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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggctcgttgtttttgccttatggtggctgggcgctcataaagttggacttgggcagGTTCTTGGAACCCCTACTCGCGAGGAGATCAAGTGTATGAATCCCAACTACACGGAATTCAAGTTCCCTCAAATCAAGGCCCACCCTTGGCACAAG

Basic information

species Selaginella moellendorffii
transcript EFJ04915
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ04915 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: LOC_Os03g62500.1 (Oryza sativa), 3'ss of exon 9
---------------gttggctcgttgt-ttttgccttatggtggctg-----ggcgctcataaagttggacttgg------gcagGTTCTTGGAACCCCTACTCGCGAGGAGATCAAGTGTATGAATCCCAACTACACGGAATTCAAGTTCCCTCAAATCAAGGCCCACCCTTGGCACAAG
               | || |      | || |  | | ||     ||     | |  | | |   || | | | |      ||||||| | || || || ||  | || ||||||||||| |||||||| ||||||||||| ||||| ||||||||||| ||||| || || |||||||||
gtaacatttttctatgatgtcctaaactgttctctcctgtgaccattgatcttgacaataacatgtttagtcatagcgccttgcagGTTTTGGGTACTCCAACAAGGGAAGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAATTCCCTCAAATTAAGGCTCATCCATGGCACAAG

upper sequence: EFJ04915 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: GRMZM2G138676_T02 (Zea mays), 3'ss of exon 9
----------------------------------------gttggctcgttgtttttgccttatggtggctgggcgctcataaagttggacttgggcagGTTCTTGGAACCCCTACTCGCGAGGAGATCAAGTGTATGAATCCCAACTACACGGAATTCAAGTTCCCTCAAATCAAGGCCCACCCTTGGCACAAG
                                         || |||   |  ||||||   |||     | |  ||  |||   |  |  |   ||||||| | || || || ||  | || ||||||||||| ||||| || ||||| ||||| ||||||||||| ||||| || || || || |||||||||
gtgattttcttacggtatccatatgaccatatctctactgttttgctgccttcttttgcaccatgacatattgaggc--atagcatctgcatcttgcagGTTTTGGGTACTCCAACAAGGGAAGAGATCAAGTGCATGAACCCAAACTATACGGAGTTCAAGTTCCCACAAATTAAAGCTCATCCGTGGCACAAG

upper sequence: EFJ04915 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: GRMZM2G131853_T01 (Zea mays), 3'ss of exon 9
--------------------------gttggctcgttgtttttgccttatggtggctgggcgctcataaagttggacttgggc---agGTTCTTGGAACCCCTACTCGCGAGGAGATCAAGTGTATGAATCCCAACTACACGGAATTCAAGTTCCCTCAAATCAAGGCCCACCCTTGGCACAAG
                           |    ||  || |  | | || | |  ||||   | |  |     |     |       || || | || || || ||  | |||||||||| ||| |||||||| || ||  | ||||||||||||||||| || || ||||| || |||||||||
gtttgcatctgctatcaaatcgtgtcatgaaatcactggtggtactttgtag--gctgaatgttttttcttctctttcttcatccaagATTTTGGGTACTCCAACAAGAGAGGAGATCAGGTGCATGAATCCAAATTATTCCGAATTCAAGTTCCCTCAGATAAAAGCCCATCCATGGCACAAG

upper sequence: EFJ04915 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: GRMZM2G121790_T01 (Zea mays), 3'ss of exon 8
---------------------------------gttggctcgttgt-ttttgccttatggtggctgggcgctcataa-agttggacttg-------ggcagGTTCTTGGAACCCCTACTCGCGAGGAGATCAAGTGTATGAATCCCAACTACACGGAATTCAAGTTCCCTCAAATCAAGGCCCACCCTTGGCACAAG
                                 ||||    |   | |  | |||  || |  ||     |   ||   | |||| |||       | ||||||||||| ||||| || |||||||| |||   ||||||||||| |||||||| || || |  || ||||| ||||| || ||||| |||||||||
gtacttggtggttctgcagactgcactatattagttgtaaagaaatgtactacctagtgttttctatttccatgtattggatggatttgctttgctgacagGTTCTTGGTACCCCAACGCGCGAGGAAATCCGATGTATGAATCCAAACTACACCGAGTTTAGATTTCCTCAGATCAAAGCTCACCCATGGCACAAG

upper sequence: EFJ04915 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: GRMZM2G043350_T02 (Zea mays), 3'ss of exon 7
------------------------------------------------------------------gttggctcgttgtttt--tgccttatgg----tggctgggcgctcat-aaagttggac-----------ttgggcagGTTCTTGGAACCCCTACTCGCGAGGAGATCAAGTGTATGAATCCCAACTACACGGAATTCAAGTTCCCTCAAATCAAGGCCCACCCTTGGCACAAG
                                                                       ||| | |  ||    ||||| |     ||| | |   ||    | | ||| ||           ||  ||||||| | || ||||| || || ||||| ||    ||||||||||||||||| || ||||||||||| ||||| || || ||    || |||||||||
gtaatggttttgcatgcattcaaaaactgactattgtaaggaagatatttgcgattgaggcggtggtccaactcctcgccttaccaccttaagaacactggtttgctactttccagaattgaacaaagattaactttttgcagGTTTTGGGCACCCCAACACGAGAGGAAATTCGTTGTATGAATCCCAACTATACAGAATTCAAGTTTCCTCAGATAAAAGCATGTCCATGGCACAAG

upper sequence: EFJ04915 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: AT4G00720.1 (Arabidopsis thaliana), 3'ss of exon 9
------------------gttggctcgttgtttttgccttatggtggctgggc--gctcataaagttggac-ttgggcagGTTCTTGGAACCCCTACTCGCGAGGAGATCAAGTGTATGAATCCCAACTACACGGAATTCAAGTTCCCTCAAATCAAGGCCCACCCTTGGCACAAG
                    ||   | |  | | |    |||  |   |   |  | | |   |  || || |    ||| ||||||| || |||||  | || || ||   |||||||||||| || ||||| || |||||||| ||||||||||| || ||||| |||||||||
gtacttaacctgatccctcgtgttccttcatctctcttctatatttaatttactagtttactcatctgtacatctaccagATTCTTGGGACGCCTACAAGAGAAGAAATACGGTGTATGAATCCGAATTACACAGAGTTCAAGTTTCCTCAAATCAAAGCTCACCCGTGGCACAAG

upper sequence: EFJ04915 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: AT2G30980.1 (Arabidopsis thaliana), 3'ss of exon 8
---------------gttggctcgttgtttttgccttatggtggctgggcgctcataaagt--tggacttgggcagGTTCTTGGAACCCCTACTCGCGAGGAGATCAAGTGTATGAATCCCAACTACACGGAATTCAAGTTCCCTCAAATCAAGGCCCACCCTTGGCACAAG
                ||   |  ||||||| || | ||      |  | |||||| | ||  ||   | |   |||||||||| || || |||||||| || |||  ||| ||||| || |||||||| || ||||  ||||| |||||||| |||||||||||||| |||
gtgaactcttcttttattatatt-ttgttttggcgtcatttcctgtctgtgctcatgatgtgctgtgttggtttagGTTCTTGGTACTCCAACTCGCGAAGAAATCCGGTGCATGAACCCAAACTACACAGACTTCAGATTCCCACAAATCAAAGCCCACCCTTGGCATAAG

upper sequence: EFJ04915 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: AT1G06390.1 (Arabidopsis thaliana), 3'ss of exon 8
-------------------------------------gttggctcgttgtttttgcct----tatggtggctgggcgctcataa----agttgg-acttggg--cagGTTCTTGGAACCCCTACTCGCGAGGAGATCAAGTGTATGAATCCCAACTACACGGAATTCAAGTTCCCTCAAATCAAGGCCCACCCTTGGCACAAG
                                      || |    | || || | ||    | | ||   |  |    |||||    | |||  || | |    |||||||||| || || ||||| || || ||    |||||||| || |||||||| || || | |||||| |||||||| || |||||||||||||||
gtgaagtctcctttattagactaatggatgtgctcttttttgtctttggtattagactagaatctagtaaatatgttaccataagtacacttgctaccttgttttagGTTCTTGGTACTCCAACTCGTGAAGAAATTCGATGTATGAACCCGAACTACACAGATTTTAGGTTCCCACAAATCAAAGCTCACCCTTGGCACAAG

upper sequence: EFJ04915 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: Vv14s0066g01050.t01 (Vitis vinifera), 3'ss of exon 9
--------------------------------------------------------------gttggctcgttgtt-tttgccttatggtggctgggcgctcataaagttggacttgggcagGTTCTTGGAACCCCTACTCGCGAGGAGATCAAGTGTATGAATCCCAACTACACGGAATTCAAGTTCCCTCAAATCAAGGCCCACCCTTGGCACAAG
                                                               |   |      |   || | || |||   |||     |  | | ||||   |     |||| ||||| || || ||||| ||||| ||||||||||||||||| ||||| || || || || ||||| ||||||||||| ||||| |||||||||
gtaaaactttctgagtcttgtatgcaagagaaacaatattaacgttttgtctgagctctgaaatcatccttcaatcactttctttgtggaacctgctgaat--tgatgttgttatctactagGTACTTGGGACGCCAACTCGTGAGGAAATCAAGTGTATGAATCCAAACTATACTGAGTTTAAATTCCCACAAATCAAGGCTCACCCCTGGCACAAG

upper sequence: EFJ04915 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: Vv07s0005g02100.t01 (Vitis vinifera), 3'ss of exon 9
--------------------------------------gttggctcgttgtttttgccttat-ggtggctgggcgctcataaagttggacttgg--gcagGTTCTTGGAACCCCTACTCGCGAGGAGATCAAGTGTATGAATCCCAACTACACGGAATTCAAGTTCCCTCAAATCAAGGCCCACCCTTGGCACAAG
                                      ||    |   | |   | ||||||   ||  |   |    |||   |   | |||   ||||||| | || ||||| ||  | ||||| || ||||| ||||||||||| ||||| ||||| || ||||| ||||| || |||||||| |||||||||
tggtgctgagtctgcagttgctcctttccatcttgtttgtgattttagtatccatcccttattaatgtgttttctacaatattttcttatttgcatgcagGTTTTGGGCACCCCAACAAGAGAGGAAATTAAGTGCATGAATCCCAATTACACAGAATTTAAATTCCCACAAATTAAAGCCCACCCATGGCACAAG

upper sequence: EFJ04915 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: Vv12s0035g01060.t01 (Vitis vinifera), 3'ss of exon 8
--------------------------------gttggctcgttgtttttgccttatggtggc-------tgggcgctcataaagttggact--tgggcagGTTCTTGGAACCCCTACTCGCGAGGAGATCAAGTGTATGAATCCCAACTACACGGAATTCAAGTTCCCTCAAATCAAGGCCCACCCTTGGCACAAG
                                        ||  |||   ||  | ||  ||       |  |    |||    ||  | |  || ||||||  | ||||| |||||  | |||||||| || ||||||||||| |||||||| ||||| || ||||| ||||| ||| | || || |||||||||
atgctacttctatttacagaatttttgaaagctcaaatctgtcatttaaacccaaaggaagcctcagaataagattccatgtgtttaaattgctgtgcagGTCTTGGGAACACCTACCAGGGAGGAGATAAAATGTATGAATCCAAACTACACCGAATTTAAATTCCCACAAATAAAGCCTCATCCATGGCACAAG

upper sequence: EFJ04915 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: PP1S60_100V6.1 (Physcomitrella patens), 3'ss of exon 8
-------------------------------------------------------gttg-gctcgttgtttttgccttatggtggctgggcgctcataaagttgga-------cttg-ggcagGTTCTTGGAACCCCTACTCGCGAGGAGATCAAGTGTATGAATCCCAACTACACGGAATTCAAGTTCCCTCAAATCAAGGCCCACCCTTGGCACAAG
                                                       |||| |   ||||     |  ||||| ||    || |   ||    |||          ||| |||||||  | || || || ||||| |||||||||||||| |||||||| ||||||||||| |||||||| || ||||||||||| ||||| |||||||| 
gtagggcacaggcgatgcacggtgttgtgttgaagggtggcgtacttgcttgctggttgtgactgttgcgggagtgttatgatgctgtggagtgtatgttattgaggaaaagttttgtggcagGTGTTGGGGACACCGACTCGTGAGGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCGCAAATCAAGGCTCACCCATGGCACAAA

upper sequence: EFJ04915 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: PP1S74_168V6.1 (Physcomitrella patens), 3'ss of exon 7
-------------------------------------------------------------------------------------------------------------------------------gttg-gctcgttgtttttgccttatggtggctgggcg---ctcataa--agttggacttgggc---agGTTCTTGGAACCCCTACTCGCGAGGAGATCAAGTGTATGAATCCCAACTACACGGAATTCAAGTTCCCTCAAATCAAGGCCCACCCTTGGCACAAG
                                                                                                                               ||   | | ||| |   | |  ||   ||| |  |     || ||    ||||||   |       ||||  | || || || || ||||||||||| ||||| |||||||| ||||||||||| |||||||| |||||||| ||||| || ||||||||||||
gtagcttacatatggtagatgttgaggaagtgcaggggtctacagcagatgtcggtgctggtgtttgggttttgtccgtttgaaatgttgtgttgcgttgaaaggttgtagctggtacttgctcggtgtgatgttagttatgacttcgctagaatggatatgtaggacttatgggtagttgggtgttaatgttagGTGTTGGGGACACCCACACGCGAGGAGATAAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCTCAAATTAAGGCTCATCCTTGGCACAAG

upper sequence: EFJ04915 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: PP1S60_85V6.1 (Physcomitrella patens), 3'ss of exon 8
----------------------------------------------------------------gttggctcgttgtttttgccttatggtggctgggcgc-tcataaagttggacttg---ggcagGTTCTTGGAACCCCTACTCGCGAGGAGATCAAGTGTATGAATCCCAACTACACGGAATTCAAGTTCCCTCAAATCAAGGCCCACCCTTGGCACAAG
                                                                ||||    | |||| |     | ||| |  || |    | ||  ||  | |||||   |||||||  | ||||| || ||||| |||||||| ||||| |||||||| ||||||||||| |||||||| || ||||||||||| ||||| |||||||| 
gtagggcacaggcggtgcacggcgttgtgttgaagggtggcgtacttgcttgctggttgtgactgttgcgggggtgttatgatgctgtggagtgtgagtatgttattgaggagtacttgtgtggcagGTGTTGGGAACACCGACTCGTGAGGAGATAAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCGCAAATCAAGGCTCACCCGTGGCACAAA

upper sequence: EFJ04915 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: PP1S52_55V6.1 (Physcomitrella patens), 3'ss of exon 8
---------------------------------------------------------------------------------------------------------------------------------------gttggctcgttgtttttgccttatggtggctgggcgctcataaagttggacttgggcagGTTCTTGGAACCCCTACTCGCGAGGAGATCAAGTGTATGAATCCCAACTACACGGAATTCAAGTTCCCTCAAATCAAGGCCCACCCTTGGCACAAG
                                                                                                                                       | | || |     |  | |  ||  |    || |    |  |  ||  ||  | | |||||  | || || ||||| || |||||||| ||||| |||||||| ||||||||||| |||||||| |||||||| ||||| ||||| |||||||||
gtatgttatacatggtagagtggaagcatatggagctgaagtcgtttgtactgatgtttgatgtgtatcgattaaaagtattgtattatatttaaagatgttagctgctcttgttgcttcgggtggtgttgcggtgatagcgcaagagtgatactgtagagcttatgagtaggcggatggt--gatgttgacagGTGTTAGGGACACCTACACGTGAGGAGATAAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCTCAAATTAAGGCTCACCCGTGGCACAAG

upper sequence: EFJ04915 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: PP1S306_62V6.1 (Physcomitrella patens), 3'ss of exon 7
----------------------------------------------------------------------gttggctcgttgtttttgccttatggtggctgggcgctcat--aaagttggacttgggcagGTTCTTGGAACCCCTACTCGCGAGGAGATCAAGTGTATGAATCCCAACTACACGGAATTCAAGTTCCCTCAAATCAAGGCCCACCCTTGGCACAAG
                                                                        |||    |||||  ||    |||   |   |||| | |    | |||    |  |||||||| | || || || ||||| |||||||||||||| |||||||| |||||||| || |||||||| || ||||||||||| ||||| |||||||| 
gtgggacacacgtggtacacgttgtttgtgtggaagggtcgccttctgggttggcggtttggtttgtagctgtggtatcttgttcgtgttggatgtgagtatggcgttgaccagacgtttccgtgtggcagGTTTTGGGGACACCGACTCGTGAGGAGATCAAGTGCATGAATCCGAACTACACAGAGTTCAAGTTTCCACAAATCAAGGCGCACCCGTGGCACAAA

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|169024806|gb|FE435485.1|FE435485
EST:     CGCTATTTCCAGGAGAAAGTGGCGTCGACCAGCTGGTGGAGATTATCAAG                         GTTCTTGGAACCCCTACTCGCGAGGAGATCAAGTGTATGAATCCCAACTAC
genomic: CGCTATTTCCAGGAGAAAGTGGCGTCGACCAGCTGGTGGAGATTATCAAGgttggctcgt ... acttgggcagGTTCTTGGAACCCCTACTCGCGAGGAGATCAAGTGTATGAATCCCAACTAC
EST: gi|169034065|gb|FE442799.1|FE442799
EST:     CGCTATTTCCAGGAGAAAGTGGCGTCGACCAGCTGGTGGAGATTATCAAG                         GTTCTTGGAACCCCTACTCGCGAGGAGATCAAGTGTATGAATCCCAACTAC
genomic: CGCTATTTCCAGGAGAAAGTGGCGTCGACCAGCTGGTGGAGATTATCAAGgttggctcgt ... acttgggcagGTTCTTGGAACCCCTACTCGCGAGGAGATCAAGTGTATGAATCCCAACTAC
EST: gi|169066575|gb|FE474135.1|FE474135
EST:     CGCTATTTCCAGGAGAAAGTGGCGTCGACCAGCTGGTGGAGATTATCAAG                         GTTCTTGGAACCCCTACTCGCGAGGAGATCAAGTGTATGAATCCCAACTAC
genomic: CGCTATTTCCAGGAGAAAGTGGCGTCGACCAGCTGGTGGAGATTATCAAGgttggctcgt ... acttgggcagGTTCTTGGAACCCCTACTCGCGAGGAGATCAAGTGTATGAATCCCAACTAC
EST: gi|169038251|gb|FE443937.1|FE443937
EST:     CGCTATTTCCAGGAGAAAGTGGTGTCGACCAGCTGGTGGAGATTATCAAG                         GTTCTTGGAACCCCTACTCGCGAGGAGATCAAGTGTATGAATCCCCACTAC
genomic: CGCTATTTCCAGGAGAAAGTGGCGTCGACCAGCTGGTGGAGATTATCAAGgttggctcgt ... acttgggcagGTTCTTGGAACCCCTACTCGCGAGGAGATCAAGTGTATGAATCCCAACTAC
EST: gi|169033900|gb|FE441932.1|FE441932
EST:     CGCTATTTCCAGGAGAAAGTGGTGTCGACCAGCTGGTGGAGATTATCAAG                         GTTCTTGGAACCCCTACTCGCGAGGAGATCAAGTGTATGAATCCCAACTAC
genomic: CGCTATTTCCAGGAGAAAGTGGCGTCGACCAGCTGGTGGAGATTATCAAGgttggctcgt ... acttgggcagGTTCTTGGAACCCCTACTCGCGAGGAGATCAAGTGTATGAATCCCAACTAC
EST: gi|169100546|gb|FE502721.1|FE502721
EST:     CGCTATTTCCAGGAGAAAGTGGTGTCGACCAGCTGGTGGAGATTATCAAG                         GTTCTTGGAACCCCTACTCGCGAGGAGATCAAGTGTATGAATCCCAACTAC
genomic: CGCTATTTCCAGGAGAAAGTGGCGTCGACCAGCTGGTGGAGATTATCAAGgttggctcgt ... acttgggcagGTTCTTGGAACCCCTACTCGCGAGGAGATCAAGTGTATGAATCCCAACTAC

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: 35 (upstream exon), 19 (downstream exon)
Score: 7

CCGCTATTTCCAGGAGAAAGTGGCGTCGACCAGCTGGTGGAGATTATCAAGgttggctcgt ... acttgggcagGTTCTTGGAACCCCTACTCGCGAGGAGATCAAGTGTATGAATCCCAACTACACGGAATTCAAGTTCCCTCAAATCAAGGCCCACCCTTGGCACAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctcgttgtttttgccttatggtggctgggcgctcataaagttggacttgggcagGTTCTTGGAACCCCTACTCGCGAGGAGATCAAGTGTATGAATCCCAACTACACGGAATTCAAGTTCCCTCAAATCAAGGCCCACCCTTGGCACAAG
     ttgttttt  TA-rich tract