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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactccaatttcttctcctctgctttgctcggccgctccagctacgtttcttcttgcgcaccagGTGATCACGAAGTTTTGCTCCGAGCGGATTGCCAAGTACGCGTTTGAGTACGCCTACCTGAACAACAGAAAGACGGTGACGGCGGTGCACAAGGCCAACA

Basic information

species Selaginella moellendorffii
transcript EFJ29002
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ29002 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os02g38200.1 (Oryza sativa), 3'ss of exon 1
---------------gtactccaatttcttctcctctgctttgctcggccgctccagctacgtttcttcttgcg--------------------caccagGTGATCACGAAGTTTTGCTCCGAGCGGATTGCCAAGTACGCGTTTGAGTACGCCTACCTGAACAACAGAAAGACGGTGACGGCGGTGCACAAGGCCAACA
               |||    ||| | ||   | ||  |    ||  |  ||  ||  |  ||| |   |  |                     || |||||||||| ||||| ||||| ||  ||||||||||||| || ||||||||||| ||||| |||||||||||||  ||||| || ||||| || || ||||
tttctgaaatagaacgtatgtaaatgtttttgtcacttttcatttcatcatctaaaggaatttttttctatatggtactgttactaaatggatttactagGTGATCACAAAGTTCTGCTCTGAAAGGATTGCCAAGTATGCTTTTGAGTACGCGTACCTCAACAACAGAAAGAAAGTGACTGCCGTGCATAAAGCAAACA

upper sequence: EFJ29002 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os04g40310.2 (Oryza sativa), 3'ss of exon 1
-------------------gtactccaatttcttctc----ctctgctttgctcggccgctccagctacgtttcttcttgcgcaccagGTGATCACGAAGTTTTGCTCCGAGCGGATTGCCAAGTACGCGTTTGAGTACGCCTACCTGAACAACAGAAAGACGGTGACGGCGGTGCACAAGGCCAACA------------
                   | || |   ||| ||  |    |||||   | ||   ||     ||   |  |   |         |||||||| || ||||||||||| ||| |||||||||| || || |||||||| || ||||| |||||| ||||||  || || || ||||| || || ||||            
attgccaatggaatgaaatgcacccttttttttttccagttctctgagcttcttttccatcttagtctcactgactaacttttgtcaggtgataacaaagTTTTGCTCTGAGAGGATTGCCAAATATGCTTTTGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACAGCAGTGCATAAAGCAAACATCATGAAGCTTG

upper sequence: EFJ29002 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os04g40310.1 (Oryza sativa), 3'ss of exon 1
-------------------------------gtactccaatttcttctc----ctctgctttgctcggccgctccagctacgtttcttcttgcgcaccagGTGATCACGAAGTTTTGCTCCGAGCGGATTGCCAAGTACGCGTTTGAGTACGCCTACCTGAACAACAGAAAGACGGTGACGGCGGTGCACAAGGCCAACA
                               | || |   ||| ||  |    |||||   | ||   ||     ||   |  |   |         |||||||| || ||||||||||| ||| |||||||||| || || |||||||| || ||||| |||||| ||||||  || || || ||||| || || ||||
ttgtgttacatgattgccaatggaatgaaatgcacccttttttttttccagttctctgagcttcttttccatcttagtctcactgactaacttttgtcagGTGATAACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCTTTTGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACAGCAGTGCATAAAGCAAACA

upper sequence: EFJ29002 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G025366_T01 (Zea mays), 3'ss of exon 1
---------------------gtactcca-atttcttctcctctgc----tttgctcggccgctccagctacgtttcttcttgcgca---------ccagGTGATCACGAAGTTTTGCTCCGAGCGGATTGCCAAGTACGCGTTTGAGTACGCCTACCTGAACAACAGAAAGACGGTGACGGCGGTGCACAAGGCCAACA
                       | |  |  ||| |  |||| | |     ||    |  |  | |  | |   ||  |||| |  |         | |||||||||| ||||||||||| ||| |||||||||| || || || ||||| || ||||| |||||| ||||||  || || || ||||| || || ||||
tgttgttgaaatagaatccactcatttaatgtttgtgatcctttacagttcttatctgaacctttcttccattattactcttactgaatggatttcctagGTGATCACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCATTCGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACTGCAGTGCATAAAGCAAACA

upper sequence: EFJ29002 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G025366_T02 (Zea mays), 3'ss of exon 1
---------gtactcca-atttcttctcctctgc----tttgctcggccgctccagctacgtttcttcttgcgca---------ccagGTGATCACGAAGTTTTGCTCCGAGCGGATTGCCAAGTACGCGTTTGAGTACGCCTACCTGAACAACAGAAAGACGGTGACGGCGGTGCACAAGGCCAACA------------
           | |  |  ||| |  |||| | |     ||    |  |  | |  | |   ||  |||| |  |         | |||||||||| ||||||||||| ||| |||||||||| || || || ||||| || ||||| |||||| ||||||  || || || ||||| || || ||||            
agaatccactcatttaatgtttgtgatcctttacagttcttatctgaacctttcttccattattactcttactgaatggatttcctaggtgatcacaaagTTTTGCTCTGAGAGGATTGCCAAATATGCATTCGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACTGCAGTGCATAAAGCAAACATTATGAAGCTTG

upper sequence: EFJ29002 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: AT4G35260.1 (Arabidopsis thaliana), 3'ss of exon 1
-------------------------------------------------------------gtactccaatttcttctcctctgctttgctcggccgctccagctacgtttcttcttgcgcaccagGTGATCACGAAGTTTTGCTCCGAGCGGATTGCCAAGTACGCGTTTGAGTACGCCTACCTGAACAACAGAAAGACGGTGACGGCGGTGCACAAGGCCAACA
                                                             ||  | ||| |  |  |  | || | ||   |   | ||        |||||   |||     |||||||||||||||| || || ||||| ||||| ||||| || |||||||| ||||||||||||||||| ||||  || || |||||||| ||||| ||||
gtgagaattccgatttctgctcctcgttttggattcaatctgtatttgtggaatcatcttcgt-ttgcaagtggtctttgtatgttatgtgtgattgttctgatcctatttcta--tgc---ttagGTGATCACGAAGTTCTGTTCGGAGCGTATTGCAAAGTATGCTTTTGAGTATGCCTACCTGAACAACAGGAAGAAAGTTACAGCGGTGCATAAGGCTAACA

upper sequence: EFJ29002 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: AT2G17130.1 (Arabidopsis thaliana), 3'ss of exon 1
-------------------------------------------------------------gtactccaatttcttctcctctgctttgctcg-gccgctccagctacgtttc---ttcttgcgcac---cagGTGATCACGAAGTTTTGCTCCGAGCGGATTGCCAAGTACGCGTTTGAGTACGCCTACCTGAACAACAGAAAGACGGTGACGGCGGTGCACAAGGCCAACA
                                                              |  |   |  | |     |  |   || ||  |      ||   | || ||   | ||   |       ||||||| || ||||| || || ||||| ||||| ||||| ||||||||||| |||||| |||||||||| ||||  || || || ||||||||||| || |
gtgcaatttctcagtttttgttgattgttttggttacaaatgtgatttgattcatagtgatttggtagtagatgtgaaagttggagatgttcatgttatatcaaagatgtctctgatgctaatgttttggtagGTGATTACAAAGTTCTGTTCAGAGCGTATTGCAAAGTATGCGTTTGAGTATGCCTACTTGAACAACAGGAAGAAAGTTACAGCAGTGCACAAGGCTAATA

upper sequence: EFJ29002 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: AT2G17130.2 (Arabidopsis thaliana), 3'ss of exon 1
-------------------------------------------------------------gtactccaatttcttctcctctgctttgctcg-gccgctccagctacgtttctt---cttgcgc---accagGTGATCACGAAGTTTTGCTCCGAGCGGATTGCCAAGTACGCGTTTGAGTACGCCTACCTGAACAACAGAAAGACGGTGACGGCGGTGCACAAGGCCAACA------------
                                                              |  |   |  | |     |  |   || ||  |      ||   | || |||    ||   |       ||||||| || ||||| || || ||||| ||||| ||||| ||||||||||| |||||| |||||||||| ||||  || || || ||||||||||| || |            
gtgcaatttctcagtttttgttgattgttttggttacaaatgtgatttgattcatagtgatttggtagtagatgtgaaagttggagatgttcatgttatatcaaagatgtctctgatgctaatgttttggtaggtgattacaaagTTCTGTTCAGAGCGTATTGCAAAGTATGCGTTTGAGTATGCCTACTTGAACAACAGGAAGAAAGTTACAGCAGTGCACAAGGCTAATATCATGAAATTGG

upper sequence: EFJ29002 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S101_151V6.1 (Physcomitrella patens), 3'ss of exon 1
-------------------------gtactc-caatttcttctcctctgctttgctcggccgct--ccagctacgtttcttcttgcgca-------ccagGTGATCACGAAGTTTTGCTCCGAGCGGATTGCCAAGTACGCGTTTGAGTACGCCTACCTGAACAACAGAAAGACGGTGACGGCGGTGCACAAGGCCAACA
                         ||      ||| |  ||| ||  |   | |  | |   |       || ||  |||   | ||         ||||| ||||| ||||| ||||| ||||| ||||| || ||||| |||||||| || || || |||||| | ||||| || || || ||||||||||||||||
atctcctcgtcatgcttcatgcattgtggaaataatcttatctactgcgtggtacctgtcaaataattctgtaagtgccttacagtgccaagatgttcagGTAATCACCAAGTTCTGCTCGGAGCGCATTGCGAAATACGCCTTTGAGTATGCTTATCTCAACAACCGCAAGACAGTAACAGCAGTGCACAAGGCCAACA

upper sequence: EFJ29002 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S212_85V6.2 (Physcomitrella patens), 3'ss of exon 2
---------------------------------gtactccaatttcttctcctctgcttt--gctcggccgctccagctacgtttcttcttgcgcaccagGTGATCACGAAGTTTTGCTCCGAGCGGATTGCCAAGTACGCGTTTGAGTACGCCTACCTGAACAACAGAAAGACGGTGACGGCGGTGCACAAGGCCAACA
                                  |   |   |   |||| |  || | |    |  | ||     ||  |      |   ||    |||||||| || || || ||||||||||| ||||| |||||||| |||||||| || || || |||||| | ||||| || || || || || ||||||||||
gcgactctatgtatattgcataatacctgtcgaatgacctgctggtttctgccttgttgtcaaatatgtcgtggatgcctcacagtgttaagcttttcagGTGATAACCAAATTCTGCTCCGAGCGAATTGCAAAGTACGCCTTTGAGTATGCTTATCTCAACAACCGTAAGACAGTAACAGCAGTACATAAGGCCAACA

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: 34 (upstream exon), 27 (downstream exon)
Score: 26

CCATGACAACGTCAACATTGTTGTGATCCGGGAGAACACCGAGGGGGAGTACGCCGGCCTGGAGCACGAGGTCGTCCCGGGTGTTGTCGAGTCTCTCAAGgtactccaat ... tgcgcaccagGTGATCACGAAGTTTTGCTCCGAGCGGATTGCCAAGTACGCGTTTGAGTACGCCTACCTGAACAACAGAAAGACGGTGACGGCGGTGCACAAGGCCAACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttctcctctgctttgctcggccgctccagctacgtttcttcttgcgcaccagGTGATCACGAAGTTTTGCTCCGAGCGGATTGCCAAGTACGCGTTTGAGTACGCCTACCTGAACAACAGAAAGACGGTGACGGCGGTGCACAAGGCCAACA
                                ctacgtttcttctt  CT-rich tract