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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaggcatttctgattgaaaatatctaccggcttgattgatttatggtgcctagGTGGTCTCTTGGAGCTATAATGTACGAGATGCTAGTCGGGTATCCGCCCTTCTATTCCGACGAACCGATGTCTACTTGCCGGAAG

Basic information

species Selaginella moellendorffii
transcript EFJ29515
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ29515 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GRMZM2G088245_T01 (Zea mays), 3'ss of exon 6
gtaagaggcatttc---tgattgaaaatatctaccggcttgatt-------gatttatggtgcctagGTGGTCTCTTGGAGCTATAATGTACGAGATGCTAGTCGGGTATCCGCCCTTCTATTCCGACGAACCGATGTCTACTTGCCGGAAG
|||||   |   |      || ||    ||  |   |  |  |         ||     ||  | |||||||| |||||  |||| ||||| ||||||||||| || ||||| || |||||||| ||||| || ||| |||||||||| |||
gtaagcatctccttgcaccatcgatcgcattgatgagtctagtctcaaacaaatcccatgtttccagGTGGTCCCTTGGTTCTATCATGTATGAGATGCTAGTGGGTTATCCTCCATTCTATTCTGACGAGCCTATGACTACTTGCCGAAAG

upper sequence: EFJ29515 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GLYMA02G00580.2 (Glycine max), 3'ss of exon 7
--------------------------------------------------------------------------------gtaagaggcatttctgattgaaaatatctaccggcttg-attgatttatggtgcctagGTGGTCTCTTGGAGCTATAATGTACGAGATGCTAGTCGGGTATCCGCCCTTCTATTCCGACGAACCGATGTCTACTTGCCGGAAG
                                                                                ||   |     |||||||      |   | |   ||    |||  | |  |   | |||||||||||||||||||||||||| || ||||| || |||||||| ||||| ||||| || ||||| ||||  |||||  | |||
gtaatatagaatatgttttctacttttctttttcaaaagtctccctaagggccaccccccttcccccttttaaacttattgtgtcaatgcattctgatgttgtgtcaatgcattctaatgttgtgtcaatgcttccagGTGGTCTCTTGGAGCTATAATGTATGAAATGCTTGTGGGGTATCCACCCTTTTATTCAGATGAACCAATGTTGACTTGTAGAAAG

upper sequence: EFJ29515 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GLYMA10G00830.1 (Glycine max), 3'ss of exon 6
------------------------------------------------------gtaagaggcatttctgattgaaaatatctac-cggcttgat--tgatttatggtgcctagGTGGTCTCTTGGAGCTATAATGTACGAGATGCTAGTCGGGTATCCGCCCTTCTATTCCGACGAACCGATGTCTACTTGCCGGAAG
                                                              | ||    | | ||  | || |  |    ||||  ||  | |  |   | ||||||||||| |||||||||||||| || ||||| || |||||||| ||||| ||||| |||||||| ||||  |||||  | |||
gtaatatagaatgtgttttctatttttctgtttcaaaagtctccccatggccacccctccccccttataaacttaatgtttcaatgcattctgatgttgtgtcaatgcttccagGTGGTCTCTAGGAGCTATAATGTATGAAATGCTTGTGGGGTATCCTCCCTTTTATTCAGACGAACCAATGTTGACTTGTAGAAAG

upper sequence: EFJ29515 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GLYMA20G35110.1 (Glycine max), 3'ss of exon 6
-----------------------------------------------------------gtaagaggcatttctgattgaa--aatatctaccggcttgattgatttatggtgcctagGTGGTCTCTTGGAGCTATAATGTACGAGATGCTAGTCGGGTATCCGCCCTTCTATTCCGACGAACCGATGTCTACTTGCCGGAAG
                                                            |       | |||  |||     ||||| | | |    |||||   ||  ||  | |||||||| || ||||| |||||||| || ||| |||| |||||||||||||| ||||| || ||||| ||||  |||||  | |||
gtattatctaatgtgtttttctacttttccttttcaaaaataccttgaagttccctttgtttttctaaacttcatattatttcaatatgttctgatgagattgtggtaatgtttccagGTGGTCCCTGGGAGCGATAATGTATGAAATGTTAGTGGGGTATCCGCCCTTTTATTCAGATGAACCAATGTTGACTTGTAGAAAG

upper sequence: EFJ29515 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GLYMA10G32480.1 (Glycine max), 3'ss of exon 6
----------------------------------------------------------------gtaagaggcatttctgattgaaaatatctaccggcttgattgatttatggtgcctagGTGGTCTCTTGGAGCTATAATGTACGAGATGCTAGTCGGGTATCCGCCCTTCTATTCCGACGAACCGATGTCTACTTGCCGGAAG
                                                                ||||    ||| |    |    ||||| | | |    ||||    ||  ||  | ||||||||  | ||||| |||||||| || ||| |||| |||||||||||||| ||||| || ||||| ||||  |||||  | |||
gtattatctaatgtgtttttctagttttccttttcaaaaataccatgaagttccctttgtttttgtaaacttcatattatttc---aatatgttctgatgagattttggtaatgtttccagGTGGTCCTTGGGAGCGATAATGTATGAAATGTTAGTGGGGTATCCGCCCTTTTATTCAGATGAACCAATGTTGACTTGTAGAAAG

upper sequence: EFJ29515 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: AT1G30640.1 (Arabidopsis thaliana), 3'ss of exon 7
------gtaagaggcatttctgattgaaaatatctaccggcttgattgatttatggtgcc----------------tagGTGGTCTCTTGGAGCTATAATGTACGAGATGCTAGTCGGGTATCCGCCCTTCTATTCCGACGAACCGATGTCTACTTGCCGGAAG
      | |  || |   |||  || | | | |  |     || ||| | ||    | |                 |||||||||||||||||| || |||| ||||||||| || |||| |||||| ||||||||||| |||||  || | || ||  | |||
gttagtgaaccagacccctctcttttacactctacaattaatttattcagttgaaattctaaaaactgttctacaatagGTGGTCTCTTGGAGCAATCATGTTCGAGATGCTTGTAGGGTTTCCGCCATTCTATTCCGAAGAACCTTTGGCAACATGTAGAAAG

upper sequence: EFJ29515 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: AT1G03920.1 (Arabidopsis thaliana), 3'ss of exon 5
-------------------------gtaagaggcatttctgattgaaaatatctaccggcttgattgatttatggtgcc---tagGTGGTCTCTTGGAGCTATAATGTACGAGATGCTAGTCGGGTATCCGCCCTTCTATTCCGACGAACCGATGTCTACTTGCCGGAAG
                           |   |  |     ||   ||||  |    |      ||   ||||      |    |||||||| || ||||||||||||||||| ||||| || |||||||| ||||| ||  ||||||| || |||||||||||  | |||
gtacgtgtacacacttgtctattttcaacttgttaacaaagaacaaaaaagtaagtccttagaatgtttttaaaaaatcctccagGTGGTCACTAGGAGCTATAATGTACGAAATGCTGGTTGGGTATCCACCCTTTTACGCCGACGACCCAATGTCTACTTGTAGAAAG

upper sequence: EFJ29515 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: AT2G20470.1 (Arabidopsis thaliana), 3'ss of exon 6
-------------------------------------gtaagaggcatttctgattgaaa----atatctac-cggcttgattgattta-tggtgcctagGTGGTCTCTTGGAGCTATAATGTACGAGATGCTAGTCGGGTATCCGCCCTTCTATTCCGACGAACCGATGTCTACTTGCCGGAAG
                                            |||||| || ||  ||    |     |  | | ||  |  ||  | || |   ||||||||||||||| |||||||||||||| |||||||| || |||||||| || ||||| || || || ||||| || ||  | |||
tagtcaaagggaccatcttgaagcattatttggtgacactgtctgcatttgtgctttgaataggacgctaatgcagttttctcaatgaaatgctatgtagGTGGTCTCTTGGTGCTATAATGTACGAAATGCTAGTAGGATATCCGCCGTTTTATTCAGATGATCCTATGTCAACCTGTAGAAAG

upper sequence: EFJ29515 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: PP1S86_100V6.1 (Physcomitrella patens), 3'ss of exon 6
-----------------------------------------------------------------gtaagaggcatttctgattgaaaatatctaccggcttgattgatttatggtgcctagGTGGTCTCTTGGAGCTATAATGTACGAGATGCTAGTCGGGTATCCGCCCTTCTATTCCGACGAACCGATGTCTACTTGCCGGAAG
                                                                 |   ||   | ||||  |||      || |   | ||||  |     |       |||||||| |||||||| || ||||||||||||||||| || || || || || || || |||||||| ||| | ||||| || |||
gtatgtgacaagtcgttctcctgaatctttctctttttatccttggctcatgatgtacttgcttagcttgataaagttcttgttgtgt---tcaaaaaggttgaacgtaagttttcctacagGTGGTCACTTGGAGCAATCATGTACGAGATGCTAGTTGGCTACCCTCCATTTTACTCTGACGAACCTATGACAACTTGTCGCAAG

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: 28 (upstream exon), 33 (downstream exon)
Score: 24

GCTTATTCAACTGTCGGGACGCCAGATTATATTGCTCCCGAAGTTCTACTGAAGAAGGGATACGGGATGGAGTGTGATTGgtaagaggca ... tggtgcctagGTGGTCTCTTGGAGCTATAATGTACGAGATGCTAGTCGGGTATCCGCCCTTCTATTCCGACGAACCGATGTCTACTTGCCGGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagaggcatttctgattgaaaatatctaccggcttgattgatttatggtgcctagGTGGTCTCTTGGAGCTATAATGTACGAGATGCTAGTCGGGTATCCGCCCTTCTATTCCGACGAACCGATGTCTACTTGCCGGAAG
              attgaaaatatcta  TA-rich tract