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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttgtccaaaatgcttctttgttaatttgttaagtgctgtatttttgcagCTTCTTTCAGAGAAGGGAGAACTTCCAACAAGATTTGGCTCTGCCACCCTTGGAATTCTTCTCTTTCAA

Basic information

species Selaginella moellendorffii
transcript EFJ25893
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ25893 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: LOC_Os12g42300.1 (Oryza sativa), 3'ss of exon 5
---------------------------------------gt-ttgttgtccaaaatgcttctttgttaatttgttaagtgctgt---atttt---tgcagCTTCTTTCAGAGAAGGGAGAACTTCCAACAAGATTTGGCTCTGCCACCCTTGGAATTCTTCTCTTTCAA
                                       || ||||    |   |  | |  || || |||| |  |||| | |   || |    ||||||||||| | ||||| || ||||| ||||||||||||||||| || || || ||||| || ||| | || 
atacaattgttcaagcaatacttcctgcttacagtagttgtattgtcactctttacacataattattgatttttggagtgtttttggatgtcatatgcagCTTCTTGCTGAGAAAGGTGAACTCCCAACAAGATTTGGCTCAGCTACACTGGGAATCCTCCTCCTGCAG

upper sequence: EFJ25893 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GRMZM2G009715_T01 (Zea mays), 3'ss of exon 5
--------------------------------------------gtt-tgttgtccaaaatgcttc---tttgttaatttgttaagtgctgtatttttgcagCTTCTTTCAGAGAAGGGAGAACTTCCAACAAGATTTGGCTCTGCCACCCTTGGAATTCTTCTCTTTCAA
                                            |||   || |  ||||   ||     ||| | |||  ||| |      || |  |||||||||| | ||||| || |||||||||||||||||||| || || || || |||||||||||| | || 
tttagttacacaaatcattcacgcaacttgtcatgcttacaacagttacattttttaaaactttttgcacttggtgattgattatgaataccatct--gcagCTTCTTGCCGAGAAAGGTGAACTTCCAACAAGATTTGGTTCAGCTACACTGGGAATTCTTCTCCTGCAG

upper sequence: EFJ25893 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GLYMA08G06890.3 (Glycine max), 3'ss of exon 6
-----------------------------------------gtttgttgtccaaaatgcttctttgttaatttgttaagtgc-----tgtatttttgcagCTTCTTTCAGAGAAGGGAGAACTTCCAACAAGATTTGGCTCTGCCACCCTTGGAATTCTTCTCTTTCAA
                                         ||  ||    | ||||     |    ||| || | |||          ||| |||| |||||||| ||||||  || || ||||| |||||||||||||| || || |||||||| ||||| || || 
atggttttaggtgttccccatgcatgagtccattgtgatatgtgagtgacactaaatatggataatgtaacttatcaagcatatatgcatatatttgtagCTTCTTGCAGAGAGAGGTGAGCTTCCTACAAGATTTGGCTCAGCAACTCTTGGAATACTTCTTTTGCAG

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|169042163|gb|FE454206.1|FE454206
EST:     TAGTTATTGGAGCGGGTTTATCATTGTCTTCTTCCGCATTTGTCTTGCAG                         CTTCTTTCAGAGAAGGGAGAACTTCCAACAAGATTTGGCTCTGCCACCCTT
genomic: TAGTTATTGGAGCGGGTTTATCATTGTCTTCTTCCGCATTTGTCTTGCAGgtttgttgtc ... atttttgcagCTTCTTTCAGAGAAGGGAGAACTTCCAACAAGATTTGGCTCTGCCACCCTT
EST: gi|169093899|gb|FE493487.1|FE493487
EST:     TAGTTATTGGAGCGGGTTTATCATTGTCTTCTTCCGCATTTGTCTTGCAG                         CTTCTTTCAGAGAAGGGAGAACTTCCAACAAGATTTGGCTCTGCCACCCTT
genomic: TAGTTATTGGAGCGGGTTTATCATTGTCTTCTTCCGCATTTGTCTTGCAGgtttgttgtc ... atttttgcagCTTCTTTCAGAGAAGGGAGAACTTCCAACAAGATTTGGCTCTGCCACCCTT
EST: gi|169047127|gb|FE457208.1|FE457208
EST:     TTGTCTTCTTCCGCATTTGTCTTGCAG                         CTTCTTTCAGAGAAGGGAGAACTTCCAACAAGATTTGGCTCTGCCACCCTT
genomic: TTGTCTTCTTCCGCATTTGTCTTGCAGgtttgttgtc ... atttttgcagCTTCTTTCAGAGAAGGGAGAACTTCCAACAAGATTTGGCTCTGCCACCCTT
EST: gi|169040292|gb|FE448370.1|FE448370
EST:     TAGTTATTGGAGCGGGTTTATCATTGTCTTCTTCCGCATTTGTCTTGCAG                         CTTCTTTCAGAGAAGGGAGAACTTCCAACAAGATTTGGCTCTGCCACCCTT
genomic: TAGTTATTGGAGCGGGTTTATCATTGTCTTCTTCCGCATTTGTCTTGCAGgtttgttgtc ... atttttgcagCTTCTTTCAGAGAAGGGAGAACTTCCAACAAGATTTGGCTCTGCCACCCTT
EST: gi|169029732|gb|FE437403.1|FE437403
EST:     TAGTTATTGGAGCGGGTTTATCATTGTCTTCTTCCGCATTTGTCTTGCAG                         CTTCTTTCAGAGAAGGGAGAACTTCCAACAAGATTTGGCTCTGCCACCCTT
genomic: TAGTTATTGGAGCGGGTTTATCATTGTCTTCTTCCGCATTTGTCTTGCAGgtttgttgtc ... atttttgcagCTTCTTTCAGAGAAGGGAGAACTTCCAACAAGATTTGGCTCTGCCACCCTT

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: 28 (upstream exon), 8 (downstream exon)
Score: 1

GTAAATATTAGAACTGTAGACGAAGCTGTAGTTATTGGAGCGGGTTTATCATTGTCTTCTTCCGCATTTGTCTTGCAGgtttgttgtc ... atttttgcagCTTCTTTCAGAGAAGGGAGAACTTCCAACAAGATTTGGCTCTGCCACCCTTGGAATTCTTCTCTTTCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttgttgtccaaaatgcttctttgttaatttgttaagtgctgtatttttgcagCTTCTTTCAGAGAAGGGAGAACTTCCAACAAGATTTGGCTCTGCCACCCTTGGAATTCTTCTCTTTCAA
                        tgttaat  putative branch site (score: 1)
                                            tattttt  putative PPT
                      tttgttaatttgttaa  TA-rich tract