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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcccatttttttttccttgcggtgtttgggtcgttaataggagttttaatgagcagTTCGAAGCTGCCTGGGCTCTTACAAATATTGCGTCCGGCACTTCCGATCACACGACGGTGGTTATAAACCATGGAGCTGTGCCTATCTTCGTGCAGCTTC

Basic information

species Selaginella moellendorffii
transcript EFJ31557
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ31557 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: LOC_Os01g14950.1 (Oryza sativa), 3'ss of exon 3
------------------gtatgcccattttttttt----ccttgcggtgtttgggtcgttaata-ggagtttt--aatga------gcagTTCGAAGCTGCCTGGGCTCTTACAAATATTGCGTCCGGCACTTCCGATCACACGACGGTGGTTATAAACCATGGAGCTGTGCCTATCTTCGTGCAGCTTC
                   |||   |||| | |  |     |         | |  |  ||| |  || | |||  ||| |      | ||||||||||||| ||||| |||||||| ||||| || |||||||| ||  | || | ||| || ||  | ||||| ||||| || || || ||| ||||||
gtgtgtgccaacacaatattattttcattatctggtaggttcaaataaaaatggatttattactgtggtgcttttgaattaaattttgtagTTCGAAGCTGCGTGGGCACTTACAAACATTGCATCTGGCACTTCGGAGAATACAAAGGTTGTCATTGATCATGGGGCTGTACCAATATTTGTGAAGCTTC

upper sequence: EFJ31557 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GRMZM2G091119_T02 (Zea mays), 3'ss of exon 3
---------------gtatgcccatttttttttccttgcggtgtt----tgggtcgttaataggagttttaatga----gcagTTCGAAGCTGCCTGGGCTCTTACAAATATTGCGTCCGGCACTTCCGATCACACGACGGTGGTTATAAACCATGGAGCTGTGCCTATCTTCGTGCAGCTTC
                ||  ||   | |  | |  |||| |  |     ||  |   | ||  |  || ||||      | |||||||||| || |||||||| ||||||||||| || |||||||| ||  | || | ||| |||||  | ||||| ||||| ||||| || ||| ||||||
gtatgttgatttaatataaaccttatatcctgttgttgctggatgaaaatgaatttctcatcagctttgtaattcttttgtagTTCGAAGCAGCATGGGCTCTCACAAATATTGCTTCTGGCACTTCAGAAAATACAAAGGTTGTTATTGATCATGGGGCTGTTCCTATATTTGTGAAGCTTC

upper sequence: EFJ31557 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: PP1S230_50V6.1 (Physcomitrella patens), 3'ss of exon 3
-----------------------------------------------------gtatgcccatttttttttccttgcggt-gtttgggtcgttaataggagttttaatgagcagTTCGAAGCTGCCTGGGCTCTTACAAATATTGCGTCCGGCACTTCCGATCACACGACGGTGGTTATAAACCATGGAGCTGTGCCTATCTTCGTGCAGCTTC
                                                         |  |||     |    | | ||  |   | ||   | |  |    | |     |||||||||||||||||||||  | ||||||||||| ||||| ||||| ||||||||   |||||||||  | || ||||||||||| || ||||| ||||| |
gtgctcactcggattttccctactgtgaactgtgtttaatctctattgtacaatcgagtacatcacgatcctgtgggggcagaacgagtatctcactgtgtgtatcgcatgcagTTCGAAGCTGCCTGGGCGTTGACAAATATTGCTTCCGGAACTTCTGATCACACCCGGGTGGTTATTGATCACGGAGCTGTGCCAATTTTCGTTCAGCTCC

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|169031969|gb|FE440669.1|FE440669
EST:     TTCCTCGATTTGTAGAGTTTTTGAAGCGCCACGATTTCCACCAGCTTCAG                         TTCGAAGCTGCCTGGGCTCTTACAAATATTGCGTCCGGCACTTCCGATCAC
genomic: TTCCTCGATTTGTAGAGTTTTTGAAGCGCCACGATTTCCACCAGCTTCAGgtatgcccat ... taatgagcagTTCGAAGCTGCCTGGGCTCTTACAAATATTGCGTCCGGCACTTCCGATCAC
EST: gi|169076897|gb|FE485290.1|FE485290
EST:     TTCCTCGATTTGTAGAGTTTTTGAAGCGCCACGATTTCCACCAGCTTCAG                         TTCGAAGCTGCCTGGGCTCTTACAAATATTGCGTCCGGCACTTCCGATCAC
genomic: TTCCTCGATTTGTAGAGTTTTTGAAGCGCCACGATTTCCACCAGCTTCAGgtatgcccat ... taatgagcagTTCGAAGCTGCCTGGGCTCTTACAAATATTGCGTCCGGCACTTCCGATCAC
EST: gi|169030898|gb|FE438166.1|FE438166
EST:     TTCCTCGATTTGTAGAGTTTTTGAAGCGCCACGATTTCCACCAGCTTCAG                         TTCGAAGCTGCCTGGGCTCTTACAAATATTGCGTCCGGCACTTCCGATCAC
genomic: TTCCTCGATTTGTAGAGTTTTTGAAGCGCCACGATTTCCACCAGCTTCAGgtatgcccat ... taatgagcagTTCGAAGCTGCCTGGGCTCTTACAAATATTGCGTCCGGCACTTCCGATCAC
EST: gi|169035711|gb|FE443180.1|FE443180
EST:     TTCCTCGATTTGTAGAGTTTTTGAAGCGCCACGATTTCCACCAGCTTCAG                         TTCGAAGCTGCCTGGGCTCTTACAAATATTGCGTCCGGCACTTCCGATCAC
genomic: TTCCTCGATTTGTAGAGTTTTTGAAGCGCCACGATTTCCACCAGCTTCAGgtatgcccat ... taatgagcagTTCGAAGCTGCCTGGGCTCTTACAAATATTGCGTCCGGCACTTCCGATCAC
EST: gi|169045304|gb|FE453617.1|FE453617
EST:     TTCCTCGATTTGTAGAGTTTTTGAAGCGCCACGATTTCCACCAGCTTCAG                         TTCGAAGCTGCCTGGGCTCTTACAAATATTGCGTCCGGCACTTCCGATCAC
genomic: TTCCTCGATTTGTAGAGTTTTTGAAGCGCCACGATTTCCACCAGCTTCAGgtatgcccat ... taatgagcagTTCGAAGCTGCCTGGGCTCTTACAAATATTGCGTCCGGCACTTCCGATCAC
EST: gi|169029571|gb|FE438932.1|FE438932
EST:     TTCCTCGATTTGTAGAGTTTTTGAAGCGCCACGATTTCCACCAGCTTCAG                         TTCGAAGCTGCCTGGGCTCTTACAAATATTGCGTCCGGCACTTCCGATCAC
genomic: TTCCTCGATTTGTAGAGTTTTTGAAGCGCCACGATTTCCACCAGCTTCAGgtatgcccat ... taatgagcagTTCGAAGCTGCCTGGGCTCTTACAAATATTGCGTCCGGCACTTCCGATCAC
EST: gi|169076232|gb|FE485262.1|FE485262
EST:     TTCCTCGATTTGTAGAGTTTTTGAAGCGCCACGATTTCCACCAGCTTCAG                         TTCGAAGCTGCCTGGGCTCTTACAAATATTGCGTCCGGCACTTCCGATCAC
genomic: TTCCTCGATTTGTAGAGTTTTTGAAGCGCCACGATTTCCACCAGCTTCAGgtatgcccat ... taatgagcagTTCGAAGCTGCCTGGGCTCTTACAAATATTGCGTCCGGCACTTCCGATCAC
EST: gi|169102471|gb|FE508021.1|FE508021
EST:     TTCCTCGATTTGTAGAGTTTTTGAAGCGCCACGATTTCCACCAGCTTCAG                         TTCGAAGCTGCCTGGGCTCTTACAAATATTGCGTCCGGCACTTCCGATCAC
genomic: TTCCTCGATTTGTAGAGTTTTTGAAGCGCCACGATTTCCACCAGCTTCAGgtatgcccat ... taatgagcagTTCGAAGCTGCCTGGGCTCTTACAAATATTGCGTCCGGCACTTCCGATCAC
EST: gi|169049984|gb|FE458076.1|FE458076
EST:     TTCCTCGATTTGTAGAGTTTTTGAAGCGCCACGATTTCCACCAGCTTCAG                         TTCGAAGCTGCCTGGGCTCTTACAAATATTGCGTCCGGCACTTCCGATCAC
genomic: TTCCTCGATTTGTAGAGTTTTTGAAGCGCCACGATTTCCACCAGCTTCAGgtatgcccat ... taatgagcagTTCGAAGCTGCCTGGGCTCTTACAAATATTGCGTCCGGCACTTCCGATCAC
EST: gi|169028583|gb|FE440440.1|FE440440
EST:     TTCCTCGATTTGTAGAGTTTTTGAAGCGCCACGATTTCCACCAGCTTCAG                         TTCGAAGCTGCCTGGGCTCTTACAAATATTGCGTCCGGCACTTCCGATCAC
genomic: TTCCTCGATTTGTAGAGTTTTTGAAGCGCCACGATTTCCACCAGCTTCAGgtatgcccat ... taatgagcagTTCGAAGCTGCCTGGGCTCTTACAAATATTGCGTCCGGCACTTCCGATCAC
EST: gi|169020321|gb|FE428305.1|FE428305
EST:     TTCCTCGATTTGTAGAGTTTTTGAAGCGCCACGATTTCCACCAGCTTCAG                         TTCGAAGCTGCCTGGGCTCTTACAAATATTGCGTCCGGCACTTCCGATCAC
genomic: TTCCTCGATTTGTAGAGTTTTTGAAGCGCCACGATTTCCACCAGCTTCAGgtatgcccat ... taatgagcagTTCGAAGCTGCCTGGGCTCTTACAAATATTGCGTCCGGCACTTCCGATCAC
EST: gi|169024266|gb|FE433060.1|FE433060
EST:     TTCCTCGATTTGTAGAGTTTTTGAAGCGCCACGATTTCCACCAGCTTCAG                         TTCGAAGCTGCCTGGGCTCTTACAAATATTGCGTCCGGCACTTCCGATCAC
genomic: TTCCTCGATTTGTAGAGTTTTTGAAGCGCCACGATTTCCACCAGCTTCAGgtatgcccat ... taatgagcagTTCGAAGCTGCCTGGGCTCTTACAAATATTGCGTCCGGCACTTCCGATCAC
EST: gi|169020135|gb|FE428522.1|FE428522
EST:     TTCCTCGATTTGTAGAGTTTTTGAAGCGCCACGATTTCCACCAGCTTCAG                         TTCGAAGCTGCCTGGGCTCTTACAAATATTGCGTCCGGCACTTCCGATCAC
genomic: TTCCTCGATTTGTAGAGTTTTTGAAGCGCCACGATTTCCACCAGCTTCAGgtatgcccat ... taatgagcagTTCGAAGCTGCCTGGGCTCTTACAAATATTGCGTCCGGCACTTCCGATCAC

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: 34 (upstream exon), 35 (downstream exon)
Score: 28

AGCGAAGGCCTCCGATCGAAGAGGTCATCAAGGCAGGCGTGGTTCCTCGATTTGTAGAGTTTTTGAAGCGCCACGATTTCCACCAGCTTCAGgtatgcccat ... taatgagcagTTCGAAGCTGCCTGGGCTCTTACAAATATTGCGTCCGGCACTTCCGATCACACGACGGTGGTTATAAACCATGGAGCTGTGCCTATCTTCGTGCAGCTTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccatttttttttccttgcggtgtttgggtcgttaataggagttttaatgagcagTTCGAAGCTGCCTGGGCTCTTACAAATATTGCGTCCGGCACTTCCGATCACACGACGGTGGTTATAAACCATGGAGCTGTGCCTATCTTCGTGCAGCTTC
                                          ttttaat  putative branch site (score: 28)
     tttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcccatttttttttccttgcggtgtttgggtcgttaataggagttttaatgagcagTTCGAAGCTGCCTGGGCTCTTACAAATATTGCGTCCGGCACTTCCGATCACACGACGGTGGTTATAAACCATGGAGCTGTGCCTATCTTCGTGCAGCTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT