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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttggaccttcacatctcagaagaccttgttttcattgaattttgtttttgtttttccagTCTGCTATTCTCGGAATGCATTCCATCCAGAAGCGTCCCGTGGTGATTGGCAACGAAATAGTCATCCGACCGATGATGTACATTGCTTTGACATACGATC

Basic information

species Selaginella moellendorffii
transcript EFJ38519
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ38519 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: Vv19s0090g00750.t01 (Vitis vinifera), 3'ss of exon 9
------------------------------------------------------------------------------------------------------------gtttggaccttcacatctcagaagaccttgtttt------cattgaattttgt---ttttg----tttttccagTCTGCTATTCTCGGAATGCATTCCATCCAGAAGCGTCCCGTGGTGATTGGCAACGAAATAGTCATCCGACCGATGATGTACATTGCTTTGACATACGATC
                                                                                                             | |||   | || |||     |  ||||   |       ||  |||  |      || |      |||  ||||| || || || || ||| | || ||   ||| |||||| ||||  ||||   | | ||| |        | ||||||||||||||||||||||||||||
gttcaaggctttactgatgcaataagttgaaattttggtgattctcttttaataatctagaagatatactttttccttcatgccctgatgataaattgtcataaaaccctctggttatccatatcagtagattcctttcgtaattaaacagagaacctcacacattctaacatctttgacagTCGGCAATCCTGGGTATGTACTCTATAGTGAAACGTCCCATGGTCGTTGGAGGCAACATAATTGCAACGTCAATGATGTACATTGCTTTGACATACGATC
















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|169056867|gb|FE466458.1|FE466458
EST:     GTGGAGTATACGGCAGTTTGATCAGCACACCCATTGTCAATCCTCCTCAG                         TCTGCTATTCTTGGAATGCATTCCATCCAGAAGCGTCCCGTGGTGATTGGC
genomic: GTGGAGTATACGGCAGTTTGATCAGCACACCCATTGTCAATCCTCCTCAGgtttggacct ... gtttttccagTCTGCTATTCTCGGAATGCATTCCATCCAGAAGCGTCCCGTGGTGATTGGC
EST: gi|169105894|gb|FE503552.1|FE503552
EST:     GTGGAGTATACGGCAGTTTGATCAGCACACCCATTGTCAATCCTCCTCAG                         TCTGCTATTCTTGGAATGCATTCCATCCAGAAGCGTCCCGTGGTGATTGGC
genomic: GTGGAGTATACGGCAGTTTGATCAGCACACCCATTGTCAATCCTCCTCAGgtttggacct ... gtttttccagTCTGCTATTCTCGGAATGCATTCCATCCAGAAGCGTCCCGTGGTGATTGGC
EST: gi|169081309|gb|FE489793.1|FE489793
EST:     GTGGAGTATACGGCAGTTTGATCAGCACACCCATTGTCAATCCTCCTCAG                         TTTGCTATTCTTGGAATGCATTCCATCCAGAAGCGTCCCGTGGTGATTGGC
genomic: GTGGAGTATACGGCAGTTTGATCAGCACACCCATTGTCAATCCTCCTCAGgtttggacct ... gtttttccagTCTGCTATTCTCGGAATGCATTCCATCCAGAAGCGTCCCGTGGTGATTGGC
EST: gi|169031261|gb|FE441129.1|FE441129
EST:     GTGGAGTATACGGCAGTTTGATCAGCACACCCATTGTCAATCCTCCTCAG                         TCTGCTATTCTCGGAATGCATTCCATCCAGAAGCGTCCCGTGGTGATTGGC
genomic: GTGGAGTATACGGCAGTTTGATCAGCACACCCATTGTCAATCCTCCTCAGgtttggacct ... gtttttccagTCTGCTATTCTCGGAATGCATTCCATCCAGAAGCGTCCCGTGGTGATTGGC
EST: gi|169070985|gb|FE478923.1|FE478923
EST:     GTGGAGTATACGGCAGTTTGATCAGCACACCCATTGTCAATCCTCCTCAG                         TCTGCTATTCTTGGAATGCATTCCATCCAGAAGCGTCCCGTGGTGATTGGC
genomic: GTGGAGTATACGGCAGTTTGATCAGCACACCCATTGTCAATCCTCCTCAGgtttggacct ... gtttttccagTCTGCTATTCTCGGAATGCATTCCATCCAGAAGCGTCCCGTGGTGATTGGC
EST: gi|169070986|gb|FE478924.1|FE478924
EST:     GTGGAGTATACGGCAGTTTGATCAGCACACCCATTGTCAATCCTCCTCAG                         TCTGCTATTCTTGGAATGCATTCCATCCAGAAGCGTCCCGTGGTGATTGGC
genomic: GTGGAGTATACGGCAGTTTGATCAGCACACCCATTGTCAATCCTCCTCAGgtttggacct ... gtttttccagTCTGCTATTCTCGGAATGCATTCCATCCAGAAGCGTCCCGTGGTGATTGGC

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), 29 (downstream exon)
Score: 43

AACCATTACTATCGATGATATGGCCGGCGGGAGCTTTACCATCTCCAACGGTGGAGTATACGGCAGTTTGATCAGCACACCCATTGTCAATCCTCCTCAGgtttggacct ... gtttttccagTCTGCTATTCTCGGAATGCATTCCATCCAGAAGCGTCCCGTGGTGATTGGCAACGAAATAGTCATCCGACCGATGATGTACATTGCTTTGACATACGATC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accttcacatctcagaagaccttgttttcattgaattttgtttttgtttttccagTCTGCTATTCTCGGAATGCATTCCATCCAGAAGCGTCCCGTGGTGATTGGCAACGAAATAGTCATCCGACCGATGATGTACATTGCTTTGACATACGATC
                                   ttttgtttttgttttt  CT-rich tract
                        ttttcattgaattttg  TA-rich tract