Skip to another splice site:
1  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttcttttcctcttcttgttcttctaagagcaacacttgtctttttagGTACACTGGAGAGGATGGGTTTGAGATCTCTGTTCCGTCGGAGCATGGTGTGGAGCTGGCGAAGGCACTTCTGGAGAAGTCGGAGGGGAAGATCCTTCTC

Basic information

species Selaginella moellendorffii
transcript EFJ06937
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ06937 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA07G39190.1 (Glycine max), 3'ss of exon 3
--------------------------------------------------------------------------------------------------------------------gtaagtttcttttcctcttcttgttcttctaagagcaacacttgtct---------ttttagGTACACTGGAGAGGATGGGTTTGAGATCTCTGTTCCGTCGGAGCATGGTGTGGAGCTGGCGAAGGCACTTCTGGAGAAGTCGGAGGGGAAGATCCTTCTC
                                                                                                                     | || |     |    |     | |     | |  |||||||   |         ||| ||||| |||||||| ||||| ||||||||||| ||||| || ||||||||  | || || || |||||| | ||||| || || || |||||| |     | 
gtatgcttttattgtcattttctttcaccaacatcacctatttattcttcaaagttcatccgagttatgaaactccatcttgtattactttaatttcattattgaatgtttgtgttatgagctcagagtttcttagggataccatgcataataacactttcttgattgagactttcagGTATACTGGAGAAGATGGATTTGAGATCTCAGTTCCTTCAGAGCATGGACTAGATCTTGCCAAGGCAATACTGGAAAAATCTGAAGGGAAGGTAAGATTG
















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|70670090|gb|DN838667.1|DN838667
EST:     TTCAGGATCCTCTCTGTCAATGGTGCCGAATGCTTCATCACTAGAACCGG                         GTACACTGGAGAGGATGGGTTTGAGATCTCTGTTCCGTCGGAGCATGCTCT
genomic: TTCAGGATCCTCTCTGTCAATGGTGCCGAATGCTTCATCACTAGAACCGGgtaagtttct ... gtctttttagGTACACTGGAGAGGATGGGTTTGAGATCTCTGTTCCGTCGGAGCATGGTGT
EST: gi|169037226|gb|FE445447.1|FE445447
EST:     TTCAGGATCCTCTCTGTCAATGGTGCCGAATGCTTCATCACTAGAACCGG                         GTACACTGGAGAGGATGGGTTTGAGATCTCTGTTCCGTCGGAGCATGCTCT
genomic: TTCAGGATCCTCTCTGTCAATGGTGCCGAATGCTTCATCACTAGAACCGGgtaagtttct ... gtctttttagGTACACTGGAGAGGATGGGTTTGAGATCTCTGTTCCGTCGGAGCATGGTGT
EST: gi|169083969|gb|FE493609.1|FE493609
EST:     TTCAGGATCCTCTCTGTCAATGGTGCCGAATGCTTCATCACTAGAACCGG                         GTACACTGGAGAGGATGGGTTTGAGATCTCTGTTCCGTCGGAGCATGGTGT
genomic: TTCAGGATCCTCTCTGTCAATGGTGCCGAATGCTTCATCACTAGAACCGGgtaagtttct ... gtctttttagGTACACTGGAGAGGATGGGTTTGAGATCTCTGTTCCGTCGGAGCATGGTGT
EST: gi|169115830|gb|FE517609.1|FE517609
EST:     TTCAGGATCCTCTCTGTCAATGGTGCCGAATGCTTCATCACTAGAACCGG                         GTACACTGGAGAGGATGGGTTTGAGATCTCTGTTCCGTCGGAGCATGGTGT
genomic: TTCAGGATCCTCTCTGTCAATGGTGCCGAATGCTTCATCACTAGAACCGGgtaagtttct ... gtctttttagGTACACTGGAGAGGATGGGTTTGAGATCTCTGTTCCGTCGGAGCATGGTGT
EST: gi|169036096|gb|FE445136.1|FE445136
EST:     TTCAGGATCCTCTCTGTCAATGGTGCCGAATGCTTCATCACTAGAACCGG                         GTACACTGGAGAGGATGGGTTTGAGATCTCTGTTCCGTCGGAGCATGCTCT
genomic: TTCAGGATCCTCTCTGTCAATGGTGCCGAATGCTTCATCACTAGAACCGGgtaagtttct ... gtctttttagGTACACTGGAGAGGATGGGTTTGAGATCTCTGTTCCGTCGGAGCATGGTGT
EST: gi|169040064|gb|FE448909.1|FE448909
EST:     TTCAGGATCCTCTCTGTCAATGGTGCCGAATGCTTCATCACTAGAACCGG                         GTACACTGGAGAGGATGGGTTTGAGATCTCTGTTCCGTCGGAGCATGGTGT
genomic: TTCAGGATCCTCTCTGTCAATGGTGCCGAATGCTTCATCACTAGAACCGGgtaagtttct ... gtctttttagGTACACTGGAGAGGATGGGTTTGAGATCTCTGTTCCGTCGGAGCATGGTGT
EST: gi|169096986|gb|FE500054.1|FE500054
EST:     TTCAGGATCCTCTCTGTCAATGGTGCCGAATGCTTCATCACTAGAACCGG                         GTACACTGGAGAGGATGGGTTTGAGATCTCTGTTCCGTCGGAGCATGGTGT
genomic: TTCAGGATCCTCTCTGTCAATGGTGCCGAATGCTTCATCACTAGAACCGGgtaagtttct ... gtctttttagGTACACTGGAGAGGATGGGTTTGAGATCTCTGTTCCGTCGGAGCATGGTGT
EST: gi|169057611|gb|FE463662.1|FE463662
EST:     TTCAGGATCCTCTCTGTCAATGGTGCCGAATGCTTCATCACTAGAACCGG                         GTACACTGGAGAGG
genomic: TTCAGGATCCTCTCTGTCAATGGTGCCGAATGCTTCATCACTAGAACCGGgtaagtttct ... gtctttttagGTACACTGGAGAGG
EST: gi|169061301|gb|FE470388.1|FE470388
EST:     TTCAGGATCCTCTCTGTCAATGGTGCCGAATGCTTCATCACTAGAACCGG                         GTACACTGGAGAGGATGGGTTTGAGATCTCTGTTCCGTCGGAGCATGCTCT
genomic: TTCAGGATCCTCTCTGTCAATGGTGCCGAATGCTTCATCACTAGAACCGGgtaagtttct ... gtctttttagGTACACTGGAGAGGATGGGTTTGAGATCTCTGTTCCGTCGGAGCATGGTGT
EST: gi|169038917|gb|FE449634.1|FE449634
EST:     TCAGGATCCTCTCTGTNCA-TGGTGCCGAATGCTTCATCACTAGAACCGG                         GTACACTGGAGAGGATGGGTTTGAGATCTCTGTTCCGTCGGAGCATGCTCT
genomic: TCAGGATCCTCTCTGT-CAATGGTGCCGAATGCTTCATCACTAGAACCGGgtaagtttct ... gtctttttagGTACACTGGAGAGGATGGGTTTGAGATCTCTGTTCCGTCGGAGCATGGTGT
EST: gi|169115235|gb|FE515638.1|FE515638
EST:     TTCAGGATCCTCTCTGTCAATGGTGCCGAATGCTTCATCACTAGAACCGG                         GTACACTGGAGAGGATGGGTTTGAGATCTCTGTTCCGTCGGAGCATGGTGT
genomic: TTCAGGATCCTCTCTGTCAATGGTGCCGAATGCTTCATCACTAGAACCGGgtaagtttct ... gtctttttagGTACACTGGAGAGGATGGGTTTGAGATCTCTGTTCCGTCGGAGCATGGTGT
EST: gi|169022956|gb|FE431543.1|FE431543
EST:     TTCAGGATCCTCTCTGTCAATGGTGCCGAATGCTTCATCACTAGAACCGG                         GTACACTGGAGAGGATGGGTTTGAGATCTCTGTTCCGTCGGAGCATGCTCT
genomic: TTCAGGATCCTCTCTGTCAATGGTGCCGAATGCTTCATCACTAGAACCGGgtaagtttct ... gtctttttagGTACACTGGAGAGGATGGGTTTGAGATCTCTGTTCCGTCGGAGCATGGTGT
EST: gi|70669740|gb|DN838317.1|DN838317
EST:     TTCAGGATCCTCTCTGTCAATGGTGCCGAATGCTTCATCACTAGAACCGG                         GTACACTGGAGAGGATGGGGTTTGAGATCTCTGTTTCCGTCCGAGCATGGT
genomic: TTCAGGATCCTCTCTGTCAATGGTGCCGAATGCTTCATCACTAGAACCGGgtaagtttct ... gtctttttagGTACACTGGAGAGGATGGG-TTTGAGATCTCTGTT-CCGTCGGAGCATGGT
EST: gi|169099533|gb|FE501045.1|FE501045
EST:     TCAGGATCCTCTCTGTNCA-TGGTGCCGAATGCTTCATCACTAGAACCGG                         GTACACTGGAGAGGATGGGTTTGAGATCTCTGTTCCGTNCG-AGCATGGTG
genomic: TCAGGATCCTCTCTGT-CAATGGTGCCGAATGCTTCATCACTAGAACCGGgtaagtttct ... gtctttttagGTACACTGGAGAGGATGGGTTTGAGATCTCTGTTCCGT-CGGAGCATGGTG

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), 34 (downstream exon)
Score: 46

CACTACAGCATCTGGTGAAGGAGGATTTGAGCAAAGTCTACTTTGGAAACTTCAGGATCCTCTCTGTCAATGGTGCCGAATGCTTCATCACTAGAACCGGgtaagtttct ... gtctttttagGTACACTGGAGAGGATGGGTTTGAGATCTCTGTTCCGTCGGAGCATGGTGTGGAGCTGGCGAAGGCACTTCTGGAGAAGTCGGAGGGGAAGATCCTTCTC




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaagtttcttttcctcttcttgttcttctaagagcaacacttgtctttttagGTACACTGGAGAGGATGGGTTTGAGATCTCTGTTCCGTCGGAGCATGGTGTGGAGCTGGCGAAGGCACTTCTGGAGAAGTCGGAGGGGAAGATCCTTCTC
                                           cttgtcttttt  CT-rich tract
       tttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttcttttcctcttcttgttcttctaagagcaacacttgtctttttagGTACACTGGAGAGGATGGGTTTGAGATCTCTGTTCCGTCGGAGCATGGTGTGGAGCTGGCGAAGGCACTTCTGGAGAAGTCGGAGGGGAAGATCCTTCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA