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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaagatctctttgtgttcgtcgaggaaaagcttgaaacttttctttttttttggccttagATGGAATACTCCTATCCACGTTGATGCCGCCAGTGGAGGATTCATCGCTCCATTCCTCTATCCAGATTTGGAGTGGGATTTTCGATTGCCTCTTGTCAAG

Basic information

species Selaginella moellendorffii
transcript EFJ36644
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ36644 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GLYMA08G09660.1 (Glycine max), 3'ss of exon 3
-----------------------------------------------------gtaaaagatctctttg-tgttcgtcgaggaaaagcttgaaacttttcttttttt-ttggccttagATGGAATACTCCTATCCACGTTGATGCCGCCAGTGGAGGATTCATCGCTCCATTCCTCTATCCAGATTTGGAGTGGGATTTTCGATTGCCTCTTGTCAAG
                                                      | |  | || ||| | | ||| | |      |        |||| ||| |  | ||     ||||||| |||| ||||| || || ||||| || ||||| || || || ||||||||||| |||||||| || || ||||||||| || | ||  | || |||
gtaagtaaattaatgtaccactaattacctctctattcactaattcaactatcttcactgttcacttagcttttcattgtcatgtactaatttgctttacttgtcatattatatatagATGGGATACACCTATTCATGTGGATGCTGCAAGTGGTGGCTTTATTGCTCCATTCCTTTATCCAGAGTTAGAATGGGATTTTAGACTCCCATTGGTGAAG

upper sequence: EFJ36644 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GLYMA08G09670.1 (Glycine max), 3'ss of exon 3
-----------------------gtaaaagatctcttt---gtgttcgtcgaggaaaagcttgaaacttttcttttt-ttttggccttagATGGAATACTCCTATCCACGTTGATGCCGCCAGTGGAGGATTCATCGCTCCATTCCTCTATCCAGATTTGGAGTGGGATTTTCGATTGCCTCTTGTCAAG
                        | ||| || | |     |  ||| |  |       ||     |||| ||| |    |      ||||||| |||| ||||| ||||| ||||| || ||||| || || || ||||||||||| ||||||||  | || ||||||||  || | ||  | || |||
gtaatgaattgatattccactaattcaaatatttttactgggctttcctttaccttgtactaattgctttacttgtcacatcaatgatagATGGGATACGCCTATTCACGTGGATGCTGCAAGTGGTGGGTTTATTGCTCCATTCCTATATCCAGAGCTAGAATGGGATTTCAGACTCCCATTGGTGAAG

upper sequence: EFJ36644 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GLYMA14G39170.1 (Glycine max), 3'ss of exon 5
-------------------------------------------gtaaaagatctctttgtgttcgtcgaggaaaagcttgaaacttttcttt----ttttttggccttagATGGAATACTCCTATCCACGTTGATGCCGCCAGTGGAGGATTCATCGCTCCATTCCTCTATCCAGATTTGGAGTGGGATTTTCGATTGCCTCTTGTCAAG
                                            |   |      |||  | |  |  |    |  |||| || |    | |    ||  ||     ||||||| | ||||| || || || ||||| |||||||| |||||||| || || || |||||||| ||  | |||||||||||||| ||||| || || |||
gtttgtattgcacatattgattgagtcttaactgcttcctattttgtgaacctagtttaaggtactttaatttagacttggaattgacatgtgaaattaattattggtagATGGGACACTCCAATTCATGTGGATGCAGCCAGTGGTGGATTCATTGCACCTTTTCTCTATCCTGAGCTTGAGTGGGATTTTCGGTTGCCACTAGTGAAG

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|169076418|gb|FE485006.1|FE485006
EST:     GACGTGAAGCTCCTCAACGAGCTCTTGGNNNNNNNGA-CAAAGACACTGG                         ATGGAATACTCCTATCCACGTTGATGCCGCCAGTGGAGGATTCATCGCTCC
genomic: GACGTGAAGCTCCTCAACGAGCTCTTGGAAAAAAAGAACAAAGACACTGGgtaaaagatc ... ttggccttagATGGAATACTCCTATCCACGTTGATGCCGCCAGTGGAGGATTCATCGCTCC
EST: gi|169075461|gb|FE483095.1|FE483095
EST:     GACGTGAAGCTCCTCAACGAGCTCTTGGNNNNNNNGAACAAAGACACTGG                         ATGGAATACTCCTATCCACGTTGATGCCGCCAGTGGAGGATTCATCGCTCC
genomic: GACGTGAAGCTCCTCAACGAGCTCTTGGAAAAAAAGAACAAAGACACTGGgtaaaagatc ... ttggccttagATGGAATACTCCTATCCACGTTGATGCCGCCAGTGGAGGATTCATCGCTCC
EST: gi|169060617|gb|FE467355.1|FE467355
EST:     GACGTGAAGCTCCTCAACGAGCTCTTGGNNNNNNNGAACAAAGACACTGG                         ATGGAATACTCCTATCCACGTTGATGCCGCCAGTGGAGGATTCATCGCTCC
genomic: GACGTGAAGCTCCTCAACGAGCTCTTGGAAAAAAAGAACAAAGACACTGGgtaaaagatc ... ttggccttagATGGAATACTCCTATCCACGTTGATGCCGCCAGTGGAGGATTCATCGCTCC
EST: gi|169066370|gb|FE473046.1|FE473046
EST:     ACGTGAAGCTCCCTCA-CGAGCTCTTGGNNNNNNNGAACAAAGACACTGG                         ATGGAATACTCCTATCCCACGT-GATGCCGCCAGTGGAGGAATCATCGCTC
genomic: ACGTGAAGCTCC-TCAACGAGCTCTTGGAAAAAAAGAACAAAGACACTGGgtaaaagatc ... ttggccttagATGGAATACTCCTATCC-ACGTTGATGCCGCCAGTGGAGGATTCATCGCTC
EST: gi|169027511|gb|FE433744.1|FE433744
EST:     GACGTGAAGCTCCTCAACGAGCTCTTGGNNNNNNNGAACAAAGACACTGG                         ATGGAATACTCCTATCCACGTTGATGCCGCCAGTGGAGGATTCATCGCTCC
genomic: GACGTGAAGCTCCTCAACGAGCTCTTGGAAAAAAAGAACAAAGACACTGGgtaaaagatc ... ttggccttagATGGAATACTCCTATCCACGTTGATGCCGCCAGTGGAGGATTCATCGCTCC
EST: gi|169093055|gb|FE494166.1|FE494166
EST:     GACGTGAAGCTCCTCAACGAGCTCTTGGGAAAAAAGAACAAAGACACTGG                         ATGGAATACTCCTATCCACGTTGATGCCGCCCGTGGAGGATTCATCGCTCC
genomic: GACGTGAAGCTCCTCAACGAGCTCTTGGAAAAAAAGAACAAAGACACTGGgtaaaagatc ... ttggccttagATGGAATACTCCTATCCACGTTGATGCCGCCAGTGGAGGATTCATCGCTCC
EST: gi|169054363|gb|FE460808.1|FE460808
EST:     GACGTGAAGCTCCTCAACGAGCTCTTGGNNNNNNNGAACAAAGACACTGG                         ATGGAATACTCCTATCCACGTTGATGCCGCCAGTGGAGGATTCATCGCTCC
genomic: GACGTGAAGCTCCTCAACGAGCTCTTGGAAAAAAAGAACAAAGACACTGGgtaaaagatc ... ttggccttagATGGAATACTCCTATCCACGTTGATGCCGCCAGTGGAGGATTCATCGCTCC
EST: gi|169080213|gb|FE488385.1|FE488385
EST:     GACGTGAAGCTCCTCAACGAGCTCTTGGNNNNNNNGAACAAAGACACTGG                         ATGGAATACTCCTATCCACGTTGATGCCGCCAGTGGAGGATTCATCGCTCC
genomic: GACGTGAAGCTCCTCAACGAGCTCTTGGAAAAAAAGAACAAAGACACTGGgtaaaagatc ... ttggccttagATGGAATACTCCTATCCACGTTGATGCCGCCAGTGGAGGATTCATCGCTCC
EST: gi|169025802|gb|FE433101.1|FE433101
EST:     GACGTGAAGCTCCTCAACGAGCTCTTGGNNNNNNNGA-CAAAGACACTGG                         ATGGAATACTCCTATCCACGTTGATGCCGCCAG
genomic: GACGTGAAGCTCCTCAACGAGCTCTTGGAAAAAAAGAACAAAGACACTGGgtaaaagatc ... ttggccttagATGGAATACTCCTATCCACGTTGATGCCGCCAG

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: 34 (upstream exon), 32 (downstream exon)
Score: 27

CCATTTGCATTGCAGCCATCCTTGGTTCCACTTACAACGGAGAGTTCGAAGACGTGAAGCTCCTCAACGAGCTCTTGGAAAAAAAGAACAAAGACACTGGgtaaaagatc ... ttggccttagATGGAATACTCCTATCCACGTTGATGCCGCCAGTGGAGGATTCATCGCTCCATTCCTCTATCCAGATTTGGAGTGGGATTTTCGATTGCCTCTTGTCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctctttgtgttcgtcgaggaaaagcttgaaacttttctttttttttggccttagATGGAATACTCCTATCCACGTTGATGCCGCCAGTGGAGGATTCATCGCTCCATTCCTCTATCCAGATTTGGAGTGGGATTTTCGATTGCCTCTTGTCAAG
                                cttttctttttttttg  CT-rich tract
                          ttgaaacttttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaagatctctttgtgttcgtcgaggaaaagcttgaaacttttctttttttttggccttagATGGAATACTCCTATCCACGTTGATGCCGCCAGTGGAGGATTCATCGCTCCATTCCTCTATCCAGATTTGGAGTGGGATTTTCGATTGCCTCTTGTCAAG

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