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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagattgtgaaccattattggctgacaaaagtcttatggtcttttggcctccagTGTTGGAAGATATCAAGAAGCAAACCCGGGAGTTTTCACCATCGTGACATTTCCATTTCTATTCGCGGTCATGTTTGGGGACTGGGGTCACGGAATTGTC

Basic information

species Selaginella moellendorffii
transcript EFJ12515
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ12515 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: GRMZM2G104418_T01 (Zea mays), 3'ss of exon 1
--------------------------------------gtaagatt--gtgaaccattattggctgacaaaagtcttatg----gtcttttggcctccagTGTTGGAAGATATCAAGAAGCAAACCCGGGAGTTTTCACCATCGTGACATTTCCATTTCTATTCGCGGTCATGTTTGGGGACTGGGGTCACGGAATTGTC
                                       | || ||  |   |  | | |  | ||   ||    | |||    ||    ||   | |||||| |  | ||||||||||||||| || ||||| |||||||||||||| || || |||||||| || ||||||||||| || ||||| || || |||  |
cttattttttgtaattaaagaagtggaattaatgtcatttgaggtttggctcaagactgtaaggtggataagtgttgatgctgtgttccatgtggtacagTGTAGCCAAATATCAAGAAGCAAATCCTGGAGTATTCACCATCGTGACTTTCCCTTTTCTATTTGCCGTCATGTTTGGTGATTGGGGCCATGGGATTTGC

upper sequence: EFJ12515 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: GRMZM2G058910_T01 (Zea mays), 3'ss of exon 10
--------------------------------------gtaagattgtgaaccattattg---gctgacaaaagtcttatggtctttt----ggcctccagTGTTGGAAGATATCAAGAAGCAAACCCGGGAGTTTTCACCATCGTGACATTTCCATTTCTATTCGCGGTCATGTTTGGGGACTGGGGTCACGGAATTGTC
                                       | || || |||  || || ||   | ||   ||   || ||| | | ||    |   | |||||| |  |  |||||||||||||| || ||||| |||||||| ||||| || || ||  |||| || ||||||||||| || ||||| || ||||||  |
cttatatcttgtaaataaagaagtgtaattcatatcatttgaggtt-tgactcaatactgtaaggtggataagtgctaatgatgtgttccatgtggtacagTGTAGCCAAGTATCAAGAAGCAAATCCTGGAGTATTCACCATTGTGACTTTCCCTTTCTTATTTGCTGTCATGTTTGGTGATTGGGGCCATGGAATTTGC

upper sequence: EFJ12515 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: GLYMA12G07740.1 (Glycine max), 3'ss of exon 10
---------------------------------gtaagattgtgaac---cattattggctgacaaaagtcttat--------ggtcttttggcctccagTGTTGGAAGATATCAAGAAGCAAACCCGGGAGTTTTCACCATCGTGACATTTCCATTTCTATTCGCGGTCATGTTTGGGGACTGGGGTCACGGAATTGTC
                                 |  |   || ||     |  ||    |||| || | || ||          | ||| |      |||||||| |||||||||||||||||| || | |||||  ||||   | | ||| |||||||| |||||||| |||||||| ||||||||||| ||||||  |
atgcccatgtcaatagatcaataggatagaactgctattctgcgattttgctataaaaactgaaaagactcctagtcctaatgagccttgtacttggcagTGTTGCAAGATATCAAGAAGCAAATCCTGCAGTTTATACCACTATTATATTCCCATTTCTTTTCGCGGTTATGTTTGGTGACTGGGGTCATGGAATTTGC

upper sequence: EFJ12515 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: GLYMA11G15730.1 (Glycine max), 3'ss of exon 10
------------------------------gtaagattgtgaaccattatt-----ggctgacaaaagtctta-------tggtcttttggcctc--cagTGTTGGAAGATATCAAGAAGCAAACCCGGGAGTTTTCACCATCGTGACATTTCCATTTCTATTCGCGGTCATGTTTGGGGACTGGGGTCACGGAATTGTC
                                |  ||| || |   ||  |       |||| || | || ||       ||  |  |||  ||   |||||||| |||||||||||||||||| || | |||||  || |   | | ||| |||||||| || ||||| |||||||| ||||||||||| ||||||  |
agagttgaataatgccagtttaggatggaaccattattttgcaattttgctataaaaactgaaaagactcctagtcctaatgagcccttgtacttggcagTGTTGCAAGATATCAAGAAGCAAATCCTGCAGTTTATACAACTATTATATTCCCATTTCTTTTTGCGGTTATGTTTGGCGACTGGGGTCATGGAATTTGC

upper sequence: EFJ12515 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: Vv03s0038g00290.t01 (Vitis vinifera), 3'ss of exon 10
-----------------------------------------gtaagattgt--gaaccattattggctgacaaaagtcttatggt-cttttggcctccagTGTTGGAAGATATCAAGAAGCAAACCCGGGAGTTTTCACCATCGTGACATTTCCATTTCTATTCGCGGTCATGTTTGGGGACTGGGGTCACGGAATTGTC
                                          | | |||    |||   ||     |  || ||| |  | || | |  ||    | ||| || |  |  |||||||| ||||| || || || ||||| || || |||||||||||||| || || ||||||||||| || ||||| || ||| |   |
tattttactttaacctatttgattttcattttgctgatgatatcaaattaacagaattgtttgcctcatactaaaattatgtgattccatttaattgcagGGTGGCCAAGTATCAAGAGGCAAATCCTGGTGTATTCACTATTGTTACATTTCCATTTCTTTTTGCTGTCATGTTTGGTGATTGGGGACATGGATTATGC

upper sequence: EFJ12515 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: PP1S115_183V6.1 (Physcomitrella patens), 3'ss of exon 11
-----------------------------------------------------------------------------------------------------------------------------------------gtaagattgtgaaccattattggctgacaaaagtcttatggtcttttggcctccagTGTTGGAAGATATCAAGAAGCAAACCCGGGAGTTTTCACCATCGTGACATTTCCATTTCTATTCGCGGTCATGTTTGGGGACTGGGGTCACGGAATTGTC
                                                                                                                                           |  ||  | ||  ||| |   |  |  |    | ||    ||||||   |  || || | ||| ||||||||||| ||||| |||   ||||| ||||| ||||| ||||| || || ||||| |||||||| |||||||| || || || |  
gtaagtttcaacaaaacatgtcgatggaaataggaattccaagaaatctagagtaggcatttttcgatcgaatacaaacgacatacactgtgaatcttttcaaagatcgaggcagagatcaaagcagagtctaaggaccagcatgttcaaaaattctgaacacattatttacataccagcttttg---tgtagGGTGGCAAGGTATCAAGAAGCGAACCCTGGATGCTTCACGATCGTTACATTCCCATTCCTCTTTGCGGTTATGTTTGGCGACTGGGGACATGGCATAGCA

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|169077636|gb|FE484898.1|FE484898
EST:     CAAGTTAATAAATTCACGTCAGCCTTCCAGGAAATCGTGGATGCATATGG                         TGTTGGAAGATATCAAGAAGCAAACCCGGGAGTTTTCACCATCGTGACATT
genomic: CAAGTTAATAAATTCACGTCAGCCTTCCAGGAAATCGTGGATGCATATGGgtaagattgt ... tggcctccagTGTTGGAAGATATCAAGAAGCAAACCCGGGAGTTTTCACCATCGTGACATT
EST: gi|169055646|gb|FE465290.1|FE465290
EST:     CAAGTTAATAAATTCACGTCAGCCTTCCAGGAAATCGTGGATGCATATGG                         TGTTGGAAGATATCAAGAAGCANACCCGGGAGTTTTCACCATCGTGACATT
genomic: CAAGTTAATAAATTCACGTCAGCCTTCCAGGAAATCGTGGATGCATATGGgtaagattgt ... tggcctccagTGTTGGAAGATATCAAGAAGCAAACCCGGGAGTTTTCACCATCGTGACATT
EST: gi|169082759|gb|FE486240.1|FE486240
EST:     CAAGTTAATAAATTCACGTCAGCCTTCCAGGAAATCGTGGATGCATATGG                         TGTTGGAAGATATCAAGAAGCAAACCCGGGAGTTTTCACCATCGTGACATT
genomic: CAAGTTAATAAATTCACGTCAGCCTTCCAGGAAATCGTGGATGCATATGGgtaagattgt ... tggcctccagTGTTGGAAGATATCAAGAAGCAAACCCGGGAGTTTTCACCATCGTGACATT
EST: gi|169096766|gb|FE499782.1|FE499782
EST:     CAAGTTAATAAATTCACGTCAGCCTTCCAGGAAATCGTGGATGCATATGG                         TGTTGGAAGATATCAAGAAGCAAACCCGGGAGTTTTCACCATCGTGACATT
genomic: CAAGTTAATAAATTCACGTCAGCCTTCCAGGAAATCGTGGATGCATATGGgtaagattgt ... tggcctccagTGTTGGAAGATATCAAGAAGCAAACCCGGGAGTTTTCACCATCGTGACATT

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: 27 (upstream exon), 35 (downstream exon)
Score: 13

CAACCATTTTCCAAGTTCTTCACACAAAGGAGGCTCCACCAACGTATTTCCAAGTTAATAAATTCACGTCAGCCTTCCAGGAAATCGTGGATGCATATGGgtaagattgt ... tggcctccagTGTTGGAAGATATCAAGAAGCAAACCCGGGAGTTTTCACCATCGTGACATTTCCATTTCTATTCGCGGTCATGTTTGGGGACTGGGGTCACGGAATTGTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taagattgtgaaccattattggctgacaaaagtcttatggtcttttggcctccagTGTTGGAAGATATCAAGAAGCAAACCCGGGAGTTTTCACCATCGTGACATTTCCATTTCTATTCGCGGTCATGTTTGGGGACTGGGGTCACGGAATTGTC
                    ggctgac  putative branch site (score: 13)
                                        tctttt  putative PPT
              attatt  TA-rich tract