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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgccattcctctctctcctctttccatctgaccgacacttcccttttctgtcactgcagGACTATCTACAACATGTGTACCCAAAAGCCTCCCCAGGACTACTCGCAGCAGCTCTATGATCGATACAGAGAAGCTTTTGAGGAGTACATCAATTCCATG

Basic information

species Selaginella moellendorffii
transcript EFJ12300
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ12300 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os05g05700.2 (Oryza sativa), 3'ss of exon 1
--------------------------------gtatgccattcctctctctcctctttccatctgaccgacacttcccttt---------tctgtca----ctgcagGACTATCTACAACATGTGTACCCAAAAGCCTCCCCAGGACTACTCGCAGCAGCTCTATGATCGATACAGAGAAGCTTTTGAGGAGTACATCAATTCCATG
                                || | || | |   || || |  | |    |||| | |   || ||            |||||      ||||||||| || ||||||||||| || || ||||| || || |||||||||||||||||||| ||    ||| | ||  | || |||||||||||||  ||||||
gtttcctcctcctcctcctcccgcccgctagggtttcccctccgattcgcttcgatctggtgctgatctagggtttccccccactccgtgtctgttgttgtctgcagGACGATATACAACATGTGCACGCAGAAGCCGCCGCACGACTACTCGCAGCAGCTCTACGACAAGTACCGGGAGTCATTCGAGGAGTACATCACCTCCATG

upper sequence: EFJ12300 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os05g05700.1 (Oryza sativa), 3'ss of exon 1
-------------------------------------------------------------------gtatgccattcctctctctcctctttccatctgaccgacacttcccttt---------tctgtca----ctgcagGACTATCTACAACATGTGTACCCAAAAGCCTCCCCAGGACTACTCGCAGCAGCTCTATGATCGATACAGAGAAGCTTTTGAGGAGTACATCAATTCCATG
                                                                   || | || | |   || || |  | |    |||| | |   || ||            |||||      ||||||||| || ||||||||||| || || ||||| || || |||||||||||||||||||| ||    ||| | ||  | || |||||||||||||  ||||||
gtacgtcccccgccgccgccgccgcctcctcctgggtttcctcctcctcctcctcccgcccgctagggtttcccctccgattcgcttcgatctggtgctgatctagggtttccccccactccgtgtctgttgttgtctgcagGACGATATACAACATGTGCACGCAGAAGCCGCCGCACGACTACTCGCAGCAGCTCTACGACAAGTACCGGGAGTCATTCGAGGAGTACATCACCTCCATG

upper sequence: EFJ12300 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os01g27150.1 (Oryza sativa), 3'ss of exon 1
------------------------------------gtatgccattcctctctctcctctttcc--atctgaccgacacttcccttttctgtcactgcagGACTATCTACAACATGTGTACCCAAAAGCCTCCCCAGGACTACTCGCAGCAGCTCTATGATCGATACAGAGAAGCTTTTGAGGAGTACATCAATTCCATG
                                     ||| | |||  | |||  ||      |  ||||||   |   |||   |   ||   || |||||| || ||||||||||| || || ||||| || || |||||||||||||||||||| ||    ||| | ||  | || |||||||||||||  ||||||
gtgcgtgtgcccgccctcctcgatttctctcccgatttattcgatttttttcttccccgcgcgctgatctgatttagggttcgtctccgtg---ctccagGACGATTTACAACATGTGCACGCAGAAGCCGCCGCACGACTACTCGCAGCAGCTCTACGAGAAGTACCGCGAGTCCTTCGAGGAGTACATCACGTCCATG

upper sequence: EFJ12300 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G166694_T01 (Zea mays), 3'ss of exon 1
------------------------------------------------------------------gtatgccattcctctct-ctcctctttccatctgaccgacacttcccttttctgtcactgcagGACTATCTACAACATGTGTACCCAAAAGCCTCCCCAGGACTACTCGCAGCAGCTCTATGATCGATACAGAGAAGCTTTTGAGGAGTACATCAATTCCATG
                                                                  || | |||   |  ||  || |  |     ||||| | |   ||    | | |||    ||||||| || ||||||||||| || || ||||| || ||||||||||| ||||||||||| ||    ||  | ||  | || ||||||||||||   ||||||
gtacgcctccctctcatctccctcgtcgccaccgccgccgctgtctccttctcggctgccgctagggtttcccacctcgatccgcttcgatccggttctgatctagggttttggtct-tgttgtcgcagGACGATATACAACATGTGCACGCAGAAGCCGCCGCAGGACTACTCACAGCAGCTCTACGACAAGTATCGGGAGTCGTTCGAGGAGTACATCGCCTCCATG

upper sequence: EFJ12300 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G166089_T01 (Zea mays), 3'ss of exon 1
--------------------------------------------------------------gtatgccattcctctctctcctctttcca--tctgaccgacacttcccttttctgtcactgcagGACTATCTACAACATGTGTACCCAAAAGCCTCCCCAGGACTACTCGCAGCAGCTCTATGATCGATACAGAGAAGCTTTTGAGGAGTACATCAATTCCATG
                                                              || |  ||   |  || | ||||  |||   ||||| | |   ||   |  |||      ||||||| || ||||||||||| || || ||||| || || |||||||||||||||||||| ||    ||  | ||  | || |||||||| ||||  ||||||
gtgcgcctccttctccccttactcctcctcgccgccaccgtctcctgcgcagcggccgcttggtttcacaccgcgatc-cgcctcgatccggttctgatctaggttttggtcctct--tgtcgcagGACGATATACAACATGTGCACGCAGAAGCCGCCGCACGACTACTCGCAGCAGCTCTACGACAAGTATCGGGAGTCGTTCGAGGAGTATATCACCTCCATG

upper sequence: EFJ12300 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA17G02800.1 (Glycine max), 3'ss of exon 1
-----------------------------------------------------------gtatgccattcctctctctcctctttccatctgaccgacacttcccttttctgtcactgcagGACTATCTACAACATGTGTACCCAAAAGCCTCCCCAGGACTACTCGCAGCAGCTCTATGATCGATACAGAGAAGCTTTTGAGGAGTACATCAATTCCATG
                                                            | |  | ||| |   | |  | | |  |||  | |     || ||||   |     |||||||| |||||||||||||| || ||||||||||| || ||||| || || || || |||||    || |  ||  ||||||| |||||||||   || | |
gtattcatctctatactctttgctctttttttttttttgtttttctttgagatctttctctctttctttctttcttttaatttctatatcccagcacttttttccttgattcgtgttgcagGACCATCTACAACATGTGCACTCAAAAGCCTCCTCATGACTATTCCCAACAACTTTATGACAAGTATAAGGAGTCTTTTGAAGAGTACATCGTATCGACG

upper sequence: EFJ12300 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: EDP03504 (Chlamydomonas reinhardtii), 3'ss of exon 2
------------------------------------------------------gtatgccattc-ctctctctcctctttccatctgaccgacacttcccttttctgtcac-tgcagGACTATCTACAACATGTGTACCCAAAAGCCTCCCCAGGACTACTCGCAGCAGCTCTATGATCGATACAGAGAAGCTTTTGAGGAGTACATCAATTCCATG
                                                       |  || | |  | | | ||   | |  |  ||  | |   ||| | |  |   || | | ||||||||||||||||||||| ||||| ||||| || || ||||| ||| ||||||| ||       ||||| || || ||  |  ||||||| ||    | |
gtaagttgtgttggtctgggcatggttggggccgcgccacaccctgccggtgccttccgcgactgacccacgcttgccctcgcgcctctcggtgccttgcgtccttcttcgccttcagGACTATCTACAACATGTGCACCCAGAAGCCGCCGCACGACTATTCGGAGCAGCTGTACAGCAAGTACAGGGACGCGTTCAACAAGTACATAAACGAGAAG

upper sequence: EFJ12300 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S144_158V6.1 (Physcomitrella patens), 3'ss of exon 1
----------------------------------gtatgccattcctctctctcctctttccatctgaccgacactt--ccctt--ttctgtcactgcagGACTATCTACAACATGTGTACCCAAAAGCCTCCCCAGGACTACTCGCAGCAGCTCTATGATCGATACAGAGAAGCTTTTGAGGAGTACATCAATTCCATG
                                     |   | |  ||| ||   |  ||| ||    |  |   ||   ||||  | ||||   | ||| || || |||||||||||||| || |||||||| ||||| ||||| ||||| ||||||||  ||||||| ||  | || || || |||||||| |||| |
gatgatatcttttattatcaatattattttagaaaattattactgttctttcaattaattcaattctccaaatttttggtccttaatgctgtttgtacagAACCATATACAACATGTGTACGCAGAAGCCTCCTCAGGATTACTCTCAGCAACTCTATGACAGATACAGGGAGTCCTTCGAAGACTACATCAAATCCAAG

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: 34 (upstream exon), 35 (downstream exon)
Score: 51

GATGGGCGTTCATGCAGAAGGGCATCACCAAGTTGATCAATCTGCTCGAGGGAGTGGCGGAGCAGCAATTCAACTCGGAGGAGTATGCCATGCTTTACACgtatgccatt ... gtcactgcagGACTATCTACAACATGTGTACCCAAAAGCCTCCCCAGGACTACTCGCAGCAGCTCTATGATCGATACAGAGAAGCTTTTGAGGAGTACATCAATTCCATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcctctctctcctctttccatctgaccgacacttcccttttctgtcactgcagGACTATCTACAACATGTGTACCCAAAAGCCTCCCCAGGACTACTCGCAGCAGCTCTATGATCGATACAGAGAAGCTTTTGAGGAGTACATCAATTCCATG
                     atctgac  putative branch site (score: 51)
                                 cttcccttttctgtca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgccattcctctctctcctctttccatctgaccgacacttcccttttctgtcactgcagGACTATCTACAACATGTGTACCCAAAAGCCTCCCCAGGACTACTCGCAGCAGCTCTATGATCGATACAGAGAAGCTTTTGAGGAGTACATCAATTCCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG