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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgatcttttcattggagtcagcatgttatgttttttaatctcgttttgcagAAAGAGCTTATAAGAACAGTGGATCTAGGTCCTTTCAAGCATACTGTGGATGACGGTCTGGAATTGAGGAAGGGTGCATTCGAGTGCGTTGACACTTTGC

Basic information

species Selaginella moellendorffii
transcript EFJ33911
intron # 23
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ33911 (Selaginella moellendorffii), 3'ss of exon 23
lower sequence: GLYMA17G00570.1 (Glycine max), 3'ss of exon 25
---------------------------------------------------------------------------------------------------------------------------------------------gtacgatctttt--cattggagtcagcatgttatgttttttaatctcgttttg-cagAAAGAGCTTATAAGAACAGTGGATCTAGGTCCTTTCAAGCATACTGTGGATGACGGTCTGGAATTGAGGAAGGGTGCATTCGAGTGCGTTGACACTTTGC
                                                                                                                                               | |||||| |   | |||||   |      |    |||||||    ||||| ||| ||||||| ||||| ||||| ||||| |||||||||||||||| ||||||||| || || |||||||||||||  || || || || || ||||| || |
gtaatctgaattgtgccattctgttccatgtatttcagttgagtatatagcattacaataaaacttgactttatactccccattattctaagaatattttaatttagtaatatattttgcaatagctgcatttaccaaaatagaagatcttgtattactggaggtgg------actcattttaatgaaattttgacagCAAGAGCTCATAAGGACAGTTGATCTTGGTCCTTTCAAGCATATTGTGGATGATGGACTTGAATTGAGGAAGGCGGCTTTTGAATGTGTAGACACATTAC

upper sequence: EFJ33911 (Selaginella moellendorffii), 3'ss of exon 23
lower sequence: GLYMA07G40230.2 (Glycine max), 3'ss of exon 26
-----------------------------gtacgatcttttcattggagtc-agcatgttatgtt---------------ttttaatctcgttttg-cagAAAGAGCTTATAAGAACAGTGGATCTAGGTCCTTTCAAGCATACTGTGGATGACGGTCTGGAATTGAGGAAGGGTGCATTCGAGTGCGTTGACACTTTGC
                             | | |||   || |    | |  |  || || | ||               |||||||    ||||| ||| ||||||| ||||| ||||| ||||| |||||||| ||||||| ||||||||| || || |||||||||||||  || || || || || ||||| ||||
atactttgtaatggctttttaatctactagaaagatgcctttaacaaaatagaagatcttgtattactggaggtgtctcattttaatgaaattttgacagCAAGAGCTCATAAGGACAGTTGATCTTGGTCCTTTTAAGCATATTGTGGATGATGGACTTGAATTGAGGAAGGCGGCTTTTGAATGTGTAGACACATTGC

upper sequence: EFJ33911 (Selaginella moellendorffii), 3'ss of exon 23
lower sequence: Vv12s0035g01840.t01 (Vitis vinifera), 3'ss of exon 26
--------------------------------------gtacgat-cttttcattggagtca-------gcatgttatgttttttaatctcgttttgcagAAAGAGCTTATAAGAACAGTGGATCTAGGTCCTTTCAAGCATACTGTGGATGACGGTCTGGAATTGAGGAAGGGTGCATTCGAGTGCGTTGACACTTTGC
                                       | | || ||||| ||||    ||       |     |||  | ||| || |   | ||||| ||||| | || |||||||| ||||| |||||||||||||||| ||||||||| ||||| ||  ||||||| |  || || || || || |||||  |||
tctgctactaaatttattgtttttatccttttccttttttgctattctttttattgataccaagtgacggttaaatattctgtttcatgtttctatgcagCAAGAGTTAATTAGAACAGTCGATCTTGGTCCTTTCAAGCATATTGTGGATGATGGTCTTGAGCTGAGGAAAGCAGCTTTTGAATGTGTAGACACACTGC

upper sequence: EFJ33911 (Selaginella moellendorffii), 3'ss of exon 23
lower sequence: PP1S35_209V6.1 (Physcomitrella patens), 3'ss of exon 25
-----------------------------------------gtacgatctttt-cattggagtcagcatgttatgttttttaatctcgt----tttgcagAAAGAGCTTATAAGAACAGTGGATCTAGGTCCTTTCAAGCATACTGTGGATGACGGTCTGGAATTGAGGAAGGGTGCATTCGAGTGCGTTGACACTTTGC
                                           ||||||| |   ||  |     |     ||  || || |   | |     | || |||||||||| || || || |||||||| |||||||||||||||| ||||||||| || |||||| | |||||||| || || || || || || || ||||
tcttctgttttgtttactccgcgtctgccttttgttcagaacaacgatctgtggtatccgcagttgttcactaaattattcatcgttggtggatgtgtagAAAGAGCTCATCAGGACCGTGGATCTTGGTCCTTTCAAGCATATTGTGGATGATGGGCTGGAACTCAGGAAGGGAGCCTTTGAATGTGTGGATACCTTGC

upper sequence: EFJ33911 (Selaginella moellendorffii), 3'ss of exon 23
lower sequence: PP1S337_6V6.1 (Physcomitrella patens), 3'ss of exon 24
----------------------------------------gtacgatcttttcattggagtcagcatgtta-tgttttttaatc-----tcgttttgcagAAAGAGCTTATAAGAACAGTGGATCTAGGTCCTTTCAAGCATACTGTGGATGACGGTCTGGAATTGAGGAAGGGTGCATTCGAGTGCGTTGACACTTTGC
                                          | ||  |    | | |     || ||  | | | | |||| |     | | |||| |||||||||| || ||||| |||||||| || ||||||||||||| ||||||||| || || ||| | || ||||| || || || || || || || ||||
tttattctctatgactggtatgtgctaatcttggttattgccaggagttcactaatcgctctggcttgccaatatgtgttaaacgtgggttggtttgtagAAAGAGCTCATCAGAACCGTGGATCTTGGACCTTTCAAGCATATTGTGGATGATGGACTAGAACTCAGAAAGGGGGCTTTTGAATGTGTGGATACCTTGC

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|169083025|gb|FE488547.1|FE488547
EST:     AACTGCTACCTGTGCTCTTTCCGCTTCTGTATGAACAGACAGTTGTAAAG                         AAAGAGCTTATAAGAACAGTGGATCTAGGTCCTTTCAAGCATACTGTGGAC
genomic: AGCTGCTACCTGTGCTCTTTCCGCTTCTGTATGAACAGACAGTTGTAAAGgtacgatctt ... cgttttgcagAAAGAGCTTATAAGAACAGTGGATCTAGGTCCTTTCAAGCATACTGTGGAT
EST: gi|169083461|gb|FE495860.1|FE495860
EST:     AGCTGCTACCTGTGCTCTTTCCGCTTCTGTATGAACAGACAGTTGTAAAG                         AAAGAGCTTATAAGAACAGTGGATCTAGGTCCTTTCAAGCATACTGTGGAT
genomic: AGCTGCTACCTGTGCTCTTTCCGCTTCTGTATGAACAGACAGTTGTAAAGgtacgatctt ... cgttttgcagAAAGAGCTTATAAGAACAGTGGATCTAGGTCCTTTCAAGCATACTGTGGAT
EST: gi|169027166|gb|FE435063.1|FE435063
EST:     AGCTGCTACCTGTGCTCTTTCCGCTTCTGTATGAACAGACAGTTGTAAAG                         AAAGAGCTTATAAGAACAGTGGATCTAGGTCCTTTCAAGCATACTGTGGAT
genomic: AGCTGCTACCTGTGCTCTTTCCGCTTCTGTATGAACAGACAGTTGTAAAGgtacgatctt ... cgttttgcagAAAGAGCTTATAAGAACAGTGGATCTAGGTCCTTTCAAGCATACTGTGGAT
EST: gi|169087454|gb|FE492530.1|FE492530
EST:     AGCTGCTACCTGTGCTCTTTCCGCTTCTGTATGAACAGACAGTTGTAAAG                         AAAGAGCTTATAAGAACAGTGGATCTAGGTCCTTTCAAGCATACTGTGGAT
genomic: AGCTGCTACCTGTGCTCTTTCCGCTTCTGTATGAACAGACAGTTGTAAAGgtacgatctt ... cgttttgcagAAAGAGCTTATAAGAACAGTGGATCTAGGTCCTTTCAAGCATACTGTGGAT
EST: gi|169095773|gb|FE498893.1|FE498893
EST:     AGCTGCTACCTGTGCTCTTTCCGCTTCTGTATGAACAGACAGTTGTAAAG                         AAAGAGCTTATAAGAACAGTGGATCTAGGTCCTTTCAAGCATACTGTGGAT
genomic: AGCTGCTACCTGTGCTCTTTCCGCTTCTGTATGAACAGACAGTTGTAAAGgtacgatctt ... cgttttgcagAAAGAGCTTATAAGAACAGTGGATCTAGGTCCTTTCAAGCATACTGTGGAT
EST: gi|169027307|gb|FE436166.1|FE436166
EST:     AGCTGCTACCTGTGCTCTTTCCGCTTCTGTATGAACAGACAGTTGTAAAG                         AAAGAGCTTATAAGAACAGTGGATCTAGGTCCTTTCAAGCATACTGTGGAT
genomic: AGCTGCTACCTGTGCTCTTTCCGCTTCTGTATGAACAGACAGTTGTAAAGgtacgatctt ... cgttttgcagAAAGAGCTTATAAGAACAGTGGATCTAGGTCCTTTCAAGCATACTGTGGAT
EST: gi|169021627|gb|FE428844.1|FE428844
EST:     AACTGCTACCTGTGCTCTTTCCGCTTCTGTATGAACAGACAGTTGTAAAG                         AAAGAGCTTATAAGAACAGTGGATCTAGGTCCTTTCAAGCATACTGTGGAC
genomic: AGCTGCTACCTGTGCTCTTTCCGCTTCTGTATGAACAGACAGTTGTAAAGgtacgatctt ... cgttttgcagAAAGAGCTTATAAGAACAGTGGATCTAGGTCCTTTCAAGCATACTGTGGAT
EST: gi|169051502|gb|FE459737.1|FE459737
EST:     GCTTCTGTATGAACAGACAGTTGTAAAG                         AAAGAGCTTATAAGAACAGTGGATCTAGGTCCTTTCAAGCATACTGTGGAT
genomic: GCTTCTGTATGAACAGACAGTTGTAAAGgtacgatctt ... cgttttgcagAAAGAGCTTATAAGAACAGTGGATCTAGGTCCTTTCAAGCATACTGTGGAT

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: 35 (upstream exon), 28 (downstream exon)
Score: 11

AGTTTCGGCTTTGAGCACTGCTGGGCACAACAAACCGAGCCTTGTGAAGGAGCTGCTACCTGTGCTCTTTCCGCTTCTGTATGAACAGACAGTTGTAAAGgtacgatctt ... cgttttgcagAAAGAGCTTATAAGAACAGTGGATCTAGGTCCTTTCAAGCATACTGTGGATGACGGTCTGGAATTGAGGAAGGGTGCATTCGAGTGCGTTGACACTTTGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtacgatcttttcattggagtcagcatgttatgttttttaatctcgttttgcagAAAGAGCTTATAAGAACAGTGGATCTAGGTCCTTTCAAGCATACTGTGGATGACGGTCTGGAATTGAGGAAGGGTGCATTCGAGTGCGTTGACACTTTGC
                                    ttttaat  putative branch site (score: 11)
                                          tctcgtttt  CT-rich tract
                          atgttatgttttttaa  TA-rich tract