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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgttttcctgcttgctagcgtttgtttctactttgtttctcttcggcagGTTCTCTCCGTTGTTGGATTGTTGCAAGACGAAGTCGATCCTATGGTGTCGGTGATGAAAGTCGAAAAAGCTCCGCTAGAGTCTTATGCCGACATCGGGG

Basic information

species Selaginella moellendorffii
transcript EFJ32659
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ32659 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os07g49150.1 (Oryza sativa), 3'ss of exon 1
-------------------------------------------------gtactg-ttttcctgcttgctagcgtttgtttctactttgtttctcttcggcagGTTCTCTCCGTTGTTGGATTGTTGCAAGACGAAGTCGATCCTATGGTGTCGGTGATGAAAGTCGAAAAAGCTCCGCTAGAGTCTTATGCCGACATCGGGG
                                                  || |  ||||  ||||  |||||     |    |||   |  || ||   |||||||| || || || ||| | |||||||| ||||| ||||||||||| || ||||||||||| || ||||||||||| || || ||||| ||||| || |
tatcattttcttatgatcgaataagtgactcaaccgtacatccatgtggctagtaattttaatgct--ctagcaagcttgctcactaaatccctatttc-cagGTTCTGTCTGTGGTCGGAATTTTGCAAGATGAAGTTGATCCTATGGTTTCTGTGATGAAAGTGGAGAAAGCTCCGCTGGAATCCTATGCTGACATTGGTG

upper sequence: EFJ32659 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os03g18690.1 (Oryza sativa), 3'ss of exon 1
----------------------------------------gtactgttttcctgcttgctagcgtttgtttctact-----ttgtt---tctcttcggcagGTTCTCTCCGTTGTTGGATTGTTGCAAGACGAAGTCGATCCTATGGTGTCGGTGATGAAAGTCGAAAAAGCTCCGCTAGAGTCTTATGCCGACATCGGGG
                                         | || ||||  | ||||  ||   || ||| ||       ||| |   ||  |||  ||||||||||| || |||||| | |||||||| || || || |||||||| || || |||||||| ||||| || ||  | ||||||||||| |||||||| |
cttataaccaatagttggctctactattaaacttgctcttatgctcttttt-tacttgtgagaagttttttataaccaaacttgataaatcatttcttcagGTTCTCTCTGTGGTTGGAATTTTGCAAGATGAGGTTGACCCTATGGTTTCTGTCATGAAAGTTGAAAAGGCACCTTTGGAGTCTTATGCGGACATCGGTG

upper sequence: EFJ32659 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G104373_T01 (Zea mays), 3'ss of exon 1
-----------------------------------gtactgttttcctgcttgct---agcgtttgttt------ctactttgtt---tctcttcggcagGTTCTCTCCGTTGTTGGATTGTTGCAAGACGAAGTCGATCCTATGGTGTCGGTGATGAAAGTCGAAAAAGCTCCGCTAGAGTCTTATGCCGACATCGGGG
                                   ||  | | | | | |||| |   |  | || |||      |  ||| |     | | | |   ||||||| || || |||||  | |||||||||||||| ||||||||||| || ||||||||||| ||||| || ||  | ||||||||||| ||||| || |
aaaatcaatgctgctcctcaagtgatgtactctgtgttttatgtacttccttgatttgaatgcttatttagtaaacagcttggccaaatgtttcccttagGTTCTGTCAGTGGTTGGTATTTTGCAAGACGAAGTTGATCCTATGGTTTCTGTGATGAAAGTTGAAAAGGCACCTTTGGAGTCTTATGCTGACATTGGTG

upper sequence: EFJ32659 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G056569_T01 (Zea mays), 3'ss of exon 1
----------------------------------------gtactgttttcctgcttgctagcgtttgtttctactttgtttctc-----ttcgg--cagGTTCTCTCCGTTGTTGGATTGTTGCAAGACGAAGTCGATCCTATGGTGTCGGTGATGAAAGTCGAAAAAGCTCCGCTAGAGTCTTATGCCGACATCGGGG
                                        | | ||||||     |    || | ||  |  |  ||  |  |||     |||    ||||||||||| || |||||  | |||||||| ||||| ||||||||||| || ||||||||||| || ||||| ||  | || |||||||| ||||| || |
tgtgctcaataaccatttgttgtaaattgcacgctttagtggattgttttgaccatcaggagaggttcatcttgtttgctcactcaaatgttcacttcagGTTCTCTCTGTGGTTGGTATATTGCAAGATGAAGTTGATCCTATGGTATCTGTGATGAAAGTTGAGAAAGCGCCTTTGGAATCTTATGCTGACATTGGTG

upper sequence: EFJ32659 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G095593_T01 (Zea mays), 3'ss of exon 1
----------------------------------------------gtactgttttcctgcttgctagcgt-ttgtttctactttgtttctcttcggcagGTTCTCTCCGTTGTTGGATTGTTGCAAGACGAAGTCGATCCTATGGTGTCGGTGATGAAAGTCGAAAAAGCTCCGCTAGAGTCTTATGCCGACATCGGGG
                                              | |  |    || ||||| |  |    |    |       | | |  ||  |||||||| || || |||||  | |||||||| ||||| ||||||||||| || ||||||||||| || ||||| ||  | || |||||||| ||||| || |
tttgttgcattgcacatgcattagtggaccgtttacaactggtaggggatagcaagccagcttgttttctcactcaaacagtcaaatgtttactcttcagGTTCTTTCTGTAGTTGGTATATTGCAAGATGAAGTTGATCCTATGGTATCTGTGATGAAAGTTGAGAAAGCACCTTTGGAATCTTATGCTGACATTGGTG

upper sequence: EFJ32659 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: AT4G29040.1 (Arabidopsis thaliana), 3'ss of exon 1
----------------------------------gtactgttttc--ctgcttgctagcgtttgttt----ctactttgtttctcttcggcagGTTCTCTCCGTTGTTGGATTGTTGCAAGACGAAGTCGATCCTATGGTGTCGGTGATGAAAGTCGAAAAAGCTCCGCTAGAGTCTTATGCCGACATCGGGG
                                  ||  || || |   ||  || |   ||   |||     | ||   ||  | |  |  |||||||||| ||||||||  |  | ||||| ||||| ||||| |||||||| ||||||||||| || ||||||||  | ||||| ||||| || || || |
gtatgtgaaattagggtttaagaatcttgtttttgttgtgattacgattgtgtgttgttgtggatttagggttgctgatttgttttatgttagGTTCTCTCTGTTGTTGGGATTCTACAAGATGAAGTGGATCCAATGGTGTCTGTGATGAAAGTTGAGAAAGCTCCTTTGGAGTCATATGCTGATATTGGAG

upper sequence: EFJ32659 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S12_207V6.1 (Physcomitrella patens), 3'ss of exon 1
-----------------------------------------------gtactgttttcctgcttgctagcgtttgtttctactttgtttct--cttcggcagGTTCTCTCCGTTGTTGGATTGTTGCAAGACGAAGTCGATCCTATGGTGTCGGTGATGAAAGTCGAAAAAGCTCCGCTAGAGTCTTATGCCGACATCGGGG
                                                || || |    |  |||  || |   |    |  ||   || |   ||  |||||| || || || ||||| ||| ||||||| || || || ||||||||||| ||||||||||| ||||||||||| |||||||| |||||||| ||||| |
gcaagcatcgaaacttttctcaactaaatttctatttttctctatggctattgatagagtagttg--agtggaggcaaatgattcacttttggtttgtgcagGTCCTTTCAGTGGTTGGGTTGCTGCAAGATGACGTGGACCCTATGGTGTCAGTGATGAAAGTTGAAAAAGCTCCTCTAGAGTCATATGCCGATATCGGTG

upper sequence: EFJ32659 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S109_234V6.1 (Physcomitrella patens), 3'ss of exon 1
--------------------------------------------gtactgttttcctgcttgctagcgtttgttt---ctactttgtttctcttcggcagGTTCTCTCCGTTGTTGGATTGTTGCAAGACGAAGTCGATCCTATGGTGTCGGTGATGAAAGTCGAAAAAGCTCCGCTAGAGTCTTATGCCGACATCGGGG
                                            |   | |   |              ||||     | | ||| ||| ||||  |||||| || || ||||| |||||| ||||||| || || || || ||||| || || |||||||| ||||||||||| |||||||| ||||| ||||| || |
aagttagagtaactgattagtcctggcggtcacgaacatggtttgagttatcaccagatcatgggaaacttgtccaaacgattttctttgtcttgtgcagGTCCTTTCAGTTGTGGGATTGCTGCAAGATGACGTGGACCCAATGGTTTCTGTTATGAAAGTTGAAAAAGCTCCTCTAGAGTCATATGCTGACATTGGTG

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|169103686|gb|FE506883.1|FE506883
EST:     TGGACAAGGACCAGCTTGAGCCCGGGTGTGCGATCCTCATGCACAATAAG                         GTTCTCTCCGTTGTTGGATTGTTGCAAGACGAAGTCGATCCTATGGTGTCG
genomic: TGGACAAGGACCAGCTTGAGCCCGGGTGTGCGATCCTCATGCACAATAAGgtactgtttt ... tcttcggcagGTTCTCTCCGTTGTTGGATTGTTGCAAGACGAAGTCGATCCTATGGTGTCG




















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: 45

TGTTTCGTCGTCGGTCGGGCCAGAGTACTATGTCAACATTCTTTCGTTTGTGGACAAGGACCAGCTTGAGCCCGGGTGTGCGATCCTCATGCACAATAAGgtactgtttt ... tcttcggcagGTTCTCTCCGTTGTTGGATTGTTGCAAGACGAAGTCGATCCTATGGTGTCGGTGATGAAAGTCGAAAAAGCTCCGCTAGAGTCTTATGCCGACATCGGGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtactgttttcctgcttgctagcgtttgtttctactttgtttctcttcggcagGTTCTCTCCGTTGTTGGATTGTTGCAAGACGAAGTCGATCCTATGGTGTCGGTGATGAAAGTCGAAAAAGCTCCGCTAGAGTCTTATGCCGACATCGGGG
                           tttgtttctactttgt  CT-rich tract
                          tttgttt  TA-rich tract