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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGAAGGAGCACGTTGTTGGATGGTACAGCACTGGTCCCAAACTACGTGAGAACGATCTTGACATTCACGAGCTCTTTAGGAAgtgagaaattttgtttctctcttcttctttttttctgtttgctcatttgtgtgattacgtctaccag

Basic information

species Selaginella moellendorffii
transcript EFJ21414
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ21414 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: LOC_Os04g56646.1 (Oryza sativa), 5'ss of exon 3
CGAAGGAGCACGTTGTTGGATGGTACAGCACTGGTCCCAAACTACGTGAGAACGATCTTGACATTCACGAGCTCTTTAGGAAg--tgagaaattttgtttctctcttcttctttttttctgtttgctcatttgtgtgattacgtctaccag-------------------------------
| |||||||| |||||||| ||||||||||| ||||| |||||  | ||||||||  | || || ||||  || || |  |||  || ||  |   |   || | |      | || |   |    | || |   ||| ||  | |                                    
CCAAGGAGCATGTTGTTGGCTGGTACAGCACCGGTCCAAAACTCAGGGAGAACGACTTGGATATACACGCACTATTCAATAAgtatgtgatgtaccgaagctttatatcctgtattgttcatgaagttatattcttgactagatatgttgttttggtgcaagtaatctttattaaattgtct

upper sequence: EFJ21414 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GRMZM2G061745_T03 (Zea mays), 5'ss of exon 3
CGAAGGAGCACGTTGTTGGATGGTACAGCACTGGTCCCAAACTACGTGAGAACGATCTTGACATTCACGAGCTCTT---TAGGAAgtgagaaattttgtttctctcttcttctttttttctgtttgc---tcatttgtgtgattacgtctaccag---------------------------
| |||||||| |||||||| |||||||||||||| || |||||| | ||||||||  | ||  | || |   | ||    ||| | || |||  | |||     | |  || || ||||    | |     || || | |   |||       ||                           
CCAAGGAGCATGTTGTTGGCTGGTACAGCACTGGCCCAAAACTAAGGGAGAACGACTTGGATGTCCATGCATTATTCAACAGgtattgtgaagctatgtcctcttgtgattgttcttttgaactcgtgtgacaattttttaggtactgtcctaagttacgagtgtgtaacttttcagccaac

upper sequence: EFJ21414 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GRMZM2G368908_T02 (Zea mays), 5'ss of exon 3
CGAAGGAGCACGTTGTTGGATGGTACAGCACTGGTCCCAAACTACGTGAGAACGATCTTGACATTCACGAGCTCTTTAGGAAgtgaga-aattttgtttctctcttcttctttttttctgtttgctcatttgtgtgattacgtctaccag--------------------------------
| |||||||| |||||||| |||||||||||||| || |||||| | ||||| ||  | ||  | || |   | || |  | ||| |   |   ||    |    |  | |  | || || ||| || |||      |||   | |||                                  
CCAAGGAGCATGTTGTTGGCTGGTACAGCACTGGCCCAAAACTAAGGGAGAATGACTTGGATGTCCATGCATTGTTCAACAGgtgtggtgaacctgcaagtgaagttatgtcctcttatggttgttcttttaaactcttaatacaacccctgagctatagacaaatatgtaaatttccaaac

upper sequence: EFJ21414 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GLYMA11G34980.1 (Glycine max), 5'ss of exon 3
CGAAGGAGCACGTTGTTGGATGGTACAGCACTGGTCCCAAACTACGTGAGAACGATCTTGACATTCACGAGCTCTTTAGGAAgtgagaaattttgt------ttctctcttc-----ttctttttttctgtttg----------ctcatttgtgtgattacgtctaccag------------
| |||||||| ||||| || ||||| ||||||||||| || || || || || ||||||||||||||||   | ||||   |||  |    ||  |      | |||| |       ||  |  ||||||| ||           ||||||| |   | |  | |  |||            
CAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAAATGATCTTGACATTCACGGCTTATTTAATGAgtatgtttattgatccaaaatcctctgtataatgatttataatttctgtgtgaatttttcacttcatttgagcattaatatttcacagttttgctgaaaa

upper sequence: EFJ21414 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GLYMA18G03360.1 (Glycine max), 5'ss of exon 3
-CGAAGGAGCACGTTGTTGGATGGTACAGCACTGGTCCCAAACTACGTGAGAACGATCTTGACATTCACGAGCTCTTTAGGAAgtgagaaattttgtttctctcttcttctttttttc-tgtttgctcatttgtgtgattac-gtctaccag----------------------------------
 | |||||||| ||||| || ||||| ||||||||||| || || ||||| || || ||||||||||| |   | ||||   |||  |    |||||| |||     |||| | | |  || ||  | |||  ||||  ||| || ||                                      
GCAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGTGAAAATGACCTTGACATTCATGGCTTATTTAATGagtatg----tttgttgctccaaatttctctgtataatgatttttaattgctgtgtgtactgtgtattcttcactttatttgagcattaatatttcacactttt

upper sequence: EFJ21414 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: Vv08s0007g01980.t01 (Vitis vinifera), 5'ss of exon 3
CGAAGGAGCACGTTGTTGGATGGTACAGCACTGGTCCCAAACTACGTGAGAACGATCTTGACATTCACGAGCTCTTTAGGAAgtgag-----aaattttgtttctctcttcttctttttttctg---tttg--ctcatttgtgtgattacgtctaccag-----------------------
| ||||||||||| ||||||||||||||||| || || ||||| || ||||| || || || |||||||  || ||     ||| ||       || ||| ||||         ||  || |||   |||   || |||   |  |     | |  ||                        
CCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGAgtaagctcatggatcttgattcttataaacgattaattactgaaatttaatcttattctggaaagcttattttgcaactgatatattagtgaagcttgat

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|169103938|gb|FE504275.1|FE504275
EST:     GGTCCCAAACTACGTGAGAACGATCTTGACATTCACGAGCTCTTTAGGAA                         CTACGCTCCTAACCCAGTCCTGGTGATTATCGACGTACAACCCAGGGAGCT
genomic: GGTCCCAAACTACGTGAGAACGATCTTGACATTCACGAGCTCTTTAGGAAgtgagaaatt ... cgtctaccagCTACGCTCCTAACCCAGTCCTGGTGATTATCGACGTACAACCCAGGGAGCT
EST: gi|169103939|gb|FE504276.1|FE504276
EST:     GGTCCCAAACTACGTGAGAACGATCTTGACATTCACGAGCTCTTTAGGAA                         CTACGCTCCTAACCCAGTCCTGGTGATTATCGACGTACAACCCAGGGAGCT
genomic: GGTCCCAAACTACGTGAGAACGATCTTGACATTCACGAGCTCTTTAGGAAgtgagaaatt ... cgtctaccagCTACGCTCCTAACCCAGTCCTGGTGATTATCGACGTACAACCCAGGGAGCT
EST: gi|169057078|gb|FE464134.1|FE464134
EST:     GGTCCCAAACTACGTGAGAACGATCTTGACATTCACGAGCTCTTTAGGAA                         CTACGCTCCTAACCCGGTCCTGGTGATCATCGACGTACAACCCAGGGAGCT
genomic: GGTCCCAAACTACGTGAGAACGATCTTGACATTCACGAGCTCTTTAGGAAgtgagaaatt ... cgtctaccagCTACGCTCCTAACCCAGTCCTGGTGATTATCGACGTACAACCCAGGGAGCT
EST: gi|169057077|gb|FE464133.1|FE464133
EST:     GGTCNCAAACTACGTGAGAACGATCTTGACATTCACGAGCTCTTTAGGAA                         CTACGCTCCTAACCCGGTCCTGGTGATCATCGACGTACAACCCAGGGAGCT
genomic: GGTCCCAAACTACGTGAGAACGATCTTGACATTCACGAGCTCTTTAGGAAgtgagaaatt ... cgtctaccagCTACGCTCCTAACCCAGTCCTGGTGATTATCGACGTACAACCCAGGGAGCT

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: 32 (upstream exon), 34 (downstream exon)
Score: 17

CGAAGGAGCACGTTGTTGGATGGTACAGCACTGGTCCCAAACTACGTGAGAACGATCTTGACATTCACGAGCTCTTTAGGAAgtgagaaatt ... cgtctaccagCTACGCTCCTAACCCAGTCCTGGTGATTATCGACGTACAACCCAGGGAGCTCGCAATCCCTACAAAGGCTTACTACTCCATCGAAGACGTCAAGGAGAAC




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