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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttctcgtgcttatacggtagatggttttctctcctctctcggtaaccacgctttggtttgcttgaatctttagGCGCTGATATCAGGAGCGTTTGCACTGAAGCCGGCATGTACGCGATCCGAGCTCGCAGGAAAACAGTGACGGAGAAAGATTTCCTCGAGGCCGTGAACAA

Basic information

species Selaginella moellendorffii
transcript EFJ29161
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ29161 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: LOC_Os06g09290.1 (Oryza sativa), 3'ss of exon 6
-----------------------------------------gtaagttctcgtgcttatacggtagatggttttctctcctctctcggtaaccacgctttggtttgcttgaatctt----tagGCGCTGATATCAGGAGCGTTTGCACTGAAGCCGGCATGTACGCGATCCGAGCTCGCAGGAAAACAGTGACGGAGAAAGATTTCCTCGAGGCCGTGAACAA
                                         |  ||||   || |  ||    |  ||  |||   ||||| | |   |   |||| || | | |   ||  | ||     ||| || || ||  |||| || ||||| || || ||||||||||| ||||| ||||||||||| || ||||| ||||| |||||| | || || ||||| ||
gtaagtgccgggaattcttgcatgacagaatccagtctctggctagtttctgttcc-atgtcatttatc-tttaacctccttttttttttctcacgtttggctatttgtgtttgttggaacagGGGCCGACATACGGAGTGTGTGCACGGAGGCTGGCATGTACGCCATCCGCGCTCGCAGGAAGACGGTGACAGAGAAGGATTTCTTGGACGCGGTGAATAA

upper sequence: EFJ29161 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: LOC_Os02g54340.1 (Oryza sativa), 3'ss of exon 9
--------------------------------gtaagttctcgtgcttatacggtagatggttttctctcctctctcgg-taa--ccacgctttggttt-----------gcttgaatctttagGCGCTGATATCAGGAGCGTTTGCACTGAAGCCGGCATGTACGCGATCCGAGCTCGCAGGAAAACAGTGACGGAGAAAGATTTCCTCGAGGCCGTGAACAA
                                ||   ||||  |   | |       || || | | |  |     ||| |||  | | |||||| | |           | |||    |  ||| |||||||| ||||| || ||||| ||||| |||||||| ||||| || || ||  ||||||||||||| ||||| || ||||| || || || |||||
gtaactggaagaactttgaaacttcgttctgggtggtttcttctagatttgtttgttatagtctccacctcaaaagcggataatgctaagctttgttctcacaaactcctgtttgctgttacagGAGCTGATATAAGGAGTGTCTGCACAGAAGCTGGCATGTATGCGATTCGCGCCCGACGGAAAACAGTGACTGAGAAGGACTTCCTTGATGCTGTAAACAA

upper sequence: EFJ29161 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: GRMZM2G110185_T01 (Zea mays), 3'ss of exon 8
gtaagttctcgtgcttatacggtagatggttttctct-cctctctcggtaa---ccacgctttggtttgcttgaatctttagGCGCTGATATCAGGAGCGTTTGCACTGAAGCCGGCATGTACGCGATCCGAGCTCGCAGGAAAACAGTGACGGAGAAAGATTTCCTCGAGGCCGTGAACAA
||  | | || |   |    |||   || |||  ||     |   || | |    | | | |||  |||||||   ||  ||| |||||||| |||||||||||||| |||||||| |||||||| || || || ||||||||||| ||||| || || ||||| ||||| || || |||||
gtgtggtttcat--ctgagtggtttctgctttattcgatgacagacgatcaggttctcacattgccttgcttgttgctccagGAGCTGATATAAGGAGCGTTTGCACAGAAGCCGGGATGTACGCCATTCGCGCCCGCAGGAAAACGGTGACAGAAAAGGATTTTCTCGATGCTGTCAACAA

upper sequence: EFJ29161 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: GRMZM2G181359_T01 (Zea mays), 3'ss of exon 9
------------------------gtaagttctcgtgcttatacggt--agatggttttct------ctcctctctcggtaaccacgcttt------ggtttgcttgaat-ctttagGCGCTGATATCAGGAGCGTTTGCACTGAAGCCGGCATGTACGCGATCCGAGCTCGCAGGAAAACAGTGACGGAGAAAGATTTCCTCGAGGCCGTGAACAA
                        | | |||   ||   |    | |  |  || ||| ||      ||   |  | | | | || | | |      |  ||||||   | ||  ||| || ||||| |||||||| ||||| |||||||| ||||| || || || || ||||||||||| ||||| ||||| ||||| ||||| || || || ||
gtgagttgctttgtggtttcagcagaatgtttgtgtttctgcttgattcaattgatttacttgaagactttgcgatagatgatcaggttctcacatagccttgctttgttactccagGAGCGGATATAAGGAGCGTCTGCACAGAAGCCGGGATGTATGCCATTCGTGCCCGCAGGAAAACGGTGACAGAGAAGGATTTTCTCGATGCTGTCAATAA

upper sequence: EFJ29161 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: GLYMA19G45140.1 (Glycine max), 3'ss of exon 9
----------------------gtaagttctcgtgctt-atacggtagatggttt-tctctcctctctcggtaaccacgctttggtttgcttgaatctttagGCGCTGATATCAGGAGCGTTTGCACTGAAGCCGGCATGTACGCGATCCGAGCTCGCAGGAAAACAGTGACGGAGAAAGATTTCCTCGAGGCCGTGAACAA
                       |      |||||||| |  |  | | | |||| |      |   |   | |||| | |    |||| ||   |||  ||| || ||||| |||||||||||||||||||| || ||||| || || |||||  | ||||| || ||||| |||||||| ||||| || || || || ||
cctttcttccctatgacccacgattgaacatcgtgcttcaggctttgggtagtttatagagattggttttttgaccaggatactttttggttc--tctccagGAGCCGATATAAGGAGCGTTTGCACTGAAGCTGGTATGTATGCTATTCGAGCCAGAAGGAAGACCGTGACAGAGAAAGACTTCCTTGACGCAGTTAATAA

upper sequence: EFJ29161 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: GLYMA03G42370.2 (Glycine max), 3'ss of exon 9
----------------------gtaagttctcgtgcttatacggtagatggttttctctcctc--tctcggtaaccacgctttggtttgcttgaatctttagGCGCTGATATCAGGAGCGTTTGCACTGAAGCCGGCATGTACGCGATCCGAGCTCGCAGGAAAACAGTGACGGAGAAAGATTTCCTCGAGGCCGTGAACAA
                         |   | |  | ||  ||  | | | ||||       |   | |   | ||   | |    |||| ||   |||  ||| || ||||| |||||||||||||||||||| || ||||| || || |||||  | ||||| || ||||| |||||||| ||||| || || || || ||
atttctgccactccctttcttccctatgacccacgattgaacattgggtagtttatagagattggtttttttgacttagatactttttggttc--tctccagGAGCCGATATAAGGAGCGTTTGCACTGAAGCTGGTATGTATGCTATTCGAGCCAGAAGGAAGACCGTGACAGAGAAAGACTTCCTTGACGCAGTTAATAA

upper sequence: EFJ29161 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: EDP03835 (Chlamydomonas reinhardtii), 3'ss of exon 11
----------------------------------------------------------------------------------------------gtaagttctcgtgcttatacggtagatggttttctctcctctctcggtaac----cacgctttggtttgcttgaatctttagGCGCTGATATCAGGAGCGTTTGCACTGAAGCCGGCATGTACGCGATCCGAGCTCGCAGGAAAACAGTGACGGAGAAAGATTTCCTCGAGGCCGTGAACAA-------------
                                                                                              |   ||  || |||    |    |||||    ||    || | |   |  |     ||  | ||    |  |   | ||  |   |   |  ||||   |||||||| || || || |||||||| ||||| |||||| ||||||| ||||||||||| || ||| | ||||| || |||||             
gtgcggcgaccgcgtgcggccgcaccccgccccaccgcatccctcatcccttgttggaatctgtggtgacgcgctaggaccttgctcctgccccgccggta-tcatgccaccatcacagatgccactcaaaactgtttgtatgtcattaaacattatgaacggtattgctgttgtgcgaccactcgcagGTCGGTTTGCACGGAGGCGGGAATGTACGCTATCCGCGCTCGCCGGAAAACTGTGACGGAGAAGGACTTCTTGGAGGCTGTTAACAAGGTCATCAAGGGC

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|169102918|gb|FE505283.1|FE505283
EST:     GCGCGACATCCGATTCGAGTTGCTAGCGCGCTTATGCCCAAACTCGACCG                         GCGCTGATATCAGGAGCGTTTGCACTGAAGCCGGCATGTACGCGATCCGAG
genomic: GCGCGACATCCGATTCGAGTTGCTAGCTCGCTTATGCCCAAACTCGACCGgtaagttctc ... gaatctttagGCGCTGATATCAGGAGCGTTTGCACTGAAGCCGGCATGTACGCGATCCGAG
EST: gi|169057196|gb|FE464174.1|FE464174
EST:     GCGCGACATCCGATTCGAGTTGCTAGCGCGCTTATGCCCAAACTCGACCG                         GCGCTGATATCAGGAGCGTTTGCACTGAAGCCGGCATGTACGCGATCCGAG
genomic: GCGCGACATCCGATTCGAGTTGCTAGCTCGCTTATGCCCAAACTCGACCGgtaagttctc ... gaatctttagGCGCTGATATCAGGAGCGTTTGCACTGAAGCCGGCATGTACGCGATCCGAG
EST: gi|169072906|gb|FE482334.1|FE482334
EST:     GCGCGACATCCGATTCGAGTTGCTAGCGCGCTTATGCCCAAACTCGACCG                         GCGCTGATATCAGGAGCGTTTGCACTGAAGCCGGCATGTACGCGATCCGAG
genomic: GCGCGACATCCGATTCGAGTTGCTAGCTCGCTTATGCCCAAACTCGACCGgtaagttctc ... gaatctttagGCGCTGATATCAGGAGCGTTTGCACTGAAGCCGGCATGTACGCGATCCGAG
EST: gi|169112395|gb|FE510137.1|FE510137
EST:     GCGCGACATCCGATTCGAGTTGCTAGCGCGCTTATGCCCAAACTCGACCG                         GCGCTGATATCAGGAGCGTTTGCACTGAAGCCGGCATGTACGCGATCCGAG
genomic: GCGCGACATCCGATTCGAGTTGCTAGCTCGCTTATGCCCAAACTCGACCGgtaagttctc ... gaatctttagGCGCTGATATCAGGAGCGTTTGCACTGAAGCCGGCATGTACGCGATCCGAG
EST: gi|169076505|gb|FE486068.1|FE486068
EST:     GCGCGACATCCGATTCGAGTTGCTAGCGCGCTTATGCCTAAACTCGACCG                         GCGCTGATATCAGGAGCGTTTGCACTGAAGCCGGCATGTACGCGATCCGAG
genomic: GCGCGACATCCGATTCGAGTTGCTAGCTCGCTTATGCCCAAACTCGACCGgtaagttctc ... gaatctttagGCGCTGATATCAGGAGCGTTTGCACTGAAGCCGGCATGTACGCGATCCGAG
EST: gi|169101241|gb|FE502479.1|FE502479
EST:     GCGCGACATCCGATTCGAGTTGCTAGCGCGCTTATGCCCAAACTCGACCG                         GCGCTGATATCAGGAGCGTTTGCACTGAAGCCGGCATGTACGCGATCCGAG
genomic: GCGCGACATCCGATTCGAGTTGCTAGCTCGCTTATGCCCAAACTCGACCGgtaagttctc ... gaatctttagGCGCTGATATCAGGAGCGTTTGCACTGAAGCCGGCATGTACGCGATCCGAG
EST: gi|169101242|gb|FE502480.1|FE502480
EST:     GCGCGACATCCGATTCGAGTTGCTAGCGCGCTTATGCCCAAACTCGACCG                         GCGCTGATATCAGGAGCGTTTGCACTGAAGCCGGCATGTACGCGATCCGAG
genomic: GCGCGACATCCGATTCGAGTTGCTAGCTCGCTTATGCCCAAACTCGACCGgtaagttctc ... gaatctttagGCGCTGATATCAGGAGCGTTTGCACTGAAGCCGGCATGTACGCGATCCGAG
EST: gi|169112394|gb|FE510136.1|FE510136
EST:     GCGCGACATCCGATTCGAGTTGCTAGCGCGCTTATGCCCAAACTCGACCG                         GCGCTGATATCAGGAGCGTTTGCACTGAAGCCGGCATGTACGCGATCCGAG
genomic: GCGCGACATCCGATTCGAGTTGCTAGCTCGCTTATGCCCAAACTCGACCGgtaagttctc ... gaatctttagGCGCTGATATCAGGAGCGTTTGCACTGAAGCCGGCATGTACGCGATCCGAG
EST: gi|169080421|gb|FE488437.1|FE488437
EST:     GCGCGACATCCGATTCGAGTTGCTAGCGCGCTTATGCCCAAACTCGACCG                         GCGCTGATATCAGGAGCGTTTGCACTGAAGCCGGCATGTACGCGATCCGAG
genomic: GCGCGACATCCGATTCGAGTTGCTAGCTCGCTTATGCCCAAACTCGACCGgtaagttctc ... gaatctttagGCGCTGATATCAGGAGCGTTTGCACTGAAGCCGGCATGTACGCGATCCGAG

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: 14

GACAGCAGAACTCAGATCTTCAAGATCCACACCAGAACCATGAACTGCGAGCGCGACATCCGATTCGAGTTGCTAGCTCGCTTATGCCCAAACTCGACCGgtaagttctc ... gaatctttagGCGCTGATATCAGGAGCGTTTGCACTGAAGCCGGCATGTACGCGATCCGAGCTCGCAGGAAAACAGTGACGGAGAAAGATTTCCTCGAGGCCGTGAACAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatggttttctctcctctctcggtaaccacgctttggtttgcttgaatctttagGCGCTGATATCAGGAGCGTTTGCACTGAAGCCGGCATGTACGCGATCCGAGCTCGCAGGAAAACAGTGACGGAGAAAGATTTCCTCGAGGCCGTGAACAA
                     cggtaac  putative branch site (score: 14)
                                                tcttt  putative PPT
                                              aatcttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttctcgtgcttatacggtagatggttttctctcctctctcggtaaccacgctttggtttgcttgaatctttagGCGCTGATATCAGGAGCGTTTGCACTGAAGCCGGCATGTACGCGATCCGAGCTCGCAGGAAAACAGTGACGGAGAAAGATTTCCTCGAGGCCGTGAACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA