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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagcacatcttgcttaactttagtaatcttcatagctcattctcctcggcagGAGTGGATCATGGAACAATGGGAGAAAAACTTCTACATTAGTGCCATTGCAGGAGCCAACAACGGCAGCTCGCTGGTTGTCATGTCAAAAG

Basic information

species Selaginella moellendorffii
transcript EFJ31718
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 10
lower sequence: GRMZM2G017835_T01 (Zea mays), 3'ss of exon 11
--------------------------gttagcacatcttgcttaactttagtaatcttcatagctcattctcctcggcagGAGTGGATCATGGAACAATGGGAGAAAAACTTCTACATTAGTGCCATTGCAGGAGCCAACAACGGCAGCTCGCTGGTTGTCATGTCAAAAG
                          |||    |   ||   |    | | |  |    | | |  |  |       |||||||||||||||||||||||||| ||||  |||||||| ||| |  |||| ||  ||||||| || || ||  | || || ||||||||||
gtaggaccttcccatctgcacctcatgttcattctcttttgatgttctcaattttgcaaaaaacaaaaacaaaaacacagGAGTGGATCATGGAACAATGGGATAAAAGTTTCTACATCAGTTCTGTTGCTGGCTCCAACAATGGAAGTTCTATTGTAGTGATGTCAAAAG

upper sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 10
lower sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 12
----------------------------------------------gttagcacatcttgcttaactttagtaatcttcata-gctcattctcctcggcagGAGTGGATCATGGAACAATGGGAGAAAAACTTCTACATTAGTGCCATTGCAGGAGCCAACAACGGCAGCTCGCTGGTTGTCATGTCAAAAG
                                              |||    |   || |||   |  | | || || ||| | |   | |      ||||| ||||| ||||||||||||||||| |||||||| || | |||  | ||||| || ||||| || || || ||||| |||||||| | ||
tagaatttggaatggagggaacaacatttaaaacttgatatatgctgttc-tgctcttttcttttttcaattgattttgatatggtgtgtgttactttcagGAATGGATAATGGAACAATGGGAGAAGAACTTCTATATCACTGCGCTAGCAGGGGCAAACAATGGTAGTTCACTGGTGGTCATGTCGAGAG

upper sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 10
lower sequence: GLYMA08G47680.3 (Glycine max), 3'ss of exon 10
-----------------------------------------gttagcacatcttgcttaactttagtaatctt--catagctcattctcctcggcagGAGTGGATCATGGAACAATGGGAGAAAAACTTCTACATTAGTGCCATTGCAGGAGCCAACAACGGCAGCTCGCTGGTTGTCATGTCAAAAG
                                          |||||  ||||   || |  | |  ||||||  |   | |  |  | ||   ||||| |||||||||||||| |||||||| ||||  ||||||| | | |||||||| || || || || ||||| || || || ||||||||||
gtgaaattatatgatttatgtaaatcagtacatgtcatataattagc-tatctgttttcatatgatgaatcttgcctgtgattctgtttcttttcagGAATGGATCATGGAACAGTGGGAGAAGAACTATTACATTACTTCTATTGCAGGGGCTAATAATGGGAGCTCTCTCGTGGTGATGTCAAAAG

upper sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 10
lower sequence: AT3G13670.1 (Arabidopsis thaliana), 3'ss of exon 12
-------------------------gttagcacatct-tgcttaactttagtaatcttc----atagctcattctcctcgg---cagGAGTGGATCATGGAACAATGGGAGAAAAACTTCTACATTAGTGCCATTGCAGGAGCCAACAACGGCAGCTCGCTGGTTGTCATGTCAAAAG
                          ||   | |||| || |         | |||||     | ||   |||||  |  |   ||||| ||||| ||||| || |||||||| |||| |||||||||| | ||||| || || | ||| || |||||  | ||||||||||||||||
gttgtctgatgtttctctgttagttatttttatatctgtgttctgtcaagatgatcttacctgagagtgaattctgttttgaatcagGAATGGATTATGGAGCAGTGGGAGAAGAACTACTACATTAGTTCTATTGCTGGTGCAAGCAATGGAAGCTCCTTAGTTGTCATGTCAAAAG

upper sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 10
lower sequence: Vv09s0002g03680.t01 (Vitis vinifera), 3'ss of exon 12
-----------------------------------------------------------------------------------------------------------------gttagcacatcttgcttaacttta----gtaatc--ttcatagctcattctcc--tcggcagGAGTGGATCATGGAACAATGGGAGAAAAACTTCTACATTAGTGCCATTGCAGGAGCCAACAACGGCAGCTCGCTGGTTGTCATGTCAAAAG
                                                                                                                  |||           |||| ||||    || |||  || ||   |  || | |  ||   |||| ||||| |||||||| ||||||||||||||||| || ||||| || |||||||| |  || || ||||| || ||||| ||||| || |
gtgcgtctcatttcttttgtttaacccatggcatacatatttatctttacatgtgtcatgcaattaaatttcatcagtatgatcgaggcatattacaaggctacttctttcagcttactgttatacatttaattttaacaagtgatcaattaatctttttttgttctgtctatagGAATGGATAATGGAACAGTGGGAGAAAAACTTCTATATCAGTGCAATAGCAGGAGCTACTAATGGGAGCTCACTAGTTGTAATGTCTAAGG

upper sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 10
lower sequence: Vv04s0008g00160.t01 (Vitis vinifera), 3'ss of exon 12
--------------------------------------------------------------------gttagcacatcttgcttaactttagtaatcttcatagctcattctcctcggcagGAGTGGATCATGGAACAATGGGAGAAAAACTTCTACATTAGTGCCATTGCAGGAGCCAACAACGGCAGCTCGCTGGTTGTCATGTCAAAAG
                                                                    |   | | ||  || | ||    ||| |      ||  |   |||   | | |||| ||||| ||||||||||||||||| ||||  ||||| ||||| || |||||||| || || || |||||  |||| || ||||| || |
gttgcttatattccttaacaggcattgcatgttagcacttcattgaacagtatgcatgtcacaaactggcacgtaaattgtgttgaaaacaagttaatactgtatttttgtctttgctgaagGAATGGATTATGGAACAATGGGAGAAGAACTATTACATCAGTGCAATAGCAGGAGCTAATAATGGGAGCTCATTGGTGGTGATGTCCAAGG

upper sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 10
lower sequence: PP1S131_16V6.1 (Physcomitrella patens), 3'ss of exon 12
---------------------------------------------------------gttagcacatct-tgcttaactttagtaat--cttcatagctcattct-cctcggcagGAGTGGATCATGGAACAATGGGAGAAAAACTTCTACATTAGTGCCATTGCAGGAGCCAACAACGGCAGCTCGCTGGTTGTCATGTCAAAAG
                                                         | ||| ||| || | | |    |  |  ||  | ||| |     |  |   |   |||||||||||||||||||| ||||| || || ||||| || |||||||| || || || || ||||| |||||  |||| |||||||| ||||
gtgggtgtgtggtgtctcgctcaagttttgggtagtatatgcagcttgtcgttcaatgatagaacagctatccctgttatgcgccatgccctcacattgagtcatatttttacagGAGTGGATCATGGAACAGTGGGAAAAGAATTTCTATATCAGTGCCATCGCTGGTGCAAATAACGGAAGCTCCTTGGTCGTCATGTCTAAAG

upper sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 10
lower sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 12
-------------------------------------------------gttagcacatcttgcttaactttagtaatcttcatagctcattctcctcggcagGAGTGGATCATGGAACAATGGGAGAAAAACTTCTACATTAGTGCCATTGCAGGAGCCAACAACGGCAGCTCGCTGGTTGTCATGTCAAAAG
                                                   |||     | |  |    | | | |||   ||| |    |  |  ||  |||||||||||||||||||| ||||| || || ||||| || ||||| ||||| ||||| || || || |||||  |||| |||||||| ||||
gtaagtgctcagtgattgtttagtgtttctgcttgttgtttttgaaggatctagttggccctcttcttttgtggaaattaacatggtcattggtattctacagGAGTGGATCATGGAACAGTGGGAAAAGAATTTCTATATCAGTGCAATTGCTGGAGCTAATAATGGGAGCTCTTTGGTCGTCATGTCGAAAG

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|169079095|gb|FE488619.1|FE488619
EST:     CAGGCTTTCAATCTCAAGTGTACGAGCTCTCCAACGTCTTCCTTCACAAG                         GAGTGGATCATGGAACAATGGGAGAAAAACTTCTACATTAGTGCCATTGCA
genomic: CAGGCTTTCAATCTCAAGTGTACGAGCTCTCCAACGTCTTCCTTCACAAGgttagcacat ... tcctcggcagGAGTGGATCATGGAACAATGGGAGAAAAACTTCTACATTAGTGCCATTGCA
EST: gi|169051034|gb|FE458204.1|FE458204
EST:     CAGGCTTTCAATCTCAAGTGTACGAGCTCTCCAACGTCTTCCTTCACAAG                         GAGTGGATCATGGAACAATGGGAGAAAAACTTCTACATTAGTGCCATTGCA
genomic: CAGGCTTTCAATCTCAAGTGTACGAGCTCTCCAACGTCTTCCTTCACAAGgttagcacat ... tcctcggcagGAGTGGATCATGGAACAATGGGAGAAAAACTTCTACATTAGTGCCATTGCA

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: 50

TAGCGTGGCTTCGTGCTCAAATCTCTGGGCGCTGATTATGGACGCGGGAACAGGCTTTCAATCTCAAGTGTACGAGCTCTCCAACGTCTTCCTTCACAAGgttagcacat ... tcctcggcagGAGTGGATCATGGAACAATGGGAGAAAAACTTCTACATTAGTGCCATTGCAGGAGCCAACAACGGCAGCTCGCTGGTTGTCATGTCAAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttagcacatcttgcttaactttagtaatcttcatagctcattctcctcggcagGAGTGGATCATGGAACAATGGGAGAAAAACTTCTACATTAGTGCCATTGCAGGAGCCAACAACGGCAGCTCGCTGGTTGTCATGTCAAAAG
              gcttaac  putative branch site (score: 50)
                                      ctcattctcctc  putative PPT
                ttaactttagtaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagcacatcttgcttaactttagtaatcttcatagctcattctcctcggcagGAGTGGATCATGGAACAATGGGAGAAAAACTTCTACATTAGTGCCATTGCAGGAGCCAACAACGGCAGCTCGCTGGTTGTCATGTCAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC