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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcttgcgttggtagatcgaagagaatagagactaacttcgcttctggttctttccagATACTGTTTGTGATCTCCAAGCCCGACGTGTTCAAGAGCCCGGCATCCGACACTCACATCATCTTTGGCGAGGCCAAGATCGAGGACTTGAGTTCCCAGC

Basic information

species Selaginella moellendorffii
transcript EFJ23805
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ23805 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: LOC_Os03g02960.1 (Oryza sativa), 3'ss of exon 2
-------------------------gtaagct-tgcgttggtagatcgaagagaatagagactaacttcgcttctggttctttccagATACTGTTTGTGATCTCCAAGCCCGACGTGTTCAAGAGCCCGGCATCCGACACTCACATCATCTTTGGCGAGGCCAAGATCGAGGACTTGAGTTCCCAGC
                           || || | | || | |      | |||||  |   |  ||  |  ||  ||   || ||||||||||| ||| | |||||||| ||||| |||||||||||| | || || ||  || |||| || || |||||||||||||||||| |||| |||||||
gtaagaaactgtgcagctgctgcaaacaatctattcattcgaatggaagacagaattaatgttttctctgaatcccgtgtgtttcagATACTGTTCGTGGTGTCCAAGCCTGACGTCTTCAAGAGCCCGACGTCGGAGACGTACGTCATATTCGGGGAGGCCAAGATCGAGGACCTGAGCTCCCAGC

upper sequence: EFJ23805 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: LOC_Os05g31000.1 (Oryza sativa), 3'ss of exon 3
------------------------------gtaagcttgcgttggtagatcgaagagaatagagactaact-tcgcttctggttctttccagATACTGTTTGTGATCTCCAAGCCCGACGTGTTCAAGAGCCCGGCATCCGACACTCACATCATCTTTGGCGAGGCCAAGATCGAGGACTTGAGTTCCCAGC
                                 |  | |   |  ||| | ||      | ||   |  || |  ||| ||   | || ||||| || ||||| |||||||| || || || |||||||||||  ||||||||||  |  |||| |||||||||||||||||||||||| |||| || ||||
gtgagcttacgactgctcttatctagccaatctaaatagttctattagttggattcctgttgatgtttgctatttcttttgccccatttcagATCCTTTTTGTCATCTCCAAACCGGATGTCTTCAAGAGCCCTACATCCGACACCTATGTCATTTTTGGCGAGGCCAAGATCGAGGACCTGAGCTCGCAGC

upper sequence: EFJ23805 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GRMZM2G465333_T01 (Zea mays), 3'ss of exon 3
------------------------------------------gtaagcttgcgttggtagatcgaagagaatagagactaacttcgcttctg-----gttctttccagATACTGTTTGTGATCTCCAAGCCCGACGTGTTCAAGAGCCCGGCATCCGACACTCACATCATCTTTGGCGAGGCCAAGATCGAGGACTTGAGTTCCCAGC
                                           |||  | |  |   |       |  |      | ||||| |      ||      || || ||||||||||||||| ||||| ||||| || |||||||||||||||   || |||||  || |||| || ||||||||||||||||||||| | || |||||||
gtaattcaccacgcaaactggcctatctttattgttgtctggctaacatggtatatattatctttattgttgtctggctaacatgataaatgcacatatttttcccagATACTGTTTGTCATCTCGAAGCCAGATGTGTTCAAGAGCCCGAACTCAGACACATACGTCATATTCGGCGAGGCCAAGATCGAGGACCTCAGCTCCCAGC

upper sequence: EFJ23805 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GRMZM2G000923_T01 (Zea mays), 3'ss of exon 3
---------------gtaagcttgcgttggtagatcgaagagaatagagactaacttcgctt--ctggttctttccagATACTGTTTGTGATCTCCAAGCCCGACGTGTTCAAGAGCCCGGCATCCGACACTCACATCATCTTTGGCGAGGCCAAGATCGAGGACTTGAGTTCCCAGC
                | || |  |       |    |     || |   |     |  | |     | | |||||||||||| ||||| |||||||| || || |||||||||||||||   ||||||||  |  |||| || |||||||| |||||||||||| | || |||||||
gtaattcaccatttactcagatcacacaaactggcttatctttattgttgcctggctaacatgatatgctatttccagATACTCTTTGTCATCTCCAAACCAGATGTGTTCAAGAGCCCGAATTCCGACACGTATGTCATATTCGGCGAGGCTAAGATCGAGGACCTCAGCTCCCAGC

upper sequence: EFJ23805 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: Vv08s0040g00600.t01 (Vitis vinifera), 3'ss of exon 3
----------------------------------------------------------------------gtaagcttgcgttggtagatcgaagagaatagagactaacttcgcttctggttctt----tccagATACTGTTTGTGATCTCCAAGCCCGACGTGTTCAAGAGCCCGGCATCCGACACTCACATCATCTTTGGCGAGGCCAAGATCGAGGACTTGAGTTCCCAGC
                                                                       | || || | ||  ||  |   |    || || |  |  ||    | ||||| ||    | ||||| || ||||| ||||| ||||| || ||||||||||||||  | || |||||| |  | || ||||||||||| ||||| ||||| |||||||| || |
gtcagtttctctttgcccactgttgattactttttatttttcatgttgggcctattgtcacctctttaatatcaggtttctttc-tattttacaatctattgaaagcagttta--ctatggtttttattattcagATTCTCTTTGTCATCTCGAAGCCAGATGTGTTCAAGAGCCCAACTTCAGACACTTATGTAATATTTGGCGAGGCAAAGATTGAGGATTTGAGTTCACAAC

upper sequence: EFJ23805 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: PP1S156_120V6.1 (Physcomitrella patens), 3'ss of exon 2
------------------------------gtaagcttgcgttggtagatcgaaga-----gaatagagactaacttcgcttctggttc----tttccagATACTGTTTGTGATCTCCAAGCCCGACGTGTTCAAGAGCCCGGCATCCGACACTCACATCATCTTTGGCGAGGCCAAGATCGAGGACTTGAGTTCCCAGC
                                 || ||| |||          |||        |   |  ||   |  ||| || ||     ||  ||||| || ||||||||||| |||||||| || ||||||||||| || || ||||| || ||||||||||| ||||||||||||||||| |||||||| ||||
ttaacttcaattctgcttgaattgtgcaataatagtttgagttatccagcaatagattttcacctgtggcttatgctttcttttgttttggaattcgcagATTCTTTTTGTGATCTCTAAGCCCGATGTATTCAAGAGCCCTGCCTCTGACACCCATATCATCTTTGGAGAGGCCAAGATCGAGGATTTGAGTTCGCAGC

upper sequence: EFJ23805 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: PP1S539_1V6.1 (Physcomitrella patens), 3'ss of exon 3
----------------------------------------gtaagcttgcgttggtaga-tcgaagagaatagagactaacttcgcttctggttctttccagATACTGTTTGTGATCTCCAAGCCCGACGTGTTCAAGAGCCCGGCATCCGACACTCACATCATCTTTGGCGAGGCCAAGATCGAGGACTTGAGTTCCCAGC
                                          |  |||| | ||  ||| |   |     | |  | |||||||   ||  |    || ||||| || ||||||||||| ||||| || |||||||||||||| ||||| |||||| || | ||||| |||||||| ||||| ||||| |||||||| ||  
tataccttcaatctttatcgcagattctacatattctttcagatccttgagatgtcagaatttcaatagcttgcaagtaacttca--tcgtgcaacttgcagATCCTCTTTGTGATCTCGAAGCCTGATGTGTTCAAGAGCCCTGCATCAGACACTTACGTAATCTTCGGCGAGGCAAAGATTGAGGATTTGAGTTCTCAAT

upper sequence: EFJ23805 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: PP1S122_100V6.1 (Physcomitrella patens), 3'ss of exon 3
--------------------------------------------gtaagcttgcgttggtagatcgaagagaatagagactaacttcgcttctggttctttccagATACTGTTTGTGATCTCCAAGCCCGACGTGTTCAAGAGCCCGGCATCCGACACTCACATCATCTTTGGCGAGGCCAAGATCGAGGACTTGAGTTCCCAGC
                                              ||| | |  | | ||    |     |||  |  ||    | ||| ||  |   |  |||||  |||| || ||||| ||||| ||||||||||||||||| ||||| ||  |||||||||||||||| ||||| ||||| ||||| ||||| || || |
gcgattctccaattgttttattttccccttgaatctggtgatttcgaagttagtttcgttattctgcctctaatgtatgct---ctggctgctaatgtat--cagATTTTGTTCGTAATCTCGAAGCCTGACGTGTTCAAGAGCCCAGCATCTGATGCTCACATCATCTTTGGAGAGGCGAAGATTGAGGATTTGAGCTCACAAC

upper sequence: EFJ23805 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: PP1S10_319V6.1 (Physcomitrella patens), 3'ss of exon 3
-----------------------------gtaagcttgcgt-tggtagatcgaagagaataga-------gactaacttcgcttctggttc--tttccagATACTGTTTGTGATCTCCAAGCCCGACGTGTTCAAGAGCCCGGCATCCGACACTCACATCATCTTTGGCGAGGCCAAGATCGAGGACTTGAGTTCCCAGC
                             |      || || ||||   |  ||   |||  |       | || ||  |   | | ||    ||| ||||| || || |||||||||   || || |||||||||||||| ||||| |||||  |||| ||||||||||| |||||||| |||||||||||||| || |
aaatatctccgaactgtatttttcagtgtgcttatctgtgtctggtctctgaaaagcaatgtattctgttggcttacgaccaatgttgtaaaatttgcagATCCTCTTCGTGATCTCCGCTCCTGATGTGTTCAAGAGCCCTGCATCAGACACGTACATTATCTTTGGCGAAGCCAAGATTGAGGACTTGAGTTCTCAAC

upper sequence: EFJ23805 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: PP1S9_207V6.1 (Physcomitrella patens), 3'ss of exon 1
----------------------------------------------gtaagcttgcgttggtagatcgaagagaatagagactaacttcgcttct-----ggttctt------tccagATACTGTTTGTGATCTCCAAGCCCGACGTGTTCAAGAGCCCGGCATCCGACACTCACATCATCTTTGGCGAGGCCAAGATCGAGGACTTGAGTTCCCAGC--
                                                ||| ||  ||| |    ||  |     |      |  || || | ||      ||| ||      | ||||| |  |||||||| || ||||| || ||||||||||||| ||  || |||||  |||| |||| ||| ||||| |||||||||||||||||||| ||||  
gtagagggttacggaaataatttcgtgcactttcctaggttatgttcaaagttttagtttgggactcacatgtcttttgtgtttcctccgttgcttatgaagtttttaatatgtgcagATCCACTTTGTGATTTCAAAGCCTGATGTGTTCAAGAGCCTGGTCTCAGACAC--ACATAATCTATGGAGAGGCTAAGATCGAGGACTTGAGTTCTCAGCTT

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

GCAAAGCCGGAGCGAGAAGAAGAGCCGGAAGGCAATGCAGAAGCTCGGGATGAAGCCCGTGACTGGAGTAACGAGGGTGACGATCAAGAAGAGCAAAAACgtaagcttgc ... ttctttccagATACTGTTTGTGATCTCCAAGCCCGACGTGTTCAAGAGCCCGGCATCCGACACTCACATCATCTTTGGCGAGGCCAAGATCGAGGACTTGAGTTCCCAGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcgttggtagatcgaagagaatagagactaacttcgcttctggttctttccagATACTGTTTGTGATCTCCAAGCCCGACGTGTTCAAGAGCCCGGCATCCGACACTCACATCATCTTTGGCGAGGCCAAGATCGAGGACTTGAGTTCCCAGC
                           gactaac  putative branch site (score: 43)
                                      cttctggttctttcc  putative PPT