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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctatggtttccaaacttttctaggccagctcgttaatagttttgcgtggtactttagGACGTGATCTTGATCGCAACCAGGCGCATCTTGAGGCCGCCGAGGAAGGGCGCCGCCGTCTCCAGACCAAGGAGCCGGACCCTCACTGCCGTGCACGACG

Basic information

species Selaginella moellendorffii
transcript EFJ26379
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ26379 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: PP1S134_167V6.1 (Physcomitrella patens), 3'ss of exon 1
------------------------------------------------------------------------------------------------------------------------------gtaagctatggtttc--caaact------tttctaggccagctcgt-taatagttttgcgtggtacttt---agGACGTGATCTTGATCGCAACCAGGCGCATCTTGAGGCCGCCGAGGAAGGGCGCCGCCGTCTCCAGACCAAGGAGCCGGACCCTCACTGCCGTGCACGACG
                                                                                                                               | |  | | ||||   |||| |       | |||    | | |   ||| | |    | || || |||   |||| ||  |  | ||||| |||||||| |||||||| || |||| ||||||| | ||||||  | | ||||||||| ||||||| || ||||||||||| |
gtgggtgctggcttccgaattgttgtgtcgggatggattgatttagtttttaagcagccgagttcaggtctcttgtcaagtctctttcctgctgttgttcagaggtgcacacatttgggagtgtcgctgaaatgtagttttgtcaaattagggttctgctataatatcactcgtaaaaatcccccttgttatttttgcagGATGTTGTTATCATCGCCACCAGGCGTATCTTGAGACCCCCGAAGAAGGGCTCAGCCGTCAACCGCCCAAGGAGCAGGACCCTGACAGCCGTGCACGAGG
















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|169066322|gb|FE472998.1|FE472998
EST:     AGATCCAACCCAGACTGGTGCGTGAGCTCGAGAAGAAATTCAGTGGCAAG                         GACGTGATCTTGATCGCAACCAGGCGCATCTTGAGGCCGCCGAGGAAGGGC
genomic: AGATCCAACCCAGACTGGTGCGTGAGCTCGAGAAGAAATTCAGTGGCAAGgtaagctatg ... ggtactttagGACGTGATCTTGATCGCAACCAGGCGCATCTTGAGGCCGCCGAGGAAGGGC
EST: gi|169096025|gb|FE497338.1|FE497338
EST:     AGATCCAACCCAGACTGGTGCGTGAGCTCGAGAAGAAATTCAGTGGCAAG                         GACGTGATCTTGATCGCAACCAGGCGCATCTTGAGGCCGCCGAGGAAGGGC
genomic: AGATCCAACCCAGACTGGTGCGTGAGCTCGAGAAGAAATTCAGTGGCAAGgtaagctatg ... ggtactttagGACGTGATCTTGATCGCAACCAGGCGCATCTTGAGGCCGCCGAGGAAGGGC
EST: gi|169066952|gb|FE475955.1|FE475955
EST:     AGATCCAACCCAGACTGGTGCGTGAGCTCGAGAAGAAATTCAGTGGCAAG                         GACGTGATCTTGATCGCAACCAGGCGCATCTTGAGGCCGCCGAGGAAGGGC
genomic: AGATCCAACCCAGACTGGTGCGTGAGCTCGAGAAGAAATTCAGTGGCAAGgtaagctatg ... ggtactttagGACGTGATCTTGATCGCAACCAGGCGCATCTTGAGGCCGCCGAGGAAGGGC
EST: gi|169034273|gb|FE445113.1|FE445113
EST:     AGATCCAACCCAGACTGGTGCGTGAGCTCGAGAAGAAATTCAGTGGCAAG                         GACGTGATCTTGATCGCAACCAGGCGCATCTTGAGGCCGCCGAGGAAGGGC
genomic: AGATCCAACCCAGACTGGTGCGTGAGCTCGAGAAGAAATTCAGTGGCAAGgtaagctatg ... ggtactttagGACGTGATCTTGATCGCAACCAGGCGCATCTTGAGGCCGCCGAGGAAGGGC
EST: gi|169034272|gb|FE445112.1|FE445112
EST:     AGATCCAACCCAGACTGGTGCGTGAGCTCGAGAAGAAATTCAGTGGCAAG                         GACGTGATCTTGATCGCAACCAGGCGCATCTTGAGGCCGCCGAGGAAGGGC
genomic: AGATCCAACCCAGACTGGTGCGTGAGCTCGAGAAGAAATTCAGTGGCAAGgtaagctatg ... ggtactttagGACGTGATCTTGATCGCAACCAGGCGCATCTTGAGGCCGCCGAGGAAGGGC
EST: gi|169078408|gb|FE488283.1|FE488283
EST:     AGATCCAACCCAGACTGGTGCGTGAGCTCGAGAAGAAATTCAGTGGCAAG                         GACGTGATCTTGATCGCAACCAGGCGCATCTTGAGGCCGCCGAGGAAGGGC
genomic: AGATCCAACCCAGACTGGTGCGTGAGCTCGAGAAGAAATTCAGTGGCAAGgtaagctatg ... ggtactttagGACGTGATCTTGATCGCAACCAGGCGCATCTTGAGGCCGCCGAGGAAGGGC
EST: gi|169062870|gb|FE472373.1|FE472373
EST:     AGATCCAACCCAGACTGGTGCGTGAGCTCGAGAAGAAATTCAGTGGCAAG                         GACGTGATCTTGATCGCAACCAGGCGCATCTTGAGGCCGCCGAGGAAGGGC
genomic: AGATCCAACCCAGACTGGTGCGTGAGCTCGAGAAGAAATTCAGTGGCAAGgtaagctatg ... ggtactttagGACGTGATCTTGATCGCAACCAGGCGCATCTTGAGGCCGCCGAGGAAGGGC
EST: gi|169037033|gb|FE442680.1|FE442680
EST:     AGATCCAACCCAGACTGGTGCGTGAGCTCGAGAAGAAATTCAGTGGCAAG                         GACGTGATCTTGATCGCAACCAGGCGCATCTTGAGGCCGCCGAGGAAGGGC
genomic: AGATCCAACCCAGACTGGTGCGTGAGCTCGAGAAGAAATTCAGTGGCAAGgtaagctatg ... ggtactttagGACGTGATCTTGATCGCAACCAGGCGCATCTTGAGGCCGCCGAGGAAGGGC
EST: gi|169093160|gb|FE494193.1|FE494193
EST:     AGATCCAACCCAGACTGGTGCGTGAGCTCGAGAAGAAATTCAGTGGCAAG                         GACGTGATCTTGATCGCAACCAGGCGCATCTTGAGGCCGCCGAGGAAGGGC
genomic: AGATCCAACCCAGACTGGTGCGTGAGCTCGAGAAGAAATTCAGTGGCAAGgtaagctatg ... ggtactttagGACGTGATCTTGATCGCAACCAGGCGCATCTTGAGGCCGCCGAGGAAGGGC
EST: gi|169057909|gb|FE465507.1|FE465507
EST:     AGATCCAACCCAGACTGGTGCGTGAGCTCGAGAAGAAATTCAGTGGCAAG                         GACGTGATCTTGATCGCAACCAGGCGCATCTTGAGGCCGCCGAGGAAGGGC
genomic: AGATCCAACCCAGACTGGTGCGTGAGCTCGAGAAGAAATTCAGTGGCAAGgtaagctatg ... ggtactttagGACGTGATCTTGATCGCAACCAGGCGCATCTTGAGGCCGCCGAGGAAGGGC
EST: gi|169073722|gb|FE483982.1|FE483982
EST:     AGATCCAACCCAGACTGGTGCGTGAGCTCGAGAAGAAATTCAGTGGCAAG                         GACGTGATCTTGATCGCAACCAGGCGCATCTTGAGGCCGCCGAGGAAGGGC
genomic: AGATCCAACCCAGACTGGTGCGTGAGCTCGAGAAGAAATTCAGTGGCAAGgtaagctatg ... ggtactttagGACGTGATCTTGATCGCAACCAGGCGCATCTTGAGGCCGCCGAGGAAGGGC
EST: gi|169037032|gb|FE442679.1|FE442679
EST:     AGATCCAACCCAGACTGGTGCGTGAGCTCGAGAAGAAATTCAGTGGCAAG                         GACGTGATTTTGATCGCAACCAGGCGCATCTTGAGGCCGCCGAGGAAGGGC
genomic: AGATCCAACCCAGACTGGTGCGTGAGCTCGAGAAGAAATTCAGTGGCAAGgtaagctatg ... ggtactttagGACGTGATCTTGATCGCAACCAGGCGCATCTTGAGGCCGCCGAGGAAGGGC
EST: gi|169109375|gb|FE514099.1|FE514099
EST:     AGATCCAACCCAGACTGGTGCGTGAGCTCGAGAAGAAATTCAGTGGCAAG                         GACGTGATCTTGATCGCAACCAGGCGCATCTTGAGGCCGCCGAGGAAGGGC
genomic: AGATCCAACCCAGACTGGTGCGTGAGCTCGAGAAGAAATTCAGTGGCAAGgtaagctatg ... ggtactttagGACGTGATCTTGATCGCAACCAGGCGCATCTTGAGGCCGCCGAGGAAGGGC
EST: gi|70670008|gb|DN838585.1|DN838585
EST:     AGATCCAACCCAGACTGGTGCGTGAGCTCGAGAAGAAATTCAGTGGCAAG                         GACGTGATCTTGATCGCAACCAGGCGCATCTTGAGGCCGCCGAGGAAGGGC
genomic: AGATCCAACCCAGACTGGTGCGTGAGCTCGAGAAGAAATTCAGTGGCAAGgtaagctatg ... ggtactttagGACGTGATCTTGATCGCAACCAGGCGCATCTTGAGGCCGCCGAGGAAGGGC
EST: gi|169096024|gb|FE497337.1|FE497337
EST:     AGATCCAACCCAGACTGGTGCGTGAGCTCGAGAAGAAATTCAGTGGCAAG                         GACGTGATCTTGATCGCAACCAGGCGCATCTTGAGGCCGCCGAGGAAGGGC
genomic: AGATCCAACCCAGACTGGTGCGTGAGCTCGAGAAGAAATTCAGTGGCAAGgtaagctatg ... ggtactttagGACGTGATCTTGATCGCAACCAGGCGCATCTTGAGGCCGCCGAGGAAGGGC
EST: gi|169031995|gb|FE440175.1|FE440175
EST:     AGATCCAACCCAGACTGGTGCGTGAGCTCGAGAAGAAATTCAGTGGCAAG                         GACGTGATCTTGATCGCAACCAGGCGCATCTTGAGGCCGCCGAGGAAGGGC
genomic: AGATCCAACCCAGACTGGTGCGTGAGCTCGAGAAGAAATTCAGTGGCAAGgtaagctatg ... ggtactttagGACGTGATCTTGATCGCAACCAGGCGCATCTTGAGGCCGCCGAGGAAGGGC
EST: gi|169106336|gb|FE506256.1|FE506256
EST:     AGATCCAACCCAGACTGGTGCGTGAGCTCGAGAAGAAATTCAGTGGCAAG                         GACGTGATCTTGATCGCAACCAGGCGCATCTTGAGGCCGCCGAGGAAGGGC
genomic: AGATCCAACCCAGACTGGTGCGTGAGCTCGAGAAGAAATTCAGTGGCAAGgtaagctatg ... ggtactttagGACGTGATCTTGATCGCAACCAGGCGCATCTTGAGGCCGCCGAGGAAGGGC
EST: gi|169069286|gb|FE480045.1|FE480045
EST:     AGATCCAACCCAGACTGGTGCGTGAGCTCGAGAAGAAATTCAGTGGCAAG                         GACGTGATCTTGATCGCAACCAGGCGCATCTTGAGGCCGCCGAGGAAGGGC
genomic: AGATCCAACCCAGACTGGTGCGTGAGCTCGAGAAGAAATTCAGTGGCAAGgtaagctatg ... ggtactttagGACGTGATCTTGATCGCAACCAGGCGCATCTTGAGGCCGCCGAGGAAGGGC
EST: gi|169045824|gb|FE451719.1|FE451719
EST:     AGATCCAACCCAGACTGGTGCGTGAGCTCGAGAAGAAATTCAGTGGCAAG                         GACGTGATCTTGATCGCAACCAGGCGCATCTTGAGGCCGCCGAGGAAGGGC
genomic: AGATCCAACCCAGACTGGTGCGTGAGCTCGAGAAGAAATTCAGTGGCAAGgtaagctatg ... ggtactttagGACGTGATCTTGATCGCAACCAGGCGCATCTTGAGGCCGCCGAGGAAGGGC
EST: gi|169046522|gb|FE457461.1|FE457461
EST:     AGATCCAACCCAGACTGGTGCGTGAGCTCGAGAAGAAATTCAGTGGCAAG                         GACGTGATCTTGATCGCAACCAGGCGCATCTTGAGGCCGCCGAGGAAGGGC
genomic: AGATCCAACCCAGACTGGTGCGTGAGCTCGAGAAGAAATTCAGTGGCAAGgtaagctatg ... ggtactttagGACGTGATCTTGATCGCAACCAGGCGCATCTTGAGGCCGCCGAGGAAGGGC
EST: gi|169069272|gb|FE480044.1|FE480044
EST:     AGATCCAACCCAGACTGGTGCGTGAGCTCGAGAAGAAATTCAGTGGCAAG                         GACGTGATTTTGATCGCAACCAGGCGCATCTTGAGGCCGCCGAGGAAGGGC
genomic: AGATCCAACCCAGACTGGTGCGTGAGCTCGAGAAGAAATTCAGTGGCAAGgtaagctatg ... ggtactttagGACGTGATCTTGATCGCAACCAGGCGCATCTTGAGGCCGCCGAGGAAGGGC
EST: gi|169073723|gb|FE483983.1|FE483983
EST:     AGATCCAACCCAGACTGGTGCGTGAGCTCGAGAAGAAATTCAGTGGCAAG                         GACGTGATCTTGATCGCAACCAGGCGCATCTTGAGGCCGCCGAGGAAGGGC
genomic: AGATCCAACCCAGACTGGTGCGTGAGCTCGAGAAGAAATTCAGTGGCAAGgtaagctatg ... ggtactttagGACGTGATCTTGATCGCAACCAGGCGCATCTTGAGGCCGCCGAGGAAGGGC
EST: gi|169064575|gb|FE471306.1|FE471306
EST:     AGATCCAACCCAGACTGGTGCGTGAGCTCGAGAAGAAATTCAGTGGCAAG                         GACGTGATCTTGATCGCAACCAGGCGCATCTTGAGGCCGCCGAGGAAGGGC
genomic: AGATCCAACCCAGACTGGTGCGTGAGCTCGAGAAGAAATTCAGTGGCAAGgtaagctatg ... ggtactttagGACGTGATCTTGATCGCAACCAGGCGCATCTTGAGGCCGCCGAGGAAGGGC
EST: gi|169036394|gb|FE443484.1|FE443484
EST:     AGATCCAACCCAGACTGGTGCGTGAGCTCGAGAAGAAATTCAGTGGCAAG                         GACGTGATCTTGATCGCAACCAGGCGCATCTTGAGGCCGCCGAGGAAGGGC
genomic: AGATCCAACCCAGACTGGTGCGTGAGCTCGAGAAGAAATTCAGTGGCAAGgtaagctatg ... ggtactttagGACGTGATCTTGATCGCAACCAGGCGCATCTTGAGGCCGCCGAGGAAGGGC
EST: gi|169066953|gb|FE475956.1|FE475956
EST:     AGATCCAACCCAGACTGGTGCGTGAGCTCGAGAAGAAATTCAGTGGCAAG                         GACGTGATCTTGATCGCAACCAGGCGCATCTTGAGGCCGCCGAGGAAGGGC
genomic: AGATCCAACCCAGACTGGTGCGTGAGCTCGAGAAGAAATTCAGTGGCAAGgtaagctatg ... ggtactttagGACGTGATCTTGATCGCAACCAGGCGCATCTTGAGGCCGCCGAGGAAGGGC

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: 114

CAAGGCGGTCGTGATCCACGTACCTTACCGCTTGAGAAAGGCGTATCAGAAGATCCAACCCAGACTGGTGCGTGAGCTCGAGAAGAAATTCAGTGGCAAGgtaagctatg ... ggtactttagGACGTGATCTTGATCGCAACCAGGCGCATCTTGAGGCCGCCGAGGAAGGGCGCCGCCGTCTCCAGACCAAGGAGCCGGACCCTCACTGCCGTGCACGACG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggtttccaaacttttctaggccagctcgttaatagttttgcgtggtactttagGACGTGATCTTGATCGCAACCAGGCGCATCTTGAGGCCGCCGAGGAAGGGCGCCGCCGTCTCCAGACCAAGGAGCCGGACCCTCACTGCCGTGCACGACG
                            cgttaat  putative branch site (score: 114)
                              ttaatagtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagctatggtttccaaacttttctaggccagctcgttaatagttttgcgtggtactttagGACGTGATCTTGATCGCAACCAGGCGCATCTTGAGGCCGCCGAGGAAGGGCGCCGCCGTCTCCAGACCAAGGAGCCGGACCCTCACTGCCGTGCACGACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG