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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttcgtcgtagttttcgttttcttctagctgttcttacgaagactttcagGGACATGATATTCTCATGGCTACGATGCTTAATGGTGCTGCGATCATGGACGGCGCTTTGCTTTTGATTGCCAGCAACGAAAGCTGCCCGCAGCCGCAAA

Basic information

species Selaginella moellendorffii
transcript EFJ14781
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ14781 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: LOC_Os12g07740.1 (Oryza sativa), 3'ss of exon 5
---------------------------------------gtaagttcgtcgtagttttcgttttcttctagctg------ttcttacgaagacttt-cagGGACATGATATTCTCATGGCTACGATGCTTAATGGTGCTGCGATCATGGACGGCGCTTTGCTTTTGATTGCCAGCAACGAAAGCTGCCCGCAGCCGCAAA
                                          | |  ||  | |||| | |||  |     |||      | | ||      |||  |||||||| ||||||||||||||||||||||||||||| ||||| |||||||| || || |||||| |||| ||    || ||||| ||||| || || || |
tgtaaaatgctatcatttcaacttcttttatgggccactaagactaggtattggtttacatttgttgaagcctgagaaattacctatttcctcttaacagGGACACGATATTCTCATGGCTACGATGCTTAATGGAGCTGCTATCATGGATGGAGCATTGCTTCTGATAGCAGCAAATGAAAGTTGCCCACAACCCCAGA

upper sequence: EFJ14781 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: LOC_Os12g41400.1 (Oryza sativa), 3'ss of exon 5
------------------------------------------gtaagttcgtcgt-agttttcgttttct-tctagc-tgttcttacgaagacttt-cagGGACATGATATTCTCATGGCTACGATGCTTAATGGTGCTGCGATCATGGACGGCGCTTTGCTTTTGATTGCCAGCAACGAAAGCTGCCCGCAGCCGCAAA
                                            ||||   |  | ||      ||   | | ||     | | ||      |||  ||||| ||||| |||||||||||||| ||||||||||| ||||| |||||||| || || ||||||||||| ||   ||| ||||||||||| || || ||||
ttttatgggtcactgcatattgttttttattttttgatctctcgaagtcaataatgagaaaatattacatatgtaatacatacctatttcttcttaacagGGGCATGACATTCTCATGGCTACAATGCTTAATGGAGCTGCTATCATGGATGGAGCATTGCTTTTGATAGCAGCCAATGAAAGCTGCCCACAACCCCAAA

upper sequence: EFJ14781 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GRMZM2G117900_T02 (Zea mays), 3'ss of exon 5
----------------------------------------------gtaagttcgtcgtagttttcgttttcttctagctgttcttacgaagactttcagGGACATGATATTCTCATGGCTACGATGCTTAATGGTGCTGCGATCATGGACGGCGCTTTGCTTTTGATTGCCAGCAACGAAAGCTGCCCGCAGCCGCAAA
                                               | |     | | |  |     | | ||  | |  | | ||           ||||||| || |||||||||||||| ||||||||||| ||||| |||||||| || ||| | |||||||| ||    || ||||| || || ||||| || |
aaaatggttatcttaatttctttgacatttcatttgatattgatcaattatgatatagaaaataattgtatgtttcaacaatacctatctccttgaatagGGACACGACATTCTCATGGCTACAATGCTTAATGGAGCTGCTATCATGGATGGAGCTCTTCTTTTGATCGCAGCAAATGAAAGTTGTCCACAGCCTCAGA

upper sequence: EFJ14781 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GRMZM2G107654_T01 (Zea mays), 3'ss of exon 5
-------------------------------------------gtaagttcgtcgtagttttcgttttcttctagctgttcttacgaagacttt---cagGGACATGATATTCTCATGGCTACGATGCTTAATGGTGCTGCGATCATGGACGGCGCTTTGCTTTTGATTGCCAGCAACGAAAGCTGCCCGCAGCCGCAAA
                                            | | || |||  |       |  |  | |   |     |||  |  | ||    ||||||| || |||||||||||||| ||||||||||| ||||| |||||||| || ||| | |||||||| ||    || ||||| || || ||||| || |
gaataattgtatgtttcaacaacacctatctccttgaatagagatgaatttgtctaacaggaaataattgtatgtttaacaatacctattccttgaatagGGACACGACATTCTCATGGCTACAATGCTTAATGGAGCTGCTATCATGGATGGAGCTCTTCTTTTGATCGCAGCAAATGAAAGTTGTCCACAGCCCCAGA

upper sequence: EFJ14781 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA15G40750.1 (Glycine max), 3'ss of exon 5
--------------------------------------------gtaagttcgtcgtagttttcgttttcttctagctgtt--cttacgaagactttcagGGACATGATATTCTCATGGCTACGATGCTTAATGGTGCTGCGATCATGGACGGCGCTTTGCTTTTGATTGCCAGCAACGAAAGCTGCCCGCAGCCGCAAA
                                             |   || ||  |    |  || |  |  | | | ||   || | ||    | ||||||||||||||||| |||||||| ||||||||||| || || |||||||| || ||||||||  | |||||   ||| ||||||||||| || || ||||
ataattacaggtcttcaatcaaatgctaaatcattgaacatatattttttttgttttgacatctgtgtgatatttgtttttacttttccaatttctgcagGGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGATGGAGCTTTGCTACTCATTGCTGCCAATGAAAGCTGCCCACAACCACAAA

upper sequence: EFJ14781 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA08G18240.1 (Glycine max), 3'ss of exon 5
-----------------------------------------gtaagttcgtcgtagttttcgttttcttctagctgttctta-----cgaagactttcagGGACATGATATTCTCATGGCTACGATGCTTAATGGTGCTGCGATCATGGACGGCGCTTTGCTTTTGATTGCCAGCAACGAAAGCTGCCCGCAGCCGCAAA
                                           | ||      |    | |    || | |   |||| |||     | ||    |  |||||||||||||||| |||||||| ||||||||||| || || |||||||| || || |||||  | || ||    || ||||||||||| || || ||||
ttccatatttttatgagtatcctttttataagcaggtaattacaggtctccaatcaaatgctaaatcatttgtttgtttttacttttccaatttctgtagGGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGATGGAGCGTTGCTACTCATAGCTGCTAATGAAAGCTGCCCACAACCACAAA

upper sequence: EFJ14781 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: AT1G04170.1 (Arabidopsis thaliana), 3'ss of exon 5
----------------------------------------------gtaagttcgtcgtagttttcgttttcttctagctgttcttacgaagactttcagGGACATGATATTCTCATGGCTACGATGCTTAATGGTGCTGCGATCATGGACGGCGCTTTGCTTTTGATTGCCAGCAACGAAAGCTGCCCGCAGCCGCAAA
                                               |    |  ||     ||   | || ||  |  | |||||         ||||||| || |||||||||||||| || ||||||||||| || || |||||||| || ||  | ||||| || ||    || ||||  || || || || ||||
gagtgagggttgatggagaagtattcattgatgtttccatcttttgcttttcttatctctacttcattcttgttgaatgtattcttgttctattcttcagGGTCACGATATTCTCATGGCAACAATGCTTAATGGAGCAGCCATCATGGATGGTGCACTACTTTTAATCGCTGCAAATGAAACTTGTCCACAACCACAAA

upper sequence: EFJ14781 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: Vv13s0074g00310.t01 (Vitis vinifera), 3'ss of exon 5
--------------------------------------------------gtaagttcgtcgtagttttc-gttttcttctagctgttcttacgaagactttcagGGACATGATATTCTCATGGCTACGATGCTTAATGGTGCTGCGATCATGGACGGCGCTTTGCTTTTGATTGCCAGCAACGAAAGCTGCCCGCAGCCGCAAA
                                                  |  ||| |     ||||||   | || ||||   |  | || | |     |  |||| |||||||||||||||||||| ||||||||||| || || || ||||| || || || ||| | || ||   |||||||||||| || ||||||||||
ctaaagacttgactttaaggttctggatgtccaggcttatatgcctggttgagagtccagtaaagttttttatgtttttctttttcatttttcaa-----tctagGGTCATGATATTCTCATGGCTACAATGCTTAATGGAGCAGCAATTATGGATGGGGCATTACTTCTTATAGCTGCCAACGAAAGCTGTCCACAGCCGCAAA

upper sequence: EFJ14781 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: Vv10s0042g01220.t01 (Vitis vinifera), 3'ss of exon 4
---------------------------------------------gtaagttcgtcgtagttttcgttttct-tctagctgttcttacgaagactttcagGGACATGATATTCTCATGGCTACGATGCTTAATGGTGCTGCGATCATGGACGGCGCTTTGCTTTTGATTGCCAGCAACGAAAGCTGCCCGCAGCCGCAAA
                                                | |   | ||  ||||  |||| | | |  || || | |      | |  |||| |||||||||||||||||||| ||||||||||| || || || ||||| || || || ||| | || ||   ||| |||||||| || ||||||||||
gaaggtggctttaagattctggatgtccaggcctaaatgcctgggtctactgtctagtgattttttttttatgtttttcttttttcatcttcccatctagGGGCATGATATTCTCATGGCTACAATGCTTAATGGAGCGGCAATTATGGATGGGGCATTACTTCTTATAGCTGCCAATGAAAGCTGTCCACAGCCGCAAA

upper sequence: EFJ14781 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: PP1S207_94V6.1 (Physcomitrella patens), 3'ss of exon 4
------------------------------------------gtaagttcgtcgtagttttcgttttcttctagct----gttcttacgaagactttcagGGACATGATATTCTCATGGCTACGATGCTTAATGGTGCTGCGATCATGGACGGCGCTTTGCTTTTGATTGCCAGCAACGAAAGCTGCCCGCAGCCGCAAA
                                          |        ||||  | ||  ||||  ||  | |     |  ||  |     || |||||||| ||||||||||||||||| ||||||||||| ||||| || ||||| || ||||| ||||||||||||||||| || || ||||| ||||| ||||
aattcgactacacacatcacttaatctgagggcttatgggaagcggtactttcgtgttcttgtttttaatccggattgaaatgtttgtgtttgtttgcagGGACACGATATTCTCATGGCTACTATGCTTAATGGAGCTGCTATTATGGATGGTGCTTTACTTTTGATTGCCAGCAATGAGAGTTGCCCCCAGCCCCAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaagttcgtcgtagttttcgttttcttctagctgttcttacgaagactttcagGGACATGATATTCTCATGGCTACGATGCTTAATGGTGCTGCGATCATGGACGGCGCTTTGCTTTTGATTGCCAGCAACGAAAGCTGCCCGCAGCCGCAAA
                                    ttcttac  putative branch site (score: 2)
                                                ctttc  putative PPT
             tagtttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttcgtcgtagttttcgttttcttctagctgttcttacgaagactttcagGGACATGATATTCTCATGGCTACGATGCTTAATGGTGCTGCGATCATGGACGGCGCTTTGCTTTTGATTGCCAGCAACGAAAGCTGCCCGCAGCCGCAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC