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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaaaaacatttttatacttgtctgctgaactaacatcttctgctggcagGGACTCGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGACATTGACATTGTTATCCATCCCCAATCCATTATACACTCCATGATCGAGA

Basic information

species Selaginella moellendorffii
transcript EFJ07179
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ07179 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: LOC_Os01g01710.2 (Oryza sativa), 3'ss of exon 8
-------------------------gtaa-aaaaacatttttatact-tgtctgctgaactaa-catcttctgctggcagGGACTCGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGACATTGACATTGTTATCCATCCCCAATCCATTATACACTCCATGATCGAGA
                          ||   |   ||| ||   | | | |   || || | | ||  |  | |   |||||  | || || |||||||| || ||||| ||||| ||||| || ||||||||||| ||||| ||||| || ||||| || |||||||| ||||| || |
gtgtttgcagtaaactttcagaattttactgaggtcatgttggcagtatttgcactaaaatgatcacttgattcatacagGGTTTAGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATACGATGACATTGAAATTGTGATCCACCCACAATCTATCATACACTCTATGATTGAAA

upper sequence: EFJ07179 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: GRMZM2G056975_T02 (Zea mays), 3'ss of exon 8
------------------------gtaaaaaaa----------catttttatacttgtctgctgaactaacatcttctgctggcagGGACTCGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGACATTGACATTGTTATCCATCCCCAATCCATTATACACTCCATGATCGAGA
                        | |||||||          ||| |||||  ||     || || | ||  |||   || | ||||  | || || |||||||| || ||||| ||||| ||||| |||||||||||||| ||||| || || || || || || |||||||| ||| | || |
gtgtcatagagctccatcttttttgaaaaaaaaatctttaatccatatttattattaaacactaaattgacgacttggtcttgtagGGTTTAGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATATGATGACATTGAGATTGTGATTCACCCACAGTCTATCATACACTCTATGGTTGAAA

upper sequence: EFJ07179 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: GRMZM2G379271_T01 (Zea mays), 3'ss of exon 2
-------------------------------------------------------------gtaaaaaaacatttttatacttgtctgctgaactaacatcttctgctggcagGGACTCGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGACATTGACATTGTTATCCATCCCCAATCCATTATACACTCCATGATCGAGA
                                                              |    | ||   |  ||   | |   || || | ||  |||   || | ||||  | || || |||||||| || ||||| ||||| ||||| |||||||||||||| ||||| || || || || || || |||||||| ||| | || |
gttgaagccatagaacaaaacgggtacgtgcctccttcctgctcctccctcctctgagttcatcgctagacgactccatgggtttggcctaaattgacgacttggtcttgtagGGTTTAGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATATGATGACATTGAGATTGTGATTCACCCACAGTCTATCATACACTCTATGGTTGAAA

upper sequence: EFJ07179 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: GRMZM2G036290_T01 (Zea mays), 3'ss of exon 8
-------------------------------gtaaaaaaacatttttatacttgtctgctgaactaacatcttctgctggcagGGACTCGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGACATTGACATTGTTATCCATCCCCAATCCATTATACACTCCATGATCGAGA
                                | ||     |||| |    ||     || || | ||| |||    | | ||||  | || || ||||| || || ||||| ||||| ||||| |||||||||||||| ||||| || || || ||||| || |||||||| ||| | || |
gtgtcttagagctccagcttttttaaatgtgtttaatccttatttattatgttaaacactaaagtgacaacttggtattgtagGGTTTAGAAGTTATTGAGGCACATTATTTATTTGGTGCTGAATATGATGACATTGAGATTGTGATTCACCCACAATCTATCATACACTCTATGGTTGAAA

upper sequence: EFJ07179 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: GLYMA17G09740.1 (Glycine max), 3'ss of exon 8
----------------------------------------------------------------gtaaaaaaacatttttatacttgtctgctgaactaacatcttctgctggcagGGACTCGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGACATTGACATTGTTATCCATCCCCAATCCATTATACACTCCATGATCGAGA
                                                                 |     |  | |||  ||  | |  | | || |         |  |  ||||| || || || |||||||| || || ||||||||||||||||||||| | ||||| ||||| || ||||| ||||| || ||||| || ||||| || |
gtttgtttctttttttatgtcaacatattggacgcaaatagcctttttataaatctgtttaattatgtggtatgaatttcctagctataaggtaaatttcttatacttcttcacagGGTCTAGAAGTAATTGAAGCACATTACTTGTTTGGAGCTGACTATGATCATATTGAGATTGTCATTCATCCACAATCAATCATACATTCAATGATTGAAA

upper sequence: EFJ07179 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: GLYMA05G02190.1 (Glycine max), 3'ss of exon 8
-------------------------------------------------------------gtaaaaaaacatttttatacttgtctgctgaactaacatcttctgctggcagGGACTCGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGACATTGACATTGTTATCCATCCCCAATCCATTATACACTCCATGATCGAGA
                                                              |     |  | |||  ||  | |  | | || |         |  |  ||||| || || || |||||||| || || ||||||||||||||||| ||| | ||||| ||||| || ||||| ||||| || ||||| || ||||| || |
gtttgcttctttttttatgtcatattgaatgaaaagagccattttataaatctgtttaattatgtggtatgaatttcctagctataaggtaaatttcttctgcttcttcacagGGTCTAGAAGTAATTGAAGCACATTACTTGTTTGGAGCTGACTACGATCATATTGAGATTGTCATTCATCCACAATCAATCATACATTCAATGATTGAAA

upper sequence: EFJ07179 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: AT5G62790.1 (Arabidopsis thaliana), 3'ss of exon 8
----------------------------------gtaaaaaaacatttttatacttgtctgctgaactaacatcttctgctggcagGGACTCGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGACATTGACATTGTTATCCATCCCCAATCCATTATACACTCCATGATCGAGA
                                   |   |||| |  |||   |  |   | |||  |      || |     ||||| || |||||||||||||| || ||||||||||||||||| ||||| || || || ||||| || ||||| |||   || ||||| |||||||| || |
gttaagattattttctcctaaggttaaactctgattttgaaaatacctttgatcaaggtagatgagttcttgattttttgaaacagGGTCTTGAGGTCATTGAAGCGCATTATTTGTTTGGAGCTGAGTATGACGATATAGAGATTGTCATTCATCCGCAAAGTATCATACATTCCATGATTGAAA

upper sequence: EFJ07179 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: PP1S62_157V6.2 (Physcomitrella patens), 3'ss of exon 10
----------------------------------------------------------------------------------------------------------------------------------------------------gtaaaaaaacatttttatacttgtctgctgaactaacatcttctgctgg-cagGGACTCGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGACATTGACATTGTTATCCATCCCCAATCCATTATACACTCCATGATCGAGA
                                                                                                                                                    | |   |  | |  || | |||      |||  | | || |  |||| | |||||  | || || ||||||||||||||| | || || ||||| || ||||||||||| |||||| ||||||||||||| || || || |||||| | ||||
gtaagctttttctgagttgcgcttgcaaagctggcaacaattcatttcactcgatgttttctcaaattttgtttttgcaaccaagtcctgctggtatctattttatggatgtcgcttcaattgaaatagttggtggatcttctttggagcatgcatgcttccttgtgcttagaaa-tgacgtcaaatgtgttgcttgtcagGGGTTGGAAGTGATTGAAGCTCACTATCTCTTCGGTGCTGATTACGATGACATTGATATTGTTGTCCATCCCCAATCAATCATTCATTCCATGGTGGAGA

upper sequence: EFJ07179 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: PP1S73_243V6.2 (Physcomitrella patens), 3'ss of exon 10
-----------------------------------------------------------------------------------------------------------------gtaaaaaaacatttttatacttgtctgct--------------gaactaacatcttctgctgg-cagGGACTCGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGACATTGACATTGTTATCCATCCCCAATCCATTATACACTCCATGATCGAGA
                                                                                                                  | |   ||  ||||| |    |    ||              ||  |  ||||   ||||   ||||| || || || |||||||| || ||| | || |||||||| || ||||| ||||| |||||| | ||||||||||| ||||| || |||||| | ||||
gtgggtcttcctgaattgcattttgatggctggcacgactttacatgaacaattttgttaacaggattttgtttcagctacctagtcttggtggtatcttcgttggatttttcatgagggaagttttttctgtcggatcactcgatgcttcggaatgacattgcatcgattgctattcagGGTCTGGAAGTGATTGAAGCCCATTATCTCTTCGGAGCTGATTACGATGATATTGATATTGTTGTTCATCCCCAATCAATTATTCATTCCATGGTGGAGA

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|169068926|gb|FE477267.1|FE477267
EST:     GGAGTATGGGAAAGAAAATTACTGTGGATTCGGCAACCTTGATGAACAAG                         GGACTCGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGAC
genomic: GGAGTATGGGAAAGAAAATTACTGTGGATTCGGCAACCTTGATGAACAAGgtaaaaaaac ... ctgctggcagGGACTCGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGAC
EST: gi|169096850|gb|FE498631.1|FE498631
EST:     GGAGTATGGGAAAGAAAATTACTGTGGATTCGGCAACCTTGATGAACAAG                         GGACTCGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGAC
genomic: GGAGTATGGGAAAGAAAATTACTGTGGATTCGGCAACCTTGATGAACAAGgtaaaaaaac ... ctgctggcagGGACTCGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGAC
EST: gi|169096851|gb|FE498632.1|FE498632
EST:     GGAGTATGGGAAAGAAAATTACTGTGGATTCGGCAACCTTGATGAACAAG                         GGACTCGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGAC
genomic: GGAGTATGGGAAAGAAAATTACTGTGGATTCGGCAACCTTGATGAACAAGgtaaaaaaac ... ctgctggcagGGACTCGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGAC
EST: gi|169034723|gb|FE443431.1|FE443431
EST:     GGAGTATGGGAAAGAAAATTACTGTGGATTCGGCAACCTTGATGAACAAG                         GGACTCGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGAC
genomic: GGAGTATGGGAAAGAAAATTACTGTGGATTCGGCAACCTTGATGAACAAGgtaaaaaaac ... ctgctggcagGGACTCGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGAC
EST: gi|169114145|gb|FE516824.1|FE516824
EST:     GGAGTATGGGAAAGAAAATTACTGTGGATTCGGCAACCTTGATGAACAAG                         GGACTCGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGAC
genomic: GGAGTATGGGAAAGAAAATTACTGTGGATTCGGCAACCTTGATGAACAAGgtaaaaaaac ... ctgctggcagGGACTCGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGAC
EST: gi|169106994|gb|FE505965.1|FE505965
EST:     GGAGTATGGGAAAGAAAATTACTGTGGATTCGGCAACCTTGATGAACAAG                         GGACTCGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGAC
genomic: GGAGTATGGGAAAGAAAATTACTGTGGATTCGGCAACCTTGATGAACAAGgtaaaaaaac ... ctgctggcagGGACTCGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGAC
EST: gi|169114144|gb|FE516823.1|FE516823
EST:     GGAGTATGGGAAAGAAAATTACTGTGGATTCGGCAACCTTGATGAACAAG                         GGACTCGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGAC
genomic: GGAGTATGGGAAAGAAAATTACTGTGGATTCGGCAACCTTGATGAACAAGgtaaaaaaac ... ctgctggcagGGACTCGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGAC
EST: gi|169025379|gb|FE435993.1|FE435993
EST:     GGAGTATGGGAAAGAAAATTACTGTGGATTCGGCAACCTTGATGAACAAG                         GGACTCGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGAC
genomic: GGAGTATGGGAAAGAAAATTACTGTGGATTCGGCAACCTTGATGAACAAGgtaaaaaaac ... ctgctggcagGGACTCGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGAC
EST: gi|169076204|gb|FE485234.1|FE485234
EST:     GGAGTATGGGAAAGAAAATTACTGTGGATTCGGCAACCTTGATGAACAAG                         GGACTCGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGAC
genomic: GGAGTATGGGAAAGAAAATTACTGTGGATTCGGCAACCTTGATGAACAAGgtaaaaaaac ... ctgctggcagGGACTCGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGAC
EST: gi|169081281|gb|FE488764.1|FE488764
EST:     GGAGTATGGGAAAGAAAATTACTGTGGATTCGGCAACCTTGATGAACAAG                         GGACTCGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGAC
genomic: GGAGTATGGGAAAGAAAATTACTGTGGATTCGGCAACCTTGATGAACAAGgtaaaaaaac ... ctgctggcagGGACTCGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGAC

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: 33 (upstream exon), 34 (downstream exon)
Score: 19

GGAAAGGCTCAAGGACGTCAAACCAGCAGATGCGCTGAAGCATCCAAACTGGAGTATGGGAAAGAAAATTACTGTGGATTCGGCAACCTTGATGAACAAGgtaaaaaaac ... ctgctggcagGGACTCGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGACATTGACATTGTTATCCATCCCCAATCCATTATACACTCCATGATCGAGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaaaaaaacatttttatacttgtctgctgaactaacatcttctgctggcagGGACTCGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGACATTGACATTGTTATCCATCCCCAATCCATTATACACTCCATGATCGAGA
                                 aactaac  putative branch site (score: 19)
                                         tcttctgct  CT-rich tract
     aaaaaaacatttttat  TA-rich tract