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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcacatttttccttcttgaccggtgtaagaacttgccatgtccagGTGATGACAGCATTCATGCCACCGCCACCAGCAGCAACGTTCCTGGCTTTTCACCCTCAAGACAACAATATCATAGCGATTGGAATGGAAGATTCTACAA

Basic information

species Selaginella moellendorffii
transcript EFJ32018
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ32018 (Selaginella moellendorffii), 3'ss of exon 20
lower sequence: LOC_Os01g15020.2 (Oryza sativa), 3'ss of exon 20
----------------------gtatgcacatttttccttcttgaccggtgtaa--gaacttgccatgtccagGTGATGACAGCATTCATGCCACCGCCACCAGCAGCAACGTTCCTGGCTTTTCACCCTCAAGACAACAATATCATAGCGATTGGAATGGAAGATTCTACAA
                      | ||  | | ||     |   |     | |||     ||| |    | |||||||||||| ||||||||||||| || |||||| |||| ||  | || ||||||||||||||||| ||||||||||| ||||||||||||||||| || |
gtaaatgctcaatatcttttttggataaatacttcaaaattcaggaaattttaattatgcttccttcatgcagGTGATGACAACATTCATGCCACCACCTCCAGCATCAACCTTTTTAGCATTTCACCCTCAAGACAATAATATCATAGCAATTGGAATGGAAGATTCAACCA

upper sequence: EFJ32018 (Selaginella moellendorffii), 3'ss of exon 20
lower sequence: LOC_Os08g06480.1 (Oryza sativa), 3'ss of exon 20
------------------------------------------------------------------------gtatgcacatttttccttcttgaccggtg----taagaacttgccatgtc----cagGTGATGACAGCATTCATGCCACCGCCACCAGCAGCAACGTTCCTGGCTTTTCACCCTCAAGACAACAATATCATAGCGATTGGAATGGAAGATTCTACAA
                                                                         ||   | || | |  ||||  |   |||    ||| |  ||   || |     ||||| |||||  | |||||| |||| ||||| || ||||| ||||| || || |||||||||||||| |||||||| || ||||||||||| || ||||| |
gtatatgatctcttcggtgtgtagcacaatcaattgttattaccctagagcataggtcatgagttactttccataaaaatatgtgttattctatagttgtgacgttaaaatttttgaattttttcacagGTCATGACTACTTTCATGGCACCTCCACCTGCTGCAACTTTCCTTGCATTCCACCCTCAAGACAATAATATCATTGCTATTGGAATGGAGGACTCTACCA

upper sequence: EFJ32018 (Selaginella moellendorffii), 3'ss of exon 20
lower sequence: LOC_Os03g14980.1 (Oryza sativa), 3'ss of exon 21
-------------gtatgcacatt-tttccttcttgaccggtgtaagaactt--gccatgtc-------cagGTGATGACAGCATTCATGCCACCGCCACCAGCAGCAACGTTCCTGGCTTTTCACCCTCAAGACAACAATATCATAGCGATTGGAATGGAAGATTCTACAA
              |||    ||| |||   ||||     |     ||||||    ||| |        |||  ||||||| | || ||||| ||||| || || |||||||| || ||||| || |||||||| ||||| || ||||| ||||||||||| || || || |
gttagttacaagtttatttctattgtttgtctcttatgtagaaattgaactttaatcatatggtgactgcagACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTCCATCCTCAAGATAACAACATTATAGCAATTGGAATGGATGACTCAACCA

upper sequence: EFJ32018 (Selaginella moellendorffii), 3'ss of exon 20
lower sequence: GRMZM2G316967_T01 (Zea mays), 3'ss of exon 20
-----------------------------------gtatgc-acatttttccttcttgaccggtgtaagaacttgccatg---------------tccagGTGATGACAGCATTCATGCCACCGCCACCAGCAGCAACGTTCCTGGCTTTTCACCCTCAAGACAACAATATCATAGCGATTGGAATGGAAGATTCTACAA
                                    || ||   ||| |    ||||||  ||    | |  | ||| |                | |||||||||||| ||||||||||||| ||||||||| |||| ||  | || ||||||||||||||||| || |||||||| || |||||||||||||| || |
atctataagcaggtcattagatgcttatataatccataagctggattatataatcttgagaggaaacaaacatggccttaatcatgcatccttcttgcagGTGATGACAACATTCATGCCACCTCCACCAGCATCAACATTTTTAGCATTTCACCCTCAAGACAATAACATCATAGCAATAGGAATGGAAGATTCAACCA

upper sequence: EFJ32018 (Selaginella moellendorffii), 3'ss of exon 20
lower sequence: GRMZM2G416836_T01 (Zea mays), 3'ss of exon 18
----------------------gtatgcacatttttccttcttgaccggtgtaa--gaacttgccatgtccagGTGATGACAGCATTCATGCCACCGCCACCAGCAGCAACGTTCCTGGCTTTTCACCCTCAAGACAACAATATCATAGCGATTGGAATGGAAGATTCTACAA
                        ||| |  |||    ||       | | |||     | | |    | |||||| ||||| |||||||||| || ||||||||| |||| ||  | || |||||||||||||| || || |||||||| || |||||||||||||| || |
gtaatgtctaactgttttattctgatgaaattttcagatttcaagaagatttaatcatgcatccttcatgcagGTGCTGACAACATTCATGCCGCCACCACCAGCATCAACATTTTTAGCATTTCACCCTCAAGATAATAACATCATAGCAATAGGAATGGAAGATTCAACCA

upper sequence: EFJ32018 (Selaginella moellendorffii), 3'ss of exon 20
lower sequence: GRMZM2G042992_T01 (Zea mays), 3'ss of exon 20
---------------------------------------------------------------------------------------------------------------gtatgcacatttttcc----ttcttgacc-ggtgtaagaacttgccatgtc---cagGTGATGACAGCATTCATGCCACCGCCACCAGCAGCAACGTTCCTGGCTTTTCACCCTCAAGACAACAATATCATAGCGATTGGAATGGAAGATTCTACAA
                                                                                                                |   | |||  || |    |||||  ||    |   | |  ||  || ||   ||||| |||||  | |||||| |||| ||||| || ||||| ||||| || || ||||| ||||| || |||||||| || ||||||||||| || ||||| |
gtagatgtccttttcagcgcctcaccataattttgttcgtctcatagatgtccatgagtcaatggtagttgtagtttgctgctgatagcttcagataaaaattgttataccatgatcgcatcattgccaatttcttaccctaaagcttggatctgggatctctgacagGTCATGACTACTTTCATGGCACCTCCACCTGCTGCAACTTTCCTTGCATTCCACCCACAAGATAATAATATCATCGCCATTGGAATGGAGGACTCTACCA

upper sequence: EFJ32018 (Selaginella moellendorffii), 3'ss of exon 20
lower sequence: GLYMA19G41840.1 (Glycine max), 3'ss of exon 20
------------------------------------gtatgcacatttttccttcttgaccggtgtaagaacttgccatgtccagGTGATGACAGCATTCATGCCACCGCCACCAGCAGCAACGTTCCTGGCTTTTCACCCTCAAGACAACAATATCATAGCGATTGGAATGGAAGATTCTACAA
                                       | |   |  |   || |         || |   |         ||||| |||||| ||||||||||||| || || ||  | || || |||||||| ||||||||||| ||||| |||||||| ||||| ||||| ||||| ||||
gtacatgtccagagatacaagtacaaccattacattccgttccgctgctatgttttctgtttacttatggtttattttctatcagGTAATGACAACATTCATGCCACCACCCCCTGCCTCTACCTTTCTGGCTTTCCACCCTCAAGATAACAACATCATAGCCATTGGGATGGAGGATTCAACAA

upper sequence: EFJ32018 (Selaginella moellendorffii), 3'ss of exon 20
lower sequence: GLYMA03G39290.1 (Glycine max), 3'ss of exon 21
----------------------------gtatgcacatttttccttcttgaccggtgtaagaacttgccatgt-ccagGTGATGACAGCATTCATGCCACCGCCACCAGCAGCAACGTTCCTGGCTTTTCACCCTCAAGACAACAATATCATAGCGATTGGAATGGAAGATTCTACAA
                             |    |||       |  ||      |        ||    | |  ||||| |||||| ||||||||||||| ||||| ||  | || || || ||||| ||||||||||| || || |||||||| ||||| ||||| ||||| ||||
gtacatgtccagagatacaaccatgacattccatacagccgcaatgtttactgtatacttaggtttattttctatcagGTAATGACAACATTCATGCCACCACCACCCGCCTCTACCTTTCTAGCTTTCCACCCTCAAGATAATAACATCATAGCCATTGGGATGGAGGATTCAACAA

upper sequence: EFJ32018 (Selaginella moellendorffii), 3'ss of exon 20
lower sequence: GLYMA13G22720.1 (Glycine max), 3'ss of exon 21
------------------------------------------------------gtatgcacatttttccttc-ttgaccggtgtaagaacttgccatgtccagGTGATGACAGCATTCATGCCACCGCCACCAGCAGCAACGTTCCTGGCTTTTCACCCTCAAGACAACAATATCATAGCGATTGGAATGGAAGATTCTACAA
                                                         || | ||| |   | | || |    |||  ||| ||  ||  | |||   |||||| | ||||||||||| |||||||| || || || || || ||||| ||||||||||||||||| || || ||||| ||||| || ||| | |
cttttgatggtttagtttagtatttccagacctcagtatcattttttttgttgcaattgtatattgtggttacattaatttctgt--gaattt--caactgcagACAATGACAACTTTCATGCCACCTCCACCAGCTGCTACATTTCTTGCATTTCATCCTCAAGACAACAATATTATTGCTATTGGCATGGAGGACTCTTCCA

upper sequence: EFJ32018 (Selaginella moellendorffii), 3'ss of exon 20
lower sequence: GLYMA17G12110.2 (Glycine max), 3'ss of exon 21
------------------------------------------------------gtatgcacatttttccttc-ttgaccggtgtaagaacttgccatgtccagGTGATGACAGCATTCATGCCACCGCCACCAGCAGCAACGTTCCTGGCTTTTCACCCTCAAGACAACAATATCATAGCGATTGGAATGGAAGATTCTACAA
                                                         || | ||| |   | | || |    |||  ||| ||  ||  | |||   |||||| | ||||||||||| |||||||| || || || || || ||||| ||||||||||| ||||| || || ||||| ||||| || ||| | |
ccttttgatggtttggtttagtatttccagaccttagtatcatttttttgttgcaattgtatattgtggttacattaatttctgt--gaattt--caactgcagACAATGACAACTTTCATGCCACCTCCACCAGCTGCGACATTTCTTGCATTTCATCCTCAAGACAATAATATTATTGCTATTGGCATGGAGGACTCTTCCA

upper sequence: EFJ32018 (Selaginella moellendorffii), 3'ss of exon 20
lower sequence: AT5G27030.1 (Arabidopsis thaliana), 3'ss of exon 20
-----------------------------------------------------------------------gtatgcacatttttccttcttgac--cggtgtaagaacttgccatgtc-cagGTGATGACAGCATTCATGCCACCGCCACCAGCAGCAACGTTCCTGGCTTTTCACCCTCAAGACAACAATATCATAGCGATTGGAATGGAAGATTCTACAA
                                                                       |||  | | |||     |  | |   |     || ||||       |   ||||||||||| |||||||||| || ||||||||| |||||||  |||| || || ||||| ||||| ||  |||| || |||||||||||||| ||||| |
gtatatattatctatatgaacttaaaaaaagccacaagatttctaactgaaaatgttctcacactaatctagtaaactcttttggttgttctaatttccacaaaaaaactattggccttatagGTGATGACAACATTCATGCCGCCTCCACCAGCATCAACGTTTTTGGCGTTCCATCCTCAGGACAATAACGTCATCGCCATTGGAATGGAAGACTCTACGA

upper sequence: EFJ32018 (Selaginella moellendorffii), 3'ss of exon 20
lower sequence: AT3G16830.1 (Arabidopsis thaliana), 3'ss of exon 20
------------------------------------------------------------------gtatgcacatttttccttcttgaccggtgtaaga---acttgccat----gtccagGTGATGACAGCATTCATGCCACCGCCACCAGCAGCAACGTTCCTGGCTTTTCACCCTCAAGACAACAATATCATAGCGATTGGAATGGAAGATTCTACAA
                                                                    ||| |  | |||   |  |   ||  |  | |   | ||  |      || ||||| |||||| | ||||||||||||||||||||  |||| ||| |||| ||||| |||||||| || ||||| || || || || ||||| || || |  |
gtaagcagcttaatccaactttttctgttctcgggagcatctcctaaatactgatacctcaggagctaatgaaactatttgagtaatatgcgaagctaaatgcatttttccctttcgtgcagGTAATGACAACTTTCATGCCACCGCCACCAGCTTCAACTTTCTTGGCATTTCATCCTCAAGATAATAATATTATTGCAATCGGGATGGAGGACTCGAGTA

upper sequence: EFJ32018 (Selaginella moellendorffii), 3'ss of exon 20
lower sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 20
-----------------------gtatgcacat----ttttccttcttgaccggtgtaa---gaacttgc---catgtccagGTGATGACAGCATTCATGCCACCGCCACCAGCAGCAACGTTCCTGGCTTTTCACCCTCAAGACAACAATATCATAGCGATTGGAATGGAAGATTCTACAA
                       | ||   |||    |||  | | |  |  ||| ||    ||  ||||   ||| |  |||| |||||| |||||||| |||| || || ||  |||| ||||| || || || ||||||||||| || |||||||| || |||||||| |||||||| |
gtatgtctaaacatcacagttttgcatcttcatcaaatttggcatttgaaatggtttagcatgatgttgctttcatttgtagGTAATGACAACATTCATGTCACCTCCCCCTGCTTCAACCTTCCTAGCCTTCCATCCTCAAGACAATAACATCATAGCCATAGGAATGGAGGATTCTACCA

upper sequence: EFJ32018 (Selaginella moellendorffii), 3'ss of exon 20
lower sequence: Vv11s0016g05620.t01 (Vitis vinifera), 3'ss of exon 21
---------------------------------------------------gtatgcacatttttccttcttgaccggtgtaagaacttgccatgtccagGTGATGACAGCATTCATGCCACCGCCACCAGCAGCAACGTTCCTGGCTTTTCACCCTCAAGACAACAATATCATAGCGATTGGAATGGAAGATTCTACAA
                                                                                                  ||   |||||| |||| ||||| || |||||||||||||| ||  |||| || || ||||||||||| |||||||| || || || ||||| || ||| | |
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnagACCATGACAACATTTATGCCCCCACCACCAGCAGCAACATTTTTGGCATTCCATCCTCAAGACAATAATATCATTGCCATAGGCATGGAGGACTCTTCTA

upper sequence: EFJ32018 (Selaginella moellendorffii), 3'ss of exon 20
lower sequence: PP1S99_260V6.1 (Physcomitrella patens), 3'ss of exon 20
-----------------------------------------------------------------------------gtatgcacatttttccttcttga--ccggtgtaagaacttgccat---gtccagGTGATGACAGCATTCATGCCACCGCCACCAGCAGCAACGTTCCTGGCTTTTCACCCTCAAGACAACAATATCATAGCGATTGGAATGGAAGATTCTACAA
                                                                              | |  ||| || ||  | || |  | |  |       | |   |      ||||| |||||  ||||||||||||| || |||||||| || || || || ||||| || ||||||||||||||||| || || |||||||||||||| ||||
gtaaagtccgcgaatcatgaggagtctattttattctttgttctaataatatggtgagaagcgttttgtttttggtaattttgacagttgtcaatttttattctgacgcttttcttcggattttgactcagGTCATGACGACATTCATGCCACCACCTCCAGCAGCTACTTTTCTTGCATTTCATCCACAAGACAACAATATCATTGCTATCGGAATGGAAGATTCGACAA

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: 32 (upstream exon), 28 (downstream exon)
Score: 12

GGAAGAAGCTGTGCCTTGCATTGCCTTGTCAAAGAATGACTCTTACGTGATGTCCGCTTCGGGAGGCAAAGTTTCTCTATTTAATATGATGACTTTCAAGgtatgcacat ... ccatgtccagGTGATGACAGCATTCATGCCACCGCCACCAGCAGCAACGTTCCTGGCTTTTCACCCTCAAGACAACAATATCATAGCGATTGGAATGGAAGATTCTACAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatgcacatttttccttcttgaccggtgtaagaacttgccatgtccagGTGATGACAGCATTCATGCCACCGCCACCAGCAGCAACGTTCCTGGCTTTTCACCCTCAAGACAACAATATCATAGCGATTGGAATGGAAGATTCTACAA
                       tcttgac  putative branch site (score: 12)
                  acattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcacatttttccttcttgaccggtgtaagaacttgccatgtccagGTGATGACAGCATTCATGCCACCGCCACCAGCAGCAACGTTCCTGGCTTTTCACCCTCAAGACAACAATATCATAGCGATTGGAATGGAAGATTCTACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA