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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacttgcgaacgttttcctagtttaaacaacgtgtcctttgttttagGCTTTGAAAGAAGCATTTGAGGTCTTCTGCAACAAAGGTGTTGGGGGAAGCACAAGTGCTGAGTTGCTAGCAACTTTCTGCGATAACCTCTTGAAGAAAG

Basic information

species Selaginella moellendorffii
transcript EFJ12300
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ12300 (Selaginella moellendorffii), 3'ss of exon 10
lower sequence: GRMZM2G166089_T05 (Zea mays), 3'ss of exon 11
-----------------------------------------gtaacttgcgaacgttttcctagtttaaacaacgtgtcctttgttttagGCTTTGAAAGAAGCATTTGAGGTCTTCTGCAACAAAGGTGTTGGGGGAAGCACAAGTGCTGAGTTGCTAGCAACTTTCTGCGATAACCTCTTGAAGAAAG
                                           || |||| || | | ||| | |     | |  |     ||     ||||  | |||||||| |||||||||||||| |||||||||||    || ||  | ||||| |||||| | || || |||||||| ||  |  |||||||||
gtcttcaactgaaacatctcattttcattttgttgttgccataaaattgcaaatggtgtcccattc----ccatataattcttaccacagGCACTTAAAGAAGCCTTTGAGGTCTTCTGTAACAAAGGTGTCTCTGGCAGTTCGAGTGCCGAGTTGTTGGCTACCTTCTGCGACAATATTCTGAAGAAAG

upper sequence: EFJ12300 (Selaginella moellendorffii), 3'ss of exon 10
lower sequence: GRMZM2G166694_T05 (Zea mays), 3'ss of exon 11
-----------------------------------------gtaacttgcgaacgttttcctagtttaaacaacgtgtcctttgttttagGCTTTGAAAGAAGCATTTGAGGTCTTCTGCAACAAAGGTGTTGGGGGAAGCACAAGTGCTGAGTTGCTAGCAACTTTCTGCGATAACCTCTTGAAGAAAG
                                           || |||  || | | ||  | | | |      |     || |  |||||  | |||||||| |||||||||||||| |||||||||||    || ||  | | |||||||||| | || || |||||||| ||  |  |||||||||
gtcttcaactaaaatatctcattttcattttgctgttgtcataaaattggaaatggtgtctcattctca----tataattcttatcgtagGCACTTAAAGAAGCCTTTGAGGTCTTCTGTAACAAAGGTGTCTCTGGCAGTTCGAATGCTGAGTTGTTGGCTACCTTCTGCGACAATATTCTGAAGAAAG

upper sequence: EFJ12300 (Selaginella moellendorffii), 3'ss of exon 10
lower sequence: GLYMA07G37850.1 (Glycine max), 3'ss of exon 11
----------------------------gtaacttgcgaacgttttcctagtttaaacaacgtgtcctttgttt---tagGCTTTGAAAGAAGCATTTGAGGTCTTCTGCAACAAAGGTGTTGGGGGAAGCACAAGTGCTGAGTTGCTAGCAACTTTCTGCGATAACCTCTTGAAGAAAG
                              || |   ||  | | |       |  | | |   |  |||| |    |||||| | ||||| || ||||||||||| ||||||||||||||||  |||||  |||| || ||  |||| ||  | ||||| |||||| |  | |||||||
gtttttgttttgagcagaaagtagctttacaattatggattgatatgtgtacatgcaaatctgatgttttgatcatatagGCTCTTAAAGAGGCTTTTGAGGTCTTTTGCAACAAAGGTGTTGCTGGAAGTTCAAGCGCAGAACTGCTTGCCTCCTTCTGTGATAACATTCTTAAGAAAG

upper sequence: EFJ12300 (Selaginella moellendorffii), 3'ss of exon 10
lower sequence: GLYMA17G02800.2 (Glycine max), 3'ss of exon 11
------------------------------gtaacttgcgaacgttttcctagtttaaacaacgtgtcctt-tgttttagGCTTTGAAAGAAGCATTTGAGGTCTTCTGCAACAAAGGTGTTGGGGGAAGCACAAGTGCTGAGTTGCTAGCAACTTTCTGCGATAACCTCTTGAAGAAAG
                               | |       |  | |    |    || |    |||  |  |  | |||||| | ||||| || ||||||||||| ||||||||||||||||  |||||  |||| || ||  |||| ||  | ||||| |||||| |  | |||||||
gttttgttttgaatagaaagtagctctacaattatggattgatatgtgtacatgcaaatctgaatgttttgatcatatagGCTCTTAAAGAGGCTTTTGAGGTCTTTTGCAACAAAGGTGTTGCTGGAAGTTCAAGCGCAGAACTGCTTGCCTCCTTCTGTGATAACATTCTTAAGAAAG

upper sequence: EFJ12300 (Selaginella moellendorffii), 3'ss of exon 10
lower sequence: Vv05s0020g01320.t01 (Vitis vinifera), 3'ss of exon 11
------------------------------gtaa-cttgcgaacgttttcct-agtttaaacaacgtgtcctttgtttta--gGCTTTGAAAGAAGCATTTGAGGTCTTCTGCAACAAAGGTGTTGGGGGAAGCACAAGTGCTGAGTTGCTAGCAACTTTCTGCGATAACCTCTTGAAGAAAG
                               | | ||      ||| | ||| |  |  ||     ||| ||||  | ||  |||  | || || || |||||||||||||||||||| |||||||  |||||| ||||||||||  | ||||| ||||| || |||||  |  | |||||||
gttggtattaacaatggctgcatattcactatgatctcatcttcgtatccctgaactagaatgttttgtgctttcctctatagGCACTCAAGGAGGCTTTTGAGGTCTTCTGCAACAAGGGTGTTGCTGGAAGCTCAAGTGCTGAACTACTAGCCACTTTTTGTGATAATATTCTTAAGAAAG

upper sequence: EFJ12300 (Selaginella moellendorffii), 3'ss of exon 10
lower sequence: PP1S177_52V6.1 (Physcomitrella patens), 3'ss of exon 7
-----------------------------------------------------------------------------------------------------------------------------gtaacttgcgaacgttttcctagtttaaacaacgtgtcctttgt----tttagGCTTTGAAAGAAGCATTTGAGGTCTTCTGCAACAAAGGTGTTGGGGGAAGCACAAGTGCTGAGTTGCTAGCAACTTTCTGCGATAACCTCTTGAAGAAAG
                                                                                                                                 |||| ||  ||| |     || || |   |||     | |    |  |||| ||||||||||| ||||| ||||||||||| || |||||||  || || |||||||| ||  | || || || || || |||||  | ||||| || |
gtgagaaagctgtttactgctcttgattttgatcgcacgttctgttctcaacgagagaatatcatgctgaagctcccttgttttctgctcggatgcagtctggaaggatttttgtgttgaaacttaatgcttg-gagtgttctttgtattgaagcttagtgaataatatggaatgcagGCATTGAAAGAAGCTTTTGAAGTCTTCTGCAATAAGGGTGTTGCTGGGAGTACAAGTGCAGAACTCCTGGCCACATTTTGTGATAATTTATTGAAAAAGG

upper sequence: EFJ12300 (Selaginella moellendorffii), 3'ss of exon 10
lower sequence: PP1S144_158V6.1 (Physcomitrella patens), 3'ss of exon 8
--------------------------------------------------------------gtaacttgcgaacgttttcctagtttaa-acaacgtgt--cctttgttttagGCTTTGAAAGAAGCATTTGAGGTCTTCTGCAACAAAGGTGTTGGGGGAAGCACAAGTGCTGAGTTGCTAGCAACTTTCTGCGATAACCTCTTGAAGAAAG
                                                               | |  || ||    |     | |||       ||| |    ||  ||  ||||  |||| ||||| ||||| |||||||||||||| |||||||  || || |||||||| ||||| || || || || || |||||  | ||||| || |
gtgagtgactcctttccttgttccgatgatgtcggcgtctttatcgttctctttagaaattcattagatgtgataaatgaagaactttggtgtggcgtttggttttacttgcagGCCCTGAAGGAAGCTTTTGAAGTCTTCTGCAACAAGGGTGTTGCAGGGAGTACAAGTGCAGAGTTACTGGCCACATTTTGTGATAATTTATTGAAAAAGG

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|70669089|gb|DN837666.1|DN837666
EST:     ATTTGCAATATGTCAGCGAGTGCTTTGTTAATCATTCCCTTTTCCACAAG                         GCTTTGAAAGAAGCATTTGAGGTCTTCTGCAACAAAGGTGTTGGGGGAAGC
genomic: ATTTGCAATATGTCAGCGAGTGCTTTGTTAATCACTCCCTTTTCCACAAGgtaacttgcg ... tttgttttagGCTTTGAAAGAAGCATTTGAGGTCTTCTGCAACAAAGGTGTTGGGGGAAGC
EST: gi|169111912|gb|FE510642.1|FE510642
EST:     ATTTGCAATATGTCAGCGAGTGCTTTGTTAATCACTCCCTTTTCCACAAG                         GCTTTGAAAGAAGCATTTGAGGTCTTCTGCAACAAAGGTGTTGGGGGAAGC
genomic: ATTTGCAATATGTCAGCGAGTGCTTTGTTAATCACTCCCTTTTCCACAAGgtaacttgcg ... tttgttttagGCTTTGAAAGAAGCATTTGAGGTCTTCTGCAACAAAGGTGTTGGGGGAAGC
EST: gi|169079161|gb|FE490908.1|FE490908
EST:     ATTTGCAATATGTCAGCGAGTGCTTTGTTAATCATTCCCTTTTCCACAAG                         GCTTTGAAAGAAGCATTTGAGGTCTTCTGCAACAAAGGTGTTGGGGGAAGC
genomic: ATTTGCAATATGTCAGCGAGTGCTTTGTTAATCACTCCCTTTTCCACAAGgtaacttgcg ... tttgttttagGCTTTGAAAGAAGCATTTGAGGTCTTCTGCAACAAAGGTGTTGGGGGAAGC
EST: gi|169027130|gb|FE435040.1|FE435040
EST:     ATTTGCAATATGTCAGCGAGTGCTTTGTTAATCACTCCCTTTTCCACA-G                         GCTTTGAAAGA-GCATTTGAGGTCTTTCTGCA-CAAAG-TGTTGGGGGAAG
genomic: ATTTGCAATATGTCAGCGAGTGCTTTGTTAATCACTCCCTTTTCCACAAGgtaacttgcg ... tttgttttagGCTTTGAAAGAAGCATTTGAGGTCTT-CTGCAACAAAGGTGTTGGGGGAAG

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: 33 (upstream exon), 35 (downstream exon)
Score: 27

GCTTTTGTTCGGAAAGTGATTGAGCTGCATGACAAATATTTGCAATATGTCAGCGAGTGCTTTGTTAATCACTCCCTTTTCCACAAGgtaacttgcg ... tttgttttagGCTTTGAAAGAAGCATTTGAGGTCTTCTGCAACAAAGGTGTTGGGGGAAGCACAAGTGCTGAGTTGCTAGCAACTTTCTGCGATAACCTCTTGAAGAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaacttgcgaacgttttcctagtttaaacaacgtgtcctttgttttagGCTTTGAAAGAAGCATTTGAGGTCTTCTGCAACAAAGGTGTTGGGGGAAGCACAAGTGCTGAGTTGCTAGCAACTTTCTGCGATAACCTCTTGAAGAAAG
                                               tcctttgtttt  CT-rich tract
                          tagtttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacttgcgaacgttttcctagtttaaacaacgtgtcctttgttttagGCTTTGAAAGAAGCATTTGAGGTCTTCTGCAACAAAGGTGTTGGGGGAAGCACAAGTGCTGAGTTGCTAGCAACTTTCTGCGATAACCTCTTGAAGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA