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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtgttccgggcttgctcttgtttatcgctaacaatctgctccagATACGATAAGTTTTGTCCGTTCTACAAGTCCGTTTGGATGATGCGAAACATCGTTCATTTCTGCGACCTGTCCACTCAG

Basic information

species Selaginella moellendorffii
transcript EFJ33015
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ33015 (Selaginella moellendorffii), 3'ss of exon 16
lower sequence: LOC_Os06g45120.1 (Oryza sativa), 3'ss of exon 16
--------------------------------------------------------gtacgtgttccgggcttgctcttgtttatcgctaacaatctgctc---cagATACGATAAGTTTTGTCCGTTCTACAAGTCCGTTTGGATGATGCGAAACATCGTTCATTTCTGCGACCTGTCCACTCAG
                                                         ||    ||      || || | || |     |  | || |  |    |||||| || ||||| ||||| ||||||||||| |||||||||||||| |||||  ||||||||       |  | | ||||
gtgagtcataccctagttttttctgatttaatacagatttattggttgtctctattttaatgattaaccattttctttagtctgatcatctctatataatgaaacagATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACATTATTCATTTCAATACATTAGCAAATCAG

upper sequence: EFJ33015 (Selaginella moellendorffii), 3'ss of exon 16
lower sequence: LOC_Os06g45120.2 (Oryza sativa), 3'ss of exon 16
--------------------------------------------------------gtacgtgttccgggcttgctcttgtttatcgctaacaatctgct---ccagATACGATAAGTTTTGTCCGTTCTACAAGTCCGTTTGGATGATGCGAAACATCGTTCATTTCTGCGACCTGTCCACTCAG---------------------
                                                         ||    ||      || || | || |     |  | || |  |    |||||| || ||||| ||||| ||||||||||| |||||||||||||| |||||  ||||||||       |  | | ||||                     
gtgagtcataccctagttttttctgatttaatacagatttattggttgtctctattttaatgattaaccattttctttagtctgatcatctctatataatgaaacagATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACATTATTCATTTCAATACATTAGCAAATCAGGTAAATCTAACGTGTTTTTAC

upper sequence: EFJ33015 (Selaginella moellendorffii), 3'ss of exon 16
lower sequence: LOC_Os02g07870.1 (Oryza sativa), 3'ss of exon 16
------------------------------------gta-cgtgttccgggcttgctc-ttgtttatcgctaacaatctgctccagATACGATAAGTTTTGTCCGTTCTACAAGTCCGTTTGGATGATGCGAAACATCGTTCATTTCTGCGACCTGTCCACTCAG
                                    ||  | |  |||    |  ||  ||| | |   ||       ||   |||||| ||||||| ||| || |||||||| || |||||||||||||| |||||  ||||||||  |    || | || |||
gtgagtgttaaacccatttgatagttctactaacctgtgtcataatccatattaactaattgatcaattctgttg-catgaaacagATATGATAAGTATTGCCCATTCTACAAATCTGTTTGGATGATGCGCAACATTATTCATTTCAACACATTGGCAACCCAG

upper sequence: EFJ33015 (Selaginella moellendorffii), 3'ss of exon 16
lower sequence: GRMZM2G421857_T02 (Zea mays), 3'ss of exon 16
---------------------------------------------gtacgtgttccgggcttgctcttgtttatcgctaacaatctgctccagATACGATAAGTTTTGTCCGTTCTACAAGTCCGTTTGGATGATGCGAAACATCGTTCATTTCTGCGACCTGTCCACTCAG
                                                  | ||    |  |  | |||   |  |||    |  |  |  ||||| |||||||| || || |||||||| ||||||||||||||||| |||||  |||| |||  |    || | | ||||
gtgagtcccctacttatttcaacacatttgatgctcatttttctccattatattttaagtatttttttgacaagtgctgtttaatta-tatagATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAACATTATTCACTTCAACACATTGGCAAATCAG

upper sequence: EFJ33015 (Selaginella moellendorffii), 3'ss of exon 16
lower sequence: GRMZM2G128877_T03 (Zea mays), 3'ss of exon 13
--------------------------------------------gtacgtgttccgggcttgctctt-gtttatcgctaacaa-------tctgctccagATACGATAAGTTTTGTCCGTTCTACAAGTCCGTTTGGATGATGCGAAACATCGTTCATTTCTGCGACCTGTCCACTCAG
                                              |  | |  |    ||  | ||    ||   || ||||       |       ||||| |||||||| || || |||||||| ||||||||||||||||| || ||  |||| |||  |    || | | ||||
atactagaccaaaaatcaagattttgggtgttacaattttctactcatatttctccattttattttttaaataattctgacaagtgttgtttaatattagATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAG

upper sequence: EFJ33015 (Selaginella moellendorffii), 3'ss of exon 16
lower sequence: GLYMA07G00430.1 (Glycine max), 3'ss of exon 17
---------------------------------------gtacgtgttccgggcttgctcttgtttatcgctaacaatctgctccagATACGATAAGTTTTGTCCGTTCTACAAGTCCGTTTGGATGATGCGAAACATCGTTCATTTCTGCGACCTGTCCACTCAG
                                        ||  |  |   |   |  | ||| |     ||      |||    ||||| ||||| ||||| || ||||||||||| |||||||||||||| |||||  | ||||||| | |  || | | ||||
gtaagggcccttgtaattggttaacttctttaacatttattatattattgtgttcttatgttggtaccttctgtgtggctgtgatagATATGATAAATTTTGCCCCTTCTACAAGTCTGTTTGGATGATGCGCAACATTATCCATTTCTACAATTTGGCAAATCAG

upper sequence: EFJ33015 (Selaginella moellendorffii), 3'ss of exon 16
lower sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 17
-------------------------------------------gtacgtgttc--cgggc---ttgctcttgtttatcgctaacaatctgctc--cagATACGATAAGTTTTGTCCGTTCTACAAGTCCGTTTGGATGATGCGAAACATCGTTCATTTCTGCGACCTGTCCACTCAG
                                            | |    ||  ||||    |  ||||||    |     |  |  |  |   |||||| || || || ||||| |||||||||||||| ||||||||||| |||||  | ||||||| | ||||  |||  |||
gtaagatttgttggctcccttcgttttggtttagtactctctctttctctctcaacgggttattcactcttgaaccttttggatgaattttttgacagATATGACAAATTCTGTCCTTTCTACAAGTCCGTGTGGATGATGCGTAACATTATCCATTTCTACAACCTAGCCAACCAG

upper sequence: EFJ33015 (Selaginella moellendorffii), 3'ss of exon 16
lower sequence: Vv04s0008g02580.t01 (Vitis vinifera), 3'ss of exon 17
-------------------------------------------------gtacgtgttccgggcttgctcttgtttatcg--ctaacaatctgctc-cagATACGATAAGTTTTGTCCGTTCTACAAGTCCGTTTGGATGATGCGAAACATCGTTCATTTCTGCGACCTGTCCACTCAG
                                                  |     || |    |    | || |||| |   |     |  | |  |||||| || ||||||||||| || |||||||| |||||||||||| | |||||  |||||||||   |  || ||| ||||
cactcttagtcactgtaggactgacatgggttattttttgttacttccaatcaaattttcattatcttccatgattattgattttttggttggttgacagATATGACAAGTTTTGTCCCTTTTACAAGTCAGTTTGGATGATGAGGAACATTATTCATTTCTATAATTTGGCCAATCAG

upper sequence: EFJ33015 (Selaginella moellendorffii), 3'ss of exon 16
lower sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 17
--------------------------------------------------------------------------------------------gtacgtgttccgggcttgctct-tgtttatcgctaaca-atctgctccagATACGATAAGTTTTGTCCGTTCTACAAGTCCGTTTGGATGATGCGAAACATCGTTCATTTCTGCGACCTGTCCACTCAG
                                                                                             ||    |||        ||   | | | |  || |     |||   |||||| |||||||| || || ||||||||||| |||||||||||||| || ||  | |||||||   |  || ||| ||||
gtaagtcccagattaagtttttgattcaaattttcgtcctttttaatttttgtttacttactatttccttatgttcccctttttatgctggtctagaaattctttttccacttaatatatgtatctcatgtggctgtgacagATATGATAAGTTCTGCCCCTTCTACAAGTCGGTTTGGATGATGCGCAATATTATCCATTTCTATAATTTGGCCAATCAG

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|169080595|gb|FE490951.1|FE490951
EST:     ACGGCCAAGCTCTTGAGAGAGGATTATTTGGCGCAAAACGCTTTCAGTGT                         ATACGATAAGTTTTGTCCGTTCTACAAGTCCGTTTGGATGATGCGAAACAT
genomic: ACGGCCAAGCTCTTGAGAGAGGATTATTTGGCGCAAAACGCTTTCAGTGTgtacgtgttc ... tctgctccagATACGATAAGTTTTGTCCGTTCTACAAGTCCGTTTGGATGATGCGAAACAT




















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: 29 (upstream exon), 29 (downstream exon)
Score: 12

CTTGTCGGCAAAGATGCGCTGGCCGAGGGAGATAAGATTATTCTTGAGACGGCCAAGCTCTTGAGAGAGGATTATTTGGCGCAAAACGCTTTCAGTGTgtacgtgttc ... tctgctccagATACGATAAGTTTTGTCCGTTCTACAAGTCCGTTTGGATGATGCGAAACATCGTTCATTTCTGCGACCTGTCCACTCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtacgtgttccgggcttgctcttgtttatcgctaacaatctgctccagATACGATAAGTTTTGTCCGTTCTACAAGTCCGTTTGGATGATGCGAAACATCGTTCATTTCTGCGACCTGTCCACTCAG
                                    cgctaac  putative branch site (score: 12)
                                             tctgctcc  putative PPT
                            ttgtttat  TA-rich tract