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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttatatcataatggcttgctatatgcactaattcttaatggatttatgtttgcagGGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACG

Basic information

species Selaginella moellendorffii
transcript EFJ34434
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ34434 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: LOC_Os01g47410.1 (Oryza sativa), 3'ss of exon 7
-------------------------------------------------------------------gttatatcataatggcttgctatatgcactaattc--ttaatggatttatgtttgcagGGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACG
                                                                    || | |   || ||       | |  |  | ||   ||  |   | | |||    ||| ||||||||    || ||||| ||||| |||||||||||||||||||||||| ||||||| |||
gtgctcaattatcaattttttttcatgctcactatacctttatttaaatgcaaaatggtctaatctttttctttttgaaaggaacatagtctaaatcattttggttgttccctatgtgtcattagGATTCTGTGCAGCTGGGTGTGCAGCAATAGCAGATTCTGGAACTTCACTGCTTACTGGTCCCACG

upper sequence: EFJ34434 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GRMZM2G153977_T01 (Zea mays), 3'ss of exon 1
------------------------gttatatcata--atggct--tgcta-tatgcactaattcttaatgg---atttat-gtttgcagGGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACG
                        |||||   |||  ||| ||  || || |  | | ||   || ||||    || ||  |||  ||||||| ||||||   || ||||| ||||| |||||||||||||||||  |||||||||| || || 
gcaggccaggttcctctcttctttgttattctatataatgtctcatgttaatgagaaatataactaaatgcgtcatctaccgttgtcagGGTTTTGTGCTGGTGGTTGTGCAGCAATAGCAGATTCTGGAACTTCCTTGCTTGCTGGCCCCACA

upper sequence: EFJ34434 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: Vv10s0116g01210.t01 (Vitis vinifera), 3'ss of exon 7
-----------------------------------------------------------------------------------------------------gttatatcataat-ggcttgctatatgcactaattcttaatggatttatgtttgcagGGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACG
                                                                                                      | |   ||||||  |  || |   |     | ||    |      ||      |||||| ||||||   ||| ||||| |||||||||||||||||||||||  || | || ||||| |||
gtgagacccctcttgaaaccattgtgtgctttataaaccaaaaagtaggaaattggaggaaagaaggaaaagcctagatttagagacctttttttaatggtataagcacataattagtatgattattatgtcagtttgacacaagcataccacctcagGGTACTGTGCCGGAGGTTGTGCAGCAATTGCAGATTCTGGAACTTCTTTGTTGGCAGGTCCAACG

upper sequence: EFJ34434 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: PP1S99_158V6.1 (Physcomitrella patens), 3'ss of exon 6
---------------------------------------gttatatcataatggcttgct-atatgcactaattcttaatggattta----tgtttgcagGGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACG
                                         || |     || |       || |   || |||   | |    |||    | |||||||| |||||||||  |||||||||||||||||||||||| |||||||| ||| | ||||||||||||
gtctatgatgtagagtcgcatcgaacatctgacctgatcactacaagtgcatagtccatagatctcatctgattaggagttatcttaaatctctttgcagGATTCTGTGCTGGAGGATGTGCTGCAATTGCAGATTCCGGAACTTCTCTGTTAGCTGGTCCTACG

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|169113000|gb|FE515480.1|FE515480
EST:     ATACTGGCAGTTCAACATGGGAGATGTGGCTGTGGATGGCCAGAGCACAG                         GGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGC
genomic: ATACTGGCAGTTCAACATGGGAGATGTGGCTGTGGATGGCCAGAGCACAGgttatatcat ... atgtttgcagGGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGC
EST: gi|169108566|gb|FE510781.1|FE510781
EST:     ATACTGGCAGTTCAACATGGGAGATGTGGTTGTGGATGGCCAGAGCACAG                         GGTTCTGTGCTAAAAGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGC
genomic: ATACTGGCAGTTCAACATGGGAGATGTGGCTGTGGATGGCCAGAGCACAGgttatatcat ... atgtttgcagGGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGC
EST: gi|169031797|gb|FE438482.1|FE438482
EST:     ATACTGGCAGTTCAACATGGGAGATGTGGCTGTGGATGGCCAGAGCACAG                         GGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGC
genomic: ATACTGGCAGTTCAACATGGGAGATGTGGCTGTGGATGGCCAGAGCACAGgttatatcat ... atgtttgcagGGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGC
EST: gi|169055215|gb|FE461076.1|FE461076
EST:     ATACTGGCAGTTCAACATGGGAGATGTGGCTGTGGATGGCCAGAGCACAG                         GGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGC
genomic: ATACTGGCAGTTCAACATGGGAGATGTGGCTGTGGATGGCCAGAGCACAGgttatatcat ... atgtttgcagGGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGC
EST: gi|169112151|gb|FE513494.1|FE513494
EST:     AGATGTGGCTGTGGATGGCCAGAGCACAG                         GGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGC
genomic: AGATGTGGCTGTGGATGGCCAGAGCACAGgttatatcat ... atgtttgcagGGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGC
EST: gi|169060203|gb|FE467565.1|FE467565
EST:     ATACTGGCAGTTCAACATGGGAGATGTGGCTGTGGATGGCCAGAGCACAG                         GGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGC
genomic: ATACTGGCAGTTCAACATGGGAGATGTGGCTGTGGATGGCCAGAGCACAGgttatatcat ... atgtttgcagGGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGC
EST: gi|169025759|gb|FE433669.1|FE433669
EST:     ATACTGGCAGTTCAACATGGGAGATGTGGCTGTGGATGGCCAGAGCACAG                         GGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTG
genomic: ATACTGGCAGTTCAACATGGGAGATGTGGCTGTGGATGGCCAGAGCACAGgttatatcat ... atgtttgcagGGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTG
EST: gi|169110929|gb|FE509334.1|FE509334
EST:     ATACGGGCAGTTCAACATGGGAGATGTGGCTGTGGATGGCCAGAGCACAG                         GGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGC
genomic: ATACTGGCAGTTCAACATGGGAGATGTGGCTGTGGATGGCCAGAGCACAGgttatatcat ... atgtttgcagGGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGC
EST: gi|169114469|gb|FE516539.1|FE516539
EST:     ATACTGGCAGTTCAACATGGGAGATGTGGCTGTGGATGGCCAGAGCACAG                         GGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGC
genomic: ATACTGGCAGTTCAACATGGGAGATGTGGCTGTGGATGGCCAGAGCACAGgttatatcat ... atgtttgcagGGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGC
EST: gi|169057177|gb|FE464688.1|FE464688
EST:     ATACTGGCAGTTCAACATGGGAGATGTGGCTGTGGATGGCCAGAGCACAG                         GGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGC
genomic: ATACTGGCAGTTCAACATGGGAGATGTGGCTGTGGATGGCCAGAGCACAGgttatatcat ... atgtttgcagGGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGC
EST: gi|169048945|gb|FE456062.1|FE456062
EST:     ATACTGGCAGTTCAACATGGGAGATGTGGCTGTGGATGGCCAGAGCACAG                         GGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGC
genomic: ATACTGGCAGTTCAACATGGGAGATGTGGCTGTGGATGGCCAGAGCACAGgttatatcat ... atgtttgcagGGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGC
EST: gi|169112990|gb|FE515470.1|FE515470
EST:     ATACTGGCAGTTCAACATGGGAGATGTGGCTGTGGATGGCCAGAGCACAG                         GGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGC
genomic: ATACTGGCAGTTCAACATGGGAGATGTGGCTGTGGATGGCCAGAGCACAGgttatatcat ... atgtttgcagGGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGC
EST: gi|169058238|gb|FE466005.1|FE466005
EST:     GGCAGTTCAACATGGGAGATGTGGCTGTGGATGGCCAGAGCACAG                         GGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGC
genomic: GGCAGTTCAACATGGGAGATGTGGCTGTGGATGGCCAGAGCACAGgttatatcat ... atgtttgcagGGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGC
EST: gi|169114468|gb|FE516538.1|FE516538
EST:     ATACTGGCAGTTCAACATGGGAGATGTGGCTGTGGATGGCCAGAGCACAG                         GGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGC
genomic: ATACTGGCAGTTCAACATGGGAGATGTGGCTGTGGATGGCCAGAGCACAGgttatatcat ... atgtttgcagGGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGC
EST: gi|169065200|gb|FE474024.1|FE474024
EST:     ATACTGGCAGTTCACCATGGGAGATGT-GCTGTGGATGGCCAGAGCACAG                         GGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGC
genomic: ATACTGGCAGTTCAACATGGGAGATGTGGCTGTGGATGGCCAGAGCACAGgttatatcat ... atgtttgcagGGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGC
EST: gi|169039673|gb|FE448607.1|FE448607
EST:     ATACTGGCAGTTCAACATGGGAGATGTGGCTGTGGATGGCCAGAGCACAG                         GGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGC
genomic: ATACTGGCAGTTCAACATGGGAGATGTGGCTGTGGATGGCCAGAGCACAGgttatatcat ... atgtttgcagGGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGC
EST: gi|169112152|gb|FE513495.1|FE513495
EST:     ATACTGGCAGTTCAACATGGGAGATGTGGCTGTGGATGGCCAGAGCACAG                         GGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGC
genomic: ATACTGGCAGTTCAACATGGGAGATGTGGCTGTGGATGGCCAGAGCACAGgttatatcat ... atgtttgcagGGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGC
EST: gi|169096046|gb|FE500024.1|FE500024
EST:     ATACTGGCAGTTCAACATGGGAGATGTGGCTGTGGATGGCCAGAGCACAG                         GGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGC
genomic: ATACTGGCAGTTCAACATGGGAGATGTGGCTGTGGATGGCCAGAGCACAGgttatatcat ... atgtttgcagGGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGC
EST: gi|169065201|gb|FE474025.1|FE474025
EST:     TACTGGCAGTTTCA-CATGGGAGATGTGGCTGTGGATGGCCAGAGCACAG                         GGTTCTGTGCTAAAGGATGTGCT
genomic: TACTGGCAGTT-CAACATGGGAGATGTGGCTGTGGATGGCCAGAGCACAGgttatatcat ... atgtttgcagGGTTCTGTGCTAAAGGATGTGCT
EST: gi|169096045|gb|FE500023.1|FE500023
EST:     ATACTGGCAGTTCACCATGGGAGATGTGGCTGTGGATGGCCAGAGCACAG                         GGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGC
genomic: ATACTGGCAGTTCAACATGGGAGATGTGGCTGTGGATGGCCAGAGCACAGgttatatcat ... atgtttgcagGGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGC
EST: gi|169093446|gb|FE495727.1|FE495727
EST:     ATACTGGCAGTTCAACATGGGAGATGTGGCTGTGGATGGCCAGAGCACAG                         GGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGC
genomic: ATACTGGCAGTTCAACATGGGAGATGTGGCTGTGGATGGCCAGAGCACAGgttatatcat ... atgtttgcagGGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGC
EST: gi|169031873|gb|FE438506.1|FE438506
EST:     ATACTGGCAGTTCAACATGGGAGATGTGGCTGTGGATGGCCAGAGCACAG                         GGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGC
genomic: ATACTGGCAGTTCAACATGGGAGATGTGGCTGTGGATGGCCAGAGCACAGgttatatcat ... atgtttgcagGGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGC

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), 35 (downstream exon)
Score: 120

AAGGATCGCTTTAAGGGAAAACATGTTTATACACCAGTTACCAGAGAGGGATACTGGCAGTTCAACATGGGAGATGTGGCTGTGGATGGCCAGAGCACAGgttatatcat ... atgtttgcagGGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatatcataatggcttgctatatgcactaattcttaatggatttatgtttgcagGGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACG
                            taattcttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttatatcataatggcttgctatatgcactaattcttaatggatttatgtttgcagGGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT