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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcaagaactcgatcgttttgatttggatccagtttctaagcattggattgttctggcagGGGGTTTTGGGGATCAAGGTGAAGATCATGCTGGACTGGGATCCAAAGGGCAAGACCGGGCCGTCGACACCGCTGCCGGACATGGTGACGATCCAAGTAC

Basic information

species Selaginella moellendorffii
transcript EFJ34676
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ34676 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: LOC_Os03g38000.2 (Oryza sativa), 3'ss of exon 3
------------------------------gtgcaagaactcgatcgttttgatttggatccagtttctaagcattggattgttctggcagGGGGTTTTGGGGATCAAGGTGAAGATCATGCTGGACTGGGATCCAAAGGGCAAGACCGGGCCGTCGACACCGCTGCCGGACATGGTGACGATCCAAGTAC
                               |  || |||   ||  | ||  ||||| || |    ||     ||   |   | | |||||| ||| | || |||||||||||||||||||| |||||||| || |||||||||   || ||| | || || ||||||||  | || || ||||| |  |
gtttgtttggttcaactcaagcatcgtagtatttaaaaacctcatgatctt--tttggctcaacgcact---tgttcattatcttttgcagGGTGTTCTTGGCATCAAGGTGAAGATCATGCTCGACTGGGACCCCAAGGGCAAGGTTGGCCCGACCACCCCTCTGCCGGATCTTGTAACCATCCATGCTC

upper sequence: EFJ34676 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GRMZM2G093902_T02 (Zea mays), 3'ss of exon 5
------------------------gtgcaagaactcgatcgttttgatttggatccagtttctaagcattggattgttctgg---cagGGGGTTTTGGGGATCAAGGTGAAGATCATGCTGGACTGGGATCCAAAGGGCAAGACCGGGCCGTCGACACCGCTGCCGGACATGGTGACGATCCAAGTAC
                         |   |  |  | | | | |  |        | |||  |||   |    |||   |||   ||||| ||  | || |||||||| ||||| |||||||||||||||||||||||||||   |||||  | |  ||  | || ||  |||| || || || || |
gtttggtgcttggtatcagatgttatcttattatgcaaacatat-aacaaaatagctgttagtaatactctagttgacttggcttcagGGTGTGCTTGGTATCAAGGTTAAGATTATGCTGGACTGGGATCCAAAGGGCAAGCAAGGGCCAACCATGCCTTTACCTGATTTGGTTACAATTCACGTGC

upper sequence: EFJ34676 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GRMZM2G074300_T03 (Zea mays), 3'ss of exon 3
--------------------------------------------gtgcaagaactcgatcgttt-tgatttggatccagtttctaagcat-tggattgttctg----gcagGGGGTTTTGGGGATCAAGGTGAAGATCATGCTGGACTGGGATCCAAAGGGCAAGACCGGGCCGTCGACACCGCTGCCGGACATGGTGACGATCCAAGTAC
                                            | | ||| |||  ||  |    | |    ||  | ||||| | ||      || |||||    |||||| ||| |||| |||||||||||||||||||| |||||||| || |||||||||   || |||   || || || |||||| ||||||| |||||    |
gtttgttttgctacaattgcccgttgtaatgtctgtttgtctctgggtaagcacttcattttcgacgttccaaatgtaatttctcaacaaacatctttttctgtcgtgcagGGTGTTCTGGGTATCAAGGTGAAGATCATGCTTGACTGGGACCCGAAGGGCAAGGTTGGCCCGATCACCCCTCTTCCGGACCTGGTGACCATCCATACCC

upper sequence: EFJ34676 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GRMZM2G099352_T01 (Zea mays), 3'ss of exon 3
------------------------------------------gtgcaagaactcgatcgttt---tgatttggatccagtttctaagca--ttggattgttctggcagGGGGTTTTGGGGATCAAGGTGAAGATCATGCTGGACTGGGATCCAAAGGGCAAGACCGGGCCGTCGACACCGCTGCCGGACATGGTGACGATCCAAGTAC
                                          | ||| | |||   |  |     || ||    |  | |  | ||  |  ||  ||   ||  |||||| ||| | || |||||||||||||||||||| |||||||| || |||||||||   || |||   || || || |||||| ||||||| |||||    |
gtttgtttgctgtaatctcctcaatgtttggtcgtctctcaagagcagggactacgttttccacgtgcttcaatttaattacccaactaacttcaatctgtcgcgcagGGTGTTCTTGGCATCAAGGTGAAGATCATGCTTGACTGGGACCCGAAGGGCAAGGTTGGCCCGATCACTCCTCTTCCGGACCTGGTGACCATCCACACCC

upper sequence: EFJ34676 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: AT2G31610.1 (Arabidopsis thaliana), 3'ss of exon 4
------------------------------gtgcaagaactcgatcgttttgatttggatccagtttctaagcattggattgttctggcagGGGGTTTTGGGGATCAAGGTGAAGATCATGCTGGACTGGGATCCAAAGGGCAAGACCGGGCCGTCGACACCGCTGCCGGACATGGTGACGATCCAAGTAC
                               |  |   | |   |      | ||||  || | | |    |  |      ||  | ||||||||| ||||| |||||||||||||||||||| |||||||| || | ||||||  | || ||   ||||||  |||| ||  | ||||  || || |  |
gtatgctttctaatgagtctcttatctaccatttagtgagtaagtataccggctttg--tctaatcttgttggttcaatccgtatttgcagGGGGTGTTGGGAATCAAGGTGAAGATCATGCTTGACTGGGACCCTACGGGCAAATCAGGACCAAAGACACCATTGCCTGATGTTGTGATCATTCATGCTC

upper sequence: EFJ34676 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: AT5G35530.1 (Arabidopsis thaliana), 3'ss of exon 5
-------------------------gtgcaagaactcgatcgttttgatttggatccagttt---ctaagcattg--gattgttctggcagGGGGTTTTGGGGATCAAGGTGAAGATCATGCTGGACTGGGATCCAAAGGGCAAGACCGGGCCGTCGACACCGCTGCCGGACATGGTGACGATCCAAGTAC
                          | |  |||    ||  |    | |  ||||  || |   || |   | |   ||       |||||| ||  | ||  ||||||||||||||||||| |||||||| || ||||||||    || |||  ||||||  |||| ||  | ||||  |||||   ||
gtcagttcttcacagtggaaacctgtttcttgaatcacattctacctagtgagatcttgtgtaacctgaatctggttaatcacatgtgcagGGTGTGCTTGGTCTCAAGGTGAAGATCATGCTTGACTGGGACCCCAAGGGCAAACAAGGACCGATGACACCATTGCCTGATGTTGTGATCATCCATACAC

upper sequence: EFJ34676 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: Vv09s0002g01460.t01 (Vitis vinifera), 3'ss of exon 5
----------------------------------gtgcaagaactcgatcgttt--tgatttggatccagttt-ctaagcattggattgttctggc--agGGGGTTTTGGGGATCAAGGTGAAGATCATGCTGGACTGGGATCCAAAGGGCAAGACCGGGCCGTCGACACCGCTGCCGGACATGGTGACGATCCAAGTAC
                                   | |||    |   | || |  |  ||   | |   ||| ||      || | |    ||||  |||| |||||||| |||||||||||||||||||| ||||||||||| |||||||||   || ||    ||||| || || ||  | || || |||||    |
aatctcctattgcatggttccttacctgctttgatttcaatgttttagttgtctattacttcccaccttttttacttttttgtgaacttaattggcacagGGTGTTTTGGGTATCAAGGTGAAGATCATGCTTGACTGGGATCCCAAGGGCAAGCAGGGCCCTAAAACACCTCTACCTGATCTTGTCACCATCCACACCC

upper sequence: EFJ34676 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: Vv04s0008g01750.t01 (Vitis vinifera), 3'ss of exon 5
-----------------------------------------gtgcaagaactcgatcgttttgatttggatccagtttctaagc--attggattgttctg------gcagGGGGTTTTGGGGATCAAGGTGAAGATCATGCTGGACTGGGATCCAAAGGGCAAGACCGGGCCGTCGACACCGCTGCCGGACATGGTGACGATCCAAGTAC
                                          ||| | | || |||    |   |||   |   |  ||   ||  |||    | ||||         |||| ||  | || |||||||| ||||||||||| ||||||||||| |||||||||   || ||  | || ||  |||| ||  ||||||| || ||   ||
gtacatgctataatgtctcctggttttggttgaattgttagctgccacatcttgatttcatcattttatttgttgaatcccggctgattttccttttctatggtgtatagGGCGTCCTTGGTATCAAGGTCAAGATCATGCTCGACTGGGATCCCAAGGGCAAGCAGGGCCCCACAACTCCATTGCCTGATCTGGTGACTATTCACACAC

upper sequence: EFJ34676 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: PP1S136_175V6.1 (Physcomitrella patens), 3'ss of exon 5
----------------------------------------------gtgcaagaactcg--atcgttttgatttgg--------atccagtttctaagcat---------tggattg----ttctggcagGGGGTTTTGGGGATCAAGGTGAAGATCATGCTGGACTGGGATCCAAAGGGCAAGACCGGGCCGTCGACACCGCTGCCGGACATGGTGACGATCCAAGTAC
                                               ||| |||  |||  ||||||||   |           ||||||| | |   | |         |  |||     |  |||||||| || ||||| |||||||| ||||||||||| |||||||| ||||||||||||   || ||   ||| || || || ||  |||| || |||||  | |
gtatgtggatcttcatagtgtttttggtcttcaattttctctgacgatgctagatttcgtcatcgtttttgctctatatacctaatccagtgtattgacgtgttacttttttaattactgttcttggcagGGAGTGTTGGGCATCAAGGTAAAGATCATGCTCGACTGGGACCCAAAGGGCAAGCAAGGCCCCATGACCCCTCTTCCAGATGTGGTTACTATCCATATGC

upper sequence: EFJ34676 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: PP1S454_3V6.1 (Physcomitrella patens), 3'ss of exon 5
----------------------------------------------------------------------------------------------gtgcaagaactcgatcgttttgatttggatccagtttctaagcattggattgttctggcagGGGGTTTTGGGGATCAAGGTGAAGATCATGCTGGACTGGGATCCAAAGGGCAAGACCGGGCCGTCGACACCGCTGCCGGACATGGTGACGATCCAAGTAC
                                                                                                | ||    |  |   |   | | || | |    |   |   ||||   | ||||   |||| |||||||| |||||||| ||||||||||| ||||||||||| |||||||||   || ||   ||| || || || ||  |||| || |||||  | |
gtatgttacatatccttggccatttctctgttaactgagtttttctggctcttcccttatacttcttgtatcaaattgagttatctcagcatttcggtaatgctttcagtttgccgttgtgaaactgaatcgaagatattgctgtcttct---agGGAGTTTTGGGTATCAAGGTCAAGATCATGCTCGACTGGGATCCCAAGGGCAAGCAAGGACCTATGACTCCACTTCCAGATGTGGTCACCATCCATATGC

upper sequence: EFJ34676 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: PP1S127_74V6.1 (Physcomitrella patens), 3'ss of exon 5
------------------------------------------------------gtgcaaga-actcgatcgttttgatttggatcc--agtttctaagcattggattgttctggcagGGGGTTTTGGGGATCAAGGTGAAGATCATGCTGGACTGGGATCCAAAGGGCAAGACCGGGCCGTCGACACCGCTGCCGGACATGGTGACGATCCAAGTAC
                                                       ||   || | ||| |  |   ||  || |||   |||     |  | |    | |  |  ||||| ||  |||| || ||||||||||||||||| ||||||||||||||||| |||   || ||   ||| || || || ||  | ||||| || ||  | |
gtacacaagatgcttgatgtccgtcagtagctcctttttcgtactagaaagatattgattgatagtcggtgttcccgaagtgaatctgaagtggaggattactttggtatgtttacagGGCGTGCTGGGCATTAAGGTGAAGATCATGCTCGACTGGGATCCAAAGGGGAAGCAAGGACCCATGACTCCACTTCCCGATGTAGTGACTATTCACATGC

upper sequence: EFJ34676 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: PP1S29_222V6.1 (Physcomitrella patens), 3'ss of exon 5
-------------------------------------------------------------------------------------------gtgcaagaactcgatcgttttgatttggatccagtttctaagc----attgga-----ttgttctggcagGGGGTTTTGGGGATCAAGGTGAAGATCATGCTGGACTGGGATCCAAAGGGCAAGACCGGGCCGTCGACACCGCTGCCGGACATGGTGACGATCCAAGTAC
                                                                                           || | | || |      |  | |||  | |     | || |||    |||| |     |  |||| |||||| || ||||| |||||||| ||||||||||| ||||||||||| || |||||    || ||   ||| || || || ||  |||| || |||||  | |
gtattaacagatttttttgatacccctatgtttactcctccttgtgcagaattaatcttcgattgtttccatccttgcattatactaaatagttctataattgaggtttcattattccgttggctctactgagcctgaattgaagctattccttcttgcagGGAGTGTTGGGTATCAAGGTCAAGATCATGCTCGACTGGGATCCCAAAGGCAAACAAGGACCCATGACTCCACTCCCAGATGTGGTTACCATCCACATGC

upper sequence: EFJ34676 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: PP1S41_146V6.1 (Physcomitrella patens), 3'ss of exon 5
--------------------------------------------------------------------------gtgcaagaactcgatcgt--tttgatttggatccagtttctaagcattggattgttctgg-cagGGGGTTTTGGGGATCAAGGTGAAGATCATGCTGGACTGGGATCCAAAGGGCAAGACCGGGCCGTCGACACCGCTGCCGGACATGGTGACGATCCAAGTAC
                                                                              || | |||| | |    |||  |   ||  |  ||  ||   ||   || || |   ||||| || ||||| ||||| || ||||||||||| |||||||| ||||||||||||   || ||   ||| || || || ||  |||| || |||||  | |
gtttgtcgagcagctattcagtggtgtcctctctgtggtctccttgctgatttctcctacggtctttgttttcaagaaaaaatctcgtttgcaagttgtctgtaatgtatcttagaaatgtttcgttatttttttcagGGTGTATTGGGTATCAAAGTTAAGATCATGCTCGACTGGGACCCAAAGGGCAAGCAAGGACCCATGACCCCTCTTCCAGATGTGGTCACCATCCATATGC

upper sequence: EFJ34676 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: PP1S487_22V6.1 (Physcomitrella patens), 3'ss of exon 4
------------------------------------------------------------------------------gtgcaagaactcgatcgttttgatttggatccagtttctaagcattggattgttctg----gcagGGGGTTTTGGGGATCAAGGTGAAGATCATGCTGGACTGGGATCCAAAGGGCAAGACCGGGCCGTCGACACCGCTGCCGGACATGGTGACGATCCAAGTAC
                                                                               |   |   ||  ||| ||||     | |    |   ||   || | |  |    |     |||||| || ||||| |||||||||||||| ||||| |||||||| || |||| ||||   ||  |   ||| |  || || ||  ||||||| || ||  | |
gcacgtgtggacattttttgtctaatggtggctgtttcttcatgctagagacctattacacttctacaacgtttcatgtttttaatgctacatcattttctacagaaatatgagacttgtcagttgtcttccttactgtgcagGGAGTATTGGGTATCAAGGTGAAGATTATGCTCGACTGGGACCCCAAGGTCAAGCAAGGATCTGTGACTCTACTTCCAGATGTGGTGACCATTCACATGC

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|169075229|gb|FE484111.1|FE484111
EST:     CCGTGAACGAGTTCATTGACAGGGCCGTGCGCCACGTCCTTTTGCGCCAG                         GGGGTTTTGGGGATCAAGGTGAAGATCATGCTGGACTGGGATCCAAAGGGC
genomic: CCGTGAACGAGTTCATTGACAGGGCCGTGCGCCACGTCCTTTTGCGCCAGgtgcaagaac ... gttctggcagGGGGTTTTGGGGATCAAGGTGAAGATCATGCTGGACTGGGATCCAAAGGGC




















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), 34 (downstream exon)
Score: 26

CGCCAAGTCGATGAAGTTCAAGGACGGATACATGATCTCGTCTGGCAGCCCCGTGAACGAGTTCATTGACAGGGCCGTGCGCCACGTCCTTTTGCGCCAGgtgcaagaac ... gttctggcagGGGGTTTTGGGGATCAAGGTGAAGATCATGCTGGACTGGGATCCAAAGGGCAAGACCGGGCCGTCGACACCGCTGCCGGACATGGTGACGATCCAAGTAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaactcgatcgttttgatttggatccagtttctaagcattggattgttctggcagGGGGTTTTGGGGATCAAGGTGAAGATCATGCTGGACTGGGATCCAAAGGGCAAGACCGGGCCGTCGACACCGCTGCCGGACATGGTGACGATCCAAGTAC
           ttttgat  putative branch site (score: 26)
                                           ttgttct  putative PPT
           ttttgattt  TA-rich tract