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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGCTGCAGACATGGTGTTGGCAGACGATAACTTCAGCACGATTGTATCAGCCGTTGCAGAAGGTCGTTCAATCTACAACAACATGAAAGCTTTTATAAGgtaaagttcctgcgtggtttgagaatgttgaaacgacgagtgaagctgattcttttcatctgctaccag

Basic information

species Selaginella moellendorffii
transcript EFJ35276
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ35276 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: GRMZM2G056014_T01 (Zea mays), 5'ss of exon 6
AAGCTGCAGACATGGTGTTGGCAGACGATAACTTCAGCACGATTGTATCAGCCGTTGCAGAAGGTCGTTCAATCTACAACAACATGAAAGCTTTTATAAGgtaaagttcctgcgtggtttgag-aatgttgaaacgacgagtgaagctgattcttttcatctgctaccag------------------------------------------
| ||  | |||||||||||||| ||||| || || ||||| || || || || || |  |||||  | || ||||||||||||||||||||||| |||||||         || || |||||  | |||| | ||   |  |    ||  | ||||||  |  || ||                                            
AGGCGTCTGACATGGTGTTGGCTGACGACAATTTTAGCACCATAGTTTCTGCAGTCGGTGAAGGAAGATCGATCTACAACAACATGAAAGCTTTCATAAGgtctgtgctgagcttgctttgattattgttcacactttg--tagtactcgtacttttcgcccccttcccttgtgggcattcttgacgtccctgtcttcctcggctgccgcag

upper sequence: EFJ35276 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: Vv15s0046g00040.t01 (Vitis vinifera), 5'ss of exon 5
AAGCTGCAGACATGGTGTTGGCAGACGATAACTTCAGCACGATTGTATCAGCCGTTGCAGAAGGTCGTTCAATCTACAACAACATGAAAGCTTTTATAAGgtaaa---gttcctgcgtggtttgagaatgttgaaacgacgagtgaag--ctgattcttttcatctgctaccag---
||||| |||| |||||  ||||||| || || ||||| || || || |||||||||||||| ||||| ||||| || ||||||||||| |||||||| ||||| |   ||       | ||||     |       ||   ||| ||   || |   |      |  | |   |   
AAGCTTCAGATATGGTTCTGGCAGATGACAATTTCAGTACCATAGTTTCAGCCGTTGCAGAGGGTCGCTCAATTTATAACAACATGAAGGCTTTTATTAGgtatatatgtcttaagttcgttttttttttccctttcgggtagtcaacatctaaccttcagtgacctcaatatgcag

upper sequence: EFJ35276 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: PP1S80_36V6.1 (Physcomitrella patens), 5'ss of exon 6
AAGCTGCAGACATGGTGTTGGCAGACGATAACTTCAGCACGATTGTATCAGCCGTTGCAGAAGGTCGTTCAATCTACAACAACATGAAAGCTTTTATAAGgtaaagttcctgcgtggtttgagaatgttgaaacgacgagtgaagctg-attcttttcatct-gcta--ccag------------------------------
||||||| ||||||||| |||||||||| || |||||||| || ||  |||| |||| ||| |||||| |||| ||||||||||||||||| || || ||||    |          |      |  || |    | |  |||  |   |||||  || ||  ||||  ||||                              
AAGCTGCTGACATGGTGCTGGCAGACGACAATTTCAGCACAATCGTGGCAGCTGTTGGAGAGGGTCGTGCAATTTACAACAACATGAAAGCCTTCATCAGgtttcatattgttccactcccgtcaactttacgtaatgcatgagtccctattctcgtcttcaagctattccagaacttgaactgcatcatgtggattctacag

upper sequence: EFJ35276 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: PP1S78_99V6.2 (Physcomitrella patens), 5'ss of exon 8
AAGCTGCAGACATGGTGTTGGCAGACGATAACTTCAGCACGATTGTATCAGCCGTTGCAGAAGGTCGTTCAATCTACAACAACATGAAAGCTTTTATAAGgtaa------------agttcctgcgtggt------ttgagaatgttgaaacgacgagtgaag--ctgattcttttcatctgctaccag
| || |||||||||||| | ||||| ||||| || |||||||||||  |||| |||| |||||||||||| || ||||| || ||||| || ||||| ||||              | |   || || ||       ||||  | ||  ||  |  | |  |   || |     ||  |   |   |||
AGGCAGCAGACATGGTGCTTGCAGATGATAATTTTAGCACGATTGTGGCAGCTGTTGGAGAAGGTCGTTCGATATACAATAATATGAAGGCCTTTATCAGgtgggtaatttgatttaataaatgagttgtattaggctgagcttattagaattaaaaattgaattctaacctgatttgtgaacctacag

upper sequence: EFJ35276 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: PP1S248_28V6.1 (Physcomitrella patens), 5'ss of exon 6
AAGCTGCAGACATGGTGTTGGCAGACGATAACTTCAGCACGATTGTATCAGCCGTTGCAGAAGGTCGTTCAATCTACAACAACATGAAAGCTTTTATAAGgtaaa-gttcctgcgtggtttgagaatgttgaaacgacgagt----gaagctgatt-cttttcatctgctaccag--------------
| || || ||||||||| | ||||| || || || ||||| |||||  ||||||||| |||||||||||| || |||||||||||||| || || || ||||    | |  |           || | ||  |  |  |  |    |||  ||| | |      | ||     ||              
AGGCAGCCGACATGGTGCTTGCAGATGACAATTTTAGCACTATTGTGGCAGCCGTTGGAGAAGGTCGTTCTATATACAACAACATGAAGGCCTTCATTAGgtgcgtgattttatactaaggatgattttttgagtggagtattttggaaattgagtaccagaagtttgactgaagttgtggatctacag

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|169115358|gb|FE515696.1|FE515696
EST:     GCCGTTGCAGAAGGTCGTTCAATCTACAACAACATGAAAGCTTTTATAAG                         GTACATGATATCTTCCAATATCGGAGAAGTCGCTTCAATCTTCTTGACGGC
genomic: GCCGTTGCAGAAGGTCGTTCAATCTACAACAACATGAAAGCTTTTATAAGgtaaagttcc ... ctgctaccagGTACATGATATCTTCCAATATCGGAGAAGTCGCTTCAATCTTCTTGACGGC




















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: 15 (upstream exon), 35 (downstream exon)
Score: 6

AAGCTGCAGACATGGTGTTGGCAGACGATAACTTCAGCACGATTGTATCAGCCGTTGCAGAAGGTCGTTCAATCTACAACAACATGAAAGCTTTTATAAGgtaaagttcc ... ctgctaccagGTACATGATATCTTCCAATATCGGAGAAGTCGCTTCAATCTTCTTGACGGCTGCATTGGGAATGCCCGAAGGCCTGATCCCAGTCCAGCTTTTGTGGGTG




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