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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggtatgtttcaagtttgtcatgagagctatgataaccagggctttgtgtagGTGTCTGCCGCTCGTGAGGAGGTGCCTGGTCGTCGTGGATATCCTGGTTATATGTATACAGATTTGGCAACAATTTACGAGCGTGCTGGACGAATTGAAG

Basic information

species Selaginella moellendorffii
transcript EFJ11911
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ11911 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: LOC_Os01g51380.2 (Oryza sativa), 3'ss of exon 9
-------------------------------------------gtatggtatgtttcaagtt-tgtcatgagagctatgataaccagggctttgtgt-agGTGTCTGCCGCTCGTGAGGAGGTGCCTGGTCGTCGTGGATATCCTGGTTATATGTATACAGATTTGGCAACAATTTACGAGCGTGCTGGACGAATTGAAG
                                           ||||  |||  |||||||    ||     | || |  |        | |    | |||| ||||| ||||| ||||| || ||||| || ||||| |||||||||||||||||||| ||||||||||| || || ||||||||||| || || ||||
aaatctagtccttttaataccacggtttatgctgatttcttaagtattatatcattcaagtcacctctacttaccttttctctgtctttcctcacatcagGTTTCTGCAGCTCGAGAGGAAGTACCTGGACGGCGTGGTTATCCTGGTTATATGTATACTGATTTGGCAACTATCTATGAGCGTGCTGGTCGCATAGAAG

upper sequence: EFJ11911 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 3'ss of exon 9
-------------------------------------------gtatggtatgtttcaagtttgtcatgagagc--tatgataaccagggctttgtgtagGTGTCTGCCGCTCGTGAGGAGGTGCCTGGTCGTCGTGGATATCCTGGTTATATGTATACAGATTTGGCAACAATTTACGAGCGTGCTGGACGAATTGAAG
                                             ||  ||| | |   | ||| ||  |   |   | | |||    |  | | ||||||| || || || || || || ||||| ||| | ||||| |||||||| ||||||||||| ||| ||||||| || || ||||| ||||| || |||||||
acatctccttttatgttcgactgcaataaatgataaattgctgaaattttatttattgtgattggcactaatacaacacggtaattgtgcttatatgtagGTATCAGCAGCCCGAGAAGAAGTGCCAGGTAGGCGTGGGTATCCTGGATATATGTATACTGATCTGGCAACCATATATGAGCGAGCTGGGCGTATTGAAG

upper sequence: EFJ11911 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: GRMZM2G094497_T01 (Zea mays), 3'ss of exon 9
---------------------------------------gtatggtatgtt----tcaagtttgtcatgagagcta--tgataaccagggctttgtgtagGTGTCTGCCGCTCGTGAGGAGGTGCCTGGTCGTCGTGGATATCCTGGTTATATGTATACAGATTTGGCAACAATTTACGAGCGTGCTGGACGAATTGAAG
                                         |||  |  ||    ||    ||   |  |  ||||  ||   |    |  ||| ||||||| ||||| || || || |||||||| ||| | ||||| |||||||| ||||||||||| |||||||||||||| || ||||||||||| || |||||||
ttttatatatttaagattaaccttttctattagctaattaaatgacaaattgatgtcgttgtttctaataatgctacatgggcattgtgcttttttgtagGTTTCTGCAGCCCGAGAAGAGGTGCCAGGTAGGCGTGGTTATCCTGGATATATGTATACTGATTTGGCAACAATATATGAGCGTGCTGGGCGTATTGAAG

upper sequence: EFJ11911 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: GRMZM2G181151_T02 (Zea mays), 3'ss of exon 9
---------------------------------------------gtatggtatgtttcaagtttgtcatgagagctatgataac-cagggctttgtgtagGTGTCTGCCGCTCGTGAGGAGGTGCCTGGTCGTCGTGGATATCCTGGTTATATGTATACAGATTTGGCAACAATTTACGAGCGTGCTGGACGAATTGAAG
                                               ||   |||||| | |||| | || |  ||||      |   | ||||| ||||||| ||||| || || || |||||||| ||| | ||||| |||||||| ||||||||||| ||| |||||||||| || ||||||||||| || |||||||
agtatttaagatcaacctttgtatttaggtaatcaaatggtaaattgatttcatgtttgatgtttctaataat-gctacatgggcattgtgctttttgtagGTTTCTGCAGCCCGAGAAGAGGTGCCAGGTAGGCGTGGTTATCCTGGATATATGTATACTGATCTGGCAACAATATATGAGCGTGCTGGGCGTATTGAAG

upper sequence: EFJ11911 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 9
--------------------------------------------gtatggtatgtttcaagtttgtcatgagagctat-gataaccagggctttgtgtagGTGTCTGCCGCTCGTGAGGAGGTGCCTGGTCGTCGTGGATATCCTGGTTATATGTATACAGATTTGGCAACAATTTACGAGCGTGCTGGACGAATTGAAG
                                             | | | |       || ||| ||   || |||| ||   |    |  |  ||||||| ||||| || || || || || |||||| | ||||| || || ||||| |||||||||||| | |||||||| ||||| ||||||||| ||||||| |
catttatttatctctttttctccgactataaaaagtaactaagtattttgcaaacaattagattgacaatggaactattgaccccttctggatcctgtagGTATCTGCTGCCCGAGAAGAAGTACCTGGTAGACGTGGGTACCCCGGTTACATGTATACAGATCTTGCAACAATATACGAACGTGCTGGAAGAATTGAGG

upper sequence: EFJ11911 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: GLYMA18G48280.1 (Glycine max), 3'ss of exon 9
--------------------------------------------gtatggtatgtttcaagtttgtcatgagagctat-gataaccagggctttgtgtagGTGTCTGCCGCTCGTGAGGAGGTGCCTGGTCGTCGTGGATATCCTGGTTATATGTATACAGATTTGGCAACAATTTACGAGCGTGCTGGACGAATTGAAG
                                             | | | |       || ||| ||   || ||||  |   |    |  |  ||||||| ||||| || || || || || |||||| | ||||| ||||| || || |||||||||||| | |||||||| ||||| ||||||||| ||||||| |
catgtatttatatctttttctcagagtattagaagtaacaaagtattttgcaaacaattagattgacaatggaactattaaccccttctggatcttgtagGTATCTGCTGCCCGAGAAGAAGTACCTGGTAGACGTGGGTATCCCGGCTACATGTATACAGATCTTGCAACAATATACGAACGTGCTGGAAGAATTGAGG

upper sequence: EFJ11911 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 10
--------------------------------------------gtatggtatgtttcaa-gtttgtcatgagagctatgataaccagggctttgtgtagGTGTCTGCCGCTCGTGAGGAGGTGCCTGGTCGTCGTGGATATCCTGGTTATATGTATACAGATTTGGCAACAATTTACGAGCGTGCTGGACGAATTGAAG
                                             |  |  ||   | ||  | | ||   |    | ||     ||     |    ||||| ||||| || || || || ||||| ||| | ||||| |||||||| ||||||||||||||| | ||||||||||| || || |||||  ||||||| |
aatgtgggacttgggttttttccaatatgacttatttttggagtatgagaaataactgaacatatttctcaaacaatttgcatgacacttgatcccatagGTATCTGCTGCCCGAGAAGAAGTGCCGGGTAGACGTGGTTATCCTGGATATATGTATACAGATCTTGCAACAATTTATGAACGAGCTGGGAGAATTGAGG

upper sequence: EFJ11911 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: GLYMA10G42940.2 (Glycine max), 3'ss of exon 9
------------------------------------------------------------------------------------------------------------------------------gtatggtatgtttc----aagtttgtcatgagagctatgataaccagggctttgtgtagGTGTCTGCCGCTCGTGAGGAGGTGCCTGGTCGTCGTGGATATCCTGGTTATATGTATACAGATTTGGCAACAATTTACGAGCGTGCTGGACGAATTGAAG
                                                                                                                              |||||  |  |  |    ||  ||   || | |  |   || ||    | |    |||||| ||||| || || || || ||||| ||  | ||||| |||||||| ||||||||||||||| | ||||||||||| || || |||||  ||||||| |
gtaatttaccttcaactgttattagtttggaagaagcaacaaaaagataggggacttgaaaccttttataggctttaatgatgatttaaaattgacattcttttatgcctttggtttattcttggagtatgagaaataactgaaaatatttctataacaatttgcatgacacttgatcc-cgtagGTATCTGCTGCCCGAGAAGAAGTGCCAGGAAGACGTGGTTATCCTGGATATATGTATACAGATCTTGCAACAATTTATGAACGAGCTGGGAGAATTGAGG

upper sequence: EFJ11911 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 9
--------------------------gtatggtatgtttcaagtttgtcatgagagctatga-------taaccagggctttgtgtagGTGTCTGCCGCTCGTGAGGAGGTGCCTGGTCGTCGTGGATATCCTGGTTATATGTATACAGATTTGGCAACAATTTACGAGCGTGCTGGACGAATTGAAG
                           | |   ||| |||||  || | ||   |||| |||       |||| |  |     | ||||| ||||| ||||| || || || |||||  | ||||||||||| || ||||||||||||||| | ||||| ||||| || || || ||||| |||||||
gtaatgagtttcactgtcctttgtgtatgtcccatgattcaaaatt-tgatttaagctttgaataaaattaacaaacgtgaactctagGTTTCTGCTGCTCGAGAAGAAGTTCCTGGAAGACGTGGATATCCGGGGTATATGTATACAGATCTTGCAACTATTTATGAACGCGCGGGACGTATTGAAG

upper sequence: EFJ11911 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: Vv18s0001g01020.t01 (Vitis vinifera), 3'ss of exon 9
-------------------------------------gtatggtatgtttcaagtttgtcatgagagcta------tgataaccagggctttg--tgtagGTGTCTGCCGCTCGTGAGGAGGTGCCTGGTCGTCGTGGATATCCTGGTTATATGTATACAGATTTGGCAACAATTTACGAGCGTGCTGGACGAATTGAAG
                                      ||| | |   |||       |  |   | |||      ||  ||     | ||||  || |||| ||||| || || ||||| || |||||  | ||||| |||||||| ||||||||||| ||| | ||||||||||| |||||||||||||| || ||||
cttcataggttttaaaatcatacggataatcgaatttctattgcaccattcccacacttactttcacctacttgactggaaatgtctgttttgactgcagGTATCTGCAGCCCGGGAGGAAGTACCTGGAAGGCGTGGGTATCCTGGGTATATGTATACTGATCTTGCAACAATTTATGAGCGTGCTGGACGTATAGAAG

upper sequence: EFJ11911 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 9
--------------------------------------gtatggtatgtttcaagtttgtca-tgagagctatgataaccagggctt--tg----tgtagGTGTCTGCCGCTCGTGAGGAGGTGCCTGGTCGTCGTGGATATCCTGGTTATATGTATACAGATTTGGCAACAATTTACGAGCGTGCTGGACGAATTGAAG
                                        || | ||  |||||  |  ||| |||    | ||||    |   |||  ||    || |||| ||||| || || || || || || ||  | ||||| |||||||| ||||||||||| ||| |||| || ||||| || ||||||||||| |||||||
cttctaattttgttcttgagtatttttaatcaagtaccccattgaattcttcaaactcatcactgatgcttgtgatgcaaactacttattgcaactgcagGTATCTGCTGCCCGAGAAGAAGTTCCCGGGAGGCGTGGGTATCCTGGGTATATGTATACTGATCTGGCGACGATTTATGAACGTGCTGGACGTATTGAAG

upper sequence: EFJ11911 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 8
----------------------------------------------------------------------------------------------------------------------------------------gtatggtatgtttcaagtttgtcatgagagctatg-ataaccagggctttgtgtagGTGTCTGCCGCTCGTGAGGAGGTGCCTGGTCGTCGTGGATATCCTGGTTATATGTATACAGATTTGGCAACAATTTACGAGCGTGCTGGACGAATTGAAG
                                                                                                                                         ||    |    |  ||| ||  |  |    | |  |    ||   |||    ||||| ||||| |||||||| || |||||||| |||||||||||||||||||| |||||||| ||| |||| || ||||| || |||||||||||||| ||||
gtacaagtgtttctcttaaagacttttcgcttggactcctttttcagaagttagctcctgtgaaattctacatgctactccgcagttggtatctgaaatagtttttaagcaaatttgtaatctattcagttggtttttaattaagaccttcagtgtgctacaaattttttccactctcaattcttcaaatagGTTTCTGCTGCTCGTGAAGAAGTGCCTGGGCGTCGTGGATATCCTGGTTACATGTATACTGATCTGGCCACCATTTATGAACGTGCTGGACGAATCGAAG

upper sequence: EFJ11911 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: PP1S85_75V6.1 (Physcomitrella patens), 3'ss of exon 8
-----------------------------------------------------------------------------------------------------------------gtatgg-tatgtttcaagtttgtcatgagagc-------tatgataaccagggctttgtgtagGTGTCTGCCGCTCGTGAGGAGGTGCCTGGTCGTCGTGGATATCCTGGTTATATGTATACAGATTTGGCAACAATTTACGAGCGTGCTGGACGAATTGAAG
                                                                                                                  || |  |     |  ||| || ||  |   |       ||||||    |    |  |   |||| ||||| |||||||| || || ||||| |||||||||||||||||||| ||||| || ||| | || || |||||||| |||||||| |||||||| |
gtaccagtctttaccttaaagatctgcttgcccttgtggtatggtacttctgactctgtttttggtttttgaaatgttagtgttctaaaaaatgcccctctattttgttggttctaagtctgcacctttagtatgccagaatgacatattcttatgatccttaactatgcgaacagGTTTCTGCAGCTCGTGAAGAAGTACCTGGGCGTCGTGGATATCCTGGTTACATGTACACGGATCTTGCCACTATTTACGAACGTGCTGGGCGAATTGAGG

upper sequence: EFJ11911 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 9
-------------------------------------------gtatggtatgtttcaagtttgtcatgagagctatg--ataaccagggctttgtgtagGTGTCTGCCGCTCGTGAGGAGGTGCCTGGTCGTCGTGGATATCCTGGTTATATGTATACAGATTTGGCAACAATTTACGAGCGTGCTGGACGAATTGAAG
                                            ||| |   || |      || |   | |  | ||   |   ||     ||    |||||||||| |||||||| || || || ||||||||||| || |||||||||||||| || ||| | || || ||||| || ||||||||||| ||||| |
gctgcactcggttacttagttaatcaagtattttgaaacctcgatatcgagggtctatgtaatgacgatatatttttgtcgttttcaattacttaaacagGTGTCTGCTGCTCGTGAAGAAGTACCCGGTCGTCGTGGGTACCCTGGTTATATGTACACCGATCTTGCCACCATTTATGAACGTGCTGGACGTATTGAGG

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|169057425|gb|FE465729.1|FE465729
EST:     TGCTNGTCATTTTGACCGACATGAGTTCGTATGCGGATGCATTGCGTGAG                         GTGTCTGCCGCTCGTGAGGAGGTGCCTGGTCGTCGTGGATATCCTGGTTAT
genomic: TGCTTGTCATTTTGACCGACATGAGTTCGTATGCGGATGCATTGCGTGAGgtatggtatg ... ctttgtgtagGTGTCTGCCGCTCGTGAGGAGGTGCCTGGTCGTCGTGGATATCCTGGTTAT
EST: gi|169036846|gb|FE443832.1|FE443832
EST:     TGCTTGTCATTTTGACCGACATGAGTTCGTATGCGGATGCATTGCGTGAG                         GTGTCTGCCGCTCGTGAGGAGGTGCCTGGTCGTCGTGGATATCCTGGTTAT
genomic: TGCTTGTCATTTTGACCGACATGAGTTCGTATGCGGATGCATTGCGTGAGgtatggtatg ... ctttgtgtagGTGTCTGCCGCTCGTGAGGAGGTGCCTGGTCGTCGTGGATATCCTGGTTAT
EST: gi|169035380|gb|FE444318.1|FE444318
EST:     ACATGAGTTCGTATGCGGATGCATTGCGTGAG                         GTGTCTGCCGCTCGTGAGGAGGTGCCTGGTCGTCGTGGATATCCTGGTTAT
genomic: ACATGAGTTCGTATGCGGATGCATTGCGTGAGgtatggtatg ... ctttgtgtagGTGTCTGCCGCTCGTGAGGAGGTGCCTGGTCGTCGTGGATATCCTGGTTAT
EST: gi|169049517|gb|FE458740.1|FE458740
EST:     TGCTTGTCATTTTGACCGACATGAGTTCGTATGCGGATGCATTGCGTGAG                         GTGTCTGCCGCTCGTGAGGAGGTGCCTGGTCGTCGTGGATATCCTGGTTAT
genomic: TGCTTGTCATTTTGACCGACATGAGTTCGTATGCGGATGCATTGCGTGAGgtatggtatg ... ctttgtgtagGTGTCTGCCGCTCGTGAGGAGGTGCCTGGTCGTCGTGGATATCCTGGTTAT
EST: gi|169088664|gb|FE491524.1|FE491524
EST:     GTCATTTTGACCGACATGAGTTCGTATGCGGATGCATTGCGTGAG                         GTGTCTGCCGCTCGTGAGGAGGTGCCTGGTCGTCGTGGATATCCTGGTTAT
genomic: GTCATTTTGACCGACATGAGTTCGTATGCGGATGCATTGCGTGAGgtatggtatg ... ctttgtgtagGTGTCTGCCGCTCGTGAGGAGGTGCCTGGTCGTCGTGGATATCCTGGTTAT
EST: gi|169114882|gb|FE515831.1|FE515831
EST:     TGAGTTTGTATGCGGATGCATTGCGTGAG                         GTGTCTGCCGCTCGTGAGGAGGTGCCTGGTCGTCGTGGATATCCTGGTTAT
genomic: TGAGTTCGTATGCGGATGCATTGCGTGAGgtatggtatg ... ctttgtgtagGTGTCTGCCGCTCGTGAGGAGGTGCCTGGTCGTCGTGGATATCCTGGTTAT
EST: gi|169057426|gb|FE465730.1|FE465730
EST:     TGCTTGTCATTTTGACCGACATGAGTTCGTATGCGGATGCATTGCGTGAG                         GTGTCTGCCGCTCGTGAGGAGGTGCCTGGTCGTCGTGGATATCCTGGTTAT
genomic: TGCTTGTCATTTTGACCGACATGAGTTCGTATGCGGATGCATTGCGTGAGgtatggtatg ... ctttgtgtagGTGTCTGCCGCTCGTGAGGAGGTGCCTGGTCGTCGTGGATATCCTGGTTAT

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), 33 (downstream exon)
Score: 35

GATTGCGTTGACGACGGCAGAGTATCTGGCTTATGATTGCGGGAAACATGTGCTTGTCATTTTGACCGACATGAGTTCGTATGCGGATGCATTGCGTGAGgtatggtatg ... ctttgtgtagGTGTCTGCCGCTCGTGAGGAGGTGCCTGGTCGTCGTGGATATCCTGGTTATATGTATACAGATTTGGCAACAATTTACGAGCGTGCTGGACGAATTGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatggtatgtttcaagtttgtcatgagagctatgataaccagggctttgtgtagGTGTCTGCCGCTCGTGAGGAGGTGCCTGGTCGTCGTGGATATCCTGGTTATATGTATACAGATTTGGCAACAATTTACGAGCGTGCTGGACGAATTGAAG
                                 tgataac  putative branch site (score: 35)
                               tatgataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggtatgtttcaagtttgtcatgagagctatgataaccagggctttgtgtagGTGTCTGCCGCTCGTGAGGAGGTGCCTGGTCGTCGTGGATATCCTGGTTATATGTATACAGATTTGGCAACAATTTACGAGCGTGCTGGACGAATTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG