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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttcctctaattttttttgttttggttgatttctttggcttaaccttctttgcattaatccacagCTCCCGTGTATTATGTGGCTGGCTGTTTACAAACCCAGAGTTTTCAGTCTTTCGTGGATGGCAAACTGG

Basic information

species Selaginella moellendorffii
transcript EFJ25874
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ10950 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GLYMA19G24540.1 (Glycine max), 3'ss of exon 7
------gtaagttcctctaattttttttgttttggttgatttctttggcttaaccttct----------ttgcattaatccaca---------------gCTCCCGTGTATTATGTGGCTGGCTGTTTACAAACCCAGAGTTTTCAGTCTTTCGTGGATGGCAAACTGG
       | | |||||  ||||| |  | | | |||  || | | ||| || |   | |           ||||||  || |||               |||||| |||||||||||||| ||| |||||||||| ||    |||||  | || |||||  | || |||
aataagattaattccttcaatttatactttataggtgtatgtgtctggttttataatttatatgactgactgcatttttcaacataatataattttgtagCTCCCCTGTATTATGTGGCTTGCTATTTACAAACCTAGGAAGTTCAGCTTATCTTGGATCACCAATTGG

upper sequence: EFJ10950 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: Vv01s0010g02640.t01 (Vitis vinifera), 3'ss of exon 9
---------------------------gtaagttcctctaattttttttgttttggttgatttctttggcttaaccttctttgcattaatc---cacagCTCCCGTGTATTATGTGGCTGGCTGTTTACAAACCCAGAGTTTTCAGTCTTTCGTGGATGGCAAACTGG
                            |||   | | | |   | ||   | |  || |       |   |||  |  |     ||  |      |||||||| ||||| |||||||| ||||||||||||||||||    | ||| | || ||| | ||||| |||
gtaaggaataaatcctcccacatccaattaaaggcatattaggctattatatatccttcacaatacagcactaatatcttaaattttggttttgtgcagCTCCCTTGTATCATGTGGCTTGCTGTTTACAAACCCAGAAGGCTTAGTTTATCATGGTTTGCAAATTGG

upper sequence: EFJ10950 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: Vv01s0010g02700.t01 (Vitis vinifera), 3'ss of exon 5
-----------------------------------------gtaagttcctctaattttttttgttttggttgatttctttggcttaaccttctttgcattaatccacagCTCCCGTGTATTATGTGGCTGGCTGTTTACAAACCCAGAGTTTTCAGTCTTTCGTGGATGGCAAACTGG
                                          | ||    |  ||| |  ||     | |   |      |  |||||   |   || |||  |   |||||||| ||||| |||||||| ||| ||||||||||||||   || ||  | || ||| | ||||| |||
gtaaggaataaatccccccacatccatgttacaggcatcatattaggctattaaatatccttcacaatagaacacgctaatatcttaaatct---tggatttgt--gcagCTCCCTTGTATCATGTGGCTTGCTATTTACAAACCCAGAAGGTTTAGCTTATCATGGTTTGCAAATTGG

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|169047534|gb|FE455118.1|FE455118
EST:     ACTTGCTGGGCTTTTTCGGAGGTTTTGCGTTTGCTCCCACGACTTACTTT                         CTCCCGTGTATTATGTGGCTGGCTGTTTACAAACCCAGAGTTTTCAGTCTT
genomic: ACTTGCTGGGCTTTTTCGGAGGTTTTGCGTTTGCTCCCACGACTTACTTTgtaagttcct ... taatccacagCTCCCGTGTATTATGTGGCTGGCTGTTTACAAACCCAGAGTTTTCAGTCTT
EST: gi|169109258|gb|FE512825.1|FE512825
EST:     ACTTGCTGGGCTTTTTCGGAGGTTTTGCGTTTGCTCCCACGACTTACTTT                         CTCCCGTGTATTATGTGGCTGGCTGTTTACAAACCCAGAGTTTTCAGTCTT
genomic: ACTTGCTGGGCTTTTTCGGAGGTTTTGCGTTTGCTCCCACGACTTACTTTgtaagttcct ... taatccacagCTCCCGTGTATTATGTGGCTGGCTGTTTACAAACCCAGAGTTTTCAGTCTT
EST: gi|169107383|gb|FE509123.1|FE509123
EST:     ACTTGCTGGGCTTTTTCGGAGGTTTTGCGTTTGCTCCCACGACTTACTTT                         CTCCCGTGTATTATGTGGCTGGCTGTTTACAAACCCAGAGTTTTCAGTCTT
genomic: ACTTGCTGGGCTTTTTCGGAGGTTTTGCGTTTGCTCCCACGACTTACTTTgtaagttcct ... taatccacagCTCCCGTGTATTATGTGGCTGGCTGTTTACAAACCCAGAGTTTTCAGTCTT
EST: gi|169100621|gb|FE502133.1|FE502133
EST:     ACTTGCTGGGCTTTTTCGGAGGTTTTGCGTTTGCTCCCACGACTTACTTT                         CTCCCGTGTATTATGTGGCTGGCTGTTTACAAACCCAGAGTTTTCAGTCTT
genomic: ACTTGCTGGGCTTTTTCGGAGGTTTTGCGTTTGCTCCCACGACTTACTTTgtaagttcct ... taatccacagCTCCCGTGTATTATGTGGCTGGCTGTTTACAAACCCAGAGTTTTCAGTCTT
EST: gi|169045221|gb|FE451454.1|FE451454
EST:     ACTTGCTGGGCTTTTTCGGAGGTTTTGCGTTTGCTCCCACGACTTACTTT                         CTCCCGTGTATTATGTGGCTGGCTGTTTACAAACCCAGAGTTTTCAGTCTT
genomic: ACTTGCTGGGCTTTTTCGGAGGTTTTGCGTTTGCTCCCACGACTTACTTTgtaagttcct ... taatccacagCTCCCGTGTATTATGTGGCTGGCTGTTTACAAACCCAGAGTTTTCAGTCTT
EST: gi|169053549|gb|FE463318.1|FE463318
EST:     ACTTGCTGGGCTTTTTCGGAGGTTTTGCGTTTGCTCCCACGACTTACTTT                         CTCCCGTGTATTATGTGGCTGGCTGTTTACAAACCCAGAGTTTTCAGTCTT
genomic: ACTTGCTGGGCTTTTTCGGAGGTTTTGCGTTTGCTCCCACGACTTACTTTgtaagttcct ... taatccacagCTCCCGTGTATTATGTGGCTGGCTGTTTACAAACCCAGAGTTTTCAGTCTT
EST: gi|169111166|gb|FE511352.1|FE511352
EST:     ACTTGCTGGGCTTTTTCGGAGGTTTTGCGTTTGCTCCCACGACTTACTTT                         CTCCCGTGTATTATGTGGCTGGCTGTTTACAAACCCAGAGTTTTCAGTCTT
genomic: ACTTGCTGGGCTTTTTCGGAGGTTTTGCGTTTGCTCCCACGACTTACTTTgtaagttcct ... taatccacagCTCCCGTGTATTATGTGGCTGGCTGTTTACAAACCCAGAGTTTTCAGTCTT
EST: gi|169083875|gb|FE492787.1|FE492787
EST:     ACTTGCTGGGCTTTTTCGGAGGTTTTGCGTTTGCTCCCACGACTTACTTT                         CTCCCGTGTATTATGTGGCTGGCTGTTTACAAACCCAGAGTTTTCAGTCTT
genomic: ACTTGCTGGGCTTTTTCGGAGGTTTTGCGTTTGCTCCCACGACTTACTTTgtaagttcct ... taatccacagCTCCCGTGTATTATGTGGCTGGCTGTTTACAAACCCAGAGTTTTCAGTCTT
EST: gi|169024838|gb|FE435504.1|FE435504
EST:     ACTTGCTGGGCTTTTTCGGAGGTTTTGCGTTTGCTCCCACGACTTACTTT                         CTCCCGTGTATTATGTGGCTGGCTGTTTACAAACCCAGAGTTTTCAGTCTT
genomic: ACTTGCTGGGCTTTTTCGGAGGTTTTGCGTTTGCTCCCACGACTTACTTTgtaagttcct ... taatccacagCTCCCGTGTATTATGTGGCTGGCTGTTTACAAACCCAGAGTTTTCAGTCTT
EST: gi|169100468|gb|FE502682.1|FE502682
EST:     ACTTGCTGGGCTTTTTCGGAGGTTTTGCGTTTGCTCCCACGACTTACTTT                         CTCCCGTGTATTATGTGGCTGGCTGTTTACAAACCCAGAGTTTTCAGTCTT
genomic: ACTTGCTGGGCTTTTTCGGAGGTTTTGCGTTTGCTCCCACGACTTACTTTgtaagttcct ... taatccacagCTCCCGTGTATTATGTGGCTGGCTGTTTACAAACCCAGAGTTTTCAGTCTT
EST: gi|169061780|gb|FE470698.1|FE470698
EST:     ACTTGCTGGGCTTTTTCGGAGGTTTTGCGTTTGCTCCCACGACTTACTTT                         CTCCCGTGTATTATGTGGCTGGCTGTTTACAAACCCAGAGTTTTCAGTCTT
genomic: ACTTGCTGGGCTTTTTCGGAGGTTTTGCGTTTGCTCCCACGACTTACTTTgtaagttcct ... taatccacagCTCCCGTGTATTATGTGGCTGGCTGTTTACAAACCCAGAGTTTTCAGTCTT
EST: gi|169072770|gb|FE484348.1|FE484348
EST:     ACTTGCTGGGCTTTTTCGGAGGTTTTGCGTTTGCTCCCACGACTTACTTT                         CTCCCGTGTATTATGTGGCTGGCTGTTTACAAACCCAGAGTTTTCAGTCTT
genomic: ACTTGCTGGGCTTTTTCGGAGGTTTTGCGTTTGCTCCCACGACTTACTTTgtaagttcct ... taatccacagCTCCCGTGTATTATGTGGCTGGCTGTTTACAAACCCAGAGTTTTCAGTCTT

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), 35 (downstream exon)
Score: 41

CTTTCACTGCCTTTATTGGGATAACTTTTCCTTTTTTTGGAGACTTGCTGGGCTTTTTCGGAGGTTTTGCGTTTGCTCCCACGACTTACTTTgtaagttcct ... taatccacagCTCCCGTGTATTATGTGGCTGGCTGTTTACAAACCCAGAGTTTTCAGTCTTTCGTGGATGGCAAACTGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttttgttttggttgatttctttggcttaaccttctttgcattaatccacagCTCCCGTGTATTATGTGGCTGGCTGTTTACAAACCCAGAGTTTTCAGTCTTTCGTGGATGGCAAACTGG
                                          cattaat  putative branch site (score: 41)
     tttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttcctctaattttttttgttttggttgatttctttggcttaaccttctttgcattaatccacagCTCCCGTGTATTATGTGGCTGGCTGTTTACAAACCCAGAGTTTTCAGTCTTTCGTGGATGGCAAACTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT