGACATCATCTTCGTTTTGCAACAGAAGGAGCAT
genomic: GAATGTCTCACAATCAAAAGATTACTTTCCAAGGAGAGGCCGACGAAGCGgtaagttagc ... gctttggcagCCGGACACAATCACCGGGGACATCATCTTCGTTTTGCAACAGAAGGAGCAT
EST: gi|169112343|gb|FE512919.1|FE512919
EST:     GAATGTCTCACAATCAGAAGATTACCTTCCAAGGAGAGGCCGACGAAGCG                         CCGGACACAATCACCGGGGACATCATCTTCGTTTTGCAACAGAAGGAGCAT
genomic: GAATGTCTCACAATCAAAAGATTACTTTCCAAGGAGAGGCCGACGAAGCGgtaagttagc ... gctttggcagCCGGACACAATCACCGGGGACATCATCTTCGTTTTGCAACAGAAGGAGCAT
EST: gi|169112344|gb|FE512920.1|FE512920
EST:     GAATGTCTCACAATCAGAAGATTACCTTCCNAGGAGAGGCCGACGAAGCG                         CCGGACACAATCACCGGGGACATCATCTTCG
genomic: GAATGTCTCACAATCAAAAGATTACTTTCCAAGGAGAGGCCGACGAAGCGgtaagttagc ... gctttggcagCCGGACACAATCACCGGGGACATCATCTTCG
EST: gi|169047451|gb|FE455646.1|FE455646
EST:     GAATGTCTCACAATCAAAAGATTACTTTCCAAGGAGAGGCCGACGAAGCG                         CCGGACACAATCACCGGGGACATCATCTTCGTTTTGCAACAGAAGGAGCAT
genomic: GAATGTCTCACAATCAAAAGATTACTTTCCAAGGAGAGGCCGACGAAGCGgtaagttagc ... gctttggcagCCGGACACAATCACCGGGGACATCATCTTCGTTTTGCAACAGAAGGAGCAT
EST: gi|169087137|gb|FE496204.1|FE496204
EST:     GAATGTCTCACAATCAGAAGATTACCTTCCAAGGAGAGGCCGACGAAGCG                         CCGGACACAATCACCGGGGACATCATCTTCGTTTTGCAACAGAAGGAGCAT
genomic: GAATGTCTCACAATCAAAAGATTACTTTCCAAGGAGAGGCCGACGAAGCGgtaagttagc ... gctttggcagCCGGACACAATCACCGGGGACATCATCTTCGTTTTGCAACAGAAGGAGCAT
EST: gi|169062696|gb|FE470782.1|FE470782
EST:     GAATGTCTCACAATCAAAAGATTACTTTCCAAGGAGAGGCCGACGAAGCG                         CCGGACACAATCACCGGGGACATCATCTTCGTTTTGCAACAGAAGGAGCAT
genomic: GAATGTCTCACAATCAAAAGATTACTTTCCAAGGAGAGGCCGACGAAGCGgtaagttagc ... gctttggcagCCGGACACAATCACCGGGGACATCATCTTCGTTTTGCAACAGAAGGAGCAT

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: 35 (upstream exon), 35 (downstream exon)
Score: 35

CAAGGTTGTCCTTCAAGAGAAGAAGCTTCTAGAGGTTTTTGTCGAGAAGGGAATGTCTCACAATCAAAAGATTACTTTCCAAGGAGAGGCCGACGAAGCGgtaagttagc ... gctttggcagCCGGACACAATCACCGGGGACATCATCTTCGTTTTGCAACAGAAGGAGCATCCCAAGTTCAAGAGGAAGGGCGACGATCTCTTTCTGGAGCACAGCCTCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagcatgttttggacgatgggcccctgaatgacgaatgtactgtgctttggcagCCGGACACAATCACCGGGGACATCATCTTCGTTTTGCAACAGAAGGAGCATCCCAAGTTCAAGAGGAAGGGCGACGATCTCTTTCTGGAGCACAGCCTCT
     atgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttagcttagcatgttttggacgatgggcccctgaatgacgaatgtactgtgctttggcagCCGGACACAATCACCGGGGACATCATCTTCGTTTTGCAACAGAAGGAGCATCCCAAGTTCAAGAGGAAGGGCGACGATCTCTTTCTGGAGCACAGCCTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA