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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcttgcaagcgtttctttaccacttccttatccattcccgtttcttcttcgtagATATGCCGATCTCTCGCTTACATCCACGGCGGGATTGGAGTCTGCCACCGTGATATCAAGCCACAAAATTTATTG

Basic information

species Selaginella moellendorffii
transcript EFJ04915
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ04915 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GLYMA20G22600.3 (Glycine max), 3'ss of exon 5
gtaagcttgcaagcgtttctttacca--cttccttatccattcccgtt--------tcttcttcgtagATATGCCGATCTCTCG--------CTTACATCCACGGCGGGATTGGAGTCTGCCACCGTGATATCAAGCCACAAAATTTATTG
||| |  ||    | || || |   |  ||| | ||    |||  | |        | || ||  || || | | ||||| | |        |||| || ||  |  | |||||||||||||| || ||||||||||| |||||| |||||
gtatgactgttgcccttcctgtcttaagctttcataattgttctggctgtaacaattatttttgatatattt-cagATCTTTAGGGCGTTATCTTATATTCATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTG

upper sequence: EFJ04915 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GLYMA10G28530.2 (Glycine max), 3'ss of exon 5
gtaagcttgcaagcgtttct-ttaccacttcc-----ttatccattcc-------cgtttcttct---tcgtagATATGCCGATCTCTCGCTTACATCCACGGCGGGATTGGAGTCTGCCACCGTGATATCAAGCCACAAAATTTATTG
||| |  ||    | || || |  |||  ||      || | ||  |          ||| || |   | | |||| |   |  |  |  |||| || ||  |  | |||||||||||||| || ||||||||||| |||||| |||||
gtatgactgttgcccttcctgtctccagctctcatcgttgttcaggctgtaacaatattttttttatgttgcagATCTTTAGGGCATTATCTTATATTCATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTG

upper sequence: EFJ04915 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GLYMA03G38850.2 (Glycine max), 3'ss of exon 5
---------------------------------------gtaagcttgcaagcgtttctt----taccacttccttatccattcccgtttcttcttcgtagATATGCCGATCTCTCGCTTACATCCACGGCGGGATTGGAGTCTGCCACCGTGATATCAAGCCACAAAATTTATTG
                                            | || |  | ||||||    | ||    |  ||||  ||  | ||  |     | |||| |   |  | ||  |||| || ||  |  | |||||||||||||| || ||||||||||| |||||| |||||
tggcttggtaaatgtagagtagatatatatccagtgttgtccttcctgtattcatttcttatcttgccgaggctgtatctgttttc-ttgatatactgcagATCTTTAGGGCACTATCTTATATTCATCGTTGCATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTG

upper sequence: EFJ04915 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GLYMA19G41420.3 (Glycine max), 3'ss of exon 5
-------------------------------------------------------------gtaagcttgcaagcgtttctttaccacttccttatccattc----ccgtttcttcttcgtagATATGCCG---ATCT--------CTCGCTTACATCCACGGCGGGATTGGAGTCTGCCACCGTGATATCAAGCCACAAAATTTATTG
                                                              |    |||  |  |||| |  |  | || ||||||           || |||  ||  | ||||| | |   ||||        ||| |||| || ||  |  | |||||||||||||| || ||||||||||| |||||| |||| 
gtatgcttaatcatgtcagtttggttttgtcatgatccttttgtcagttttattttggaaaatggctttgttaatgttt-tggattattttcttatcttactgaggttgtatctgttttcttgatatactgcagATCTTTAGGGCACTCTCTTATATTCATCGTTGCATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTA

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|169026283|gb|FE432646.1|FE432646
EST:     GAATGAATCAGAGAATGCCACTCTTGTATGTAAAATTGTATACATACCAG                         ATATGCCGATCTCTCGCTTACATCCACGGCGGGATTGGAGTCTGCCACCGT
genomic: GAATGAATCAGAGAATGCCACTCTTGTATGTAAAGTTGTATACATACCAGgtaagcttgc ... ttcttcgtagATATGCCGATCTCTCGCTTACATCCACGGCGGGATTGGAGTCTGCCACCGT
EST: gi|169024806|gb|FE435485.1|FE435485
EST:     GAATGAATCAGAGAATGCCACTCTTGTATGTAAAGTTGTATACATACCAG                         ATATGCCGATCTCTCGCTTACATCCACGGCGGGATTGGGGTCTGCCACCGT
genomic: GAATGAATCAGAGAATGCCACTCTTGTATGTAAAGTTGTATACATACCAGgtaagcttgc ... ttcttcgtagATATGCCGATCTCTCGCTTACATCCACGGCGGGATTGGAGTCTGCCACCGT
EST: gi|169034065|gb|FE442799.1|FE442799
EST:     GAATGAATCAGAGAATGCCACTCTTGTATGTAAAGTTGTATACATACCAG                         ATATGCCGATCTCTCGCTTACATCCACGGCGGGATTGGGGTCTGCCACCGT
genomic: GAATGAATCAGAGAATGCCACTCTTGTATGTAAAGTTGTATACATACCAGgtaagcttgc ... ttcttcgtagATATGCCGATCTCTCGCTTACATCCACGGCGGGATTGGAGTCTGCCACCGT
EST: gi|169036066|gb|FE446772.1|FE446772
EST:     GAATGAATCACAGAATGCCACTCTTGTATGTAAAATTGTATACATACCAG                         ATATGCCGATCTCTCGCTTACATCCACGGCGGGATTGGAGTCTGCCACCGT
genomic: GAATGAATCAGAGAATGCCACTCTTGTATGTAAAGTTGTATACATACCAGgtaagcttgc ... ttcttcgtagATATGCCGATCTCTCGCTTACATCCACGGCGGGATTGGAGTCTGCCACCGT
EST: gi|169111672|gb|FE511910.1|FE511910
EST:     GAATGAATCAGAGAATGCCACTCTTGTATGTAAAGTTGTATACATACCAG                         ATATGCCGATCTCTCGCTTACATCCCACGGCG
genomic: GAATGAATCAGAGAATGCCACTCTTGTATGTAAAGTTGTATACATACCAGgtaagcttgc ... ttcttcgtagATATGCCGATCTCTCGCTTACATCC-ACGGCG
EST: gi|169051268|gb|FE457618.1|FE457618
EST:     GAATGAATCAGAGAATGCCACTCTTGTATGTAAAGTTGTATACATACCAG                         ATATGCCGATCTCTCGCTTACATCCACGGCGGGATTGGGGTCTGCCACCGT
genomic: GAATGAATCAGAGAATGCCACTCTTGTATGTAAAGTTGTATACATACCAGgtaagcttgc ... ttcttcgtagATATGCCGATCTCTCGCTTACATCCACGGCGGGATTGGAGTCTGCCACCGT
EST: gi|169038251|gb|FE443937.1|FE443937
EST:     GAATGAATCAGAGAATGCCACTCTTGTATGTAAAATTGTATACATACCAG                         ATATGCCGATCTCTCGCTTACATCCACGGCGGGATTGGAGTCTGCCACCGT
genomic: GAATGAATCAGAGAATGCCACTCTTGTATGTAAAGTTGTATACATACCAGgtaagcttgc ... ttcttcgtagATATGCCGATCTCTCGCTTACATCCACGGCGGGATTGGAGTCTGCCACCGT
EST: gi|169020214|gb|FE430317.1|FE430317
EST:     GAATGAATCAGAGAATGCCACTCTTGTATGTAAAATTGTATACATACCAG                         ATATGCCGATCTCTCGCTTACATCCCACG-CGGGATTGGAGTCTGCCACCG
genomic: GAATGAATCAGAGAATGCCACTCTTGTATGTAAAGTTGTATACATACCAGgtaagcttgc ... ttcttcgtagATATGCCGATCTCTCGCTTACATCC-ACGGCGGGATTGGAGTCTGCCACCG
EST: gi|169033900|gb|FE441932.1|FE441932
EST:     GAATGAATCAGAGAATGCCACTCTTGTATGTAAAATTGTATACATACCAG                         ATATGCCGATCTCTCGCTTACATCCACGGCGGGATTGGAGTCTGCCACCGT
genomic: GAATGAATCAGAGAATGCCACTCTTGTATGTAAAGTTGTATACATACCAGgtaagcttgc ... ttcttcgtagATATGCCGATCTCTCGCTTACATCCACGGCGGGATTGGAGTCTGCCACCGT
EST: gi|169046998|gb|FE454570.1|FE454570
EST:     GAATGAATCAGAGAATGCCACTCTTGTATGTAAAGTTGTATACATACCAG                         ATATGCCGATCTCTCGCTTACATCCACGGCGGGATTGGGGTCTGCCACCGT
genomic: GAATGAATCAGAGAATGCCACTCTTGTATGTAAAGTTGTATACATACCAGgtaagcttgc ... ttcttcgtagATATGCCGATCTCTCGCTTACATCCACGGCGGGATTGGAGTCTGCCACCGT
EST: gi|169100546|gb|FE502721.1|FE502721
EST:     GAATGAATCAGAGAATGCCACTCTTGTATGTAAAATTGTATACATACCAG                         ATATGCCGATCTCTCGCTTACATCCACGGCGGGATTGGAGTCTGCCACCGT
genomic: GAATGAATCAGAGAATGCCACTCTTGTATGTAAAGTTGTATACATACCAGgtaagcttgc ... ttcttcgtagATATGCCGATCTCTCGCTTACATCCACGGCGGGATTGGAGTCTGCCACCGT
EST: gi|169054529|gb|FE462613.1|FE462613
EST:     GAATGAATCAGAGAATGCCACTCTTGTATGTAAAGTTGTATACATACCAG                         ATATGCCGATCTCTCGCTTACATCCACGGCGGGATTGGNGTCTGC
genomic: GAATGAATCAGAGAATGCCACTCTTGTATGTAAAGTTGTATACATACCAGgtaagcttgc ... ttcttcgtagATATGCCGATCTCTCGCTTACATCCACGGCGGGATTGGAGTCTGC
EST: gi|169057379|gb|FE466814.1|FE466814
EST:     GAATGAATCAGAGAATGCCACTCTTGTATGTAAAATTGTATACATACCAG                         ATATGCCGATCTCTCGCTTACATC
genomic: GAATGAATCAGAGAATGCCACTCTTGTATGTAAAGTTGTATACATACCAGgtaagcttgc ... ttcttcgtagATATGCCGATCTCTCGCTTACATC
EST: gi|169051816|gb|FE458998.1|FE458998
EST:     GAATGAATCAGAGAATGCCACTCTTGTATGTAAAATTGTATACATACCAG                         ATATGCCGATCTCTCGCTTACATCCACGGCGGGATTGGAGTCTGCCACCGT
genomic: GAATGAATCAGAGAATGCCACTCTTGTATGTAAAGTTGTATACATACCAGgtaagcttgc ... ttcttcgtagATATGCCGATCTCTCGCTTACATCCACGGCGGGATTGGAGTCTGCCACCGT

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: 67

CCTCGAGTATGTTCCGGAAACCGTGTATCGCATCGCAAAGCATCACAACAGAATGAATCAGAGAATGCCACTCTTGTATGTAAAGTTGTATACATACCAGgtaagcttgc ... ttcttcgtagATATGCCGATCTCTCGCTTACATCCACGGCGGGATTGGAGTCTGCCACCGTGATATCAAGCCACAAAATTTATTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcttgcaagcgtttctttaccacttccttatccattcccgtttcttcttcgtagATATGCCGATCTCTCGCTTACATCCACGGCGGGATTGGAGTCTGCCACCGTGATATCAAGCCACAAAATTTATTG
            tttctttaccacttcc  CT-rich tract
            tttcttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcttgcaagcgtttctttaccacttccttatccattcccgtttcttcttcgtagATATGCCGATCTCTCGCTTACATCCACGGCGGGATTGGAGTCTGCCACCGTGATATCAAGCCACAAAATTTATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG