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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtcgagtttttcgagttcctctgttacaaagtttctttttttcttgcttcacagGGTGCATTGGACGGTGGACTAGACATCCCGCACAGCGAGAAGCGTTTCGCCGGCTACAGCAAGGAGGACAAGTCCCTGAATGCCGAAGTGCACCGGAAGT

Basic information

species Selaginella moellendorffii
transcript EFJ17161
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ17161 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: PP1S38_329V6.1 (Physcomitrella patens), 3'ss of exon 7
-------------------------------------------------------------------------------------gtttgtcgagtttttcgagttcctctgttacaaagtttctttttttcttgcttcacagGGTGCATTGGACGGTGGACTAGACATCCCGCACAGCGAGAAGCGTTTCGCCGGCTACAGCAAGGAGGACAAGTCCCTGAATGCCGAAGTGCACCGGAAGT
                                                                                      ||    | |     |||| |   |   || |      || |  | ||   ||  |||||||| ||||| || ||  ||||  | || |||||||||||||| |||||||||||||||||||| ||||||||| ||||||||||  | ||||||||||
gtaagtattctggatgactctctacggaggttactgccactcctgtcattccgtttcactttcaccaatactagtaaggaaatagattccgagtgacagccgagcttaacc-ctagacgtcacctatcatcctgcttttccagGGTGCGTTGGATGGAGGTTTAGATGTTCCTCACAGCGAGAAGCGCTTCGCCGGCTACAGCAAGGAAGACAAGTCCTTGAATGCCGAGATTCACCGGAAGT

upper sequence: EFJ17161 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: PP1S364_3V6.1 (Physcomitrella patens), 3'ss of exon 6
--------------------------------------gtttgtcg--agtttttcgagttcctctgt-tacaaagtttctttttttcttgc-ttcacagGGTGCATTGGACGGTGGACTAGACATCCCGCACAGCGAGAAGCGTTTCGCCGGCTACAGCAAGGAGGACAAGTCCCTGAATGCCGAAGTGCACCGGAAGT
                                      | || ||    ||   || ||| | |   | |  | |   |  |||| | |    |    ||||||| |||||||||||| ||||| | || |||||||||||||| || || || |||| ||||||||| ||||| |||||||||||  | ||||| ||||
ttatcatcaaatggaaacgaaaatgttcatctcggtgaggttctcagtggtcggtcaagtccattcatatttatatcctggttttctgtcatatctttagGGTGCTTTGGACGGTGGATTAGACGTTCCCCACAGCGAGAAGCGCTTTGCAGGTTACAACAAGGAGGATAAGTCTCTGAATGCCGAGATTCACCGCAAGT

upper sequence: EFJ17161 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: PP1S371_31V6.3 (Physcomitrella patens), 3'ss of exon 5
--------------------------------------------------------------------------------------------------------gtttgt---cgagtttttcgagttcctctgttacaaagtttctttttttcttgct------tcacagGGTGCATTGGACGGTGGACTAGACATCCCGCACAGCGAGAAGCGTTTCGCCGGCTACAGCAAGGAGGACAAGTCCCTGAATGCCGAAGTGCACCGGAAGT
                                                                                                        | |||     || ||   ||| |   |   |||||     ||||| ||| ||  |      | |||||| || || || || ||| | ||  | || ||||| |||||||| |||||||| | |||||||||||| || ||| ||||||| ||    || || ||||
gtatccttatcttcccaactttctcacatgttatgatgcatttacaatacaagagaaaatgcattgatgtcggtacaagacctggcataatttcggtatgtgttgcttgcgtaagaattcagcgaatgtttgctttacagcacatctttgtttgtttatctattattacagGGAGCTTTAGATGGAGGATTGGATGTTCCTCACAGTGAGAAGCGGTTCGCCGGTTTCAGCAAGGAGGATAAATCCTTGAATGCTGAGACACATCGCAAGT

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|169079162|gb|FE490909.1|FE490909
EST:     TTGGCCTCGTCCGGACTACAACGGGCAACCGAGTCTTTGGTGCCTTGAAG                         GGTGCATTGGACGGTGGACTAGATATCCCGCACAGCGAGAAACGTTTTGCC
genomic: TTGGCCTGGTCCGGACTACAACGGGCAACCGAGTCTTTGGTGCCTTGAAGgtttgtcgag ... tgcttcacagGGTGCATTGGACGGTGGACTAGACATCCCGCACAGCGAGAAGCGTTTCGCC
EST: gi|169079163|gb|FE490910.1|FE490910
EST:     TTGGCCTCGTCCGGACTACAACGGGCAACCGAGTCTTTGGTGCCTTGAAG                         GGTGCATTGGACGGTGGACTAGATATCCCGCACAGCGAGAAACGTTTTGCC
genomic: TTGGCCTGGTCCGGACTACAACGGGCAACCGAGTCTTTGGTGCCTTGAAGgtttgtcgag ... tgcttcacagGGTGCATTGGACGGTGGACTAGACATCCCGCACAGCGAGAAGCGTTTCGCC
EST: gi|169033526|gb|FE442078.1|FE442078
EST:     TTGGCCTGGTCCGGACTACAACGGGCAACCGAGTCTTTGGTGCCTTGAAG                         GGTGCATTGGACGGTGGACTAGACATCCCGCACAGCGAGAAGCGTTTCGCC
genomic: TTGGCCTGGTCCGGACTACAACGGGCAACCGAGTCTTTGGTGCCTTGAAGgtttgtcgag ... tgcttcacagGGTGCATTGGACGGTGGACTAGACATCCCGCACAGCGAGAAGCGTTTCGCC
EST: gi|169110841|gb|FE509324.1|FE509324
EST:     TTGGCCTCGTCCGGACTACAACGGGCAACCGAGTCTTTGGTGCCTTGAAG                         GGTGCATTGGACGGTGGACTAGATATCCCGCACAGCGAGAAACGTTTTGCC
genomic: TTGGCCTGGTCCGGACTACAACGGGCAACCGAGTCTTTGGTGCCTTGAAGgtttgtcgag ... tgcttcacagGGTGCATTGGACGGTGGACTAGACATCCCGCACAGCGAGAAGCGTTTCGCC
EST: gi|169026340|gb|FE433431.1|FE433431
EST:     TTGGCCTCGTCCGGACTACAACGGGCAACCGAGTCTTTGGTGCCTTGAAG                         GGTGCATTGGACGGTGGACTAGATATCCCGCACAGCGAGAAACGTTTTGCC
genomic: TTGGCCTGGTCCGGACTACAACGGGCAACCGAGTCTTTGGTGCCTTGAAGgtttgtcgag ... tgcttcacagGGTGCATTGGACGGTGGACTAGACATCCCGCACAGCGAGAAGCGTTTCGCC
EST: gi|169051355|gb|FE459213.1|FE459213
EST:     TTGGCCTGGTCCGGACTACAACGGGCAACCGAGTCTTTGGTGCCTTGAAG                         GGTGCATTGGACGGTGGACTAGACATCCCGCACAGCGAGAAGCGTTTCGCC
genomic: TTGGCCTGGTCCGGACTACAACGGGCAACCGAGTCTTTGGTGCCTTGAAGgtttgtcgag ... tgcttcacagGGTGCATTGGACGGTGGACTAGACATCCCGCACAGCGAGAAGCGTTTCGCC
EST: gi|169110842|gb|FE509325.1|FE509325
EST:     TTGGCCTCGTCCGGACTACAACGGGCAACCGAGTCTTTGGTGCCTTGAAG                         GGTGCATTGGACGGTGGACTAGATATCCCGCACAGCGAGAAACGTTTTGCC
genomic: TTGGCCTGGTCCGGACTACAACGGGCAACCGAGTCTTTGGTGCCTTGAAGgtttgtcgag ... tgcttcacagGGTGCATTGGACGGTGGACTAGACATCCCGCACAGCGAGAAGCGTTTCGCC
EST: gi|169051354|gb|FE459212.1|FE459212
EST:     TTGGCCTGGTCCGGACTACAACGGGCAACCGAGTCTTTGGTGCCTTGAAG                         GGTGCATTGGACGGTGGACTAGACATCCCGCACAGCGAGAAGCGTTTCGCC
genomic: TTGGCCTGGTCCGGACTACAACGGGCAACCGAGTCTTTGGTGCCTTGAAGgtttgtcgag ... tgcttcacagGGTGCATTGGACGGTGGACTAGACATCCCGCACAGCGAGAAGCGTTTCGCC
EST: gi|70670052|gb|DN838629.1|DN838629
EST:     TTGGCCTCGTCCGGACTACAACGGGCAACCGAGTCTTTGGTGCCTTGAAG                         GGTGCATTGGACGGTGGACTAGATATCCCGCACAGCGAGAAACGTTTTGCC
genomic: TTGGCCTGGTCCGGACTACAACGGGCAACCGAGTCTTTGGTGCCTTGAAGgtttgtcgag ... tgcttcacagGGTGCATTGGACGGTGGACTAGACATCCCGCACAGCGAGAAGCGTTTCGCC
EST: gi|169041727|gb|FE449298.1|FE449298
EST:     TTGGCCTCGTCCGGACTACAACGGGCAACCGAGTCTTTGGTGCCTTGAAG                         GGTGCATTGGACGGTGGACTAGATATCCCGCACAGCGAGAAACGTTTTGCC
genomic: TTGGCCTGGTCCGGACTACAACGGGCAACCGAGTCTTTGGTGCCTTGAAGgtttgtcgag ... tgcttcacagGGTGCATTGGACGGTGGACTAGACATCCCGCACAGCGAGAAGCGTTTCGCC
EST: gi|169033527|gb|FE442079.1|FE442079
EST:     TTGGCCTGGTCCGGACTACAACGGGCAACCGAGTCTTTGGTGCCTTGAAG                         GGTGCATTGGACGGTGGACTAGACATCCCGCACAGCGAGAAGCGTTTCGCC
genomic: TTGGCCTGGTCCGGACTACAACGGGCAACCGAGTCTTTGGTGCCTTGAAGgtttgtcgag ... tgcttcacagGGTGCATTGGACGGTGGACTAGACATCCCGCACAGCGAGAAGCGTTTCGCC

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: 109

CGTTGAAACTCTGGACGAGAACAGGCGTCCATTCAGGGCCCTTCTTGATGTTGGCCTGGTCCGGACTACAACGGGCAACCGAGTCTTTGGTGCCTTGAAGgtttgtcgag ... tgcttcacagGGTGCATTGGACGGTGGACTAGACATCCCGCACAGCGAGAAGCGTTTCGCCGGCTACAGCAAGGAGGACAAGTCCCTGAATGCCGAAGTGCACCGGAAGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtcgagtttttcgagttcctctgttacaaagtttctttttttcttgcttcacagGGTGCATTGGACGGTGGACTAGACATCCCGCACAGCGAGAAGCGTTTCGCCGGCTACAGCAAGGAGGACAAGTCCCTGAATGCCGAAGTGCACCGGAAGT
                                tttctttttttcttgc  CT-rich tract
                            aaagtttcttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtcgagtttttcgagttcctctgttacaaagtttctttttttcttgcttcacagGGTGCATTGGACGGTGGACTAGACATCCCGCACAGCGAGAAGCGTTTCGCCGGCTACAGCAAGGAGGACAAGTCCCTGAATGCCGAAGTGCACCGGAAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA