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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagagcgcgcggctatcgcgggatcttacgattcttgtgttgtgcagGTGCGCGGGCCGAAGAAGCATCTGAAGGTGCTCAATGCCCCCAAGCATTGGATGCTGAGCAAGCTCGGCGGTGCCTTC

Basic information

species Selaginella moellendorffii
transcript EFJ26570
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ26570 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os02g01560.1 (Oryza sativa), 3'ss of exon 1
-------------------------------------------gtgagagcgcgcggctatcgcgg--gatc--ttacgattcttgtgttgtg----cagGTGCGCGGGCCGAAGAAGCATCTGAAGGTGCTCAATGCCCCCAAGCATTGGATGCTGAGCAAGCTCGGCGGTGCCTTC
                                            ||       |  | |||    |  ||||  || |  |||   |   ||     ||||   | ||   ||||||||||||||||  ||||||||| |||||||||||||||||   |||||| || || || || 
accttgtgatttcattgtgtcattgtattcatgtcgtgctactctgcagttatgttgttatttgtgctgatcatttccttttcccttaccgtaataccagGCAAGGGGTTTGAAGAAGCATCTGAAGAGGCTCAATGCGCCCAAGCATTGGATGCTCGACAAGCTTGGTGGAGCTTTT

upper sequence: EFJ26570 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os05g30530.1 (Oryza sativa), 3'ss of exon 1
---------------------------------------------------gtgagagcgcgcggctatcgcgggatcttacgattcttgtgttgtgcagGTGCGCGGGCCGAAGAAGCATCTGAAGGTGCTCAATGCCCCCAAGCATTGGATGCTGAGCAAGCTCGGCGGTGCCTTC
                                                    | |    |      | | |    |     |   | || || |    ||| | | ||   ||||||||||||||||  ||||||||||||||  |||||||||||   |||||| || || || || 
tttactgtattgcccccttttcatttctctcatttggattggttaaacgctatcaatatgtatttatcttgttaaaagaatctccttttctgcttaatagGCGAGGGGTTTGAAGAAGCATCTGAAGAGGCTCAATGCCCCCAGCCATTGGATGCTTGACAAGCTTGGTGGAGCATTT

upper sequence: EFJ26570 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os01g25610.1 (Oryza sativa), 3'ss of exon 1
------------------------------------------gtgagagcgcgcggctatcgcgggatcttacgat-------tcttgtgttgtg--cagGTGCGCGGGCCGAAGAAGCATCTGAAGGTGCTCAATGCCCCCAAGCATTGGATGCTGAGCAAGCTCGGCGGTGCCTTC
                                           || |||   | || ||       |  | ||| |       | || | || ||  |||| | | ||   |||||||||||| |||  ||||||||| |||||||| ||||||||   |||||||||||| || || 
agaattatattgttgtactggcttttaagaagcatcacaattctgtgagtatgtggttaataacatacttaacgttgtcaacctgttattttctgaacagGCGAGGGGATTGAAGAAGCATCTCAAGAGGCTCAATGCGCCCAAGCACTGGATGCTCGACAAGCTCGGCGGAGCTTTT

upper sequence: EFJ26570 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G125271_T01 (Zea mays), 3'ss of exon 1
----------------------------------------------------gtgagagcgcgcggctatcgcgggatcttacgattcttgtgttgtgcagGTGCGCGGGCCGAAGAAGCATCTGAAGGTGCTCAATGCCCCCAAGCATTGGATGCTGAGCAAGCTCGGCGGTGCCTTC
                                                    |   ||    |  |   |     ||||    | || || ||   | ||||   | ||   |||||||||| |||||  ||||||||||||||||||||||||||||  |||||| ||||| || || 
ttgagaaggaatcattccgtgaaatcaggttgcgatgcctatgataacacttgctggaatctgttgtgcttttctgatcac-tgttttttttgcaatccagGCTAGAGGATTGAAGAAGCATTTGAAGAGGCTCAATGCCCCCAAGCATTGGATGCTGGACAAGCTTGGCGGAGCTTTT

upper sequence: EFJ26570 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G542753_T01 (Zea mays), 3'ss of exon 5
----------------------------------------------------gtgagagcgcgcggctatcgcgggatcttacgattcttgtgttgtgcagGTGCGCGGGCCGAAGAAGCATCTGAAGGTGCTCAATGCCCCCAAGCATTGGATGCTGAGCAAGCTCGGCGGTGCCTTC
                                                        ||    |  ||  |   |     | |  ||| || ||   | ||||   | ||  ||||||||||  |||||  ||||||||| |||||||||||||||||   |||||| ||||| || || 
ctgttacttttaacagctaatgcaatctggatgagtcacctatgaatgccatactggaatctgttgcgcttttgttga-tcattattattttgcaatccagGCTAGGGGATCGAAGAAGCACTTGAAGAGGCTCAATGCGCCCAAGCATTGGATGCTCGACAAGCTTGGCGGAGCTTTT

upper sequence: EFJ26570 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G301096_T01 (Zea mays), 3'ss of exon 2
-----------------------------------------------------gtgagagcgcgcggctatcgcgggatcttacgattcttgtgttgtgcagGTGCGCGGGCCGAAGAAGCATCTGAAGGTGCTCAATGCCCCCAAGCATTGGATGCTGAGCAAGCTCGGCGGTGCCTTC
                                                       ||    |    ||| | |  |    |||  ||| ||    | |  |||   | ||   |||||||||  |||||  ||||||||| ||||||||||||||||| | |||||| ||| | || || 
tgttacttttaacagctaatgcaatctgaatgagtcacctatgaatgccatactggaatttgttgcgcttttgttgatcattattatttttacaatct--agGCTAGGGGATTGAAGAAGCACTTGAAGAGGCTCAATGCGCCCAAGCATTGGATGCTCAACAAGCTTGGCAGAGCTTTT

upper sequence: EFJ26570 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G158584_T04 (Zea mays), 3'ss of exon 5
----------------------------------------------------gtgagagcgcgcggctatcgcgggatcttacgattcttgtgttgtgcagGTGCGCGGGCCGAAGAAGCATCTGAAGGTGCTCAATGCCCCCAAGCATTGGATGCTGAGCAAGCTCGGCGGTGCCTTC
                                                        ||    |  ||  |   |     | |  ||| || ||   | ||||   | ||   |||||||||  |||||  ||||||||| |||||||||||||||||   |||||| ||||| || || 
ctgttacttttaacagctaatgcaatctggatgagtcacctatgaattccatactggaatctgttgcgcttttgttga-tcattattattttgcaatccagGCTAGGGGATTGAAGAAGCACTTGAAGAGGCTCAATGCGCCCAAGCATTGGATGCTCGACAAGCTTGGCGGAGCTTTT

upper sequence: EFJ26570 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G469061_T01 (Zea mays), 3'ss of exon 2
----------------------------------------------------gtgagagcgcgcggctatcgcgggatcttacgattcttgtgttgtgcagGTGCGCGGGCCGAAGAAGCATCTGAAGGTGCTCAATGCCCCCAAGCATTGGATGCTGAGCAAGCTCGGCGGTGCCTTC
                                                        ||    |  ||  |   |     | |  ||| || ||   | ||||   | ||   |||||||||  |||||  ||||||||| |||||||||||||||||   |||||| || || || || 
ctgttacttttaacagctaatgcaatctggatgagtcacctatgaatgccatactggaatctgttgcgcttttgttga-tcattattattttgcaatccagGCTAGGGGATTGAAGAAGCACTTGAAGAGGCTCAATGCGCCCAAGCATTGGATGCTCGACAAGCTTGGTGGAGCTTTT

upper sequence: EFJ26570 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G176641_T01 (Zea mays), 3'ss of exon 3
----------------------------------------------------gtgagagcgcgcggctatcgcgggatcttacgattcttgtgttgtgcagGTGCGCGGGCCGAAGAAGCATCTGAAGGTGCTCAATGCCCCCAAGCATTGGATGCTGAGCAAGCTCGGCGGTGCCTTC
                                                        ||    |  ||  |   |     | |  ||| || ||   | ||||   | ||   |||||||||  |||||  ||||||||| |||||||||||||||||   |||||| ||||| || || 
ctgttacttttaacagctaaagcaatctggatgagtcacctatgaatgccatactggaatctgttgcgcttttgttga-tcattattattttgcaatccagGCTAGGGGATTGAAGAAGCACTTGAAGAGGCTCAATGCGCCCAAGCATTGGATGCTCGACAAGCTTGGCGGAGCTTTT

upper sequence: EFJ26570 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G158584_T05 (Zea mays), 3'ss of exon 1
----------------------------------------------------gtgagagcgcgcggctatcgcgggatcttacgattcttgtgttgtgcagGTGCGCGGGCCGAAGAAGCATCTGAAGGTGCTCAATGCCCCCAAGCATTGGATGCTGAGCAAGCTCGGCGGTGCCTTC----------------------
                                                        ||    |  ||  |   |     | |  ||| || ||   | ||||   | ||   |||||||||  |||||  ||||||||| |||||||||||||||||   |||||| ||||| || ||                       
ctgttacttttaacagctaatgcaatctggatgagtcacctatgaattccatactggaatctgttgcgcttttgttga-tcattattattttgcaatccagGCTAGGGGATTGAAGAAGCACTTGAAGAGGCTCAATGCGCCCAAGCATTGGATGCTCGACAAGCTTGGCGGAGCTTTTGTAAGTAAAAAATATTTTCTAG

upper sequence: EFJ26570 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G035017_T01 (Zea mays), 3'ss of exon 1
------------------------------------------------------gtgagagcgcgcggctatcgcgggatcttacgattcttgtgttgtgcagGTGCGCGGGCCGAAGAAGCATCTGAAGGTGCTCAATGCCCCCAAGCATTGGATGCTGAGCAAGCTCGGCGGTGCCTTC
                                                        ||    |    ||| | |  |    | |  ||| || ||   | ||||   | ||   |||||||||  |||||  ||||||||| |||||||||||||||||   |||||| ||||| || || 
ctgttacttttaacagctgatgcaatcaggatgagtcgcctatgaatgccccactcgaatctgttgtgcttttgttga---tcattattattttgcaatccagGCTAGGGGATTGAAGAAGCACTTGAAGAGGCTCAATGCGCCCAAGCATTGGATGCTCGACAAGCTTGGCGGAGCTTTT

upper sequence: EFJ26570 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA16G23730.1 (Glycine max), 3'ss of exon 1
---------------------------------------------gtgagagcgcgcggctatcgcgggatcttacgattc----ttgtg-ttgtg-cagGTGCGCGGGCCGAAGAAGCATCTGAAGGTGCTCAATGCCCCCAAGCATTGGATGCTGAGCAAGCTCGGCGGTGCCTTC
                                              |             | | |   || |||   | |     || || ||||  |||| | | ||    |||||||||||||||  ||| |||||||| ||||||||||||||   ||| || || ||||| || 
cccgagttttatttgtttagtgttagatttgatattcaagattttttatttttaattaatttttgtttgagctttgaacttcaatttatgattgtaacagGCGAGAGGATTAAAGAAGCATCTGAAGAGGCTTAATGCCCCAAAGCATTGGATGCTTGACAAACTGGGTGGTGCATTT

upper sequence: EFJ26570 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA02G43080.2 (Glycine max), 3'ss of exon 1
-------------------------------------------gtgagagcgcgcggctatcgcgggatcttacgattcttgtgttg--------tgcagGTGCGCGGGCCGAAGAAGCATCTGAAGGTGCTCAATGCCCCCAAGCATTGGATGCTGAGCAAGCTCGGCGGTGCCTTC
                                            |      |      |   |   ||  ||   | | | ||| |         | ||||   | ||   |||||||||||| |||  ||||||||| || ||||||||||||||   ||| || || ||||| || 
ctaccataggttttggtcatttaatgtcagacttgctgtttgaatctttttgtttaatttgtgtttgagttttaaactttcgtgcttatgactgttacagGCTAGGGGATTGAAGAAGCATCTCAAGAGGCTCAATGCTCCTAAGCATTGGATGCTTGACAAACTGGGTGGTGCATTT

upper sequence: EFJ26570 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA02G05370.1 (Glycine max), 3'ss of exon 1
---------------------------------------------------gtgag-agcgcgcggctatcgcgggatcttacgattcttgtgttgtgcagGTGCGCGGGCCGAAGAAGCATCTGAAGGTGCTCAATGCCCCCAAGCATTGGATGCTGAGCAAGCTCGGCGGTGCCTTC
                                                    | |  |    | | ||       || ||| | ||   ||  |    |||| | | ||   |||||||||| |||||  ||| |||||||| ||||||||||||||   ||| || || ||||| || 
gtaatgctgagttttatttgtttattgttagacttgatattgaaggtttttttaattaatttgtgtctgagctttgaactt-caatatatgattgtaacagGCGAGAGGATTGAAGAAGCATTTGAAGAGGCTTAATGCCCCAAAGCATTGGATGCTTGACAAACTGGGTGGTGCATTT

upper sequence: EFJ26570 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: Vv08s0058g00390.t01 (Vitis vinifera), 3'ss of exon 2
------------------------------------------------gtgagagcg-cgcggctatcgcggga--tcttacgattcttgtgttgtgcagGTGCGCGGGCCGAAGAAGCATCTGAAGGTGCTCAATGCCCCCAAGCATTGGATGCTGAGCAAGCTCGGCGGTGCCTTC
                                                ||     |  |     ||| || | |  ||||   ||    |||   | ||||   | |||  |||||| ||| |||||  |||||||||||| ||||||||||||||   |||||| || ||||| || 
gtatgaaaatatgatttggaactgtgatttttgtaatctgccttttttgtttttccaacatttttattgctgaacttcttgtcatgtgggtgcattacagGCTAGAGGGTTGAAGAAACATTTGAAGAGGCTCAATGCCCCTAAGCATTGGATGCTTGACAAGCTTGGAGGTGCATTT

upper sequence: EFJ26570 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S461_1V6.1 (Physcomitrella patens), 3'ss of exon 1
---------------------------------------------------gtgagagcgcgcggctatcgcgggatcttacgattcttgtgttgtgcagGTGCGCGGGCCGAAGAAGCATCTGAAGGTGCTCAATGCCCCCAAGCATTGGATGCTGAGCAAGCTCGGCGGTGCCTTC
                                                   | |  ||   | | |     | |  |  |     |||||||   |  |||  || ||   ||||||||||||||||  ||||||||| |||||||||||||||||   |||| | || |||||||||
cctgcaagcttaaaatgggggtggtttagggttttgaagttggttgatgatgaggaagtttgagtcgtgttctgagttctgtttctcttgtgcgttttagGCTCGTGGTTTGAAGAAGCATCTGAAGAGGCTCAATGCGCCCAAGCATTGGATGCTTGACAAGTTGGGTGGTGCCTTC

upper sequence: EFJ26570 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S81_172V6.1 (Physcomitrella patens), 3'ss of exon 1
----------------------------------------------------gtgagagcgcgcggctatcgcgggatcttacgattcttgtgttgtgcagGTGCGCGGGCCGAAGAAGCATCTGAAGGTGCTCAATGCCCCCAAGCATTGGATGCTGAGCAAGCTCGGCGGTGCCTTC
                                                     | |         | | |    |  | ||  | || || | || | ||||  || ||   |||||||||| |||||  ||||||||| |||||||||||||||||   |||  | || || ||||| 
gaggttggtttcgtagcatatttttgaaatgtgcgctgatttttttcttttttttatttttttacgttgtttttgttttttttg-ttatttttttcttcagGCTCGTGGTTTGAAGAAGCATTTGAAGAGGCTCAATGCGCCCAAGCATTGGATGCTCGACAAATTGGGTGGCGCCTTT

upper sequence: EFJ26570 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S282_25V6.1 (Physcomitrella patens), 3'ss of exon 1
---------------------------------------------gtgagagcgcgcggctatcgcgggatcttacgattctt----gtgttg--tgcagGTGCGCGGGCCGAAGAAGCATCTGAAGGTGCTCAATGCCCCCAAGCATTGGATGCTGAGCAAGCTCGGCGGTGCCTTC
                                              | |    |  |   |    || |  || |  ||   |    ||||||  | ||||  |||||   |||||||||| |||||  ||||||||| || ||||||||||||||   |||||| || || ||||||
atgctggagtgagaatcagggtcttcggtattttgggactggctgatcaccctgttcaattggtacgtgtgctaaacatgtgttgcggtgttgattccagGCTCGCGGTTTGAAGAAGCATTTGAAGAGGCTCAATGCGCCTAAGCATTGGATGCTTGACAAGCTGGGTGGCGCCTTC

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), 35 (downstream exon)
Score: 67

CCTAATTCCTGTTTTTGAGGGTTTCCACGGCGGCTAGGGTTCTAGGCGGAGGAGCGTGCAGCAATGgtgagagcgc ... tgttgtgcagGTGCGCGGGCCGAAGAAGCATCTGAAGGTGCTCAATGCCCCCAAGCATTGGATGCTGAGCAAGCTCGGCGGTGCCTTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgagagcgcgcggctatcgcgggatcttacgattcttgtgttgtgcagGTGCGCGGGCCGAAGAAGCATCTGAAGGTGCTCAATGCCCCCAAGCATTGGATGCTGAGCAAGCTCGGCGGTGCCTTC
                              atcttac  putative branch site (score: 67)
                                       ttcttgt  putative PPT
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagagcgcgcggctatcgcgggatcttacgattcttgtgttgtgcagGTGCGCGGGCCGAAGAAGCATCTGAAGGTGCTCAATGCCCCCAAGCATTGGATGCTGAGCAAGCTCGGCGGTGCCTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT