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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcgtcgtagaaattgtcgtttgtgtagatcgagcatctctaaaaattttgtccttgtttcttcgtagGTGGTCGCGATCTTGCCGCTGGCATTGGTGCACACCATGGGGAATCTCTTTACCAACATGAGCCTTGGAAAGGTTGCGGTGTCATTTACTCACACAATCA

Basic information

species Selaginella moellendorffii
transcript EFJ05868
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ05868 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: LOC_Os09g12600.2 (Oryza sativa), 3'ss of exon 2
-----------------------gtatcgtcgtagaaattgtcgtttgtgtagatcgagcatctctaaaaattttgtccttgtttct-tcgtagGTGGTCGCGATCTTGCCGCTGGCATTGGTGCACACCATGGGGAATCTCTTTACCAACATGAGCCTTGGAAAGGTTGCGGTGTCATTTACTCACACAATCA
                         |||||   |  | | |       ||||   | |  ||      || | ||||   |||   | |   || | |  || ||| | || || ||  |||| ||||||||||| ||||| || || ||||||||||||||||||||||| ||||||||||| || || ||||
gtaattatatttctctataagatacatcgtgacaacattcgatacacatgtattgc-actatgaagccaactattgtaactgtccttatttcagCTTGCTGCTATCCTTCCTCTCGCTATGGTCCACACCATGGGCAATCTTTTCACGAACATGAGCCTTGGAAAGGTTGCAGTGTCATTTACACATACTATCA

upper sequence: EFJ05868 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G103047_T01 (Zea mays), 3'ss of exon 2
-----------gtatcgtcgtagaaattgtcgtttgtgtagatcgagcatctctaaaaattttg--tccttgtttcttcgtagGTGGTCGCGATCTTGCCGCTGGCATTGGTGCACACCATGGGGAATCTCTTTACCAACATGAGCCTTGGAAAGGTTGCGGTGTCATTTACTCACACAATCA
           || ||||||   ||| | ||  |  |  | || | |||||   |  ||| | |   | || ||  |||  || |  | || ||| | || || ||  | || || |||||||| ||||| || || ||||||||||||||||||||||||||||||||||| || || ||||
gtgaatatttagtttcgtcgagcaaactttcagt-ataaacatagtgcatcaaaattaatgtcggtgctttcttgtttcccagCTTTTTGCTATCCTTCCTCTAGCTATCGTTCATACCATGGGCAATCTTTTCACAAACATGAGCCTTGGAAAGGTTGCGGTGTCATTTACACATACTATCA

upper sequence: EFJ05868 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G047404_T02 (Zea mays), 3'ss of exon 2
-----------gtatcgtcgtagaaattgtcgtttgtgtagatcgagcatctctaaaaattttgtccttgtttc---ttcgtagGTGGTCGCGATCTTGCCGCTGGCATTGGTGCACACCATGGGGAATCTCTTTACCAACATGAGCCTTGGAAAGGTTGCGGTGTCATTTACTCACACAATCA
           || | |  |   ||| | ||  |  |  | |  | |||||   |  ||| |||    ||||     |||  || |  |||| ||| | || || ||  | || || |||||||| ||||| || || ||||||||||||||||||||||| ||||||||||| || || || |
gtgaatatttagttttgctgggcaaactttcagt-ataaacacagtgcatcaaaattaatgttggtgctgttcttgtttcccagCTTTTCGCTATCCTTCCTCTAGCTATTGTCCATACCATGGGCAATCTTTTCACAAACATGAGCCTTGGAAAGGTTGCAGTGTCATTTACACATACTATAA

upper sequence: EFJ05868 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G174107_T01 (Zea mays), 3'ss of exon 2
----------gtatcgtcgtagaaattgtcgtttgtgtagatcgagcatctctaaaaattttgtccttgtttc---ttcgtagGTGGTCGCGATCTTGCCGCTGGCATTGGTGCACACCATGGGGAATCTCTTTACCAACATGAGCCTTGGAAAGGTTGCGGTGTCATTTACTCACACAATCA
            ||  || || || || |    | | ||  | ||       ||| | |  ||| | | ||     ||   || | || || ||| | || |||||  | || || || ||||| |||||||| ||||||||||||||||| || ||||| ||||||||||| ||||| ||||
gtaacctttaacattttcttacaacttttacgctatttacttggatatatattaatactcatgttcattttaacaattttcagCTTGTAGCCATCCTACCTCTGGCTATTGTTCATACTATGGGCAATCTCTTCACCAACATGAGCCTTGGGAAAGTTGCAGTGTCATTTACGCACACCATCA

upper sequence: EFJ05868 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA19G00270.1 (Glycine max), 3'ss of exon 2
--------------------------------------gtatcgtcgtagaaattgtcgtttgtgtagatcgagcatctctaaaaattttgtccttgtttcttcgtagGTGGTCGCGATCTTGCCGCTGGCATTGGTGCACACCATGGGGAATCTCTTTACCAACATGAGCCTTGGAAAGGTTGCGGTGTCATTTACTCACACAATCA
                                         | |  |  | |||     |   |  | ||     || | ||||   |   |   | | | |||  || | |  || ||| | || |||||  |||  ||||| ||||| || ||||| |||||||| || ||||| |||||||| || || || |||||||||||||
gtattttgaattgtgtggtgaaaaaggggtggttcattaatttggtggggtaatcactctaatttcaaattattaatttataaattataattatatttgtgttcacagTTTGCAGCAATCCTTCCACTGGCTGTGGCTCACACAATGGGAAACCTCTTGACCAACATTAGTCTTGGCAAGGTTGCTGTATCTTTCACTCACACAATCA

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|169055811|gb|FE465377.1|FE465377
EST:     TCATGTGGACTACGGGACTGTACAAGCGTCCAAGTCTCACCACTGCACAG                         GTGGTCGCGATCTTGCCGCTGGCATTGGTGCACACCATGGGGAATCTCTTT
genomic: TCATGTGGACTACGGGACTGTACAAGCGTCCAAGTCTCACCACTGCACAGgtatcgtcgt ... ttcttcgtagGTGGTCGCGATCTTGCCGCTGGCATTGGTGCACACCATGGGGAATCTCTTT




















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), 20 (downstream exon)
Score: 4

GATCACGATCACTGAGATCCAATTCGCCATTGGGTCCGCTGCCGTGCTCTTCATGTGGACTACGGGACTGTACAAGCGTCCAAGTCTCACCACTGCACAGgtatcgtcgt ... ttcttcgtagGTGGTCGCGATCTTGCCGCTGGCATTGGTGCACACCATGGGGAATCTCTTTACCAACATGAGCCTTGGAAAGGTTGCGGTGTCATTTACTCACACAATCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtcgtttgtgtagatcgagcatctctaaaaattttgtccttgtttcttcgtagGTGGTCGCGATCTTGCCGCTGGCATTGGTGCACACCATGGGGAATCTCTTTACCAACATGAGCCTTGGAAAGGTTGCGGTGTCATTTACTCACACAATCA
                        ctctaaa  putative branch site (score: 4)
                                 ttttgtccttgtttct  putative PPT
                      atctctaaaaatttt  TA-rich tract