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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGATGAGTGACTACAAGGTGGAGATGGTAAACGATGGGATGAACGAGTTTAATGTGGAGTTCCATGGACCTCGGGATAgtaagtcctccacactgccctcttctcttcctcttgtctccctgtggttttcgtgcctctgtgtctctcggcttgtttgaaagagagatttcttcttgtt...

Basic information

species Selaginella moellendorffii
transcript EFJ34378
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ34378 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: LOC_Os10g31000.1 (Oryza sativa), 5'ss of exon 2
GATGATGAGTGACTACAAGGTGGAGATGGTAAACGATGGGATGAACGAGTTTAATGTGGAGTTCCATGGACCTCGGGATAgtaagtcctccacactgccctcttctcttcctcttgtctccctgtggttttcgtgcctctgtgtctctcggcttgtttgaaagagagatttcttcttgtt-
||||||||| |||||||||||||||||||| |||||||||||| | |||||    ||||| ||||  || |||   || |||| |  | |  |||     |      ||  | ||  ||||   |||||   |  |   ||   | |    |||||||    |       |||   |||  
GATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAGTTCTTCGTGGAATTCCGGGGGCCTACTGAAAgtacgatcgc-gcacgcaaattccgattttgtttttcctcctcctggttcctggcctgatgatccgcgtttcttgttttccggtctctgatctagatgtag

upper sequence: EFJ34378 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: AC149818.2_FGT006 (Zea mays), 5'ss of exon 2
GATGATGAGTGACTACAAGGTGGAGATGGTAAACGATGGGATGAACGAGTTTAATGTGGAGTTCCATGGACCTCGGGATAgtaagtcctccacactgccctcttctcttcctcttgtctccctgtggttttcgtgcctctgtgtctctcggcttgt--ttgaaagagagatttcttcttgtt
||||||||| |||||||||||||||||||| |||||||||||| | |||||   ||| || || | ||| |||   || |||| |   |    ||         |  ||    || | |  || |||      ||  |||||  |||  || || |  |  | | |||      | |  || 
GATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAGTTCTTTGTTGAATTTCGTGGGCCTAACGAAAgtacggattattaacgcaaaaggacgatttaggttttgtttctatggccg--atgattctgtagctcctggtttatgatctatatagaccgaagtgcaagtc

upper sequence: EFJ34378 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GRMZM2G053764_T03 (Zea mays), 5'ss of exon 2
GATGATGAGTGACTACAAGGTGGAGATGGTAAACGATGGGATGAACGAGTTTAATGTGGAGTTCCATGGACCTCGGGATAgtaa-gtcctccacactgccctcttctcttcctcttgtctccctgtggttttcgtgcctctgtgtctctcggcttgtt-tgaaagagagatttcttcttgtt
||||||||| |||||||||||||||||||| |||||||||||| | || ||    || || ||| | || ||    || |||||   ||  | | |||    |   |    || || ||||||||    |  |||||   ||   | | |  ||  || |||   |||  ||       |  
GATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAAgtaatagccctcgcgctgaatcccggttgctcttttctctccctgc--ctcccgtgctgatggtgcacgctcctgattctgatctagatgttgtggggggaa

upper sequence: EFJ34378 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GRMZM2G146374_T02 (Zea mays), 5'ss of exon 2
GATGATGAGTGACTACAAGGTGGAGATGGTAAACGATGGGATGAACGAGTTTAATGTGGAGTTCCATGGACCTCGGGATAgtaa-gtcctccacactgccctcttctcttcctcttgtctccctgtggttttcgtgcctctgtgtctctcggcttgtttgaaagagagatttcttcttgtt-
||||||||| |||||||||||||||||||| ||||| |||||| | || ||    || || ||| | || ||    || |||||   ||  | | | |    |    || || | | || | | |   |    ||  |||    || ||| || |    |   |       ||  | ||   
GATGATGAGCGACTACAAGGTGGAGATGGTGAACGACGGGATGCAGGAATTCTTCGTCGAATTCAAGGGCCCGGCCGAAAgtaataaccctcgcgccgaatcccagcctcccccctctcgcgccg-aatcccggtttctcccc-tccctctgcctcccggcgggctgatgatccacgtgggc

upper sequence: EFJ34378 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GRMZM2G150867_T03 (Zea mays), 5'ss of exon 1
--------------------GATGATGAGTGACTACAAGGTGGAGATGGTAAACGATGGGATGAACGAGTTTAATGTGGAGTTCCATGGACCTCGGGATAgtaagtcctccacactgccctcttctcttcctcttgtctccctgtggttttcgtgcctctgtgtctctcggcttgt--ttgaaagagagatttcttcttgtt
                    ||||||||| |||||||||||||| ||||| |||||||||||| | |||||   ||| || || | ||| |||   || |||| |   |   |||         |  ||    || |||  ||  ||      ||| |||||  |||  |  || |  |  | | |||      | |  |||
CTGCATGTTGATGCCTGCAGGATGATGAGCGACTACAAGGTGGATATGGTGAACGATGGGATGCAGGAGTTCTTTGTTGAATTTCGTGGGCCTAACGAAAgtacggttttttcacacaaaaggccgatttaggttttctttctagggccg--atgcttctgtagctcctgatttataatctatatagaccgaattgcaagtt

upper sequence: EFJ34378 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GRMZM2G053764_T02 (Zea mays), 5'ss of exon 2
GATGATGAGTGACTACAAGGTGGAGATGGTAAACGATGGGATGAACGAGTTTAATGTGGAGTTCCATGGACCTCGGGATAgtaa-gtcctccacactgccctcttctcttcctcttgtctccctgtggttttcgtgcctctgtgtctctcggcttgtt-tgaaagagagatttcttcttgtt
||||||||| ||||||||||| |||||||| |||||||||||| | || ||    || || ||| | || ||    || |||||   ||  | | |||    |  |  || ||||| |||| |  ||  |  |||||   ||   | | |  ||  || |||   |||  ||      ||  
GATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAAgtaatagccctcgcgctgaatcc--cggttgctcttctctctccctgcctcccgtgctgatggtgcacgctcctgattctgatctagatgttgtggggtgga

upper sequence: EFJ34378 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GRMZM2G150867_T02 (Zea mays), 5'ss of exon 2
GATGATGAGTGACTACAAGGTGGAGATGGTAAACGATGGGATGAACGAGTTTAATGTGGAGTTCCATGGACCTCGGGATAgtaagtcctccacactgccctcttctcttcctcttgtctccctgtggttttcgtgcctctgtgtctctcggcttgt--ttgaaagagagatttcttcttgtt
||||||||| |||||||||||||| ||||| |||||||||||| | |||||   ||| || || | ||| |||   || |||| |   |   |||         |  ||    || |||  ||  ||      ||| |||||  |||  |  || |  |  | | |||      | |  |||
GATGATGAGCGACTACAAGGTGGATATGGTGAACGATGGGATGCAGGAGTTCTTTGTTGAATTTCGTGGGCCTAACGAAAgtacggttttttcacacaaaaggccgatttaggttttctttctagggccg--atgcttctgtagctcctgatttataatctatatagaccgaattgcaagtt

upper sequence: EFJ34378 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GLYMA07G07540.3 (Glycine max), 5'ss of exon 1
--------------------GATGATGAGTGACTACAAGGTGGAGATGGTAAACGATGGGATGAACGAGTTTAATGTGGAGTTCCATGGACCTCGGGATAgtaagtcctccacactgccctcttctcttcctcttgtctccctgtggttttcg---tgcctctgtgtctctcggcttgtttgaaagagagatttcttcttgtt
                    |||||||||||||||||||||||||||| | || ||||| ||| | |||||| ||||| | |||||||||||    || ||||||| ||||    ||   |  ||| |    ||||  |    |   |||| |   ||  | ||         | | | |||  |  | |  |   |  |   
TTTTTTTTTTTAATTAATAGGATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTTTTATGTGCATTTCCATGGACCCAATGAGAgtaagttctcctt--tgtttttatctatgttacttgctttagagctttttttgaattgtttttggtgaaaaaagttgggttgctattgcgggtgtgtggtaa-

upper sequence: EFJ34378 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GLYMA16G03940.2 (Glycine max), 5'ss of exon 2
GATGATGAGTGACTACAAGGTGGAGATGGTAAACGATGGGATGAACGAGTTTAATGTGGAGTTCCATGGACCTCGGGATAgtaagtcctccacactgccctcttctcttcctcttgtctccctgtggttttcgtgcctctgtgtctctcggcttgtttgaaagagagatttcttcttgtt----
|||||||||||||||||||||||||||| | || ||||| ||| | |||||| ||||| | |||||||||||    || ||||| | ||||    |    | || ||||  |    | |      | |||| |||  |   | | | |        |||         | |     |||     
GATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTTTTATGTGCACTTCCATGGACCCAATGAGAgtaaattctcc----tttgtttttatctttgttacatgttttgaagctttttgtgaattgttttttgtgaaaaaagttgggttgctattgtgggtatgtggtaa

upper sequence: EFJ34378 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GLYMA07G07540.2 (Glycine max), 5'ss of exon 2
GATGATGAGTGACTACAAGGTGGAGATGGTAAACGATGGGATGAACGAGTTTAATGTGGAGTTCCATGGACCTCGGGATAgtaagtcctccacactgccctcttctcttcctcttgtctccctgtggttttcg---tgcctctgtgtctctcggcttgtttgaaagagagatttcttcttgtt
|||||||||||||||||||||||||||| | || ||||| ||| | |||||| ||||| | |||||||||||    || ||||||| ||||    ||   |  ||| |    ||||  |    |   |||| |   ||  | ||         | | | |||  |  | |  |   |  |   
GATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTTTTATGTGCATTTCCATGGACCCAATGAGAgtaagttctcctt--tgtttttatctatgttacttgctttagagctttttttgaattgtttttggtgaaaaaagttgggttgctattgcgggtgtgtggtaa-

upper sequence: EFJ34378 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GLYMA08G01940.1 (Glycine max), 5'ss of exon 2
GATGATGAGTGACTACAAGGTGGAGATGGTAAACGATGGGATGAACGAGTTTAATGTGGAGTTCCATGGACCTCGGGATAgtaagtcctccacactgccctcttctcttcctcttgtctccctgtggttt--tcgtgcctctgtgtctctcggcttgtttgaaagagagatttcttcttgtt
|||||||||||| ||||||||||||| ||| |||||||| ||| | |||||   |||||| ||||| |||||    || ||||| |  |    ||        ||  ||  | |    |   | |  |||  ||    ||  ||     | |  |||||  |    | |    ||| |  | 
GATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGTTCTTTGTGGAATTCCACGGACCCAAAGACAgtaaatttttgcaaccctttgtgtcattttatttccaattattattttttgttcagttcttggttgagatagtgttgttctatttggtg-caacttttaat-

upper sequence: EFJ34378 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GLYMA08G01940.4 (Glycine max), 5'ss of exon 1
--------------------GATGATGAGTGACTACAAGGTGGAGATGGTAAACGATGGGATGAACGAGTTTAATGTGGAGTTCCATGGACCTCGGGATAgtaagtcctccacactgccctcttctcttcctcttgtctccctgtggttt--tcgtgcctctgtgtctctcggcttgtttgaaagagagatttcttcttgtt
                    |||||||||||| ||||||||||||| ||| |||||||| ||| | |||||   |||||| ||||| |||||    || ||||| |  |    ||        ||  ||  | |    |   | |  |||  ||    ||  ||     | |  |||||  |    | |    ||| |  | 
GACATGGATCAGGTCATCAGGATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGTTCTTTGTGGAATTCCACGGACCCAAAGACAgtaaatttttgcaaccctttgtgtcattttatttccaattattattttttgttcagttcttggttgagatagtgttgttctatttggtg-caacttttaat-

upper sequence: EFJ34378 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GLYMA08G01940.3 (Glycine max), 5'ss of exon 2
--------GATGATGAGTGACTACAAGGTGGAGATGGTAAACGATGGGATGAACGAGTTTAATGTGGAGTTCCATGGACCTCGGGATAgtaagtcct--ccacactgccctcttctcttcctcttgtctccctgtggttttcgtgcctctgtgtctctcggcttgtttgaaagagagatttcttcttgtt
        |||||||||||| ||||||||||||| ||| |||||||| ||| | |||||   |||||| ||||| |||||    || ||||| |  |  | || ||         | |   ||   |     | |  | |||    ||  ||     | |  |||||  |    | |    ||| |  | 
GTCATCAGGATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGTTCTTTGTGGAATTCCACGGACCCAAAGACAgtaaatttttgcaaccctttgtgtcattttatttccaattattattttttgttcagttcttggttgagatagtgttgttctatttggtg-caacttttaat-

upper sequence: EFJ34378 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: AT1G63800.1 (Arabidopsis thaliana), 5'ss of exon 2
GATGATGAGTGACTACAAGGTGGAGATGGTAAACGATGGGATGAACGAGTTTAATGTGGAGTTCCATGGACCTCGGGATAgtaagtcctccacactgccctcttctc--ttcctcttgtctccctgtggttttcgtgcctctgtgtctctcggct-----tgtttgaaagagagatttcttcttgtt-------------------------------------------------------------------
|||||||||||||||||||||||||||| | || ||||| ||| | |||||   ||| || |||  ||||||    || |||||||    ||    | ||  |      ||    |  |     | || || |  |   |||   |||  | |||     || |    | || | ||| |     ||                                                                   
GATGATGAGTGACTACAAGGTGGAGATGATCAATGATGGCATGCAAGAGTTCTTTGTCGAATTCAGTGGACCCAAAGACAgtaagtaactcaattcgtcccgtgaataatttaaatcatagagttttgattctgttttttcttgttcttgctgctgatgatgatcatcatagggttttgtgtcaatttcaacttatcagtatcaacttgttaatttttggtgattttatctctgtgtgtttgtactatggacag

upper sequence: EFJ34378 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: Vv02s0025g00070.t01 (Vitis vinifera), 5'ss of exon 2
GATGATGAGTGACTACAAGGTGGAGATGGTAAACGATGGGATGAACGAGTTTAATGTGGAGTTCCATGGACCTCGGGATAgtaagtcctccacac---tgccct-cttctcttcctcttgtctccctg--tggttttcgtgcctctgtgtctctcggcttgtttgaaagagagatttcttcttgtt
|||||||||||| || |||||||||||||| || ||||| ||| | |||||  |||| || |||||||||||  | || ||||| || || ||||   | || |  || | ||  | ||| ||   ||  || |     ||    ||||| |||  |  || |||||     ||  | ||      
GATGATGAGTGATTATAAGGTGGAGATGGTGAATGATGGCATGCAAGAGTTCTATGTCGATTTCCATGGACCCGGTGACAgtaaatcttcaacacccataccttatttttttttattttgcctttttggttgatcaggatggggatgtgtatctttg--tgattgaagattcgaggtattta----

upper sequence: EFJ34378 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: Vv15s0046g02280.t01 (Vitis vinifera), 5'ss of exon 2
GATGATGAGTGACTACAAGGTGGAGATGGTAAACGATGGGATGAACGAGTTTAATGTGGAGTTCCATGGACCTCGGGATAgtaagtcctccacactgccctcttctcttcctcttgtctccctgtggttttcgtgcctctgtgtctctcggcttgtttgaaagagagatttcttcttgtt---
|||||||||||| ||||||||||||||| | || ||||| ||| | |||||  ||||| | |||||||||||  | || ||||| || || | ||   | | | || ||  | ||   |   | |  ||   |    ||      | | ||  |   |||| || | ||||   ||  ||   
GATGATGAGTGATTACAAGGTGGAGATGATCAATGATGGCATGCAAGAGTTCTATGTGCATTTCCATGGACCCAGTGACAgtaaatcttcaatacccacatatccttttgttttttggtttttttttttcctggttttcccaaattgttggtct--ctgaatgaaa-atttgagctcattaag

upper sequence: EFJ34378 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: PP1S37_166V6.1 (Physcomitrella patens), 5'ss of exon 2
GATGATGAGTGACTACAAGGTGGAGATGGTAAACGATGGGATGAACGAGTTTAATGTGGAGTTCCATGGACCTCGGGATAgtaagtcctccacactgccctcttctcttcctcttgtctccctgtggttttcgtgcctctgtgtctctcggcttgtttgaaagagagatttcttcttgtt-
||||||||||||||||||||| |||||||| || ||||| |||| ||| ||  |||||||||| |||||||| || || |||| ||  |      |      ||| || | |  ||| | |     || | |||  || | |     |  |   |   |   | ||   |  | || | | 
GATGATGAGTGACTACAAGGTCGAGATGGTGAATGATGGAATGAGCGAATTCTATGTGGAGTTTCATGGACCGCGTGAGAgtacgttttttcatttcttaaattcactcctttctgt-tgcggaccgtatgcgtaactatttcgagttgtgtaaggccgtttgtgaagctgatgctcgatg

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), 30 (downstream exon)
Score: 20

GATGATGAGTGACTACAAGGTGGAGATGGTAAACGATGGGATGAACGAGTTTAATGTGGAGTTCCATGGACCTCGGGATAgtaagtcctc ... tttccaacagGTCCATATCAAACGGGGACTTGGAAGGTTCGTGTCGAACTTCCAGAGGCTTACCCGTATAAATCTCCATCCATCGGTTTTGTGAACAGGATATTTCACCC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGATGAGTGACTACAAGGTGGAGATGGTAAACGATGGGATGAACGAGTTTAATGTGGAGTTCCATGGACCTCGGGATAgtaagtcctccacactgccctcttctcttcctcttgtctccctgtggttttcgtgcctctgtgtctctcggcttgtttgaaagagagatttcttcttgtt

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttctct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgtctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttttcgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtctct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttgttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agagaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tttcttc