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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccgtgttcacttacaaaacaacactttgatcattcgttttctctctctgtctcgccagGCCGGGCTATTCGTATATGACATCTTCTGGGTATTCTTCACTCCTGTGATGGTCACCGTTGCGAAGTCCTTTGATGCTCCCATCAAG

Basic information

species Selaginella moellendorffii
transcript EFJ21978
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ21978 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: LOC_Os05g36070.2 (Oryza sativa), 3'ss of exon 7
-------------------------------------gtaccgtgtt---cacttacaaaacaacactttgatcattcgttttctctctctgtctcgccagGCCGGGCTATTCGTATATGACATCTTCTGGGTATTCTTCACTCCTGTGATGGTCACCGTTGCGAAGTCCTTTGATGCTCCCATCAAG
                                     |||  ||||    || ||  ||      |||||  |   ||||  | | || || |     |||  ||| || ||  | ||||| || |||||||| ||||||||||| || |||||||  ||||| ||||| ||||||||||| || |||
gcttgcgaaattaaagtccatatttgtatacaccaccgtattgtgtaaagcatttttaatttgtaacttttgtgtatcgtggtat-tcccttttaattcagAGCGGACTCTTTTTCTATGATATTTTCTGGGTCTTCTTCACTCCAGTTATGGTCAGTGTTGCCAAGTCATTTGATGCTCCAATAAAG

upper sequence: EFJ21978 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: LOC_Os02g02530.3 (Oryza sativa), 3'ss of exon 6
------------------------------------gtaccgtgt---tcacttacaaaacaacactttgatcattcgttttctctctctgtctcgccagGCCGGGCTATTCGTATATGACATCTTCTGGGTATTCTTCACTCCTGTGATGGTCACCGTTGCGAAGTCCTTTGATGCTCCCATCAAG
                                    ||||  |||   |||||   ||      ||  | ||   ||      | ||  | |     ||||| || || ||  | ||||| || |||||||| |||||||||||||| |||||||  ||||| || || |||||||| || || |||
cctgttatatttgtagaaactattgcactgcttgctgtactttgtaaatcactattaagttgtaacgcttatgtatcacgggatttcctttttgattcagGCTGGCCTCTTTTTCTATGATATTTTCTGGGTTTTCTTCACTCCTGTTATGGTCAGTGTTGCAAAATCATTTGATGCACCGATAAAG

upper sequence: EFJ21978 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GRMZM2G150251_T01 (Zea mays), 3'ss of exon 7
-------------------------------------------gtaccgtgttcacttacaaaacaacactttgatcattcgttttctctctctgtctcgccagGCCGGGCTATTCGTATATGACATCTTCTGGGTATTCTTCACTCCTGTGATGGTCACCGTTGCGAAGTCCTTTGATGCTCCCATCAAG
                                            | |  |||||| |   | |   | |  |  ||      || ||  | ||  | ||  ||||  || || || || |||||||| |||||||| ||||||||||| || |||||||  || || || || ||||||||||| || |||
gagttgatttcttctacttgtttcaacattgtgccagtgaatcattctctgttcattattacatgcatatgtgaatg--caattgtccttttccatttc--cagGGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATGGTCAGTGTGGCTAAATCTTTTGATGCTCCTATAAAG

upper sequence: EFJ21978 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GLYMA14G21190.1 (Glycine max), 3'ss of exon 2
---------------------------------gtaccgtgttcacttacaaaacaaca----ctttgatc--attcgttttctctctc-tgtctcgccagGCCGGGCTATTCGTATATGACATCTTCTGGGTATTCTTCACTCCTGTGATGGTCACCGTTGCGAAGTCCTTTGATGCTCCCATCAAG
                                 ||      |||| ||    | |  ||    ||||| |   | || ||| |  |||| ||| | || |||| || || || || |||||||| |||||||| ||||||||||| |||||||||| |||||| || || ||||||||||| || |||
gctacaataagattcatatttgttttgtaatttgtttttcattcattttttcatcttcatggtctttgctttgaatcttttccaatctcatgttttgc-agGCTGGACTCTTTGTTTATGACATTTTCTGGGTTTTCTTCACTCCAGTGATGGTCAGCGTTGCAAAATCATTTGATGCTCCAATAAAG

upper sequence: EFJ21978 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GLYMA06G08620.2 (Glycine max), 3'ss of exon 7
-------------------------------------gtaccgtgttcacttacaaaacaacactttgatcattcgttttctc---tctctgt-ctcgccagGCCGGGCTATTCGTATATGACATCTTCTGGGTATTCTTCACTCCTGTGATGGTCACCGTTGCGAAGTCCTTTGATGCTCCCATCAAG
                                     |||   |  || |||         || | || || ||   | |||    |   |||  |   ||||| || ||||| || |||||||| |||||||| ||||||||||| |||||||| | |||||| || || ||||||||||| || |||
agtcagttattaaaagatcaaacatatgcttttcattgtataattctctctttttgttt--caatatggtctttgactctcttacattcatgtattttacagGCTGGTCTATTTGTGTATGACATTTTCTGGGTTTTCTTCACTCCAGTGATGGTTAGCGTTGCAAAATCATTTGATGCTCCAATAAAG

upper sequence: EFJ21978 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GLYMA04G08510.1 (Glycine max), 3'ss of exon 7
-----------------------------------------gtaccgtgttcacttacaaaacaacactttgatcattcgttttctctctctgtctcgccagGCCGGGCTATTCGTATATGACATCTTCTGGGTATTCTTCACTCCTGTGATGGTCACCGTTGCGAAGTCCTTTGATGCTCCCATCAAG
                                          || |   ||   ||    || |  |  ||  | | ||  || |  ||      |   ||||| || ||||| || |||||||| |||||||| |||||||| || |||||||||| |||||| || || ||||||||||| || |||
ttagtcagttattaaaagattaagcatatgcttttcattgtataactccttttttttttcaatatgatctt--tgactctcttacattcatgtattttacagGCTGGTCTATTTGTGTATGACATTTTCTGGGTTTTCTTCACCCCAGTGATGGTCAGCGTTGCAAAATCATTTGATGCTCCAATAAAG

upper sequence: EFJ21978 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: Vv06s0009g03520.t01 (Vitis vinifera), 3'ss of exon 7
-------------------------------------gtaccgtgttcacttacaaaacaacactt--tgatcattcgttttctctctctgtctcgccagGCCGGGCTATTCGTATATGACATCTTCTGGGTATTCTTCACTCCTGTGATGGTCACCGTTGCGAAGTCCTTTGATGCTCCCATCAAG
                                      | | |  |||| ||       |   ||   ||||  ||    |     ||         ||||| || || || || ||||| || |||||||| ||||||||||| ||||||||||  ||||| |||||||| |||||||| || |||
ttgatgccagtatttttgtccctcatatctatgcctgttcctgcattcagtttgtttgtacttctaagtgatttttgacatgggtacttgcgaattgcagGCAGGACTTTTTGTTTATGATATTTTCTGGGTCTTCTTCACTCCAGTGATGGTCAGTGTTGCAAAGTCCTTCGATGCTCCTATTAAG

upper sequence: EFJ21978 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: PP1S47_5V6.2 (Physcomitrella patens), 3'ss of exon 7
-----------------------------------------gtaccgtgttcacttacaaaacaacactttgatcattcgttttctctctctgtctcgccagGCCGGGCTATTCGTATATGACATCTTCTGGGTATTCTTCACTCCTGTGATGGTCACCGTTGCGAAGTCCTTTGATGCTCCCATCAAG
                                         |||   ||   | | |      |  | |||||    | | |   || |  ||    || |||| || || ||| |||| |||||||||||||| |||||||| ||||| ||||| | ||| || ||||| || |||||||||||||||
ggtttgtgtgaaaaggtgcaagagtgttgagttttgggattgtaaattggcaattaattggggaggagtttgagatgttggtgg-tcacgatggagtgc-agGCAGGACTGTTCATATACGACATCTTCTGGGTGTTCTTCACGCCTGTAATGGTGAGCGTGGCAAAGTCGTTCGATGCTCCCATCAAG

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: 33 (upstream exon), 35 (downstream exon)
Score: 17

GGAATCGAGATGCTGTCTCTAGGCTCATTCAAGATCGGGGCGATTCTTCTGgtaccgtgtt ... gtctcgccagGCCGGGCTATTCGTATATGACATCTTCTGGGTATTCTTCACTCCTGTGATGGTCACCGTTGCGAAGTCCTTTGATGCTCCCATCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttcacttacaaaacaacactttgatcattcgttttctctctctgtctcgccagGCCGGGCTATTCGTATATGACATCTTCTGGGTATTCTTCACTCCTGTGATGGTCACCGTTGCGAAGTCCTTTGATGCTCCCATCAAG
                          tcattcgttttctctc  CT-rich tract
       ttacaaaa  TA-rich tract