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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgatcctggcatcaaaatctatgcgctaaagtgtgtctttgttgtttagATTGCCTGCTGTGTTTGATGATCCTAGCTTTTCGACAGTGACTATACAGCGTGATCTCTTCTATGGCTACGACACTCTTATGGAGAACGTTTCCGATCCA

Basic information

species Selaginella moellendorffii
transcript EFJ23274
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ23274 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA11G19800.1 (Glycine max), 3'ss of exon 2
-----------------------------------------------------------------------------------------------------------gtaagtgat-cctggcatcaaaatctat-gcgctaaagtgtgtctttgt---tgtttagATTGCCTGCTGTGTTTGATGATCCTAGCTTTTCGACAGTGACTATACAGCGTGATCTCTTCTATGGCTACGACACTCTTATGGAGAACGTTTCCGATCCA
                                                                                                            ||||   |   | |  |     | ||| |  ||  |  ||   |||||   ||||||| ||||||| ||  |||||  | ||    ||| | || || |  || ||||||||||| |||||||| ||||| ||||| |||||||| || || ||||| 
gtaattgatttaatttaattcggttttgttctgaggaataatgttaaattaattgtaattgggtcctttataatggatgttatcctgtgtttattattttatgttggctaaggagtgttttgttttgtgttttattgacctggatggtaaatttgtgtttgtttagGTTGCCTGATGACTTTGACAAACCGGAGTTTGCCACGGTCAACATTCAGCGTGATCTGTTCTATGGTTACGATACTCTCATGGAGAATGTCTCTGATCCT

upper sequence: EFJ23274 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA12G08740.1 (Glycine max), 3'ss of exon 2
------------------------------------------------------------------------------------------------------------------------gtaagtgatcctggcatcaaaatctat----gcgctaaagtgtgtctttgtt-gtttagATTGCCTGCTGTGTTTGATGATCCTAGCTTTTCGACAGTGACTATACAGCGTGATCTCTTCTATGGCTACGACACTCTTATGGAGAACGTTTCCGATCCA
                                                                                                                         |      |  | |  |     | |||      |  |  ||   | | |||| |||||| ||||||| ||  |||||  | ||    ||| | || || |  || ||||||||||| |||||||| ||||| ||||| |||||||| || || ||||| 
gtgattgatttaattgaatttgattcggtctttttctgaggaataatgttaaattaattgtaattgggccccttataatggatgttgttctgtgtatagtattattattttattttggctatggagtgtttttgttttgtgttttattgacctgtgatggtaaatttgtgtttgtttagGTTGCCTGATGACTTTGACAAACCGGAGTTTGCCACGGTCAACATTCAGCGTGATCTGTTCTATGGTTACGATACTCTCATGGAGAATGTCTCTGATCCT
















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|169024006|gb|FE436479.1|FE436479
EST:     TGGCCTGACGAGAAAGGCTGGGAAAGCGCTCAAAGAACACAACCTCCTCA                         ATTGCCTGCTGTGTTTGATGATCCTAGCTTTTCGACAGTGACTATACAGCG
genomic: TGGCCTGACGAGAAAGGCTGGGAAAGCGCTCAAAGAACACAGCCTCCTCAgtaagtgatc ... tgttgtttagATTGCCTGCTGTGTTTGATGATCCTAGCTTTTCGACAGTGACTATACAGCG
EST: gi|169087365|gb|FE492194.1|FE492194
EST:     TGGCCTGACGAGAAAGGCTGGGAAAGCGCTCAAAGAACACAGCCTCCTCA                         ATTGCCTGCTGTGTTTGATGATCCTAGCTTTTCGACAGTGACTATACAGCG
genomic: TGGCCTGACGAGAAAGGCTGGGAAAGCGCTCAAAGAACACAGCCTCCTCAgtaagtgatc ... tgttgtttagATTGCCTGCTGTGTTTGATGATCCTAGCTTTTCGACAGTGACTATACAGCG
EST: gi|169098689|gb|FE498589.1|FE498589
EST:     TGGCCTGACGAGAAAGGCTGGGAAAGCGCTCAAAGAACACAGCCTCCTCA                         ATTGCCTGCTGTGTTTGATGATCCTAGCTTTTCGACAGTGACTATACAGCG
genomic: TGGCCTGACGAGAAAGGCTGGGAAAGCGCTCAAAGAACACAGCCTCCTCAgtaagtgatc ... tgttgtttagATTGCCTGCTGTGTTTGATGATCCTAGCTTTTCGACAGTGACTATACAGCG
EST: gi|169094557|gb|FE492442.1|FE492442
EST:     TGGCCTGACGAGAAAGGCTGGGAAAGCGCTCAAAGAACACAGCCTCCTCA                         ATTGCCTGCTGTGTTTGATGATCCTAGCTTTTCGACAGTGACTATACAGCG
genomic: TGGCCTGACGAGAAAGGCTGGGAAAGCGCTCAAAGAACACAGCCTCCTCAgtaagtgatc ... tgttgtttagATTGCCTGCTGTGTTTGATGATCCTAGCTTTTCGACAGTGACTATACAGCG
EST: gi|169080025|gb|FE489952.1|FE489952
EST:     TGGCCTGACGAGAAAGGCTGGGAAAGCGCTCAAAGAACACAGCCTCCTCA                         ATTGCCTGCTGTGTTTGATGATCCTAGCTTTTCGACAGTGACTATACAGCG
genomic: TGGCCTGACGAGAAAGGCTGGGAAAGCGCTCAAAGAACACAGCCTCCTCAgtaagtgatc ... tgttgtttagATTGCCTGCTGTGTTTGATGATCCTAGCTTTTCGACAGTGACTATACAGCG
EST: gi|169116420|gb|FE517783.1|FE517783
EST:     TGGCCTGACGAGAAAGGCTGGGAAAGCGCTCAAAGAACACAACCTCCTCA                         ATTGCCTGCTGTGTTTGATGATCCTAGCTTTTCGACAGTGACTATACAGCG
genomic: TGGCCTGACGAGAAAGGCTGGGAAAGCGCTCAAAGAACACAGCCTCCTCAgtaagtgatc ... tgttgtttagATTGCCTGCTGTGTTTGATGATCCTAGCTTTTCGACAGTGACTATACAGCG
EST: gi|169027513|gb|FE433746.1|FE433746
EST:     TGGCCTGACGAGAAAGGCTGGGAAAGCGCTCAAAGAACACAACCTCCTCA                         ATTGCCTGCTGTGTTTGATGATCCTAGCTTTTCGACAGTGACTATACAGCG
genomic: TGGCCTGACGAGAAAGGCTGGGAAAGCGCTCAAAGAACACAGCCTCCTCAgtaagtgatc ... tgttgtttagATTGCCTGCTGTGTTTGATGATCCTAGCTTTTCGACAGTGACTATACAGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaagtgatcctggcatcaaaatctatgcgctaaagtgtgtctttgttgtttagATTGCCTGCTGTGTTTGATGATCCTAGCTTTTCGACAGTGACTATACAGCGTGATCTCTTCTATGGCTACGACACTCTTATGGAGAACGTTTCCGATCCA
                             cgctaaa  putative branch site (score: 3)
                                         tctttgtt  putative PPT
                   aaaatctat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgatcctggcatcaaaatctatgcgctaaagtgtgtctttgttgtttagATTGCCTGCTGTGTTTGATGATCCTAGCTTTTCGACAGTGACTATACAGCGTGATCTCTTCTATGGCTACGACACTCTTATGGAGAACGTTTCCGATCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA