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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagattggggaacttttaaactgttctgagttctagttttttggattttagACGGCCGCTAGCTACCATGCCATAGCTATCGCCCTTTCGCTAATGGAAGCGTACTCCCTCAGTGTACAGCACGAGCAAACAACGCTTCAAATCTTGCAAG

Basic information

species Selaginella moellendorffii
transcript EFJ26734
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ26734 (Selaginella moellendorffii), 3'ss of exon 19
lower sequence: LOC_Os07g23990.1 (Oryza sativa), 3'ss of exon 18
-----------------------------------------------gtaaagattggggaacttttaaactgttctga-gttctagttttttggattttagACGGCCGCTAGCTACCATGCCATAGCTATCGCCCTTTCGCTAATGGAAGCGTACTCCCTCAGTGTACAGCACGAGCAAACAACGCTTCAAATCTTGCAAG
                                                   | ||||    | | |     |   || |  | || || | ||  ||||||||| || || ||||||||||||||||| || || || ||  | |||||||| || ||| | ||||| ||||| |||||||||||  | |||||  | |  |
agtacaggtttcactgttgactacttcacttaatgctttcatcatttaatgatattgcttgattatctgtttcaactaacatacttgtctgtt--attttagACTGCTGCGAGCTACCATGCCATAGCCATTGCTCTCTCATTGATGGAAGCTTATTCCTTGAGTGTTCAGCATGAGCAAACAACCTTGCAAATTCTTCGTG

upper sequence: EFJ26734 (Selaginella moellendorffii), 3'ss of exon 19
lower sequence: GRMZM2G086030_T01 (Zea mays), 3'ss of exon 19
----------------------------------------gtaaagattggggaacttttaaactgttctgagtt--ctagt--tttttggatt--ttagACGGCCGCTAGCTACCATGCCATAGCTATCGCCCTTTCGCTAATGGAAGCGTACTCCCTCAGTGTACAGCACGAGCAAACAACGCTTCAAATCTTGCAAG
                                         | | |    | || |   | |  | || |||  |  | ||   |||||  ||     |||| || || ||||||||||||||||| || ||||||||  | ||||| ||||||||||| || || || || || ||||||||  | || ||  | || |
cgacatttgatttataattcattgaacaatatgataaagaattaggtcctgtgatcgaattacttattatgaactaacaagcaatttttcaatcaaacagACTGCTGCAAGCTACCATGCCATAGCCATAGCCCTTTCAATGATGGACGCGTACTCCCTAAGCGTGCAACATGAACAAACAACCTTGCAGATACTTCAGG

upper sequence: EFJ26734 (Selaginella moellendorffii), 3'ss of exon 19
lower sequence: GRMZM5G892758_T01 (Zea mays), 3'ss of exon 2
-------------------------------------gtaaagattggggaacttttaaactgttctgagtt--ctag-----ttttttggatt--ttagACGGCCGCTAGCTACCATGCCATAGCTATCGCCCTTTCGCTAATGGAAGCGTACTCCCTCAGTGTACAGCACGAGCAAACAACGCTTCAAATCTTGCAAG
                                      |   |    | ||  |  | |  |  | |||  |  | ||     ||||||  ||   | |||| || || ||||||||||| ||||| || ||||||||  | ||||| ||||||||||| ||||| || || || ||||||||  | || ||  | || |
cacctgatttataattcattgaataatatgatgaataattgggtcctgtgatttaattacttactatgaactaacaagcaattttttttcaatcaatcagACTGCTGCAAGCTACCATGCTATAGCCATAGCCCTTTCAATGATGGATGCGTACTCCCTAAGTGTGCAACATGAACAAACAACCATGCAGATACTTCAGG

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), 34 (downstream exon)
Score: 11

AATGATGGAAGAAGGTCTAGGGAATGTGCATATAGCGCTTAGATATCTTCACGAAGCTTTGAAATGCAACCAGCGACTTTTAGGAGCGGACCACATCCAGgtaaagattg ... tggattttagACGGCCGCTAGCTACCATGCCATAGCTATCGCCCTTTCGCTAATGGAAGCGTACTCCCTCAGTGTACAGCACGAGCAAACAACGCTTCAAATCTTGCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaaagattggggaacttttaaactgttctgagttctagttttttggattttagACGGCCGCTAGCTACCATGCCATAGCTATCGCCCTTTCGCTAATGGAAGCGTACTCCCTCAGTGTACAGCACGAGCAAACAACGCTTCAAATCTTGCAAG
                                        tttttt  CT-rich tract
                                        ttttttggatttta  TA-rich tract