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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggctatagtttctggttatactctatctttggttggtctaatctgttattaaatccagGTGGATGATTTGGAGGAAGTGAGTGACTACTACCAGAATAGGGGACGATTCGATGAACTGATTTCTCTAATGGAAAGTGGTCTTGGACTCGACCGCGCAC

Basic information

species Selaginella moellendorffii
transcript EFJ24508
intron # 24
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ24508 (Selaginella moellendorffii), 3'ss of exon 24
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 24
---------------------------gtaaggctatagttt----ctggttatactctatctttggttggtctaatctgttattaaatccagGTGGATGATTTGGAGGAAGTGAGTGACTACTACCAGAATAGGGGACGATTCGATGAACTGATTTCTCTAATGGAAAGTGGTCTTGGACTCGACCGCGCAC
                              |    ||| ||     |  ||  |    |||||    ||  |||||     | ||   |  |||| ||||||||||||||||| ||||| ||||||||||| || ||| | ||| ||||||| ||||| || |||||||||||||| ||||| || || || |
gtatatatacaggagcaacctgttagaactaaaacatatttcagtacaagtcttttcttatctagattttttctaacacccttttttgtatagGTTGATGATTTGGAGGAAGTAAGTGAATACTACCAGAACAGAGGATGTTTCAATGAACTTATTTCCCTCATGGAAAGTGGTCTAGGACTGGAGCGTGCTC

upper sequence: EFJ24508 (Selaginella moellendorffii), 3'ss of exon 24
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 24
---------------------------gtaaggctatagttt----ctggttatactctatctttggttggtctaa--tctgttattaaatccagGTGGATGATTTGGAGGAAGTGAGTGACTACTACCAGAATAGGGGACGATTCGATGAACTGATTTCTCTAATGGAAAGTGGTCTTGGACTCGACCGCGCAC
                              |    ||| ||     |  ||  |    |||||    ||  |||||   |  || ||   |  |||| ||||||||||||||||| ||||| ||||||||||| || ||| | ||| ||||||| ||||| || |||||||||||||| ||||| || || || |
gtatatatacaggaccaacctgttagaactaaaacatatttcagtacaagtcttttcttatctagattttttctaacacccttttttttgtatagGTTGATGATTTGGAGGAAGTAAGTGAATACTACCAGAACAGAGGATGTTTCAATGAACTTATTTCCCTCATGGAAAGTGGTCTAGGACTGGAGCGTGCTC

upper sequence: EFJ24508 (Selaginella moellendorffii), 3'ss of exon 24
lower sequence: GRMZM5G822591_T01 (Zea mays), 3'ss of exon 1
----------------------------------------------------gtaaggctatagtttctg-gttatactctatctttggttggtctaatctgttattaaatccagGTGGATGATTTGGAGGAAGTGAGTGACTACTACCAGAATAGGGGACGATTCGATGAACTGATTTCTCTAATGGAAAGTGGTCTTGGACTCGACCGCGCAC
                                                    | |  |||    |  ||| | | || | | | ||    |       | |||  ||   |  |||| ||||| ||||| ||||| ||||| |||||||| ||||| ||| | ||| ||||||| ||| |||| ||||| |||||||||||||| || || ||||
gtatacaagtaggagcacatacttgataattttttgtagtatctgctttatagcagagcttctatcactgtgatctatttttttttctcatatctgcttttgtatttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAAAATAGAGGATGCTTCAATGAACTCATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC

upper sequence: EFJ24508 (Selaginella moellendorffii), 3'ss of exon 24
lower sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 1
--------------------------------------------gtaaggctatagtttctggttatactctatctttggttggtctaatctgttattaa-atccagGTGGATGATTTGGAGGAAGTGAGTGACTACTACCAGAATAGGGGACGATTCGATGAACTGATTTCTCTAATGGAAAGTGGTCTTGGACTCGACCGCGCAC
                                             | |    | || ||||        | | | | ||    |||| || |  ||||    |  |||| ||||| ||||| ||||| ||||| |||||||||||||| ||| | |||  |||||| ||| |||| ||||| |||||||||||||| || || ||||
gtatacaagtaggagcacatacttgataattttttctagtctgttttataacagagcttctatgatctatttctgtctgacatgtctgattttgtatttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAGAATAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC

upper sequence: EFJ24508 (Selaginella moellendorffii), 3'ss of exon 24
lower sequence: GRMZM2G325285_T01 (Zea mays), 3'ss of exon 14
-----------------------------------------------gtaaggctatagtttctg--gttatactctatctttggttggtcta---atctgttattaaatccagGTGGATGATTTGGAGGAAGTGAGTGACTACTACCAGAATAGGGGACGATTCGATGAACTGATTTCTCTAATGGAAAGTGGTCTTGGACTCGACCGCGCAC
                                                | |    | || ||||     |||  ||||| |||   |  | |     | |||  ||   |  |||| ||||| ||||| ||||| ||||| |||||||| ||||| ||| | ||| ||||||| ||| |||| ||||| |||||||||||||| || || ||||
gtatacaagtaggagcacatacttaataatttttttgtagtatctgctttatagcagagcttctatcactatgatctatttttttctcatatctgcttttgtatttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAAAATAGAGGATGCTTCAATGAACTCATTGCTCTCATGGAGAGTGGTCTTGGACTAGAACGTGCAC

upper sequence: EFJ24508 (Selaginella moellendorffii), 3'ss of exon 24
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 22
-----------------------------------------------gtaaggctatagtttctg-gttatactctatctttggttggtctaatctgttattaaatccagGTGGATGATTTGGAGGAAGTGAGTGACTACTACCAGAATAGGGGACGATTCGATGAACTGATTTCTCTAATGGAAAGTGGTCTTGGACTCGACCGCGCAC
                                                | |    | |||||||  | |||| |   | | ||      ||  ||| || ||   |  |||| || ||  |||| ||||| ||||| ||||||||||| || ||| | |||  |||||| ||| |||| ||||| |||||||||||||| || || ||||
gtatacaagtaggagggcatacttgatgatttttccctagtctttgttttattgcaaagtttctatgatatatttc-tttctgacatacctgctcttttttttg-tttagGTTGACGACCTGGAAGAAGTCAGTGAGTACTACCAGAACAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC

upper sequence: EFJ24508 (Selaginella moellendorffii), 3'ss of exon 24
lower sequence: GRMZM2G395549_T01 (Zea mays), 3'ss of exon 9
--------------------------------------------------------------------------------------------------------------------gtaaggctatagtttctg-gttatactctatctttggttggtctaatctgttattaaatccagGTGGATGATTTGGAGGAAGTGAGTGACTACTACCAGAATAGGGGACGATTCGATGAACTGATTTCTCTAATGGAAAGTGGTCTTGGACTCGACCGCGCAC
                                                                                                                     | |    | |||||||  | |||| |   | | ||      ||  ||| || ||   |  |||| |||||  | || ||||| ||||| ||||||||||| || ||| | |||  |||||| ||| |||| ||||| |||||||||||||| || || ||||
gtctgctttgcttgtgttgacgtggaggagttccgtcttgcacaaatatgtggtctcaatattattgttcagatatacaagtaggagggcatacttgatttttccctattctttgttttattgcaaagtttctatgatatatttc-tttctgacatagctgctctttttttg--tttagGTTGATGACCTCGAAGAAGTCAGTGAGTACTACCAGAACAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC

upper sequence: EFJ24508 (Selaginella moellendorffii), 3'ss of exon 24
lower sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 24
----------------------------------gtaaggctatagttt--ctggttatactctatc-tttggttggtctaatctgttattaa-atccagGTGGATGATTTGGAGGAAGTGAGTGACTACTACCAGAATAGGGGACGATTCGATGAACTGATTTCTCTAATGGAAAGTGGTCTTGGACTCGACCGCGCAC
                                  |  || |  | | ||   | |||||  ||| |  |||| ||  |        ||||||  ||  |||||||||||||||| || || ||||| |  |||||||| || ||| | ||  |||||||||| ||||||||||| ||||| |||||||| || || || |
attgggaaatgtagaacattggcaacaagtggcagatagacagttgattagtttgttattttctgttgtttgattactaattctctttattattatgaagGTGGATGATTTGGAAGAGGTTAGTGAGTTTTACCAGAACAGAGGATGCTTTAATGAACTGATATCTCTAATGGAGAGTGGACTTGGACTGGAGCGTGCCC

upper sequence: EFJ24508 (Selaginella moellendorffii), 3'ss of exon 24
lower sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 24
-----------------------------gtaaggct----atagtttctggttatactctatctttggttgg-----tctaatctgttattaaatccagGTGGATGATTTGGAGGAAGTGAGTGACTACTACCAGAATAGGGGACGATTCGATGAACTGATTTCTCTAATGGAAAGTGGTCTTGGACTCGACCGCGCAC
                             | ||  ||    || | ||    | |   | |  | |||  ||      |   ||||||| |  | |  ||||||||||||||||||| || || || ||||| ||||| || ||| | ||| ||||||| || ||||||||||| |||||  | ||| | || || ||||
tagtagcaaaatactaaaaacaagtgacagaaaaacttttgattgctttgtctaaccttttgaccttgtctgaatacttactatctgttttatattgaagGTGGATGATTTGGAGGAGGTTAGCGAGTACTATCAGAACAGAGGATGCTTCAATGAACTCATATCTCTAATGGAGAGTGGGTTAGGATTGGAGCGTGCAC

upper sequence: EFJ24508 (Selaginella moellendorffii), 3'ss of exon 24
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 24
----------------------------------gtaaggctat---agtttctggttatactctatctttggttggtctaatctgttat-taaatccagGTGGATGATTTGGAGGAAGTGAGTGACTACTACCAGAATAGGGGACGATTCGATGAACTGATTTCTCTAATGGAAAGTGGTCTTGGACTCGACCGCGCAC
                                  || |  ||||      | || ||  |  |  |    |  ||| |||    | || | | | || |||||||||||||||| ||||| |||||||| |||||||| |||||| | ||  |||| || || ||||| ||||| |||||  | ||| | || || ||||
aatgcagctagctattcatttataacctcagtatgttactctatttagaatcctagtcctgtttgaatcctctttgatcttggatattttatgattctagGTGGATGATTTGGAAGAAGTCAGTGACTATTACCAGAACAGGGGATGCTTTAATGAGCTCATATCTCTCATGGAGAGTGGATTGGGATTGGAACGTGCAC

upper sequence: EFJ24508 (Selaginella moellendorffii), 3'ss of exon 24
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 24
--------------------------------------------------------------------------------------gtaaggctatagtttctggttatactctatc---tttggttggtctaatctgtta--ttaaatcc---agGTGGATGATTTGGAGGAAGTGAGTGACTACTACCAGAATAGGGGACGATTCGATGAACTGATTTCTCTAATGGAAAGTGGTCTTGGACTCGACCGCGCAC
                                                                                        ||| |||  ||||  | || |    ||||   | |  ||   ||| | | ||   || |||     |||| |||||||||||||| || ||||| || ||||||||||| ||| | ||| |||| || || || || ||||| |||||||| ||  | || || ||||
gtaatgtattgttttttaagggtagggtgggatgataacatcataaaaatggattgttgtttcaaaatttccttctgtatgagcttccaagcctaatgttttcgcttttttattatcaggtctaattt-cctagtgtattgatttgaattttgtagGTCGATGATTTGGAGGAGGTCAGTGATTATTACCAGAATAGAGGATGCTTCAATGAGCTAATATCACTCATGGAGAGTGGTCTGGGCTTGGAGCGTGCAC

upper sequence: EFJ24508 (Selaginella moellendorffii), 3'ss of exon 24
lower sequence: PP1S147_10V6.1 (Physcomitrella patens), 3'ss of exon 12
---------------------------------gtaaggctatagtttctggttatactcta---tctttggttggtctaatc-tgtt-attaaatccagGTGGATGATTTGGAGGAAGTGAGTGACTACTACCAGAATAGGGGACGATTCGATGAACTGATTTCTCTAATGGAAAGTGGTCTTGGACTCGACCGCGCAC
                                 | |  | | | ||||   |  |  ||  |      ||   |    | ||| || | | |   | |||||||| |||||||| || || ||||| || ||||||||||| || || || ||||| || || || || ||||||||||| |||||  | || ||||| |
ggagtattggattctctggtccaagtagagtatgcattgattttgttttctggaaggctagaaaacaattatataacatgatcatgctgaatttttgcagGTGGACGATTTGGAAGAGGTCAGTGAATATTACCAGAATAGAGGTCGCTTTGATGAGCTCATCTCACTTATGGAAAGTGGGCTTGGTTTGGAGCGCGCTC

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|169097272|gb|FE497649.1|FE497649
EST:     CGGAAGAGTTCAGGCTCGCACAAATATGTGGTCTCAACATCATTGTCCAG                         GTGGATGATTTGGAGGAAGTGAGTGACTACTACCAGAATAGGGGACGATTC
genomic: CGGAAGAGTTCAGGCTCGCACAAATATGTGGTCTCAACATCATTGTCCAGgtaaggctat ... ttaaatccagGTGGATGATTTGGAGGAAGTGAGTGACTACTACCAGAATAGGGGACGATTC
EST: gi|169045878|gb|FE451734.1|FE451734
EST:     CGGAAGAGTTCAGGCTCGCACAAATATGTGGTCTCAACGTCATTGTCCAG                         GTGGATGATTTGGAGGAAGTGAGTGACTACTACCAGAATAGGGGACGATTC
genomic: CGGAAGAGTTCAGGCTCGCACAAATATGTGGTCTCAACATCATTGTCCAGgtaaggctat ... ttaaatccagGTGGATGATTTGGAGGAAGTGAGTGACTACTACCAGAATAGGGGACGATTC
EST: gi|169082005|gb|FE486448.1|FE486448
EST:     CGGAAGAGTTCAGGCTCGCACAAATATGTGGTCTCAACGTCATTGTCCAG                         GTGGATGATTTGGAGGAAGTGAGTGACTACTACCAGAATAGGGGACGATTC
genomic: CGGAAGAGTTCAGGCTCGCACAAATATGTGGTCTCAACATCATTGTCCAGgtaaggctat ... ttaaatccagGTGGATGATTTGGAGGAAGTGAGTGACTACTACCAGAATAGGGGACGATTC
EST: gi|169047382|gb|FE456215.1|FE456215
EST:     CGGAAGAGTTCAGGCTCGCACAAATATGTGGTCTCAACATCATTGTCCAG                         GTGGATGATTTGGAGGAAGTGAGTGACTACTACCAGAATAGGGGACGATTC
genomic: CGGAAGAGTTCAGGCTCGCACAAATATGTGGTCTCAACATCATTGTCCAGgtaaggctat ... ttaaatccagGTGGATGATTTGGAGGAAGTGAGTGACTACTACCAGAATAGGGGACGATTC
EST: gi|169114799|gb|FE516060.1|FE516060
EST:     CGGAAGAGTTCAGGCTCGCACAAATATGTGGTCTCAACATCATTGTCCAG                         GTGGATGATTTGGAGGAAGTGAGTGACTACTACCAGAATAGGGGACGATTC
genomic: CGGAAGAGTTCAGGCTCGCACAAATATGTGGTCTCAACATCATTGTCCAGgtaaggctat ... ttaaatccagGTGGATGATTTGGAGGAAGTGAGTGACTACTACCAGAATAGGGGACGATTC
EST: gi|169025122|gb|FE434709.1|FE434709
EST:     CGGAAGAGTTCAGGCTCGCACAAATATGTGGTCTCAACATCATTGTCCAG                         GTGGATGATTTGGAGGAAGTGAGTGACTACTACCAGAATAGGGGACGATTC
genomic: CGGAAGAGTTCAGGCTCGCACAAATATGTGGTCTCAACATCATTGTCCAGgtaaggctat ... ttaaatccagGTGGATGATTTGGAGGAAGTGAGTGACTACTACCAGAATAGGGGACGATTC

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: 35

GGCCAACAGTGCGAAGACGTGGAAAGAAGTTTGCTTCGCTTGTGTTGACGCGGAAGAGTTCAGGCTCGCACAAATATGTGGTCTCAACATCATTGTCCAGgtaaggctat ... ttaaatccagGTGGATGATTTGGAGGAAGTGAGTGACTACTACCAGAATAGGGGACGATTCGATGAACTGATTTCTCTAATGGAAAGTGGTCTTGGACTCGACCGCGCAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatagtttctggttatactctatctttggttggtctaatctgttattaaatccagGTGGATGATTTGGAGGAAGTGAGTGACTACTACCAGAATAGGGGACGATTCGATGAACTGATTTCTCTAATGGAAAGTGGTCTTGGACTCGACCGCGCAC
                                gtctaat  putative branch site (score: 35)
                                   taatctgttattaaat  TA-rich tract