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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggacgaactctcggcattttgctcttcaggttgtaactttattcctggctcctttcagGTGATTGTGAGCGGCAAGCTCCGAGCCCAACGCGCCAAGTCGATGAAGTTCAAGGACGGATACATGATCTCGTCTGGCAGCCCCGTGAACGAGTTCATTG

Basic information

species Selaginella moellendorffii
transcript EFJ34676
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ34676 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: LOC_Os03g38000.2 (Oryza sativa), 3'ss of exon 2
-----------------------gtatggacgaactctcggcattttgctc-----ttcaggttgtaactttattcctggctcct-ttcagGTGATTGTGAGCGGCAAGCTCCGAGCCCAACGCGCCAAGTCGATGAAGTTCAAGGACGGATACATGATCTCGTCTGGCAGCCCCGTGAACGAGTTCATTG
                        ||     | |     |  ||||||  |     || | |||| ||||     | |   || | ||||||| ||||| || || |||||| | |||||| | |||||||| |||||||||||||| || ||||||||||| |||||    || || || |||| |||||
gtgagttccttgtacaataaaaattacatgtgcaaatgtgatattttgtacacacattaaagttg-aactgatccctttattcttattcagGTCATTGTAAGTGGAAAGCTCAGGGCCCAAAGAGCCAAGTCCATGAAGTTCAAGGATGGTTACATGATCTCATCTGGTCAGCCAGTCAATGAGTACATTG

upper sequence: EFJ34676 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: LOC_Os07g41750.1 (Oryza sativa), 3'ss of exon 4
------------------------gtatggacgaactctcggcattttgctcttcaggttgtaactttattcctggctcctttcagGTGATTGTGAGCGGCAAGCTCCGAGCCCAACGCGCCAAGTCGATGAAGTTCAAGGACGGATACATGATCTCGTCTGGCAGCCCCGTGAACGAGTTCATTG
                        ||||||     ||        |   || || | ||  | | ||  |          || ||||| |||||||| || |||||  | || || || || || || |||||||||||||||||||||||||| || |||||    || || |||  ||  ||||
gtactctcatgcaaaacgaaagctgtatggttttgcttggattcctgctctatttatgtattgatttgctgttctttggtttacagGTTATTGTGAGTGGGAAGCTTAGGGCTCAGCGTGCTAAATCCATGAAGTTCAAGGACGGATACATGATTTCTTCTGGTTATCCTGTTAACTTGTATATTG

upper sequence: EFJ34676 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GRMZM2G099352_T02 (Zea mays), 3'ss of exon 1
------gtatggacgaact-ctcggcattttgctcttcaggttgtaactttattcc---------tggctccttt-------cagGTGATTGTGAGCGGCAAGCTCCGAGCCCAACGCGCCAAGTCGATGAAGTTCAAGGACGGATACATGATCTCGTCTGGCAGCCCCGTGAACGAGTTCATTG
      ||      | ||| |  |  |   || || |  | | || | |  ||  |         || ||| |||       |||||||| ||||| || |||||| | |||||| | |||||||| |||||||||||||| || ||||||||||| |||||    || |||||||||| |||||
gtgagtgttcctttgtacttcctgagaacatgttcatttgttagtgaatgcatctcgacagcctttgtctcttttaaaataacagGTGATCGTGAGTGGAAAGCTCAGGGCCCAAAGAGCCAAGTCCATGAAGTTCAAGGATGGCTACATGATCTCATCTGGTCAGCCAGTGAACGAGTACATTG

upper sequence: EFJ34676 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GRMZM2G074300_T03 (Zea mays), 3'ss of exon 2
-------------------------gtatggacgaactctcggcattttgctcttcaggttg-taactttattcctggctcctttcagGTGATTGTGAGCGGCAAGCTCCGAGCCCAACGCGCCAAGTCGATGAAGTTCAAGGACGGATACATGATCTCGTCTGGCAGCCCCGTGAACGAGTTCATTG
                         || ||  |    |||    |||      | || || |  | | |||||  ||      | ||||| |||||||| || |||||| | || ||| | |||||||| |||||||||||||| || ||||||||||| |||||    || ||||| |||| ||| |
gttagtgctcctgtgcactatgagggtctgttcattttctgatgattggtgaatgcatgtcgacagccttatt--tgttctaatacagGTCATTGTGAGTGGAAAGCTCAGGGCTCAAAGAGCCAAGTCCATGAAGTTCAAGGATGGCTACATGATCTCATCTGGTCAGCCAGTGAATGAGTACATCG

upper sequence: EFJ34676 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: Vv04s0008g01750.t01 (Vitis vinifera), 3'ss of exon 4
----gtatggacgaactctcggcattttgctct------tcaggttgtaactt---tattcctggctccttt---cagGTGATTGTGAGCGGCAAGCTCCGAGCCCAACGCGCCAAGTCGATGAAGTTCAAGGACGGATACATGATCTCGTCTGGCAGCCCCGTGAACGAGTTCATTG
    || |  | || || ||    ||||  |||      ||| ||    | ||    | ||    |||  ||   ||||| |||||||| || |||||||| || || || |||||||| |||||||| ||||| || ||||||||||| |||||    || || || || | |||||
gtttgtctata-gagctttccatgttttcatctaccatttcatgtgagcagttggaaaatctaatctctcttctgcagGTTATTGTGAGTGGGAAGCTCCGTGCTCAGCGTGCCAAGTCAATGAAGTTTAAGGATGGGTACATGATCTCCTCTGGTCAACCTGTTAAGGATTACATTG

upper sequence: EFJ34676 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: PP1S31_178V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------------------------------gtatggacga-actctcggcattttgctcttcaggttgtaactttattcctggctcctttcagGTGATTGTGAGCGGCAAGCTCCGAGCCCAACGCGCCAAGTCGATGAAGTTCAAGGACGGATACATGATCTCGTCTGGCAGCCCCGTGAACGAGTTCATTG
                                      |  || | || | | |  | |  ||  ||||    |  | | ||| |   ||||   |  |||||||| ||||| || ||||| || ||    || || ||||| |||||||||||||||||||||||||| || ||||| ||||| || ||||| | |||||
aattgagctttagcactgcttcactgttacatctggaagattgcaggatattgtatgtagattcatctttgtctaattagtttgtgggtggcgg-tcacagGTGATAGTGAGTGGAAAGCTTCGTGCAGCTCGTGCAAAGTCCATGAAGTTCAAGGACGGATACATGATATCATCTGGAAGCCCTGTCAACGACTACATTG

upper sequence: EFJ34676 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: PP1S127_74V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------------------------gtatggacgaactctcggcattttgctcttcaggtt---gtaactttattcctg---gctcctttcagGTGATTGTGAGCGGCAAGCTCCGAGCCCAACGCGCCAAGTCGATGAAGTTCAAGGACGGATACATGATCTCGTCTGGCAGCCCCGTGAACGAGTTCATTG
                                      |  |  |  |    ||||  |  | |  |     | |  |  || |||   | |  |  ||||| ||||||||||| ||||| || ||    || || ||||| |||||||||||||| || ||||||||||| ||||| ||||| || ||||| | ||| |
acatcttctctagtatgcggcaagtatctgtcaagcaaaaaactttacaatttttttttaattaaatgcaaatgatctcgttgctgtatgttggtaacagGTTATTGTGAGCGGAAAGCTGCGTGCAGCTCGTGCTAAGTCCATGAAGTTCAAGGATGGTTACATGATCTCATCTGGGAGCCCTGTCAACGATTACATCG

upper sequence: EFJ34676 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: PP1S454_3V6.1 (Physcomitrella patens), 3'ss of exon 4
---------------------------------gtatggacgaactctcggcattttgctcttcaggttgt--aactttattcctggctc---ctttcagGTGATTGTGAGCGGCAAGCTCCGAGCCCAACGCGCCAAGTCGATGAAGTTCAAGGACGGATACATGATCTCGTCTGGCAGCCCCGTGAACGAGTTCATTG
                                     | |     ||| |  |  | | |       ||||   ||  | ||   || |    ||| ||||| ||||| || |||||||| || |||    | |||||||| ||||||||||||||||| |||||||| || || || ||||| || || || | ||| |
tcctttttctcatggagtagtgcgtctgaagacacccgaatactttctggttaagtaggtgcaagcattgtgtgacgatgttagcgggtttggcttgcagGTCATTGTCAGTGGCAAGCTGCGTGCCGCTAGGGCCAAGTCTATGAAGTTCAAGGACGGCTACATGATTTCATCCGGAAGCCCTGTCAATGATTACATCG

upper sequence: EFJ34676 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: PP1S41_146V6.1 (Physcomitrella patens), 3'ss of exon 4
----------------------------gtatggacgaactctcggcattttgctcttcagg---ttgtaactttattcctggctcc-------tttcagGTGATTGTGAGCGGCAAGCTCCGAGCCCAACGCGCCAAGTCGATGAAGTTCAAGGACGGATACATGATCTCGTCTGGCAGCCCCGTGAACGAGTTCATTG
                            |    |||  ||  ||  |  |    |   |||     |||||  | |||  | |           ||  |||| ||||| || || ||||| || ||    || |||||||| |||||||||||||| || |||||||| || || || |||||||| ||||| | ||| |
acttgataatgtgatgtatggagtagtggctctgacttacagtcatcgctacagttagcagaattgtgtaatctgattagttgacgtgtgggaattgtagGTCATTGTCAGTGGAAAGCTGCGTGCAGCTCGAGCCAAGTCTATGAAGTTCAAGGATGGCTACATGATTTCATCAGGAAGCCCCGTCAACGATTACATCG

upper sequence: EFJ34676 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: PP1S29_222V6.1 (Physcomitrella patens), 3'ss of exon 4
---------------------------------------gtatggacgaactctcggcattt-tgctcttcaggttgtaactttattcctggctcctttcagGTGATTGTGAGCGGCAAGCTCCGAGCCCAACGCGCCAAGTCGATGAAGTTCAAGGACGGATACATGATCTCGTCTGGCAGCCCCGTGAACGAGTTCATTG
                                       || || |  |  |  | | || |  | |  |        ||        |||| |  || ||||| ||||| || || ||| | || |||    | |||||||| ||||| |||||||| || ||||||||||| || || |||||||| || || |  ||||
aagcatttgagtgtgatcatatgccgtgaagtagccctcgtttgtagaatatagcagaatgtgcgatgcttgtaacacaatcaaggggctgggt--ttacagGTCATTGTCAGTGGAAAGTTGCGTGCCGCTAGGGCCAAGTCTATGAAATTCAAGGATGGCTACATGATCTCATCCGGAAGCCCCGTCAATGATTATATTG

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|169075229|gb|FE484111.1|FE484111
EST:     GAGCCAAGGGTTGTGAG                         GTGATTGTGAGCGGCAAGCTCCGAGCCCAACGCGCCAAGTCGATGAAGTTC
genomic: GAGCCAAGGGTTGTGAGgtatggacga ... ctcctttcagGTGATTGTGAGCGGCAAGCTCCGAGCCCAACGCGCCAAGTCGATGAAGTTC




















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: 58

AGTTCTCTACTTCGTCAGGGCCTGCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTGTGAGgtatggacga ... ctcctttcagGTGATTGTGAGCGGCAAGCTCCGAGCCCAACGCGCCAAGTCGATGAAGTTCAAGGACGGATACATGATCTCGTCTGGCAGCCCCGTGAACGAGTTCATTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgaactctcggcattttgctcttcaggttgtaactttattcctggctcctttcagGTGATTGTGAGCGGCAAGCTCCGAGCCCAACGCGCCAAGTCGATGAAGTTCAAGGACGGATACATGATCTCGTCTGGCAGCCCCGTGAACGAGTTCATTG
                           ttgtaac  putative branch site (score: 58)
                                      ttcctggctcctttc  putative PPT
                              taactttatt  TA-rich tract