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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCATGAGATATCCGAGCGCGTGAGAACTGGCTTATGGGTAGGCGATTGTTTCATTTACAACAACTCGTCATGGAGACTGAACTACTGCGTTGGAGGAGAGgtctgcttttgtattgtcgtttatatttgtttcacacttcctcttccag

Basic information

species Selaginella moellendorffii
transcript EFJ36319
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ36319 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: GRMZM2G443953_T03 (Zea mays), 5'ss of exon 16
GCATGAGATATCCGAGCGCGTGAGAACTGGCTTATGGGTAGGCGATTGTTTCATTTACAACAACTCGTCATGGAGACTGAACTACTGCGTTGGAGGAGAGgtctgcttttg----tattgtcgtttata-----tttgtttcacacttcctc--ttccag-------------------------------------------------
 |||||||||   || || ||  | ||||| |||||||| || || ||||| || ||||| || || |||||| | ||||||||||||||||||||||||||   |  ||      |   |  | | ||     ||   | || |  |  |   |||| |                                                 
TCATGAGATAAATGAACGTGTCCGTACTGGGTTATGGGTCGGAGACTGTTTTATATACAATAATTCTTCATGGCGCCTGAACTACTGCGTTGGAGGAGAGgttaacacttaatttcaccataatctgtagaatcttgaatgcatatctgtttgattcctgagagtgtttggttttatgtgctatctatttaccatctcatgtgttacag

upper sequence: EFJ36319 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: GRMZM2G141587_T05 (Zea mays), 5'ss of exon 15
---GCATGAGATATCCGAGCGCGTGAGAACTGGCTTATGGGTAGGCGATTGTTTCATTTACAACAACTCGTCATGGAGACTGAACTACTGCGTTGGAGGAGAGgtctgcttttgtattgtcgtttatatttgtttcacacttcctcttccag------------------------------------------------------------
    ||||||||   ||| || ||  | |||||  ||||||| |||||||||||||| ||||| || || |||||| | || || ||||| || |||||||||||  | ||||   |  ||  ||| |      ||  |  |    ||| ||                                                            
GCTTCATGAGATCAACGAACGTGTCCGGACTGGGCTATGGGTTGGCGATTGTTTCATCTACAATAATTCTTCATGGCGTCTTAATTACTGTGTAGGAGGAgaggtgagttttt---tcatcacttaaaaagacatcctatatatctttcaagttagatcatttatggatagagtgctttcatgtcataaccatttcatattttcatgtgtta

upper sequence: EFJ36319 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: GRMZM2G141587_T02 (Zea mays), 5'ss of exon 15
GCATGAGATATCCGAGCGCGTGAGAACTGGCTTATGGGTAGGCGATTGTTTCATTTACAACAACTCGTCATGGAGACTGAACTACTGCGTTGGAGGAGAGgtctgcttttgtattgtcgtttatatttgtttcacacttcctcttccag---------------------------------------------------------------
 ||||||||   ||| || ||  | |||||  ||||||| |||||||||||||| ||||| || || |||||| | || || ||||| || |||||||||||  | ||||   |  ||  ||| |      ||  |  |    ||| ||                                                               
TCATGAGATCAACGAACGTGTCCGGACTGGGCTATGGGTTGGCGATTGTTTCATCTACAATAATTCTTCATGGCGTCTTAATTACTGTGTAGGAGGAGAGgtgagttttt---tcatcacttaaaaagacatcctatatatctttcaagttagatcatttatggatagagtgctttcatgtcataaccatttcatattttcatgtgttacag

upper sequence: EFJ36319 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: GRMZM2G124886_T01 (Zea mays), 5'ss of exon 15
GCATGAGATATCCGAGCGCGTGAGAACTGGCTTATGGGTAGGCGATTGTTTCATTTACAACAACTCGTCATGGAGACTGAACTACTGCGTTGGAGGAGAGgtctgctttt--------gtattgtcgt-ttatatttgtttcacacttcctcttccag------------------------------------------
 ||||||||    || || ||  | |||||  ||||||| ||||||||||| || |||||||| || || ||| | || || |||||||| |||||||||||  | ||||          |  | | | |||||| | |||||   |   || |  ||                                          
TCATGAGATCAATGAACGTGTCCGGACTGGGCTATGGGTTGGCGATTGTTTTATCTACAACAATTCTTCGTGGCGGCTTAATTACTGCGTAGGAGGAGAGgtgggttttttgtcacttaaaaagacatcttatatatctttcaagttagatcatttagtgatagagcgctttcatgtcataaccatttcatgtgttacag

upper sequence: EFJ36319 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: AT1G52360.2 (Arabidopsis thaliana), 5'ss of exon 15
GCATGAGATATCCGAGCGCGTGAGAACTGGCTTATGGGTAGGCGATTGTTTCATTTACAACAACTCGTCATGGAGACTGAACTACTGCGTTGGAGGAGAGgt-ctgcttttgtattgtcgtttatatttgtttcacacttcctct--tccag----------------------------------
 ||||| |     || || || || || ||  ||||||| || || |||||||||||||||||||| || ||||  || |||||||| |||||||| |||||  ||    | ||| || | |||   |  |||   | ||  | |   |  |                                  
CCATGAAAATGATGAACGTGTTAGGACAGGTATATGGGTTGGTGACTGTTTCATTTACAACAACTCTTCCTGGAAGCTTAACTACTGTGTTGGAGGCGAGgtattgtgcatatat-gttggttactctgatttggaagttgttatgaactggattctaatgatggttgctaacatcgtaatactag

upper sequence: EFJ36319 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: PP1S243_63V6.1 (Physcomitrella patens), 5'ss of exon 15
GCATGAGATATCCGAGCGCGTGAGAACTGGCTTATGGGTAGGCGATTGTTTCATTTACAACAACTCGTCATGGAGACTGAACTACTGCGTTGGAGGAGAGgtc-----tgcttttgtattgtcgtttatatt-tgtttcacacttcctcttccag---------------------------------------------
||| || ||  | |||||  | ||||||||||| ||||| || || || |||||||||||||| ||  |||||||||| |||||||| ||||| ||||||||      || |  |  ||  | | | |  |  || | |||  |  |  || |||                                             
GCACGAAATTCCTGAGCGAATTAGAACTGGCTTGTGGGTTGGTGACTGCTTCATTTACAACAATTCAGCATGGAGACTCAACTACTGTGTTGGTGGAGAGgtaagtaatggtcatacatgatggatcagctaatgctgcaccgtatccatttcagatactagtagattacattttagcttatgagttacttgcatccaat

upper sequence: EFJ36319 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: PP1S79_180V6.2 (Physcomitrella patens), 5'ss of exon 15
GCATGAGATATCCGAGCGCGTGAGAACTGGCTTATGGGTAGGCGATTGTTTCATTTACAACAACTCGTCATGGAGACTGAACTACTGCGTTGGAGGAGAGgtctgcttttgtat-tgtcgtttatatttgtttcacacttcctcttccag--------------------------------------------------
 || || || ||||| ||  | ||||||||||| ||||| ||||| || |||||||||||||| ||| ||||||| || ||||| || || || ||||||||  |       |  |     ||| |     |      | | ||||  |                                                   
ACACGAAATCTCCGAACGAATTAGAACTGGCTTGTGGGTGGGCGACTGCTTCATTTACAACAATTCGGCATGGAGGCTCAACTATTGTGTCGGTGGAGAGgtaaggaaaaacaagtaaaccttagacacaatgtcatttgcttctttgaaggtgatctttgtgttgctcgaactagtagaccaccctctggtgagatggt

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|169094662|gb|FE494555.1|FE494555
EST:     TCATTTACAACAACTCGTCATGGAGACTGAACTACTGCGTTGGAGGAGAG                         GTAACTACTATGTATCACCTGGACAAGCCAATGTATTTGCTTGGCTATCTG
genomic: TCATTTACAACAACTCGTCATGGAGACTGAACTACTGCGTTGGAGGAGAGgtctgctttt ... cctcttccagGTAACTACTATGTATCACCTGGACAAGCCAATGTATTTGCTTGGCTATCTG
EST: gi|169083821|gb|FE492733.1|FE492733
EST:     TCATTTACAACAACTCGTCATGGAGACTGAACTACTGCGTTGGAGGAGAG                         GTAACTACTATGTATCACCTGGACAAGC-AATGTATTTGCTTGGCTATCTG
genomic: TCATTTACAACAACTCGTCATGGAGACTGAACTACTGCGTTGGAGGAGAGgtctgctttt ... cctcttccagGTAACTACTATGTATCACCTGGACAAGCCAATGTATTTGCTTGGCTATCTG
EST: gi|169067594|gb|FE475297.1|FE475297
EST:     TCATTTACAACAACTCGTCATGGAGACTGAACTACTGCGTTGGAGGAGAG                         GTAACTACTATGTATCACCTGGACAAGCCAATGTATTTGCTTGGCTATCTG
genomic: TCATTTACAACAACTCGTCATGGAGACTGAACTACTGCGTTGGAGGAGAGgtctgctttt ... cctcttccagGTAACTACTATGTATCACCTGGACAAGCCAATGTATTTGCTTGGCTATCTG
EST: gi|169056508|gb|FE464916.1|FE464916
EST:     TCATTTACAACAACTCGTCATGGAGACTGAACTACTGCGTTGGAGGAGAG                         GTAACTACTATGTATCACCTGGACAAGCCAATGTATTTGCTTGGCTATCTG
genomic: TCATTTACAACAACTCGTCATGGAGACTGAACTACTGCGTTGGAGGAGAGgtctgctttt ... cctcttccagGTAACTACTATGTATCACCTGGACAAGCCAATGTATTTGCTTGGCTATCTG
EST: gi|169021101|gb|FE431412.1|FE431412
EST:     TCATTTACAACAACTCGTCATGGAGACTGAACTACTGCGTTGGAGGAGAG                         GTAACTACTATGTATCACCTGGACAAGC-AATGTATTTGCTTGGCTATCTG
genomic: TCATTTACAACAACTCGTCATGGAGACTGAACTACTGCGTTGGAGGAGAGgtctgctttt ... cctcttccagGTAACTACTATGTATCACCTGGACAAGCCAATGTATTTGCTTGGCTATCTG
EST: gi|169025538|gb|FE435008.1|FE435008
EST:     TCATTTACAACAACTCGTCATGGAGACTGAACTACTGCGTTGGAGGAGAG                         GTAACTACTATGTATCACCTGGACAAGCCAATGTATTTGCTTGGCTATCTG
genomic: TCATTTACAACAACTCGTCATGGAGACTGAACTACTGCGTTGGAGGAGAGgtctgctttt ... cctcttccagGTAACTACTATGTATCACCTGGACAAGCCAATGTATTTGCTTGGCTATCTG
EST: gi|169066106|gb|FE475645.1|FE475645
EST:     TCATTTACAACAACTCGTCATGGAGACTGAACTACTGCGTTGGAGGAGAG                         GTAACTACTATGTATCACCTGGACAAGCCAATGTATTTGCTTGGCTATCTG
genomic: TCATTTACAACAACTCGTCATGGAGACTGAACTACTGCGTTGGAGGAGAGgtctgctttt ... cctcttccagGTAACTACTATGTATCACCTGGACAAGCCAATGTATTTGCTTGGCTATCTG
EST: gi|169082250|gb|FE490606.1|FE490606
EST:     TCATTTACAACAACTCGTCATGGAGACTGAACTACTGCGTTGGAGGAGAG                         GTAACTACTATGTATCACCTGGACAAGCCAATGTATTTGCTTGGCTATCTG
genomic: TCATTTACAACAACTCGTCATGGAGACTGAACTACTGCGTTGGAGGAGAGgtctgctttt ... cctcttccagGTAACTACTATGTATCACCTGGACAAGCCAATGTATTTGCTTGGCTATCTG

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: 31 (upstream exon), 34 (downstream exon)
Score: 18

GCATGAGATATCCGAGCGCGTGAGAACTGGCTTATGGGTAGGCGATTGTTTCATTTACAACAACTCGTCATGGAGACTGAACTACTGCGTTGGAGGAGAGgtctgctttt ... cctcttccagGTAACTACTATGTATCACCTGGACAAGCCAATGTATTTGCTTGGCTATCTGGCAAATCAAAGCCGAGTGTATCTGATCGACAAGGAGTTCAA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCATGAGATATCCGAGCGCGTGAGAACTGGCTTATGGGTAGGCGATTGTTTCATTTACAACAACTCGTCATGGAGACTGAACTACTGCGTTGGAGGAGAGgtctgcttttgtattgtcgtttatatttgtttcacacttcctcttccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA