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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaacgatgcttcttttttcttttctccctctttcgttctgatttgagattcgtgaccagGCGACACTTGCTTTCGTGGGTATGGGCGACGCGATGGTGAGCGGAGGAGGAAGTCAGTTCGTGGTTGCATTGTCAGCCATGATCTGTCTGTTCTCAATCT

Basic information

species Selaginella moellendorffii
transcript EFJ26393
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ14726 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: LOC_Os03g27260.1 (Oryza sativa), 3'ss of exon 4
-------------------------gtaaaacgatgcttcttttttcttttctccc---tctttcgttctga---tttgagattcgtgac--cagGCGACACTTGCTTTCGTGGGTATGGGCGACGCGATGGTGAGCGGAGGAGGAAGTCAGTTCGTGGTTGCATTGTCAGCCATGATCTGTCTGTTCTCAATCT
                         | |     ||| ||| |||| |||| ||  |   | ||    | |||   ||  |  ||  |     ||||   | | ||||| ||||| |||||  | || ||||||||||| || ||||||||||| |||||||||||||||||||| ||||| |||||| ||||  |
gtagatgtttaagatgcttacatttgaatggttatgtttcattttgctttgctggcaggtgttctaatgtgaatgttccatttttatactgacagGTACCCCCTGCTTCCGTGGATATGGCAGGCGTGATGGTGAGCGCAGAAGGAAGTCAGTCCGTGGTTGCATTGTCAGCCAAGATCTCTCTGTTATCAACTT

upper sequence: EFJ14726 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: LOC_Os07g42950.1 (Oryza sativa), 3'ss of exon 4
gtaaaacgatgcttcttttttc-----ttttc------tccctctttcgttctgatt------tgagattcgtg-accagGCGACACTTGCTTTCGTGGGTATGGGCGACGCGATGGTGAGCGGAGGAGGAAGTCAGTTCGTGGTTGCATTGTCAGCCATGATCTGTCTGTTCTCAATCT
|||||| |   ||  || | |       ||||      ||   |  | | |||||        ||  | | ||    |||||    ||||||| |||||||||||  | || ||||||||||| ||||||||||| || ||||||||||| |||||||| || || |||||| | ||  |
gtaaaaaggctctatttctattattgactttcggatattcatgcccttgctctgaccatattatgttacttgtatggcagGCACACCTTGCTTCCGTGGGTATGGCAGGCGTGATGGTGAGCGCAGGAGGAAGTCTGTCCGTGGTTGCATCGTCAGCCAGGACCTATCTGTTATTAACTT

upper sequence: EFJ14726 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GRMZM5G851698_T01 (Zea mays), 3'ss of exon 4
gtaaaacgatgcttcttttttcttttctccctctttcgttctgatttgagattcgtgaccagGCGACACTTGCTTTCGTGGGTATGGGCGACGCGATGGTGAGCGGAGGAGGAAGTCAGTTCGTGGTTGCATTGTCAGCCATGATCTGTCTGTTCTCAATCT-----------------------------------------------------------------------
                               |||     | |||| |||  |  ||    ||||    | ||||| || || |||||  | ||  |||||||||| ||||||||||| || |||||||| ||||| ||||| || || |||||| ||||  |                                                                       
-----------------------------tatctgaacatttgatatgaattgtgt----aggcactccctgcttccgcggttatggcaggcgtaatggtgagcgcaggaggaagtctgtccgtggttgtattGTGAGCCAAGACCTATCTGTTATCAACTTGGTAATTGTTAAGAAGGGTGAGAACGATCTGCCTGGTTTAACTGACACTGAGAAGCCAAGGATGAGGGGTC

upper sequence: EFJ14726 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GRMZM2G054136_T06 (Zea mays), 3'ss of exon 3
-------------------------------------gtaaaacgatgcttcttttttcttttctccctctttcgttctgatttgagattcgtgac-cagGCGACACTTGCTTTCGTGGGTATGGGCGACGCGATGGTGAGCGGAGGAGGAAGTCAGTTCGTGGTTGCATTGTCAGCCATGATCTGTCTGTTCTCAATCT
                                     ||  |         |  | || |  |||   ||||   |    ||| || ||   |     ||||    | ||||| ||||| |||||  | ||  |||||||||| ||||||||||| || ||||||||||| || ||||| || || |||||| ||||  |
ttctgctccataggggtatagagacttcctatgtccagtgtactctcaacaccatcttttactctgattcttatctgaacattcgatatcaattctgtagGCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGAAGTCTGTCCGTGGTTGCATCGTGAGCCAAGACCTATCTGTTATCAACTT

upper sequence: EFJ14726 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GRMZM2G054136_T01 (Zea mays), 3'ss of exon 4
----------------------gtaaaacgatgcttcttttttcttttctccctctttcgttctgatttgagattcgtgac-cagGCGACACTTGCTTTCGTGGGTATGGGCGACGCGATGGTGAGCGGAGGAGGAAGTCAGTTCGTGGTTGCATTGTCAGCCATGATCTGTCTGTTCTCAATCT
                      ||  |         |  | || |  |||   ||||   |    ||| || ||   |     ||||    | ||||| ||||| |||||  | ||  |||||||||| ||||||||||| || ||||||||||| || ||||| || || |||||| ||||  |
gtatagagacttcctatgtccagtgtactctcaacaccatcttttactctgattcttatctgaacattcgatatcaattctgtagGCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGAAGTCTGTCCGTGGTTGCATCGTGAGCCAAGACCTATCTGTTATCAACTT

upper sequence: EFJ14726 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GRMZM5G851698_T02 (Zea mays), 3'ss of exon 4
----------------------gtaaaa-cgatgcttcttttttcttttctccctctttcgttctgatttgagattcgt-gaccagGCGACACTTGCTTTCGTGGGTATGGGCGACGCGATGGTGAGCGGAGGAGGAAGTCAGTTCGTGGTTGCATTGTCAGCCATGATCTGTCTGTTCTCAATCT
                      |||    | |  |  | | |||    | |   ||||   |    |||||| ||   | |   ||||    | ||||| || || |||||  | ||  |||||||||| ||||||||||| || |||||||| ||||| ||||| || || |||||| ||||  |
gtatatagactgtatctccattgtactctcaacaccccctcttttacctgtggttcttatctgaacatttgatatgaattgtgtagGCACTCCCTGCTTCCGCGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGAAGTCTGTCCGTGGTTGTATTGTGAGCCAAGACCTATCTGTTATCAACTT

upper sequence: EFJ14726 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GRMZM2G054136_T02 (Zea mays), 3'ss of exon 3
----------------------gtaaaacgatgcttcttttttcttttctccctctttcgttctgatttgagattcgtgaccagGCGACACT-TGCTTTCGTGGGTATGGGCGACGCGATGGTGAGCGGAGGAGGAAGTCAGTTCGTGGTTGCATTGTCAGCCATGATCTGTCTGTTCTCAATCT
                      ||  |         |  | || |  |||   ||||   |    ||| || ||   |      | ||| |  ||||| ||||| |||||  | ||  |||||||||| ||||||||||| || ||||||||||| || ||||| || || |||||| ||||  |
gtatagagacttcctatttacagtgtactctcagcaccatcttttactctgattcttatctgaacattcgatatcaattctgtagGGACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGAAGTCTGTCCGTGGTTGCATCGTGAGCCAAGACCTATCTGTTATCAACTT

upper sequence: EFJ14726 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA13G31130.1 (Glycine max), 3'ss of exon 5
------------------------------------gtaaaacgatgcttcttttttcttttctccctctttcgttctgatttgagattcg--tgaccagGCGACACTTGCTTTCGTGGGTATGGGCGACGCGATGGTGAGCGGAGGAGGAAGTCAGTTCGTGGTTGCATTGTCAGCCATGATCTGTCTGTTCTCAATCT
                                     |   |  |    | | | || ||    |  | ||   ||    ||||    |    ||| ||||     |||| || ||||| || ||  | ||| |||| ||||| ||||||||||| |||||||| ||||||||||||| ||| || |||||||||||  |
agtaaggtcatgtatatttgttttttaggtactgctttttcataaccaatttatgttattggtccaatgttaaatttctgtttgttgcttacctgagcagGAACTCCTTGTTTCCGTGGTTACGGAAGGCGCAATGGAGAGCGTAGGAGGAAGTCTGTTCGTGGGTGCATTGTCAGCCCTGACCTCTCTGTTCTCAACTT

upper sequence: EFJ14726 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA15G08210.1 (Glycine max), 3'ss of exon 4
---------------------------------gtaaaacgat--gct--tcttttttcttttctccctctttcgttctgatttgagatt-cgtgaccagGCGACACTTGCTTTCGTGGGTATGGGCGACGCGATGGTGAGCGGAGGAGGAAGTCAGTTCGTGGTTGCATTGTCAGCCATGATCTGTCTGTTCTCAATCT
                                    ||||  |  ||    |||| || |||| ||  | ||   ||    ||   | || |     ||||     |||| || ||||| |||||  | ||| |||| ||||| ||||||||||| |||||||| ||||||||||||| ||| || |||||||||||  |
tttgaggtactgtttttttttataactggactcaggaaacttttagccaacctttgttattttttcaatgttaaatttcatttgttgcttacccatgcagGAACTCCTTGTTTCCGTGGTTATGGAAGGCGCAATGGAGAGCGTAGGAGGAAGTCTGTTCGTGGGTGCATTGTCAGCCCTGACCTCTCTGTTCTCAACTT

upper sequence: EFJ14726 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA07G31840.3 (Glycine max), 3'ss of exon 3
---------------------------------------gtaaaacgatgcttcttttttcttttctccctctttcgttctgatttgagattcgtgaccagGCGACACTTGCTTTCGTGGGTATGGGCGACGCGATGGTGAGCGGAGGAGGAAGTCAGTTCGTGGTTGCATTGTCAGCCATGATCTGTCTGTTCTCAATCT
                                        |   | ||| ||      |  || | | |    ||  |  || |||  |  |  ||| ||||     |||| || ||||| |||||  | ||| |||| ||||| || |||||||| |||||||||||||||||||| |  ||||| |||||| | || ||
tttatgcaatgatttttagctttaactagaaaccttttcattgcaggattctcagccatgtttatttgcagacttgttaatgttttttgcatt-tgagcagGAACTCCTTGTTTCCGTGGATATGGAAGGCGCAATGGAGAGCGTAGAAGGAAGTCTGTTCGTGGTTGCATTGTCAGTCCAGATCTCTCTGTTTTGAACCT

upper sequence: EFJ14726 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA08G45770.1 (Glycine max), 3'ss of exon 4
--------------------------------gtaaaac--gatgcttcttttttcttttctc------cctctttcgttctgatttgagattcgtgaccagGCGACACTTGCTTTCGTGGGTATGGGCGACGCGATGGTGAGCGGAGGAGGAAGTCAGTTCGTGGTTGCATTGTCAGCCATGATCTGTCTGTTCTCAATCT
                                || | |   | ||  |   ||||||||| ||      |   |||  || | |||||  | |  ||| ||||     ||||||| ||||| |||||  | ||  |||| ||||| ||||| ||||| |||||||| |||||||||||||  || || |||||| | ||  |
ttattaatttttaatagtgtaatgcatttgttgttatatcaggtgtctacattttcttttgtctacaaactaattttctttttatttgttact--tgaacagGAACTCCTTGCTTCCGTGGATATGGAAGGCGTAATGGAGAGCGTAGGAGAAAGTCTGTTCGTGGGTGCATTGTCAGCCCAGACCTCTCTGTTTTGAACTT

upper sequence: EFJ14726 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: AT4G31700.1 (Arabidopsis thaliana), 3'ss of exon 4
------------------------------------------gtaaaacgatgcttcttttttcttttctccctctttcgttc-----tgatttgagattcgtgaccagGCGACACTTGCTTTCGTGGGTATGGGCGACGCGATGGTGAGCGGAGGAGGAAGTCAGTTCGTGGTTGCATTGTCAGCCATGATCTGTCTGTTCTCAATCT
                                           |  |    |  || | | |   | | |    || | | |      || || |  ||  |||| ||||     |||||||  | ||  ||||  |  |   ||||||| |||| || ||||| ||||||||||||||||| |||| |||||| |||||||| || ||
gtaactaaacataataccttttcttacacttttgcatctataatggatttgtatttgtgtgtgtgtgtgttttgctgtagattaacattgtttcgtaatgggtgaacagGAACTCCTTGCTTCAGAGGACATGGAAGGAGAACTGGTGAGAGGAGAAGAAAGTCTGTTCGTGGTTGCATTGTGAGCCCTGATCTCTCTGTTCTGAACCT

upper sequence: EFJ14726 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: Vv03s0017g01350.t01 (Vitis vinifera), 3'ss of exon 4
-----------------------------------------------gtaaaacgatgcttcttttttcttt---tctccctctttcgttctgatttgagatt-cgtgaccagGCGACACTTGCTTTCGTGGGTATGGGCGACGCGATGGTGAGCGGAGGAGGAAGTCAGTTCGTGGTTGCATTGTCAGCCATGATCTGTCTGTTCTCAATCT
                                                |||    ||  || | |     ||   |||      ||  ||    |||  | ||   ||| ||||   | | ||||| ||||| |||||  ||||  |||| ||||| ||||||||| | |||||||| |||||||||||||| || || |||||| | ||  |
gtgagtaaactgggactgttctaatccttaaaaactgatcacaacccttaagttcatatttttatgcaagttgggtctatgagatttattacactttatgcttatttgagcagGTACCCCATGCTTCCGTGGATATGGAAGACGTAATGGAGAGCGAAGGAGGAAGGCTGTTCGTGGGTGCATTGTCAGCCAAGACCTCTCTGTTTTGAACTT

upper sequence: EFJ14726 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: Vv18s0001g06290.t01 (Vitis vinifera), 3'ss of exon 4
------------------------------------------------------------------------------------------gtaaaacgatgcttcttttttcttttctccctctttcgtt----ctgatttgagatt-cgtgaccagGCGACACTTGCTTTCGTGGGTATGGGCGACGCGATGGTGAGCGGAGGAGGAAGTCAGTTCGTGGTTGCATTGTCAGCCATGATCTGTCTGTTCTCAATCT
                                                                                           ||  || ||| ||  ||    | |  |   |  |   |     ||| | |    || | | | ||||   | |||||||||| || |||||  | ||  |||| ||| ||||||||||| | || ||||| |||||||||||||| || || |||||||| ||  |
gtgggtttttggtggtatattagtgttggtgcactgaccaccattccttcaagtttaagatggatcacggccagttagaagcatgttttgctaggaccatgttttgttgccttgtcatagatgatggatgaaaactgttctagttttgcttaagcagGAACCCCTTGCTTTCGAGGATATGGTAGGCGTAATGGAGAGAGGAGGAGGAAGGCTGTACGTGGGTGCATTGTCAGCCAGGACCTTTCTGTTCTGAACTT

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|169073801|gb|FE484022.1|FE484022
EST:     GAAGCAGGGCGTCCTCAAGACGAAGCGTGTGCGCCTCCTGTTAAACCGAG                         GCGACACTTGCTTTCGTGGGTATGGGCGACGCGATGGTGAGCGGAGGAGGA
genomic: GAAGCAGGGCGTTCTCAAGACGAAGCGTGTGCGCCTCCTGTTAAACCGAGgtaaaacgat ... tcgtgaccagGCGACACTTGCTTTCGTGGGTATGGGCGACGCGATGGTGAGCGGAGGAGGA
EST: gi|70670389|gb|DN838966.1|DN838966
EST:     GAAGCAGGGCGTTCTCAAGACGAAGCGTGTGCGCCTCCTGTTAAACCGAG                         GCGACACTTGCTTTCGTGGGTATGGGCGACGCGATGGTGAGCGGAGGAGGA
genomic: GAAGCAGGGCGTTCTCAAGACGAAGCGTGTGCGCCTCCTGTTAAACCGAGgtaaaacgat ... tcgtgaccagGCGACACTTGCTTTCGTGGGTATGGGCGACGCGATGGTGAGCGGAGGAGGA
EST: gi|169055041|gb|FE462956.1|FE462956
EST:     GAAGCAGGGCGTCCTCAAGACGAAGCGTGTGCGCCTCCTGTTAAACCGAG                         GCGACACTTGCTTTCGTGGGTATGGGCGACGCGATGGTGAGCGGAGGAGGA
genomic: GAAGCAGGGCGTTCTCAAGACGAAGCGTGTGCGCCTCCTGTTAAACCGAGgtaaaacgat ... tcgtgaccagGCGACACTTGCTTTCGTGGGTATGGGCGACGCGATGGTGAGCGGAGGAGGA
EST: gi|169039410|gb|FE449124.1|FE449124
EST:     GAAGCAGGGCGTCCTCAAGACGAAGCGTGTGCGCCTCCTGTTAAACCGAG                         GCGACACTTGCTTTCGTGGGTATGGGCGACGCGATGGTGAGCGGAGGAGGA
genomic: GAAGCAGGGCGTTCTCAAGACGAAGCGTGTGCGCCTCCTGTTAAACCGAGgtaaaacgat ... tcgtgaccagGCGACACTTGCTTTCGTGGGTATGGGCGACGCGATGGTGAGCGGAGGAGGA
EST: gi|169076015|gb|FE480997.1|FE480997
EST:     GAAGCAGGGCGTCCTCAAGACGAAGCGTGTGCGCCTCCTGTTAAACCGAG                         GCGACACTTGCTTTCGTGGGTATGGGCGACGCGATGGTGAGCGGAGGAGGA
genomic: GAAGCAGGGCGTTCTCAAGACGAAGCGTGTGCGCCTCCTGTTAAACCGAGgtaaaacgat ... tcgtgaccagGCGACACTTGCTTTCGTGGGTATGGGCGACGCGATGGTGAGCGGAGGAGGA
EST: gi|169061908|gb|FE470202.1|FE470202
EST:     GAAGCAGGGCGTTCTCAAGACGAAGCGTGTGCGCCTCCTGTTAAACCGAG                         GCGACACTTGCTTTCGTGGGTATGGGCGACGCGATGGTGAGCGGAGGAGGA
genomic: GAAGCAGGGCGTTCTCAAGACGAAGCGTGTGCGCCTCCTGTTAAACCGAGgtaaaacgat ... tcgtgaccagGCGACACTTGCTTTCGTGGGTATGGGCGACGCGATGGTGAGCGGAGGAGGA

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), 35 (downstream exon)
Score: 59

GGCTATGTCTTCAAGATCATGGGAGGATGTGACAAGGATGGCTTCCCTATGAAGCAGGGCGTTCTCAAGACGAAGCGTGTGCGCCTCCTGTTAAACCGAGgtaaaacgat ... tcgtgaccagGCGACACTTGCTTTCGTGGGTATGGGCGACGCGATGGTGAGCGGAGGAGGAAGTCAGTTCGTGGTTGCATTGTCAGCCATGATCTGTCTGTTCTCAATCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgcttcttttttcttttctccctctttcgttctgatttgagattcgtgaccagGCGACACTTGCTTTCGTGGGTATGGGCGACGCGATGGTGAGCGGAGGAGGAAGTCAGTTCGTGGTTGCATTGTCAGCCATGATCTGTCTGTTCTCAATCT
                               ttctgat  putative branch site (score: 59)
     ttcttttttctttt  TA-rich tract