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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaagctttctctctctctcttttttttttacttctctccagccgtgatagatcttgatggatgatcgactcaaacttttcatttcttcttgtgtgtgtccttctcccagATATTCTCTATGATTCGTGGTCGCCAGCCATGACCGTCAGCTCCATCTGCATCAGCATCCTCTCGATGCTCTCGAGCTCCACAGTCAAG

Basic information

species Selaginella moellendorffii
transcript EFJ21480
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ21480 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: AT1G75440.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgaagctttctctctctctcttttttttttacttctctccagccgtgatagatcttgatggatgatcgac-tcaaacttttcatttcttcttgtgtgtgtccttctcccagATATTCTCTATGATTCGTGGTCGCCAGCCATGACCGTCAGCTCCATCTGCATCAGCATCCTCTCGATGCTCTCGAGCTCCACAGTCAAG
             | |   | |   |       | | ||| |       ||| |  | ||  |  || | | ||          | |||  |  ||||| || |  |  |||||||| | |||||||||||||| ||||||||||| || || || |||||||| ||||||||||| |||||||| ||||| || |  |||
------------ttttgcttttagatccaagggtacactcaaatttcagtagcttattatttaacataggcctcctggaagaagtatctgatgttgtgtatcatcgttgcagATATTTTGTATGATTCGTGGTCTCCAGCCATGACGGTGAGTTCTATCTGCATTAGCATCCTCTCCATGCTCTCAAGCTCGACTGAAAAG

upper sequence: EFJ21480 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: AT5G42990.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgaagctttctctctctctcttttttttttacttctctccagccgtgatagatcttgatggatgatcgactcaaacttttcatttcttcttgtgtgtgtccttctcccagATATTCTCTATGATTCGTGGTCGCCAGCCATGACCGTCAGCTCCATCTGCATCAGCATCCTCTCGATGCTCTCGAGCTCCACAGTCAAG
  |   |  |   |        || |      | ||  |  ||  | || ||  | | | |||| ||   || ||   |  ||     |||  |     ||||| |   ||||||||| ||||| || ||||| ||||| ||||| || || ||  ||||||||||||||||||| ||||| || || ||| | |  |||
--gttacaatacataatcacgattatacccggcctcattttag--gagaaagtccatta-ggattatgcgcttaa-tataacacactctctaat-----tcctttttgtagATATTCTGTATGACTCATGGTCTCCAGCAATGACAGTGAGTTCAGTCTGCATCAGCATCCTCTCAATGCTATCAAGTTCCCCCGAAAAG

upper sequence: EFJ21480 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: Vv04s0023g02620.t01 (Vitis vinifera), 3'ss of exon 4
gtgaagctttctctctctctcttttttttttacttctctccagccgtgatagatcttgatggatgatcgactcaaacttttcatttcttcttgtgtgtgtccttctcccagATATTCTCTATGATTCGTGGTCGCCAGCCATGACCGTCAGCTCCATCTGCATCAGCATCCTCTCGATGCTCTCGAGCTCCACAGTCAAG
       ||| |   ||    | | ||  ||   |        |    |   |  |   |   |      || ||| |||  |||| ||      ||||   | |    ||||||| | |||||||| ||||| ||||||||||| || || || |||||||||||||| ||||| ||||| || ||||| || || |||
-------tttatggatccaaatatgttagtttgattatgatgtctaaaactaacttatgtacctttcaatctgaaattttatatttattgactcatgtgatgtgc----agATATTTTGTATGATTCTTGGTCCCCAGCCATGACAGTTAGTTCTATCTGCATCAGCATTCTCTCCATGCTATCAAGCTCAACTGTGAAG

upper sequence: EFJ21480 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: Vv18s0001g13180.t01 (Vitis vinifera), 3'ss of exon 4
gtgaagctttctctctctctcttttttttttacttctctccagccgtgatagatcttgatggatgatcgactca--aacttttcatttcttcttgtgtgtgtccttctcccagATATTCTCTATGATTCGTGGTCGCCAGCCATGACCGTCAGCTCCATCTGCATCAGCATCCTCTCGATGCTCTCGAGCTCCACAGTCAAG
     | ||  | | ||  ||   || |||||  ||     |  |    | |   ||||| |   ||| || ||   || | | || || |    | | |||   | || |||||||||| |||||||| ||||| ||||||||||| || || || ||||| |||||||| ||||| ||| | |||||||| || || |||
-----ggttcttatttcaatcccattatttta--tcaactgattctctgtgg---ttgattgtccatcaacacactgacatctaatatcatagcttatttgt---tttcacagATATTCTATATGATTCATGGTCCCCAGCCATGACAGTTAGTTCAATCTGTATCAGCATACTCTCCATGTTATCGAGCTCAACTGTGAAG

upper sequence: EFJ21480 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: PP1S211_21V6.1 (Physcomitrella patens), 3'ss of exon 4
gtgaagctttctctctctctcttttttttttacttctctccagccgtgatagatcttgatggatgatcgactcaaacttttcatttcttcttgtgtgtgtccttctc-ccagATATTCTCTATGATTCGTGGTCGCCAGCCATGACCGTCAGCTCCATCTGCATCAGCATCCTCTCGATGCTCTCGAGCTCCACAGTCAAG
           |  |   ||          ||  ||| |  |   |  ||  | | || ||  |  |  | | | |||    |||||| |     ||  | | | || ||||||||||| ||||| || ||||| ||||| |||||||| || || ||||||||||||||||| || ||| | || || || || || |||
------acgagttcccaacttaacgaaaactatctctgtgtacttg-aatttaacatgttgcgt--ttaattaagacta---atttctgcaaacttggcttcgtttcaccagATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAG

upper sequence: EFJ21480 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: PP1S193_49V6.1 (Physcomitrella patens), 3'ss of exon 4
gtgaagctttctctctctctcttttttttttacttctctccagccgtgatagatcttgatgga---tgatcgactca-aacttttcatttcttcttgtgtgtgtccttctcccagATATTCTCTATGATTCGTGGTCGCCAGCCATGACCGTCAGCTCCATCTGCATCAGCATCCTCTCGATGCTCTCGAGCTCCACAGTCAAG
               ||      |       |||   | | || | |||  ||   || || |   | ||  | | |  | ||||||||      | | | | |  |||  ||||||||  | ||||| || ||||| ||||| ||||| || |||||||||||||||||||||||||| ||| | || || || ||||| |||
-------------aatcatagaatgaagaacactcgacgc-agtcatgagggagagtggtgcacgttaatgaaatgatgatttttcattctgggatttattt-ttgttcaaccagATATATTGTATGACTCTTGGTCACCAGCAATGACTGTGAGCTCCATCTGCATCAGCATCCTCTCTATGTTATCTAGTTCAACAGTGAAG

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|169069479|gb|FE480563.1|FE480563
EST:     CAATCCTCCCTTTCATCCCCATGTCTACAGCAACGGGCACATTTGCTTAG                         ATATTCTCTATGATTCGTGGTCGCCAGCCATGACCGTCAGCTCCATCTGCA
genomic: CAATCCTCCCTTTCATCCCCATGTCTACAGCAACGGGCACATTTGCTTAGgtgaagcttt ... cttctcccagATATTCTCTATGATTCGTGGTCGCCAGCCATGACCGTCAGCTCCATCTGCA
EST: gi|169058657|gb|FE466866.1|FE466866
EST:     CAATCCTCCCTTTCATCCCCATGTCTACAGCAACGGGCACATTTGCTTAG                         ATATTCTCTATGATTCGTGGTCGCCAGCCATGACCGTCAGCTCCATCTGCA
genomic: CAATCCTCCCTTTCATCCCCATGTCTACAGCAACGGGCACATTTGCTTAGgtgaagcttt ... cttctcccagATATTCTCTATGATTCGTGGTCGCCAGCCATGACCGTCAGCTCCATCTGCA
EST: gi|169097750|gb|FE497477.1|FE497477
EST:     CAATCCTCCCTTTCATCCCCATGTCTACAGCAACGGGCACATTTGCTTAG                         ATATTCTCTATGATTCGTGGTCGCCAGCCATGACCGTCAGCTCCATCTGCA
genomic: CAATCCTCCCTTTCATCCCCATGTCTACAGCAACGGGCACATTTGCTTAGgtgaagcttt ... cttctcccagATATTCTCTATGATTCGTGGTCGCCAGCCATGACCGTCAGCTCCATCTGCA
EST: gi|169058658|gb|FE466867.1|FE466867
EST:     CAATCCTCCCTTTCATCCCCATGTCTACAGCAACGGGCACATTTGCTTAG                         ATATTCTCTATGATTCGTGGTCGCCAGCCATGACCGTCAGCTCCATCTGCA
genomic: CAATCCTCCCTTTCATCCCCATGTCTACAGCAACGGGCACATTTGCTTAGgtgaagcttt ... cttctcccagATATTCTCTATGATTCGTGGTCGCCAGCCATGACCGTCAGCTCCATCTGCA
EST: gi|169069480|gb|FE480564.1|FE480564
EST:     CAATCCTCCCTTTCATCCCCATGTCTACAGCAACGGGCACATTTGCTTAG                         ATATTCTCTATGATTCGTGGTCGCCAGCCATGACCGTCAGCTCCATCTGCA
genomic: CAATCCTCCCTTTCATCCCCATGTCTACAGCAACGGGCACATTTGCTTAGgtgaagcttt ... cttctcccagATATTCTCTATGATTCGTGGTCGCCAGCCATGACCGTCAGCTCCATCTGCA
EST: gi|169096580|gb|FE499492.1|FE499492
EST:     CAATCCTCCCTTTCATCCCCATGTCTACAGCAACGGGCACATTTGCTTAG                         ATATTCTCTATGATTCGTGGTCGCCAGCCATGACCGTCAGCTCCATCTGCA
genomic: CAATCCTCCCTTTCATCCCCATGTCTACAGCAACGGGCACATTTGCTTAGgtgaagcttt ... cttctcccagATATTCTCTATGATTCGTGGTCGCCAGCCATGACCGTCAGCTCCATCTGCA

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), 35 (downstream exon)
Score: 93

GTTATCTTCATCCACAATCCTCCCTTTCATCCCCATGTCTACAGCAACGGGCACATTTGCTTAGgtgaagcttt ... cttctcccagATATTCTCTATGATTCGTGGTCGCCAGCCATGACCGTCAGCTCCATCTGCATCAGCATCCTCTCGATGCTCTCGAGCTCCACAGTCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatggatgatcgactcaaacttttcatttcttcttgtgtgtgtccttctcccagATATTCTCTATGATTCGTGGTCGCCAGCCATGACCGTCAGCTCCATCTGCATCAGCATCCTCTCGATGCTCTCGAGCTCCACAGTCAAG
 tcttgat  putative branch site (score: 93)
                                       tgtgtccttctccc  putative PPT
                     ttttcattt  TA-rich tract