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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcgacgtcttgaatcttctgtaagatcgatcgattgacagatcgcgacttccagGTTCAAATGTATCGATCTGGATTGTGACGGAGTGGTGACTCCAAACGAGATGCAGTACTTTTATGAGGAGCAATTGCATCGCATGGAGTGCCTAGCTCAA

Basic information

species Selaginella moellendorffii
transcript EFJ32791
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ32791 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: GLYMA10G32500.1 (Glycine max), 3'ss of exon 9
------------------------------------------gtaagcgacgtcttgaatcttctgtaagatcgatcgattgacagatcgcgacttccagGTTCAAATGTATCGATCTGGATTGTGACGGAGTGGTGACTCCAAACGAGATGCAGTACTTTTATGAGGAGCAATTGCATCGCATGGAGTGCCTAGCTCAA
                                          | |   ||  |  || || |  |  ||  || |    |      |      |||  ||||||||||| || ||| ||||| |  | |||||| |||| ||||| || ||||||| ||||||||||||||| |||||||| ||||||||| | || |||
atatttctagattgtaaattcagtatttcagtagcaagttcagaatttgatttgctgcatttaatagaaactcaacatttgtttttaaaaattcttgtagGTTCAAATGCATTGATTTGGATGGAAATGGAGTGCTGACACCAAATGAAATGCAGTTCTTTTATGAGGAGCAGTTGCATCGGATGGAGTGCATGGCCCAA

upper sequence: EFJ32791 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: GLYMA20G35090.1 (Glycine max), 3'ss of exon 9
-------------------------------------------gtaagcgacgtcttgaatcttctgtaagatcgatcgattgacagatcgcgacttccagGTTCAAATGTATCGATCTGGATTGTGACGGAGTGGTGACTCCAAACGAGATGCAGTACTTTTATGAGGAGCAATTGCATCGCATGGAGTGCCTAGCTCAA
                                           | |   ||  |  || || |  |  ||  || |    || | | |      |||  ||||||||||| || ||| ||||| |  | |||||| |||| || || || ||||||| ||||||||||||||| |||||||| ||||||||| | || |||
tatatttatagattgtaaattcagtattttggtagcaaattcagaatttgatttgctgcatttaatagaaactcaacattttcaaaaaaaa-atcttgtagGTTCAAATGCATTGATTTGGATGGAAATGGAGTGCTGACACCTAATGAAATGCAGTTCTTTTATGAGGAGCAGTTGCATCGGATGGAGTGCATGGCCCAA

upper sequence: EFJ32791 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: GLYMA19G43790.1 (Glycine max), 3'ss of exon 9
-----------------------------------------gtaag--cgacgtcttgaatcttctgtaag--atcgatcgattgacagatcgcgacttccagGTTCAAATGTATCGATCTGGATTGTGACGGAGTGGTGACTCCAAACGAGATGCAGTACTTTTATGAGGAGCAATTGCATCGCATGGAGTGCCTAGCTCAA
                                         | |||   ||  | |    |   || | ||  ||   |   |||||   ||  || |   |||||||| || || ||| ||||| |  | |||||  |||| |  || ||  |||| |  ||||||||||||||||||||||| ||||||||| | || |||
ttttccaccttgcctcctaagtacactcttaggcgaacattggaagtttgatctttgtggttgactattagctatttgtgatttgacgtgtcatgatt---agGTTCAAGTGCATTGATTTGGATGGAAATGGAGTTCTGACACGGAATGAACTGCAATTTTTTTATGAGGAGCAATTGCATCGAATGGAGTGCATGGCCCAA

upper sequence: EFJ32791 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: GLYMA03G41180.1 (Glycine max), 3'ss of exon 9
--------------------------------------------gtaagcgacgtc-ttgaatcttctgtaagatcgatcgattgacagatcgcgacttccagGTTCAAATGTATCGATCTGGATTGTGACGGAGTGGTGACTCCAAACGAGATGCAGTACTTTTATGAGGAGCAATTGCATCGCATGGAGTGCCTAGCTCAA
                                             | | |   ||  |||| |||| |     ||   |   ||||    ||  || |   |||||||| || || ||| ||||| |  | |||||  |||| |  || ||  |||| |  ||||||||||||||||||||||| ||||||||| | || |||
tccaccttgcctcctaagtacactcttaggcgaacattggaagtttgacctttgtggttgactcttgttagctatttgtgatttgatgtgtcatgatt---agGTTCAAGTGCATTGATTTGGATGGAAATGGAGTTCTGACACGGAATGAACTGCAATTTTTTTATGAGGAGCAATTGCATCGAATGGAGTGCATGGCCCAA

upper sequence: EFJ32791 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: GLYMA20G36530.1 (Glycine max), 3'ss of exon 9
-------------------------------------gtaagcgacgtcttgaatcttctgt-----aagatcgatcgattgacagatcgcgacttccagGTTCAAATGTATCGATCTGGATTGTGACGGAGTGGTGACTCCAAACGAGATGCAGTACTTTTATGAGGAGCAATTGCATCGCATGGAGTGCCTAGCTCAA
                                      | |      |  ||| | ||  ||     |||  ||| |       | |  |  |||   |||||||| || || ||| ||||| |  | |||||  ||||    || ||  |||| |  ||||||||||| ||||||||||| ||||||||| | || |||
atgctatttggtaaacagtggatatttgacattgtggttgacttgttttctgatttttaagtcgtcaaagtacgagctgacttgaaaatgtcactattagGTTCAAGTGCATAGATTTGGATGGAAATGGAGTTCTGACAAGGAATGAACTGCAATTTTTTTATGAGGAACAATTGCATCGGATGGAGTGCATGGCCCAA

upper sequence: EFJ32791 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: GLYMA10G30930.1 (Glycine max), 3'ss of exon 9
---------------------------------gtaagcgacgtcttgaatcttctgtaag--atcga----tcgattgac---agatcgcgacttccagGTTCAAATGTATCGATCTGGATTGTGACGGAGTGGTGACTCCAAACGAGATGCAGTACTTTTATGAGGAGCAATTGCATCGCATGGAGTGCCTAGCTCAA
                                 ||    ||| | ||   |  | | ||||  ||| |         ||||   | |  |  |||   |||||||| || || ||| ||||| |  | |||||  | ||    || ||  |||| |  ||||||||||||||||||||||| ||||| ||| | || |||
atgctatttggtaaacagtggatatttgacatcgtggttgacttgttttctggtttttaagtcatcaaagtacgagctgacttgaaaatgtcactattagGTTCAAGTGCATAGATTTGGATGGAAATGGAGTTCTAACAAGGAATGAACTGCAATTTTTTTATGAGGAGCAATTGCATCGGATGGAATGCATGGCCCAA

upper sequence: EFJ32791 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: Vv07s0005g03730.t01 (Vitis vinifera), 3'ss of exon 10
----------------------------------------gtaagcgacgtcttgaatcttctgtaag-atcgatcgattgacagatcgcgactt-ccagGTTCAAATGTATCGATCTGGATTGTGACGGAGTGGTGACTCCAAACGAGATGCAGTACTTTTATGAGGAGCAATTGCATCGCATGGAGTGCCTAGCTCAA
                                          ||   |  | ||   |  ||  |  | |||  ||  ||     ||    | || |||||||||| || || ||| ||||| |  | |||||| | || |  || || ||||||| |||||||||||||||||||||||| ||||| ||| | || |||
tatgggattaggtttgaggcagtagcttaatttgatgctctaaatttatttgttatgtaatcaatgtgcatcactcactttgtgaatttttattttccagGTTCAAGTGCATAGATTTGGATGGAAATGGAGTGCTTACACTGAATGAAATGCAGTTCTTTTATGAGGAGCAATTGCATCGAATGGAATGCATGGCCCAA

upper sequence: EFJ32791 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 9
----------------------------------------------------------------------------------------------------------------------------------------gtaagcgacgtcttgaatcttctgtaagatcgatcgattgacagatcgcgacttccagGTTCAAATGTATCGATCTGGATTGTGACGGAGTGGTGACTCCAAACGAGATGCAGTACTTTTATGAGGAGCAATTGCATCGCATGGAGTGCCTAGCTCAA
                                                                                                                                         ||    ||  |  | |  |   ||   ||  ||   ||     | | |    | ||||||||||||| | || ||||||||||| || ||| | || ||||| |||||||| || ||||||||||||||| | ||||| ||||||||| | ||||| 
gtacgtacctttatatggcctctaaaatgctctccacttttttggcatgaagttgatgtttttgaatgcaaatcatgtgctttctgacaaaacagtatttaggataaaggattgaattttcactcggattgattagttacataacaacgaggacatcgagtctaatttattttttcttgta-cacctgatgcagGTTCAAATGTGTGGACCTGGATTGTGATGGTGTGATAACACCAAATGAGATGCAATATTTTTATGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAG

upper sequence: EFJ32791 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: PP1S191_94V6.1 (Physcomitrella patens), 3'ss of exon 10
------------------------------------------------------------------------------------------------------gtaagcga-cgtcttgaatcttctgtaag-atcgatcgattgacagatcgcgacttc-----cagGTTCAAATGTATCGATCTGGATTGTGACGGAGTGGTGACTCCAAACGAGATGCAGTACTTTTATGAGGAGCAATTGCATCGCATGGAGTGCCTAGCTCAA
                                                                                                        |   || | |  |||    ||| ||   |  |||    | |||  | | ||          |||||||| ||| | ||| | |||||||| || ||| | ||| |||| || ||||| || ||||||||||||||||| ||||| ||||| ||  | || |||
gtaatttttttgtttttttcttattctttttaattttatttattaatttatttattttattatctcccatgtagttatttctttttacaagcttgaattcttaaacatgatcattgtgatatatctatatttaatgattatctaacaagtggtgaaaataaaattagGTTCAAGTGTGTGGATTTAGATTGTGATGGGGTGATCACTGCAAATGAAATGCATTATTTTTATGAGGAGCAATTACATCGAATGGAATGTATGGCACAA

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|169021252|gb|FE429613.1|FE429613
EST:     TTCATTTTATCGGAGGAGGACAAAACGTCTGAACCAAGCTTGGAGTACTG                         GTTCAAATGTATCGATCTGGATTGTGACGGAGTGGTGACTCCAAACGAGAT
genomic: TTCATTTTATCGGAGGAGGACAAAACGTCTGAACCAAGCTTGGAGTACTGgtaagcgacg ... cgacttccagGTTCAAATGTATCGATCTGGATTGTGACGGAGTGGTGACTCCAAACGAGAT




















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), 31 (downstream exon)
Score: 10

AGTTTACGAGTTCCGTGGAAGGAAAGATGGGTTACGAGGACTTTGTGTGGTTCATTTTATCGGAGGAGGACAAAACGTCTGAACCAAGCTTGGAGTACTGgtaagcgacg ... cgacttccagGTTCAAATGTATCGATCTGGATTGTGACGGAGTGGTGACTCCAAACGAGATGCAGTACTTTTATGAGGAGCAATTGCATCGCATGGAGTGCCTAGCTCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcgacgtcttgaatcttctgtaagatcgatcgattgacagatcgcgacttccagGTTCAAATGTATCGATCTGGATTGTGACGGAGTGGTGACTCCAAACGAGATGCAGTACTTTTATGAGGAGCAATTGCATCGCATGGAGTGCCTAGCTCAA
                                gattgac  putative branch site (score: 10)
                                                cttcc  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcgacgtcttgaatcttctgtaagatcgatcgattgacagatcgcgacttccagGTTCAAATGTATCGATCTGGATTGTGACGGAGTGGTGACTCCAAACGAGATGCAGTACTTTTATGAGGAGCAATTGCATCGCATGGAGTGCCTAGCTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA