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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttggtccttaaatgcaattacagtctaacatgtgcttttacagGTTCGTTTTGTAGTAATGGGAAACATGTTCTGCACAGACCTTCGTATACACCGGAGGTTCGATTTGAAGGGGTCGTCGCTGGGGCGGTCGACGGAAAATG

Basic information

species Selaginella moellendorffii
transcript EFJ31327
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ31327 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GRMZM2G076392_T02 (Zea mays), 3'ss of exon 4
------------------------------------------------------gtttggtccttaaatgcaat-tacagtctaacatgtgcttttacagGTTCGTTTTGTAGTAATGGGAAACATGTTCTGCACAGACCTTCGTATACACCGGAGGTTCGATTTGAAGGGGTCGTCGCTGGGGCGGTCGACGGAAAATG
                                                       | | ||| || |   |||  ||  |  |    |  |  ||| ||| | || |||||||| |||||||||||||| ||||| || ||| | || ||||||||||| || ||||| || || ||  | || || || || || || |
ctagtgtcattttcatttcttaaacagtcagagcagtttatgatatcatttaaattatagtcatttatcccaaaataatgcatgttgttcgtgtttgcagTTCCGGTTTGTAGTGATGGGAAACATGTTTTGCACTGAACTTAGAATTCACCGGAGGTTTGACTTGAAAGGTTCATCCTTAGGCCGCTCAACAGACAAAG

upper sequence: EFJ31327 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GLYMA05G30320.1 (Glycine max), 3'ss of exon 4
--------------------------------------------------------------------------------------------------gtt-tggtccttaaatgca-attacagtctaacatg---------tgcttttac-agGTTCGTTTTGTAGTAATGGGAAACATGTTCTGCACAGACCTTCGTATACACCGGAGGTTCGATTTGAAGGGGTCGTCGCTGGGGCGGTCGACGGAAAATG
                                                                                                  ||| | ||  ||  ||  | ||| |  |||  | |          || ||| |  ||||||| ||||| || |||||||| |||||||||||||| |||| ||| |||||  | |  ||| ||||||||||  | |  ||  | |  || || || |
gtataacaaatatctgtctctagcttcttcttttcaattagtactactggtatgaataaccttgttttccaccccacctagtgagaaaagggttggttgttgttgtttttgtataaatatttctttctttcttcattggttgttgttttcattagGTTCGCTTTGTGGTCATGGGAAATATGTTCTGCACAGAACTTCATATTCACCGTCGTTATGATCTGAAGGGGTCTACTCAAGGAAGATATACAGACAAAG

upper sequence: EFJ31327 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GLYMA03G34340.1 (Glycine max), 3'ss of exon 4
----------------------------------------------gtttggt-ccttaaatgcaa---ttacagtctaacatgtgctt-----ttacagGTTCGTTTTGTAGTAATGGGAAACATGTTCTGCACAGACCTTCGTATACACCGGAGGTTCGATTTGAAGGGGTCGTCGCTGGGGCGGTCGACGGAAAATG
                                              ||    | ||| ||||   |   | | | |  || |||   ||     || ||| |||| ||||| ||||||||||| ||||||||||||||| |  | || || |||||||| ||||| || || || || || ||  | ||  | || ||  
atgatcaaatatttgagcctatcataacttgcatcttcaatttcatgtacatttcctcaaataggaggctaatacttgaatatgattttctgtcttgcagTTTCGCTTTGTTGTAATGGGAAATATGTTCTGCACAGACTTAAGGATCCATCGGAGGTTTGATTTAAAAGGTTCTTCCCTTGGAAGATCATCAGACAAGA

upper sequence: EFJ31327 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GLYMA13G20980.1 (Glycine max), 3'ss of exon 5
-------------------------------------------------gtttggtcc---ttaaatgcaattac---agtctaacatgtgcttttacagGTTCGTTTTGTAGTAATGGGAAACATGTTCTGCACAGACCTTCGTATACACCGGAGGTTCGATTTGAAGGGGTCGTCGCTGGGGCGGTCGACGGAAAATG
                                                  |||  ||    | | | || | |||     |||||  |    |||| ||| |||| ||||| ||||||||||| ||||||||||||||  |  | || ||  |||| |  |||||||| || || || || || || ||  |||| ||  
caaatgtaccacatcaaatatttgaacctatcatgacttaataatctaaattttatctcattaagaggctaatacttatatctaattttctattttgcagTTTCGCTTTGTCGTAATGGGAAATATGTTCTGCACAGAATTAAGGATCCATAGGAGATATGATTTGAAAGGTTCATCTCTTGGACGTTCTTCGGACAAGA

upper sequence: EFJ31327 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: Vv08s0007g04700.t01 (Vitis vinifera), 3'ss of exon 4
------------------------------------------------------gtttggtccttaaatgcaattacagtctaacatgtgct--tttacagGTTCGTTTTGTAGTAATGGGAAACATGTTCTGCACAGACCTTCGTATACACCGGAGGTTCGATTTGAAGGGGTCGTCGCTGGGGCGGTCGACGGAAAATG
                                                       | ||  |  | ||   ||||   ||  |  |||| ||  ||| ||| |||| ||||||||||||||||||||||||||||||||  | || || ||  |||| || |||||||| || || ||  | ||||| ||  | || || |
attcttgttggcttatccaaaaaaacaaaactactgttgagcatatgattgcatatatgtacaatgaac-taatttttgtaaactatgtcctactttgcagTTTCGCTTTGTAGTAATGGGAAACATGTTCTGCACAGAATTACGAATCCATAGGAGATTTGATTTGAAAGGTTCCTCCTTAGGGCGTTCTGCAGACAAGG

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|169044977|gb|FE450873.1|FE450873
EST:     TTACAAAGTTTTTTGGCCTTCATCGTATCAAGCCTCANNNNNNNCGAAAG                         GTTCGTTTTGTAGTAATGGGAAACATGTTCTGCACAGACCTTCGTATACAC
genomic: TTACAAAGTTTTTTGGCCTTCATCGTATCAAGCCTCAGGGGGGGCGAAAGgtttggtcct ... gcttttacagGTTCGTTTTGTAGTAATGGGAAACATGTTCTGCACAGACCTTCGTATACAC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttggtccttaaatgcaattacagtctaacatgtgcttttacagGTTCGTTTTGTAGTAATGGGAAACATGTTCTGCACAGACCTTCGTATACACCGGAGGTTCGATTTGAAGGGGTCGTCGCTGGGGCGGTCGACGGAAAATG
                                  gtctaac  putative branch site (score: 2)
                                            tgctttt  putative PPT
                   ttaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttggtccttaaatgcaattacagtctaacatgtgcttttacagGTTCGTTTTGTAGTAATGGGAAACATGTTCTGCACAGACCTTCGTATACACCGGAGGTTCGATTTGAAGGGGTCGTCGCTGGGGCGGTCGACGGAAAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG