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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttgtgatagttttcattgaatttatattcttagttgtttggctggtttcagGAACAGGAGAAAGCTAACCTCGCAACTGATACTGGACTCGACCAGAAGCAAATTAACAACTGGTTTATCAACCAGAGAAAGCGTCATTGGAATCCTTCAG

Basic information

species Selaginella moellendorffii
transcript EFJ07540
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ07541 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: LOC_Os03g56110.2 (Oryza sativa), 3'ss of exon 4
-------------------------------------gtatgttgtg-atagttttcattgaatttatattcttagttgtttggctggtttc--agGAACAGGAGA-----AAGCTAACCTCGCAACTGAT-ACTGGACTCGACCAGAAGCAAATTAACAACTGGTTTATCAACCAGAGAAAGCGTCATTGGAATCCTTCAG
                                       || || || |     || | |   || | | |    |   |||    ||||    | || |||||||     ||| | ||   |   | ||  || || || ||||||||||| || ||||||||||| ||||||||||| ||||| || ||||| ||  |  
gtacgcacgcatcacatcccgtttgatcaattcaaccacattttctgcaccaaattaactcgtttgaaaatgcgtgaaatttacggggttgtgtatgagcagGAGATGGAGAAGATGACGCTGGCGCAGACGACGGGGCTGGACCAGAAGCAGATCAACAACTGGTTCATCAACCAGAGGAAGCGGCACTGGAAGCCGACGC

upper sequence: EFJ07541 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: LOC_Os05g03884.1 (Oryza sativa), 3'ss of exon 4
-----------------------------gtatgttgtgatagttttcattgaatttatattcttagtt--gtttggctggtttcagGAACAGGAGAAAGCTAACCTCGCAACTGATACTGGACTCGACCAGAAGCAAATTAACAACTGGTTTATCAACCAGAGAAAGCGTCATTGGAATCCTTCAG
                               |        ||     || |||  |   | |||   ||    |||     |  |||||| |||| || |  |  || ||  |    ||||| ||||||| |||||| || ||||||||||| ||||||||||| ||| | || ||||| || || |
gtaatgtcgcgaaaacgccttttcgacacacaaaagcctctaacccacactgacctgggactctgtcttccaattgatctttcacagGAAGAGGATAAGGTGAGGCTGGCCGCGATGACTGGCCTCGACCCGAAGCAGATCAACAACTGGTTCATCAACCAGAGGAAGAGGCACTGGAAGCCATCGG

upper sequence: EFJ07541 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: LOC_Os03g56140.2 (Oryza sativa), 3'ss of exon 4
--------------------------------------------------gtatgttgtgatagttttcattgaat----ttatattcttagttgtttggctg-gttt---cagGAACAGGAGAAAGCTAACCTCGCAACTGATACTGGACTCGACCAGAAGCAAATTAACAACTGGTTTATCAACCAGAGAAAGCGTCATTGGAATCCTTCAG
                                                   |         | | | | ||  ||     | |  ||||  | |||     || || |   |||||   ||||||    |  || ||       || || || ||||||||||| || | ||||||||| ||||||||||| ||||| || ||||| ||  |  
gtacgcacgcatatatatgcttcccatttgatcaattcaaccacatttttctgcaccaaactcgatcttatgaaaatgcgtgaacttctcgggtgtacatgtgtgtatgagcagGAGGTGGAGAAGATGACGCTGGCGCAGACGACGGGGCTGGACCAGAAGCAGATCAGCAACTGGTTCATCAACCAGAGGAAGCGGCACTGGAAGCCGACGC

upper sequence: EFJ07541 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: LOC_Os03g51690.3 (Oryza sativa), 3'ss of exon 3
-----------------------------gtatgttgtgatagttttcatt-----gaatttatattcttagttgtttggctggttt-ca---gGAACAGGAGA-----AAGCTAAC-CTCGCAACTGATACTGGACTCGACCAGAAGCAAATTAACAACTGGTTTATCAACCAGAGAAAGCGTCATTGGAATCCTTCAG
                               || |  ||  || | ||        || ||  |  || | ||| | |  ||  ||| ||   ||| |||||||     ||| |  | || ||       || || || |||| |||||| || ||||||||||| ||||||||||| ||||| || ||||| || || |
tagttatctactaccatttctgtgctataaaatataatgcaagctatcgccatgcagatttcctgatcatggttatgtatctattttacatgtggagcagGAGAGTCAGAAGGTGGCACTGGCGGAGTCGACGGGGCTGGACCTGAAGCAGATCAACAACTGGTTCATCAACCAGAGGAAGCGGCACTGGAAGCCCTCCG

upper sequence: EFJ07541 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GRMZM2G087741_T01 (Zea mays), 3'ss of exon 4
-----------------------------------------gtatgttgtgatagttt--tcattgaatttatattcttagttgtttggctggtttcagGAACAGGAGAAAGCTAACCTCGCAACTGATACTGGACTCGACCAGAAGCAAATTAACAACTGGTTTATCAACCAGAGAAAGCGTCATTGGAATCCTTCAG
                                            ||  |    | | |   || |||  | ||| ||| |  || |  |||| |  |||||  | || || |  |  |||||| |    || || ||||||| |||||| || ||||||||||| ||||||||||| ||| | |||||||| || || |
gtatgtaggcgctggccattttttttcaccaaacaatctgaacctgcaggtgcactgtgaccagtga-ctgataatctga--tgctgtgctgctgacagGAGGAAGACAAGGTGAGGCTCGCAGCAATGACCGGTCTCGACCCGAAGCAGATCAACAACTGGTTCATCAACCAGAGGAAGAGGCATTGGAAGCCATCTG

upper sequence: EFJ07541 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GRMZM5G832409_T01 (Zea mays), 3'ss of exon 4
-----------------------------------------------------gtatgttgtgatagttttcattgaatttatattcttagttgtttggctggttt--cagGAACAGGAGAAAGCTAACCTCGCAACTGATACTGGACTCGACCAGAAGCAAATTAACAACTGGTTTATCAACCAGAGAAAGCGTCATTGGAATCCTTCAG
                                                             |   |  | | || |   || |  ||  |  |   |  || |||   |||||  |||| || |  |  || ||  |    ||||| || |||| |||||| || ||||||||||| ||||||||| | ||||| |||||||| || || |
gtaacatgctcacagcacacacctgtgctgtgactgatctttcctcgctttgaacgaacaatcgaatctgtgatcggcattttgctcaga-ctaagtatcttgttcggcagGAGGAGGATAAGGTGAGGCTGGCGGCCATGACTGGGCTGGACCCGAAGCAGATCAACAACTGGTTCATCAACCAGCGGAAGCGGCATTGGAAGCCGTCGG

upper sequence: EFJ07541 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GRMZM2G028041_T01 (Zea mays), 3'ss of exon 4
----------------------------------------gtatgttgtgatagttttcattgaatttatattcttagttgtttg--gctggttt---cagGAACAGGAGAAAGCTAACCTCGCAACTGATACTGGACTCGACCAGAAGCAAATTAACAACTGGTTTATCAACCAGAGAAAGCGTCATTGGAATCCTTCAG
                                         |    ||    ||  |  |||| ||  | ||| ||| |  |||   | | |||    |||||   ||||||   |   ||||||      || || || ||||||||||| || ||||||||||| ||||||||||| || || || ||||| || || |
ttccgtgacctttacgcgatgttaacactgcttcagaaccatgaactgaagcagaatgtattgtata-acattgttactgatttaatgtttgttcgagcagGAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAGATCAACAACTGGTTCATCAACCAGAGGAAACGGCACTGGAAGCCATCGG

upper sequence: EFJ07541 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GRMZM2G452178_T01 (Zea mays), 3'ss of exon 4
----------------------------------------------------------------------gtatgt-tgtgatagttttcattgaatttatattcttagttgtttggctggt--ttcagGAACAGGAGAAAGCTAACCTCGCAACTGATACTGGACTCGACCAGAAGCAAATTAACAACTGGTTTATCAACCAGAGAAAGCGTCATTGGAATCCTTCAG
                                                                      | | |   |||     |  | |||  |   | | |||   |||||| |||    | |||||   ||||||       || |||   |  ||||| || ||||||||||| || ||||||||||| ||||||||| | ||||| || ||||| || || |
gtgagagactaatctcccgtgcggccgtgccttaacacaatgctgacagatcgattaccgtactcatacagcacgcgcgtgccttgtgcccttggctcgctgtgcttg--tgtttgtctgaacatgcagGAGACGGAGAAGATCGCGCTGGCAGAGGCGACTGGCCTGGACCAGAAGCAGATCAACAACTGGTTCATCAACCAGCGGAAGCGGCACTGGAAGCCGTCGG

upper sequence: EFJ07541 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GLYMA08G39170.1 (Glycine max), 3'ss of exon 4
------------------------------------gtatgttgtgatagttttcattgaatttatattcttagttgtttg------gctggt--ttcagGAACAGGAGAAAGCTAACCTCGCAACTGATACTGGACTCGACCAGAAGCAAATTAACAACTGGTTTATCAACCAGAGAAAGCGTCATTGGAATCCTTCAG
                                    ||   |    ||| ||     |     || ||| | |   | |||      | || |  ||||||||   || ||   |   || || |     |||||  | ||||||||||||||||||||||||||||| || |||||||||||||| ||||| || || |
tatagtttattataggaaaaacattgcttgacatcagttaatgaatataattaagtctacgcctacattatcaaaagcttgtttcttgatgatctttcagGAAGGTGATAAGATTGCACTGGCTAAATCAACTGGGTTAGACCAGAAGCAAATTAACAACTGGTTTATTAATCAGAGAAAGCGTCACTGGAAACCATCTG

upper sequence: EFJ07541 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GLYMA17G01370.1 (Glycine max), 3'ss of exon 4
------------------------------------gtatgttgtgatagttttcattgaatttatattcttagttgtt--tggctggtttcagGAACAGGAG-----AAAGCTAAC-CTCGCAACTGATACTGGACTCGACCAGAAGCAAATTAACAACTGGTTTATCAACCAGAGAAAGCGTCATTGGAATCCTTCAG
                                      ||||| ||  |||||| |  | |   || | |   ||| |   ||  |   | ||  |||||||       |||||| | || |||      || || || || ||||||||||||||||||||||||||||| || |||||||| || ||||| |||||||
atattataatagcaataatttttcggtatataagaaacatgttatggaagtttttaggggaacaatttacaaggttttacatgattttatgcattaacagGAATCTCAGAAGCTAGCTCTTGCAGAGTCAACAGGGCTGGATCAGAAGCAAATTAACAACTGGTTTATCAATCAAAGAAAGCGGCACTGGAAGCCTTCAG

upper sequence: EFJ07541 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GLYMA02G04190.1 (Glycine max), 3'ss of exon 4
--------------------------------------------gtatgttgtgatagttttcattgaatttatattcttagttgtttggctggtttcagGAACAGGAGAAAGCTAACCTCGCAACTGATACTGGACTCGACCAGAAGCAAATTAACAACTGGTTTATCAACCAGAGAAAGCGTCATTGGAATCCTTCAG
                                             |||  | |  |   | | ||| || || |||| |   ||  |||      |  |||||   || ||   | | || || |     || || || |||||||||||||||||||| |||||||| ||||| ||||| ||||||||||| || ||||
aaagataagcataaaaaatgttggttgtatgaattattatacaaatatcatttttttaatattattaaacttgtattttgttttacttgatcatctatagGAAGCTGATAAGATTGAACTGGCTAAGTCAACAGGGCTGGACCAGAAGCAAATTAACAATTGGTTTATTAACCAAAGAAAACGTCATTGGAAACCATCAG

upper sequence: EFJ07541 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GLYMA18G20460.1 (Glycine max), 3'ss of exon 1
------------------------gtatgttgtgatagttttcattgaatt------------tatattcttagttgtttg------gctggt--ttcagGAACAGGAGAAAGCTAACCTCGCAACTGATACTGGACTCGACCAGAAGCAAATTAACAACTGGTTTATCAACCAGAGAAAGCGTCATTGGAATCCTTCAG
                         ||| |  ||| |    | | |||| |            || ||| | |   | |||      | || |  ||||||||   || ||   |   || || |     |||||| | ||||||||||||||||||||||||||||| || |||||||||||  | ||||| || || |
tattttctcatggattacttgaaaatatttcttgacatcagttagtgaactgaagtcttagcctacattatcaaaagcttgttccttgttgatctttcagGAAGGTGATAAGATTGCACTGGCTAAATCAACTGGATTAGACCAGAAGCAAATTAACAACTGGTTTATTAATCAGAGAAAGCGCTACTGGAAACCATCTG

upper sequence: EFJ07541 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GLYMA01G03450.1 (Glycine max), 3'ss of exon 5
---------------------------------------------gtatgttgtgatagttttcattgaatttatattcttagttgtttggctggtttcagGAACAGGAGAAAGCTAACCTCGCAACTGATACTGGACTCGACCAGAAGCAAATTAACAACTGGTTTATCAACCAGAGAAAGCGTCATTGGAATCCTTCAG
                                               || || |  |  | || ||| || || |||| |   ||  |||      |  |||||   || ||   | | || || |     || || || |||||||||||||||||||| |||||||| ||||| ||||| || |||||||| || || |
tgaaaaaaatgtactaaaaaattgttggatgaattattttacagataatattttttttatatt-attaaacttgtattttgttttacttgatcatgtatagGAAGCTGATAAGATTGAACTGGCTAAGTCAACAGGGCTAGACCAGAAGCAAATTAACAATTGGTTTATAAACCAAAGAAAACGACATTGGAAACCATCCG

upper sequence: EFJ07541 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GLYMA14G05150.1 (Glycine max), 3'ss of exon 5
-----------------------------------------gtatgttgtgatagttttcattgaatttatattcttagt-tgtttggctggt--ttcagGAACAGGAGAAAGCTAACCTCGCAACTGATACTGGACTCGACCAGAAGCAAATTAACAACTGGTTTATCAACCAGAGAAAGCGTCATTGGAATCCTTCAG
                                          |||    |||    | | ||   ||    ||  | | | || |||| |     |  |||||    | ||       || |||      || || || || | ||| ||||| ||||||||||| ||||| |||||||| ||||||||||| ||||| |
tgtgcattaattaattcataagttttgtttactatttatatatatccgatgactaatcttatattatggcaatggtgaatgtgcttggataaacatgtagGAATCTCAAAAGCAGGCACTTGCAGAATCCACAGGCCTAGATCTGAAACAAATCAACAACTGGTTCATCAATCAGAGAAAACGTCATTGGAAGCCTTCTG

upper sequence: EFJ07541 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GLYMA07G39350.1 (Glycine max), 3'ss of exon 3
-----------------------------gtatgttgtgatagttttcattg----aatttatat--tcttagttgtttggctggttt---cagGAACAGGAG-----AAAGCTAAC-CTCGCAACTGATACTGGACTCGACCAGAAGCAAATTAACAACTGGTTTATCAACCAGAGAAAGCGTCATTGGAATCCTTCAG
                               ||||| ||   ||||| |  |    |||||| |   |  ||  || ||   |  |||   ||  |||||||       |||||  | || |||      || || || || ||||||||||||||||||||||||||||| || || ||| | || ||||| |||||||
gacaacaattatttttcggtatatatgaaacatgttatggctgtttttaggggaataatttacaagattctacatgcttaattaatttatgcattaacagGAATCTCAGAAGCTGGCTCTTGCAGAGTCAACAGGCCTGGATCAGAAGCAAATTAACAACTGGTTTATCAATCAAAGGAAGAGGCACTGGAAGCCTTCAG

upper sequence: EFJ07541 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: Vv14s0060g01180.t01 (Vitis vinifera), 3'ss of exon 4
-----------------------------------------gtatgttgtgatagttttcatt---gaatttatattcttagttgtttggctg-gtttcagGAACAGGAGAAAGCTAACCTCGCAACTGATACTGGACTCGACCAGAAGCAAATTAACAACTGGTTTATCAACCAGAGAAAGCGTCATTGGAATCCTTCAG
                                         | |   | || |   |||||||   | |    |||    |   | |||     | | |||||| | ||||||   || ||  ||   | ||||||||| ||||||||||| |||||||||||||| || |||||||| ||||| |||||||| || ||||
aaaagttcatattggagttgtatttagaactgctatcgctgggacact-tgtttactttcatttctggacacgtatctgaaaaggattgatgatgatacagGAAGATGAGAAATTGAAGCTATCAGAGGTTACTGGACTAGACCAGAAGCAGATTAACAACTGGTTCATAAACCAGAGGAAGCGGCATTGGAAACCATCAG

upper sequence: EFJ07541 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: Vv01s0127g00210.t01 (Vitis vinifera), 3'ss of exon 4
-------------------------------------gtatgttgtgatagttttcattgaatttatattcttagttgtttggctggt-------ttcagGAACAGGAGAAAGCTAACCTCGCAACTGATACTGGACTCGACCAGAAGCAAATTAACAACTGGTTTATCAACCAGAGAAAGCGTCATTGGAATCCTTCAG
                                     ||  |     ||| | ||   ||| | | |   | ||    |||  ||  |       | ||||||   || |||  |   || ||       || || || |||||||||||||||||||| |||||||| || ||  ||||||| || ||||| || ||||
gtaagtctgcactttgtgttttcatttcctttatagggtgggaatgcatactattttctgagtctttgaccataccgctttttcttatataataatccagGAAGCTGATAAAATTGCACTTGCTGAAACAACGGGTCTGGACCAGAAGCAAATTAACAATTGGTTTATAAATCAACGAAAGCGGCACTGGAAACCATCAG

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: 31 (upstream exon), 35 (downstream exon)
Score: 5

GGAGTTTCTCAAGAAGAAGAAGAAAGGAAAGCTGCCCAAGCACTCGACCGAGAAGCTGTATGAGTGGTGGGAAGCTCATATCAAGTGGCCATATCCATCGgtatgttgtg ... ctggtttcagGAACAGGAGAAAGCTAACCTCGCAACTGATACTGGACTCGACCAGAAGCAAATTAACAACTGGTTTATCAACCAGAGAAAGCGTCATTGGAATCCTTCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgttgtgatagttttcattgaatttatattcttagttgtttggctggtttcagGAACAGGAGAAAGCTAACCTCGCAACTGATACTGGACTCGACCAGAAGCAAATTAACAACTGGTTTATCAACCAGAGAAAGCGTCATTGGAATCCTTCAG
         atagttttcattgaat  TA-rich tract