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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatggatgcgtgacgccagtctcatgccgtcgtccatttgtgttcttgctgctgactctcactctcttctctctcgtcagTACATCTTGCAAGTTGGAGAGGGAGCAGCGGCGCAGTGCATTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTG

Basic information

species Selaginella moellendorffii
transcript EFJ34434
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ34434 (Selaginella moellendorffii), 3'ss of exon 10
lower sequence: Vv10s0116g01210.t01 (Vitis vinifera), 3'ss of exon 12
-----------gtgatggatgc--gtgacgccagtctcatg-ccgtcgtccatttgtgttcttgctgctgactctcac-tctcttctctc---tcgtcagTACATCTTGCAAGTTGGAGAGGGAGCAGCGGCGCAGTGCATTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTG
              | ||   |  || |    |    |||  | |   |   ||||  ||| |  |  |    ||||| |  ||| |||    |  ||||||| |  || | || || ||||| || || || |||||||||||||||||||  |  ||||||||||||||||||   || ||  ||||
atttgctcaattaaacggtcaccagtaaacatacatacatatctgaacttggtttgcattccttttcattgtcctcacattacttttcttggttgatcagTACGTGCTGAAGGTGGGCGAGGGTGCTGCTGCACAGTGCATTAGTGGCTTTATTGCCATGGACGTCCCTCCTCCACGAGGACCCCTCTG
















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|169031797|gb|FE438482.1|FE438482
EST:     ACGTCTCATTCACCATCGCAAATCAAACGTTCGAGCTGACGCCTAAACAG                         TACATCTTGCAAGTTGGAGAGGGAGCAGCGGCGCAGTGCATTAGTGGCTTT
genomic: ACGTCTCATTCACCATCGCAAATCAAACGTTCGAGCTGACGCCTAAACAGgtgatggatg ... ctctcgtcagTACATCTTGCAAGTTGGAGAGGGAGCAGCGGCGCAGTGCATTAGTGGCTTT
EST: gi|169031872|gb|FE438505.1|FE438505
EST:     ACGTCTCATTCACCATCGCAAATCAAACGTTCGAGCTGACGCCTAAACAG                         TACATCTTGCAAGTTGGAGAGGGAGCAGCGGCGCAGTGCATTAGTGGCTTT
genomic: ACGTCTCATTCACCATCGCAAATCAAACGTTCGAGCTGACGCCTAAACAGgtgatggatg ... ctctcgtcagTACATCTTGCAAGTTGGAGAGGGAGCAGCGGCGCAGTGCATTAGTGGCTTT
EST: gi|169112151|gb|FE513494.1|FE513494
EST:     ACGTCTCATTCACCATCGCAAATCAAACGTTCGAGCTGACGCCTAAACAG                         TACATCTTGCAAGTTGGAGAGGGAGCAGCGGCGCAGTGCATTAGTGGCTTT
genomic: ACGTCTCATTCACCATCGCAAATCAAACGTTCGAGCTGACGCCTAAACAGgtgatggatg ... ctctcgtcagTACATCTTGCAAGTTGGAGAGGGAGCAGCGGCGCAGTGCATTAGTGGCTTT
EST: gi|169095717|gb|FE498876.1|FE498876
EST:     ACGTCTCATTCACCATCGCAAATCAAACGTTCGAGCTGACGCCTAAACAG                         TACATCTTGCAAGTTGGAGAGGGAGCAGCGGCGCAGTGCATTAGTGGCTTT
genomic: ACGTCTCATTCACCATCGCAAATCAAACGTTCGAGCTGACGCCTAAACAGgtgatggatg ... ctctcgtcagTACATCTTGCAAGTTGGAGAGGGAGCAGCGGCGCAGTGCATTAGTGGCTTT
EST: gi|169060203|gb|FE467565.1|FE467565
EST:     ACGTCTCATTCACCATCGCAAATCAAACGTTCGAGCTGACGCCTAAACAG                         TACATCTTGCAAGTTGGAGAGGGAGCAGCGGCGCAGTGCATTAGTGGCTTT
genomic: ACGTCTCATTCACCATCGCAAATCAAACGTTCGAGCTGACGCCTAAACAGgtgatggatg ... ctctcgtcagTACATCTTGCAAGTTGGAGAGGGAGCAGCGGCGCAGTGCATTAGTGGCTTT
EST: gi|169110929|gb|FE509334.1|FE509334
EST:     ACGTCTCATTCACCATCGCAAATCAAACGTTCGAGCTGACGCCTAAACAG                         TACATCTTGCAAGTTGGAGAGGGAGCAGCGGCGCAGTGCATTAGTGGCTTT
genomic: ACGTCTCATTCACCATCGCAAATCAAACGTTCGAGCTGACGCCTAAACAGgtgatggatg ... ctctcgtcagTACATCTTGCAAGTTGGAGAGGGAGCAGCGGCGCAGTGCATTAGTGGCTTT
EST: gi|169112990|gb|FE515470.1|FE515470
EST:     ACGTCTCATTCACCATCGCAAATCAAACGTTCGAGCTGACGCCTAAACAG                         TACATCTTGCAAGTTGGAGAGGGAGCAGCGGCGCAGTGCCTTAGTGGCTTT
genomic: ACGTCTCATTCACCATCGCAAATCAAACGTTCGAGCTGACGCCTAAACAGgtgatggatg ... ctctcgtcagTACATCTTGCAAGTTGGAGAGGGAGCAGCGGCGCAGTGCATTAGTGGCTTT
EST: gi|169058238|gb|FE466005.1|FE466005
EST:     ACGTCTCATTCACCATCGCAAATCAAACGTTCGAGCTGACGCCTAAACAG                         TACATCTTGCAAGTTGGAGAGGGAGCAGCGGCGCAGTGCATTAGTGGCTTT
genomic: ACGTCTCATTCACCATCGCAAATCAAACGTTCGAGCTGACGCCTAAACAGgtgatggatg ... ctctcgtcagTACATCTTGCAAGTTGGAGAGGGAGCAGCGGCGCAGTGCATTAGTGGCTTT
EST: gi|169031935|gb|FE440661.1|FE440661
EST:     ACGTCTCATTCACCATCGCAAATCAAACGTTCGAGCTGACGCCTAAACAG                         TACATCTTGCAAGTTGGAGAGGGAGCAGCGGCGCAGTGCATTAGTGGCTTT
genomic: ACGTCTCATTCACCATCGCAAATCAAACGTTCGAGCTGACGCCTAAACAGgtgatggatg ... ctctcgtcagTACATCTTGCAAGTTGGAGAGGGAGCAGCGGCGCAGTGCATTAGTGGCTTT
EST: gi|169114468|gb|FE516538.1|FE516538
EST:     ACGTCTCATTCACCATCGCAAATCAAACGTTCGAGCTGACGCCTAAACAG                         TACATCTTGCAAGTTGGAGAGGGAGCAGCGGCGCAGTGCATTAGTGGCTTT
genomic: ACGTCTCATTCACCATCGCAAATCAAACGTTCGAGCTGACGCCTAAACAGgtgatggatg ... ctctcgtcagTACATCTTGCAAGTTGGAGAGGGAGCAGCGGCGCAGTGCATTAGTGGCTTT
EST: gi|169065200|gb|FE474024.1|FE474024
EST:     ACGTCTCATTCACCATCGCAAATCAAACGTTCGAGCTGACGCCTAAACAG                         TACATCTTGCAAGTTGGAGAGGGAGCAGCGGCGCAGTGCATTAGTGGCTTT
genomic: ACGTCTCATTCACCATCGCAAATCAAACGTTCGAGCTGACGCCTAAACAGgtgatggatg ... ctctcgtcagTACATCTTGCAAGTTGGAGAGGGAGCAGCGGCGCAGTGCATTAGTGGCTTT
EST: gi|169040181|gb|FE448948.1|FE448948
EST:     ACGTCTCATTCACCATCGCAAATCAAACGTTCGAGCTGACGCCTAAACAG                         TACATCTTGCAAGTTGGAGAGGGAGCAGCGGCGCAGTGCATTAGTGGCTTT
genomic: ACGTCTCATTCACCATCGCAAATCAAACGTTCGAGCTGACGCCTAAACAGgtgatggatg ... ctctcgtcagTACATCTTGCAAGTTGGAGAGGGAGCAGCGGCGCAGTGCATTAGTGGCTTT
EST: gi|169021618|gb|FE432137.1|FE432137
EST:     ACGTCTCATTCACCATCGCAAATCAAACGTTCGAGCTGACGCCTAAACAG                         TACATCTTGCAAGTTGGAGAGGGAGCAGCGGCGCAGTGCATTAGTGGCTTT
genomic: ACGTCTCATTCACCATCGCAAATCAAACGTTCGAGCTGACGCCTAAACAGgtgatggatg ... ctctcgtcagTACATCTTGCAAGTTGGAGAGGGAGCAGCGGCGCAGTGCATTAGTGGCTTT
EST: gi|169096045|gb|FE500023.1|FE500023
EST:     ACGTCTCATTCACCATCGCAAATCAAACGTTCGAGCTGACGCCTAAACAG                         TACATCTTGCAAGTTGGAGAGGGAGCAGCGGCGCAGTGCATTAGTGGCTTT
genomic: ACGTCTCATTCACCATCGCAAATCAAACGTTCGAGCTGACGCCTAAACAGgtgatggatg ... ctctcgtcagTACATCTTGCAAGTTGGAGAGGGAGCAGCGGCGCAGTGCATTAGTGGCTTT
EST: gi|169093446|gb|FE495727.1|FE495727
EST:     ACGTCTCATTCACCATCGCAAATCAAACGTTCGAGCTGACGCCTAAACAG                         TACATCTTGCAAGTTGGAGAGGGAGCAGCGGCGCAGTGCATTAGTGGCTTT
genomic: ACGTCTCATTCACCATCGCAAATCAAACGTTCGAGCTGACGCCTAAACAGgtgatggatg ... ctctcgtcagTACATCTTGCAAGTTGGAGAGGGAGCAGCGGCGCAGTGCATTAGTGGCTTT
EST: gi|169039672|gb|FE448606.1|FE448606
EST:     ACGTCTCATTCACCATCGCAAATCAAACGTTCGAGCTGACGCCTAAACAG                         TACATCTTGCAAGTTGGAGAGGGAGCAGCGGCGCAGTGCATTAGTGGCTTT
genomic: ACGTCTCATTCACCATCGCAAATCAAACGTTCGAGCTGACGCCTAAACAGgtgatggatg ... ctctcgtcagTACATCTTGCAAGTTGGAGAGGGAGCAGCGGCGCAGTGCATTAGTGGCTTT
EST: gi|169044448|gb|FE451072.1|FE451072
EST:     ACGTCTCATTCACCATCGCAAATCAAACGTTCGAGCTGACGCCTAAACAG                         TACATCTTGCAAGTTGGAGAGGGAGCAGCGGCGCAGTGCATTAGTGGCTTT
genomic: ACGTCTCATTCACCATCGCAAATCAAACGTTCGAGCTGACGCCTAAACAGgtgatggatg ... ctctcgtcagTACATCTTGCAAGTTGGAGAGGGAGCAGCGGCGCAGTGCATTAGTGGCTTT
EST: gi|169021619|gb|FE432138.1|FE432138
EST:     ACGTCTCATTCACCATCGCAAATCAAACGTTCGAGCTGACGCCTAAACAG                         TACATCTTGCAAGTTGGAGAGGGAGCAGCGGCGCAGTGCATTAGTGGCTTT
genomic: ACGTCTCATTCACCATCGCAAATCAAACGTTCGAGCTGACGCCTAAACAGgtgatggatg ... ctctcgtcagTACATCTTGCAAGTTGGAGAGGGAGCAGCGGCGCAGTGCATTAGTGGCTTT
EST: gi|169021385|gb|FE431176.1|FE431176
EST:     ACGTCTCATTCACCATCGCAAATCAAACGTTCGAGCTGACGCCTAAACAG                         TACATCTTGCAAGTTGGAGAGGGAGCAGCGGCGCAGTGCATTAGTGGCTTT
genomic: ACGTCTCATTCACCATCGCAAATCAAACGTTCGAGCTGACGCCTAAACAGgtgatggatg ... ctctcgtcagTACATCTTGCAAGTTGGAGAGGGAGCAGCGGCGCAGTGCATTAGTGGCTTT

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: 192

CCCGAATGGCCAGTCCGTTGTTGAGTGCGCGAAAATCTCCTCCCTCCCGAACGTCTCATTCACCATCGCAAATCAAACGTTCGAGCTGACGCCTAAACAGgtgatggatg ... ctctcgtcagTACATCTTGCAAGTTGGAGAGGGAGCAGCGGCGCAGTGCATTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccgtcgtccatttgtgttcttgctgctgactctcactctcttctctctcgtcagTACATCTTGCAAGTTGGAGAGGGAGCAGCGGCGCAGTGCATTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTG
                       ctgctgactctcactc  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgatggatgcgtgacgccagtctcatgccgtcgtccatttgtgttcttgctgctgactctcactctcttctctctcgtcagTACATCTTGCAAGTTGGAGAGGGAGCAGCGGCGCAGTGCATTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC