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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattcggcgtggattgcttaattcaagagtttctttttgctgacagacgtcattttagGCTGCTGTTAGCGCTTTGCAGGCGCAGCCCGTTGTAAACGCTGTGATCGACGGAGATGACATCATTTACAGAGACTACGTCGACATCAGCATTGCTGTTG

Basic information

species Selaginella moellendorffii
transcript EFJ38519
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ38519 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: LOC_Os04g32330.1 (Oryza sativa), 3'ss of exon 10
-------------------------gtattcgg--cgtggattgcttaattcaagagtttctt---tttgctga---cagacgtcattttagGCTGCTGTTAGCGCTTTGCAGGCGCAGCCCGTTGTAAACGCTGTGATCGACGGAGATGACATCATTTACAGAGACTACGTCGACATCAGCATTGCTGTTG
                         | |   |     | | ||| | | || |  | | | ||   | ||||     ||   |   | | ||||||||||||  ||  | ||    || ||  |||| || ||||| || || || ||||||||||| ||||||||||| || ||||||||  |||||||||
gtactgaccaatcttgtgtactgctgaagctgaactattgcttggtaattttactaatatattcaatgtgctcgttccatttgctttgtcagGCTGCTGTTACAGCACTTCAAAACCAACCAATTGTCAATGCTGTCATTGATGGTGATGACATCATATACAGAGACTATGTTGACATCAGTGTTGCTGTTG

upper sequence: EFJ38519 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GRMZM2G079538_T02 (Zea mays), 3'ss of exon 11
----------gtattcggcgtgg--attgcttaattcaagagtttctttttgctgacagacgtcattt-------tagGCTGCTGTTAGCGCTTTGCAGGCGCAGCCCGTTGTAAACGCTGTGATCGACGGAGATGACATCATTTACAGAGACTACGTCGACATCAGCATTGCTGTTG
          || || ||||| |  |    ||    | | | |||  | | |||| |  |    ||||       ||||||||||||   ||  | ||    |||||  |||| || ||||| || || || ||||||||||| |||||||||||||| ||||||||  |||||||||
gtatttgccagtcttaggcgttgcaaagcttttgcaccatacttttatgtggctggctaattatatttgttttggtagGCTGCTGTTTCTGCACTTCAAAACCAGCCAATTGTCAATGCTGTCATTGATGGTGATGACATCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTG

upper sequence: EFJ38519 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GRMZM5G807639_T03 (Zea mays), 3'ss of exon 10
----------gtattcggcgtggattgcttaattcaagagtttctttttgctgacagacgtcattt-------tagGCTGCTGTTAGCGCTTTGCAGGCGCAGCCCGTTGTAAACGCTGTGATCGACGGAGATGACATCATTTACAGAGACTACGTCGACATCAGCATTGCTGTTG
           |||  |  |   |    || |  ||    ||| | |  |||| |  |  | ||||        |||||||||||   ||  | ||    |||||  |||| || ||||| || || || ||||||||||| |||||||||||||| ||| ||||  |||||||||
gtacttagtcttatgtgttgcaaagcttttgaaccatacatttatatg-gctggctaattttatttattttgtcagGCTGCTGTTTCTGCACTTCAAAACCAGCCAATTGTTAATGCTGTCATTGATGGCGATGACATCATATACAGAGACTACGTAGACGTCAGTGTTGCTGTTG

upper sequence: EFJ38519 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: AT5G55070.1 (Arabidopsis thaliana), 3'ss of exon 12
------------------------------gtattcggcgtggattgcttaattcaagagtttctttttgctgacagacgtcattttagGCTGCTGTTAGCGCTTTGCAGGCGCAGCCCGTTGTAAACGCTGTGATCGACGGAGATGACATCATTTACAGAGACTACGTCGACATCAGCATTGCTGTTG
                               ||||  || |     |  | |  | |     |  | ||  |||   |  |  ||| ||||||||||||| ||  | |||   || || || ||||| || || ||||| |||||||| |||||||||||||||||||| || ||||| || |||||||
gtatggtaaaaaactcaaaagtttcctgaactatttagcatatcaggactcaaccgattaagtaatcttcttgaactat-ttgtttcagGCTGCTGTTAGTGCCCTCCAGCACCAACCTGTAGTAAATGCAGTTATCGATGGAGATGATATCATTTACAGAGACTACGTGGATATCAGTATCGCTGTTG

upper sequence: EFJ38519 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: PP1S2_220V6.1 (Physcomitrella patens), 3'ss of exon 6
-------------------------------------gtattcggcgtggattgcttaattcaagagtttctttttgctgacagacgtcat----tttagGCTGCTGTTAGCGCTTTGCAGGCGCAGCCCGTTGTAAACGCTGTGATCGACGGAGATGACATCATTTACAGAGACTACGTCGACATCAGCATTGCTGTTG
                                        ||||| ||| ||      | || |  |  |   |    ||       |  |    | ||||| ||||| || ||  |  ||      || |  ||||| || || ||||| |||||||| ||||| |||||||||||| | |||||||||||||||||||
gttttcccgctcgacattcctccgctggtgtttttccactttcggtgtgaatactgggagtctattgactggctcgcatgcgctttattgtggaatctagGCAGCTGTGAGTGCACTTAAGCAATTTCCTGCAGTAAATGCGGTAATCGATGGAGATGATATCATATACAGAGACTACATTGACATCAGCATTGCTGTTG

upper sequence: EFJ38519 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: PP1S154_6V6.2 (Physcomitrella patens), 3'ss of exon 10
--------------------------------gtattcggcgtggattgctta-attcaagagtttct----ttttgctgac---agacgtcatttt--agGCTGCTGTTAGCGCTTTGCAGGCGCAGCCCGTTGTAAACGCTGTGATCGACGGAGATGACATCATTTACAGAGACTACGTCGACATCAGCATTGCTGTTG
                                    ||| | |  | ||||   | ||||    | ||     ||||  ||    || | |   |||  |||| || || || ||  |  ||      || | ||| || ||||| || || |||||||||||||| ||| |||| ||||| |||||||||||||||||||
ttgctcggttgttatggcccaccataaaccctaagctcgtcatc-actgctggtaatcaatgactactacaactttgacgattttagtcttggatttacagGCAGCCGTGAGTGCACTCAAGCAATTTCCTGCTGTCAATGCTGTAATTGATGGAGATGACATCATCTACCGAGATTACGTTGACATCAGCATTGCTGTTG

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|169056867|gb|FE466458.1|FE466458
EST:     TTCAAGAAAAACATGGAGCAAAGCTTGGGTTCATGTCGGTGTTTGTCAAG                         GCTGCTGTTAGCGCTTTGCAGGCGCAGCCCGTTGTAAACGCTGTGATCGAC
genomic: TTCAAGAAAAACATGGAGCAAAGCTTGGGTTCATGTCGGTGTTTGTCAAGgtattcggcg ... gtcattttagGCTGCTGTTAGCGCTTTGCAGGCGCAGCCCGTTGTAAACGCTGTGATCGAC
EST: gi|169105894|gb|FE503552.1|FE503552
EST:     TTCAAGAAAAACATGGAGCAAAGCTTGGGTTCATGTCGGTGTTTGTCAAG                         GCTGCTGTTAGCGCTTTGCAGGCGCAGCCCGTTGTAAACGCTGTGATCGAC
genomic: TTCAAGAAAAACATGGAGCAAAGCTTGGGTTCATGTCGGTGTTTGTCAAGgtattcggcg ... gtcattttagGCTGCTGTTAGCGCTTTGCAGGCGCAGCCCGTTGTAAACGCTGTGATCGAC
EST: gi|169081309|gb|FE489793.1|FE489793
EST:     TTCAAGAAAAACATGGAGCAAAGCTTGGGTTCATGTCGGTGTTTGTCAAG                         GCTGCTGTTAGCGCTTTGCAGGCGCAGCCCGTTGTAAACGCTGTGATCGAC
genomic: TTCAAGAAAAACATGGAGCAAAGCTTGGGTTCATGTCGGTGTTTGTCAAGgtattcggcg ... gtcattttagGCTGCTGTTAGCGCTTTGCAGGCGCAGCCCGTTGTAAACGCTGTGATCGAC
EST: gi|169031261|gb|FE441129.1|FE441129
EST:     TTCAAGAAAAACATGGAGCAAAGCTTGGGTTCATGTCGGTGTTTGTCAAG                         GCTGCTGTTAGCGCTTTGCAGGCGCAGCCCGTTGTAAACGCTGTGATCGAC
genomic: TTCAAGAAAAACATGGAGCAAAGCTTGGGTTCATGTCGGTGTTTGTCAAGgtattcggcg ... gtcattttagGCTGCTGTTAGCGCTTTGCAGGCGCAGCCCGTTGTAAACGCTGTGATCGAC
EST: gi|169070985|gb|FE478923.1|FE478923
EST:     TTCAAGAAAAACATGGAGCAAAGCTTGGGTTCATGTCGGTGTTTGTCAAG                         GCTGCTGTTAGCGCTTTGCAGGCGCAGCCCGTTGTAAACGCTGTGATCGAC
genomic: TTCAAGAAAAACATGGAGCAAAGCTTGGGTTCATGTCGGTGTTTGTCAAGgtattcggcg ... gtcattttagGCTGCTGTTAGCGCTTTGCAGGCGCAGCCCGTTGTAAACGCTGTGATCGAC
EST: gi|169070986|gb|FE478924.1|FE478924
EST:     TTCAAGAAAAACATGGAGCAAAGCTTGGGTTCATGTCGGTGTTTGTCAAG                         GCTGCTGTTAGCGCTTTGCAGGCGCAGCCCGTTGTAAACGCTGTGATCGAC
genomic: TTCAAGAAAAACATGGAGCAAAGCTTGGGTTCATGTCGGTGTTTGTCAAGgtattcggcg ... gtcattttagGCTGCTGTTAGCGCTTTGCAGGCGCAGCCCGTTGTAAACGCTGTGATCGAC

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), 31 (downstream exon)
Score: 32

GACAAATGCAATGGCTTTGCGTGCAAAGTACAAGGACGAGTTTCAAGAAAAACATGGAGCAAAGCTTGGGTTCATGTCGGTGTTTGTCAAGgtattcggcg ... gtcattttagGCTGCTGTTAGCGCTTTGCAGGCGCAGCCCGTTGTAAACGCTGTGATCGACGGAGATGACATCATTTACAGAGACTACGTCGACATCAGCATTGCTGTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcggcgtggattgcttaattcaagagtttctttttgctgacagacgtcattttagGCTGCTGTTAGCGCTTTGCAGGCGCAGCCCGTTGTAAACGCTGTGATCGACGGAGATGACATCATTTACAGAGACTACGTCGACATCAGCATTGCTGTTG
                                  tgctgac  putative branch site (score: 32)
                                              tcatttt  putative PPT
              ttaattcaa  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattcggcgtggattgcttaattcaagagtttctttttgctgacagacgtcattttagGCTGCTGTTAGCGCTTTGCAGGCGCAGCCCGTTGTAAACGCTGTGATCGACGGAGATGACATCATTTACAGAGACTACGTCGACATCAGCATTGCTGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT