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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactcattcatctagttgtttgttttccaaatcatagtttttactgatcttctcgatgggcagCGTACTTCAATGACGCACAGAGGCAGGCAACGAAGGATGCCGGTGCCATCGCCGGACTGAATGTGGCTCGTATTATCAACGAGCCCACTGCGGCAGCAAT

Basic information

species Selaginella moellendorffii
transcript EFJ29073
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ29073 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: LOC_Os02g02410.1 (Oryza sativa), 3'ss of exon 3
-----------------------gtactca-ttcatctagttgtttgttttcc--aaatcatagttt-ttactgatcttctcgatgggcagCGTACTTCAATGACGCACAGAGGCAGGCAACGAAGGATGCCGGTGCCATCGCCGGACTGAATGTGGCTCGTATTATCAACGAGCCCACTGCGGCAGCAAT
                       || || | || |   |   | |  || |    ||  ||| | |   | ||| ||||     |   ||||||||||||||||||| |||||||||||||| ||||||||||||| ||| || || |||||||| ||| | || ||||| ||||| ||||| || || ||
gttagtaatgacaagacattcatgtgcttagttaactcaagcggtgattctgtggaagccattgctcacttctgctctttcatgttttcagCGTACTTCAATGACGCGCAGAGGCAGGCAACCAAGGATGCCGGTGTCATTGCTGGCCTGAATGTTGCTAGGATCATCAATGAGCCAACTGCTGCTGCTAT

upper sequence: EFJ29073 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GRMZM2G114793_T01 (Zea mays), 3'ss of exon 3
------------------gtactcatt-catctagttgtttgttttccaaatcatagt------ttttactg-atcttctcgatgggcagCGTACTTCAATGACGCACAGAGGCAGGCAACGAAGGATGCCGGTGCCATCGCCGGACTGAATGTGGCTCGTATTATCAACGAGCCCACTGCGGCAGCAAT
                   | ||  || | |||||| |||  | |   ||| | | |        ||   ||  |  | |   |  ||||||||||||||||| || |||||||||||||| |||||||| |||| ||| ||||| || ||||| ||| | || ||||| ||||| ||||| || || ||
gttagtaactgaacaattctgctggttacctctagtagttgttatgtaaaaacgtggcggctcacttccttgtgttgtgtttttttgcagCGTACTTCAATGATGCGCAGAGGCAGGCAACCAAGGATGCTGGTGTCATTGCCGGCCTCAATGTTGCTAGGATCATCAATGAGCCAACTGCTGCTGCTAT

upper sequence: EFJ29073 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GRMZM2G415007_T01 (Zea mays), 3'ss of exon 3
------------------gtactcatt-catctagttgtttgttttccaaatcatagtt-----tttactgatcttct-cgatgggcagCGTACTTCAATGACGCACAGAGGCAGGCAACGAAGGATGCCGGTGCCATCGCCGGACTGAATGTGGCTCGTATTATCAACGAGCCCACTGCGGCAGCAAT
                   | ||  || | |||||| |||  | |   |||   | ||       || || || || |    |  ||||| ||||||||||| || |||||||||||||| |||||||| |||| ||| ||||| || ||||| ||| | || ||||| ||||| ||||| || || ||
gttagtaactgaaccattctgctggttacctctagtagttgttatgtaaaaatgtggtggcttacttccttatgttttgttttttgcagCATACTTCAATGATGCGCAGAGGCAGGCAACCAAGGATGCTGGTGTCATTGCCGGCCTCAATGTTGCTAGGATCATCAATGAGCCAACTGCTGCTGCTAT

upper sequence: EFJ29073 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA08G02940.1 (Glycine max), 3'ss of exon 3
-----------------------------------------------gtactcattcatctagttgtttgttttccaaatcatagtttttac--tgatcttctcgatgggcagCGTACTTCAATGACGCACAGAGGCAGGCAACGAAGGATGCCGGTGCCATCGCCGGACTGAATGTGGCTCGTATTATCAACGAGCCCACTGCGGCAGCAAT
                                                |  |  ||   ||   || || |  |   | ||  | || | ||  |  | ||    |||  |||| ||||||||||| || ||||||||||| || |||||||| |||| ||| || || || ||||| ||| | ||||||||||| |||||||| || || ||
gtaactggaagtctgaaacaatttgcgccttatttctccccttcaatttgattgttttcctc-ctgcttttgcttttattccaatttctcacatttttgtttcaaatgcacagCTTACTTCAATGATGCTCAGAGGCAGGCCACCAAGGATGCTGGTGTCATTGCTGGTCTCAATGTTGCTAGAATTATCAACGAACCCACTGCCGCTGCCAT

upper sequence: EFJ29073 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA05G36620.1 (Glycine max), 3'ss of exon 3
---------------------------------------------gtactcattcatctagttgtttgttttccaaatca-tagtttttactgatcttctcgatgggcagCGTACTTCAATGACGCACAGAGGCAGGCAACGAAGGATGCCGGTGCCATCGCCGGACTGAATGTGGCTCGTATTATCAACGAGCCCACTGCGGCAGCAAT
                                              |  |  ||   ||  |  |||    |  |  ||| ||  |   | |   |||    |||  |||| ||||||||||| || ||||||||||| || |||||||| |||| ||| || || || ||||| ||| | |||||||| || |||||||| || || ||
gtaactggaagtctggaacaattcacgacttatttcaactgcaatttgattgttttcctcctgcttttgcctttatttcaatatctcacattttcctttaaaatgcacagCTTACTTCAATGATGCTCAGAGGCAGGCCACCAAGGATGCTGGTGTCATTGCTGGTCTCAATGTTGCTAGAATTATCAATGAACCCACTGCTGCTGCCAT

upper sequence: EFJ29073 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: Vv02s0025g02140.t01 (Vitis vinifera), 3'ss of exon 3
------------------------------------------------------------gtactcattcatctagttgtttgttttccaaatcatagtttt--tactgatcttct---cgatgggcagCGTACTTCAATGACGCACAGAGGCAGGCAACGAAGGATGCCGGTGCCATCGCCGGACTGAATGTGGCTCGTATTATCAACGAGCCCACTGCGGCAGCAAT
                                                             |      | |  |||   ||||||    |     |  |  |  || |    |||    | |   ||||| ||||||||||| || ||||||||||| || |||||||| || |  || || || |||||||| || || ||||| || ||||| ||||| ||||| ||
gtgagtatcactcttctagatataacgtgtgaggttttgaactgcccgcttacactcttcttgaaatgtgaattagcattttgttcattaggatgttttactcatattagctttccatgcaacccgcagCTTACTTCAATGATGCCCAGAGGCAGGCTACAAAGGATGCTGGCGTTATTGCTGGCCTGAATGTTGCACGAATTATTAATGAGCCAACTGCTGCAGCTAT

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|169038081|gb|FE445834.1|FE445834
EST:     CCGTTGTCACAGTTCCAG                         CGTACTTCAATGACGCACAGAGGCAGGCAACGAAGGATGCCGGTGCCATCG
genomic: CCGTTGTCACAGTTCCAGgtactcattc ... cgatgggcagCGTACTTCAATGACGCACAGAGGCAGGCAACGAAGGATGCCGGTGCCATCG
EST: gi|169080680|gb|FE487188.1|FE487188
EST:     GGCAAGAAGATCAAGGACGCCGTTGTCACAGTTCCAG                         CGTACTTCAATGACGCACAGAGGCAGGCAACGAAGGATGCCGGTGCCATCG
genomic: GGCAAGAAGATCAAGGACGCCGTTGTCACAGTTCCAGgtactcattc ... cgatgggcagCGTACTTCAATGACGCACAGAGGCAGGCAACGAAGGATGCCGGTGCCATCG
EST: gi|169115292|gb|FE517008.1|FE517008
EST:     GCAAGAAGATCAAGGACGCCGTTGTCACAGTTCCAG                         CGTACTTCAATGACGCACAGAGGCAGGCAACGAAGGATGCCGGTGCCATCG
genomic: GCAAGAAGATCAAGGACGCCGTTGTCACAGTTCCAGgtactcattc ... cgatgggcagCGTACTTCAATGACGCACAGAGGCAGGCAACGAAGGATGCCGGTGCCATCG
EST: gi|169079294|gb|FE490183.1|FE490183
EST:     CGCCGTTGTCACAGTTCCAG                         CGTACTTCAATGACGCACAGAGGCAGGCAACGAAGGATGCCGGTGCCATCG
genomic: CGCCGTTGTCACAGTTCCAGgtactcattc ... cgatgggcagCGTACTTCAATGACGCACAGAGGCAGGCAACGAAGGATGCCGGTGCCATCG
EST: gi|169087152|gb|FE493099.1|FE493099
EST:     CGAGTCATACTTGGGCAAGAAGATCAAGGACGCCGTTGTCACAGTTCCAG                         CGTACTTCAATGACGCACAGAGGCAGGCAACGAAGGATGCCGGTGCCATCG
genomic: CGAGTCATACTTGGGCAAGAAGATCAAGGACGCCGTTGTCACAGTTCCAGgtactcattc ... cgatgggcagCGTACTTCAATGACGCACAGAGGCAGGCAACGAAGGATGCCGGTGCCATCG
EST: gi|169034527|gb|FE444574.1|FE444574
EST:     CGAGTCATACTTGGGCAAGAAGATCAAGGACGCCGTTGTCACAGTTCCAG                         CGTACTTCAATGACGCACAGAGGCAGGCAACGAAGGATGCCGGTGCCATCG
genomic: CGAGTCATACTTGGGCAAGAAGATCAAGGACGCCGTTGTCACAGTTCCAGgtactcattc ... cgatgggcagCGTACTTCAATGACGCACAGAGGCAGGCAACGAAGGATGCCGGTGCCATCG

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), 34 (downstream exon)
Score: 48

AGTCCAGAGGAGATAAGCGCCATGATCTTGACGAGAATGAAGGAGACGGCCGAGTCATACTTGGGCAAGAAGATCAAGGACGCCGTTGTCACAGTTCCAGgtactcattc ... cgatgggcagCGTACTTCAATGACGCACAGAGGCAGGCAACGAAGGATGCCGGTGCCATCGCCGGACTGAATGTGGCTCGTATTATCAACGAGCCCACTGCGGCAGCAAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catctagttgtttgttttccaaatcatagtttttactgatcttctcgatgggcagCGTACTTCAATGACGCACAGAGGCAGGCAACGAAGGATGCCGGTGCCATCGCCGGACTGAATGTGGCTCGTATTATCAACGAGCCCACTGCGGCAGCAAT
                                 tactgat  putative branch site (score: 48)
                                       tcttctc  CT-rich tract
                    aaatcatagttttta  TA-rich tract