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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctgtcttccaagaaaaaaacaacttgtttctcaaactttttgtttttcatgttgctctttctagCCTCAAGATGCTTATGGACTAGAGAAGCTCTGCAGTGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGAATCGAGTGCCGGATTGGAAGATTTCACA

Basic information

species Selaginella moellendorffii
transcript EFJ09286
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ12864 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: LOC_Os10g28200.1 (Oryza sativa), 3'ss of exon 3
----------------------------gtatgctgtcttccaagaaaaaaacaacttgtttctcaaactttttgtttttcatgttgctctttctagCCTCAAGATGCTTATGGACTAGAGAAGCTCTGCAGTGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGAATCGAGTGCCGGATTGGAAGATTTCACA
                               || | | ||  |  ||||  | || ||| ||  | |      ||||||   |  ||     || ||||||||||||| |||||  | ||||||||    | ||| ||||| |||||||||||||||||||| ||||| || ||||||||  ||||  | || ||||
gtttgtccatcaaaataattttaggctttagtgttatgttttagtaaaaccagaagttgatttccta-----ctgttttaactactg-----tccagCCTCAAGATGCCTATGGTTTGGAGAAGCTTGCAACTGAGGAGCTCTGCAAGCACTACACCAAGGACTTTGGCATTGAGTGCCGTGTTGGCCGCTTCCACA

upper sequence: EFJ12864 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G138907_T01 (Zea mays), 3'ss of exon 3
-----------------------------------gtatgctgtcttccaagaaaaaaacaacttgtt-tctcaaactttttgtttttca--tgttgctc--tttctagCCTCAAGATGCTTATGGACTAGAGAAGCTCTGCAGTGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGAATCGAGTGCCGGATTGGAAGATTTCACA
                                   ||  ||||||  | |    |      |||||   |  |||| |  || ||  | |  || |||    ||| |||||||||||||| ||||| || || || |||   | ||| ||||||||||||||||| || ||||||||||| |||||||||||||||||  | |||||||
gtttctaataaacttctgcatttctttacgctcgtgttagctgtcacctacttgagctgtgacttgcgatggcaaaatggtttttactgaactgatgcctaatttttagCCTCAAGATGCCTATGGCCTGGAAAAACTCGCGACTGAGGAGCTGTGCAAGCACTATACAAAGGATTTTGGCATCGAGTGCCGGATTGGTCGCTTTCACA

upper sequence: EFJ12864 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G124434_T01 (Zea mays), 3'ss of exon 3
--------------gtatgctgtc-ttccaagaaaaaaacaacttgtttctcaaactttttgtttttcatgttgctctttctagCCTCAAGATGCTTATGGACTAGAGAAGCTCTGCAGTGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGAATCGAGTGCCGGATTGGAAGATTTCACA
               ||   || | ||||        |   |  | |      || | |   |       ||    | ||  ||||||||||||| |||||  | ||||||||    |  || |||||||||||||||||||||||||| ||||| |||||||||||  | ||  | || ||||
gtgtgttcatcgaaatacaatgacgttcctgtttgttagacatatatacagtcaaatctaaatcccctcggtgttacgtttcagCCTCAAGATGCCTATGGCTTGGAGAAGCTTGCAACCGAGGAGCTGTGCAAGCACTACACCAAGGACTTTGGCATCGAGTGCCGCGTCGGCCGCTTCCACA

upper sequence: EFJ12864 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA19G43400.1 (Glycine max), 3'ss of exon 3
----------------------------------gtatgctgtcttccaagaaaaaaacaacttgtttctcaaactttttgtttttcatgttgctctttctagCCTCAAGATGCTTATGGACTAGAGAAGCTCTGCAGTGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGAATCGAGTGCCGGATTGGAAGATTTCACA
                                   ||| |||  |    |    |||| |  | | ||  ||    | |  |||   || |  || ||| ||||| |||||||| ||||| || ||||||||    |  |||||| | |||||||| || | ||||||||||||||| |||||||||||||| ||||| || |
gtttgttgctgattcttttaattagttgttcaacttattctggttattcacttgaaaatacttaggttagcagggatat-atttaatatttgactttttatagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAGCATTATAACAAGGATTTTGGAATTGAGTGCCGGATTGGGAGATTCCATA

upper sequence: EFJ12864 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA20G36740.2 (Glycine max), 3'ss of exon 3
------------------------------gtatgctgtcttccaagaaaaaaac--aacttgtttctcaaactttttgtttttcatgttgctctttctagCCTCAAGATGCTTATGGACTAGAGAAGCTCTGCAGTGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGAATCGAGTGCCGGATTGGAAGATTTCACA
                               |||| ||  |    |     | |      |||    | |    |||  ||||    ||  || ||| ||||| |||||||| ||||| |||||||||||    |  || ||  | ||||||||||| | ||||||||||||||| |||||||| ||||| || || ||||
gtttgttggtgatcttttcaattgttcaatttatgttggttcttgattttcacattgggattgggattaatgtgtttaatttt----gtgactgtttttagCCACAAGATGCATATGGGCTAGAGAAGCTTGCAACAGAGGAATTATGCAAGCACTATAACAAGGATTTTGGAATTGAGTGCCGCATTGGGAGGTTCCACA

upper sequence: EFJ12864 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA10G30400.1 (Glycine max), 3'ss of exon 2
------------------------------gtatgctgtcttccaagaaaaaaacaacttgtttctcaaactttttgtttttcatgttgctctttctagCCTCAAGATGCTTATGGACTAGAGAAGCTCTGCAGTGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGAATCGAGTGCCGGATTGGAAGATTTCACA
                               |||| ||  |     ||     |||    | ||   |    |||  ||  |  |||  || ||| |||||||||||||| ||||| |||||||| ||    |  || ||  | ||||||||||| | ||||||||||||||| |||||||| ||||| || || ||||
gttagttggtgatcttttgaattgttcaatttatgttggttctt--gattttcacattgggattgggattaatttgtttaattttgtgactttttttagCCTCAAGATGCATATGGGCTAGAGAAACTTGCAACAGAGGAATTATGCAAGCACTATAACAAGGATTTTGGAATTGAGTGCCGCATTGGGAGGTTCCACA

upper sequence: EFJ12864 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA03G40720.1 (Glycine max), 3'ss of exon 3
----------------------------------gtatgctgtcttccaagaaaaaaacaacttgtttctcaaactttttgtttttcatgttgctctttctagCCTCAAGATGCTTATGGACTAGAGAAGCTCTGCAGTGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGAATCGAGTGCCGGATTGGAAGATTTCACA
                                   ||| |||  |    |   ||||| |  | |  |  ||    | |  ||  |  | |||   ||| ||||| |||||||| ||||| || ||||||||    |  |||||| | |||||||| || | ||||||||||||||| |||||||| ||||| ||||| || |
gtatgttgctgattctttgaattacttgttcaagttattctggttattcacttaaaaatacttaggctagcagggatatatttaat--ttttgacttttatagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAGCATTATAACAAGGATTTTGGAATTGAGTGCCGCATTGGGAGATTCCATA

upper sequence: EFJ12864 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: Vv05s0020g04510.t01 (Vitis vinifera), 3'ss of exon 3
----------------------gtatgctgtcttccaagaaaaaaacaacttgtttctcaaactttttgtttttcatgttgctctt-tctagCCTCAAGATGCTTATGGACTAGAGAAGCTCTGCAGTGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGAATCGAGTGCCGGATTGGAAGATTTCACA
                        ||      |   || | |   |      | || |     |   || |   | | ||||| || | |||||||||||||| |||||  |||||||||||   | ||| ||| | |||||||||||||| ||||| |||||||| ||||| || |||||| | || || |
gtttttcctctaatcttataaaaaatatcagttctaaatatattcatttgaggattattggcataactgatgagctttttgcttttgtttagCCTCAAGATGCCTATGGCTTAGAGAAGCTCGCAACTGAGGAGTTATGCAAGCACTACACTAAGGACTTTGGAATTGAGTGTCGCATTGGACGGTTCCATA

upper sequence: EFJ12864 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: EDP09235 (Chlamydomonas reinhardtii), 3'ss of exon 5
---------------------------gtatgctgtcttccaagaaaaaaacaacttgtttctcaaactttttgtttttc----atgttgctctttctagCCTCAAGATGCTTATGGACTAGAGAAGCTCTGCAGTGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGAATCGAGTGCCGGATTGGAAGATTTCACA
                           |   ||||  | |         |      |||  ||     || ||     ||    | ||          |||| |||||||| || || || ||||||||   ||  || ||||||||||||||||||| |||||| || || || |||||||| || |   | || ||||
gtcctctcggccgtgtgtctgcgtgtcgccggctgcttgctgcaccgcgacgccgctgtcactgctgattcttacacctcccaaacgtcttcgcccgcagCCCCAAGATGCGTACGGCCTGGAGAAGCTGGCCACCGAGGAGCTGTGCAAGCACTACAACAAGGACTTCGGCATTGAGTGCCGCATCGCGCGCTTCCACA

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|70670289|gb|DN838866.1|DN838866
EST:     AACTTGAAACGAACGTGAGTCTCAAGGAATCGGATGCTTGGCCAGCAGAG                         CCTCAAGATGCTTATGGACTAGAGAAGCTCTGCAGTGAAGAGCTGTGCAAG
genomic: AACTTGAAACGAACGTGAGTCTCAAGGAATCGGATGCTTGGCCAGCAGAGgtatgctgtc ... ctctttctagCCTCAAGATGCTTATGGACTAGAGAAGCTCTGCAGTGAAGAGCTGTGCAAG
EST: gi|169100903|gb|FE502233.1|FE502233
EST:     AGGAATCGGATGCTTGCCCAGCAGAG                         CCTCAAGATGCTTATGGACTAGAGAAGCTCTGCAGTGAAGAGCTGTGCAAG
genomic: AGGAATCGGATGCTTGGCCAGCAGAGgtatgctgtc ... ctctttctagCCTCAAGATGCTTATGGACTAGAGAAGCTCTGCAGTGAAGAGCTGTGCAAG
EST: gi|169078884|gb|FE489656.1|FE489656
EST:     AC-TGAAAACGAACGTGAGTCTCAAGGAATCGGATGCTTGGCCAGCAGAG                         CCTCAAGATGCTTATGGACTAGAGAAGCTCTGCAGTGAAGAGCTGTGCAAG
genomic: ACTTG-AAACGAACGTGAGTCTCAAGGAATCGGATGCTTGGCCAGCAGAGgtatgctgtc ... ctctttctagCCTCAAGATGCTTATGGACTAGAGAAGCTCTGCAGTGAAGAGCTGTGCAAG
EST: gi|169046275|gb|FE456408.1|FE456408
EST:     AACTTGAAACGAACGTGAGTCTCAAGGAATCGGATGCTTGGCCAGCAGAG                         CCTCAAGATGCTTATGGACTAGAGAAGCTCTGCAGTGAAGAGCTGTGCAAG
genomic: AACTTGAAACGAACGTGAGTCTCAAGGAATCGGATGCTTGGCCAGCAGAGgtatgctgtc ... ctctttctagCCTCAAGATGCTTATGGACTAGAGAAGCTCTGCAGTGAAGAGCTGTGCAAG
EST: gi|70670419|gb|DN838996.1|DN838996
EST:     AACTTGAAACGAACGTGAGTCTCAAGGAATCGGATGCTTGGCCAGCAGAG                         CCTCAAGATGCTTATGGACTAGAGAAGCTCTGCAGTGAAGAGCTGTGCAAG
genomic: AACTTGAAACGAACGTGAGTCTCAAGGAATCGGATGCTTGGCCAGCAGAGgtatgctgtc ... ctctttctagCCTCAAGATGCTTATGGACTAGAGAAGCTCTGCAGTGAAGAGCTGTGCAAG
EST: gi|169066576|gb|FE474136.1|FE474136
EST:     AAC-TGAAACGAACGTGAGTCTCAAGGAATCGGATGCTTGGCCAGCAGAG                         CCTCAAGATGCTTATGGACTAGAGAAGCTCTGCAGTGAAGAGCTGTGCAAG
genomic: AACTTGAAACGAACGTGAGTCTCAAGGAATCGGATGCTTGGCCAGCAGAGgtatgctgtc ... ctctttctagCCTCAAGATGCTTATGGACTAGAGAAGCTCTGCAGTGAAGAGCTGTGCAAG
EST: gi|169047515|gb|FE455710.1|FE455710
EST:     AACTTGAAACGAACGTGAGTCTCAAGGAATCGGATGCTTGGCCAGCAGAG                         CCTCAAGATGCTTATGGACTATAGAAGCTCTGCAGTGAAGAGCTGTGCAAG
genomic: AACTTGAAACGAACGTGAGTCTCAAGGAATCGGATGCTTGGCCAGCAGAGgtatgctgtc ... ctctttctagCCTCAAGATGCTTATGGACTAGAGAAGCTCTGCAGTGAAGAGCTGTGCAAG
EST: gi|169115072|gb|FE516645.1|FE516645
EST:     AACTTGAAACGAACGTGAGTCTCAAGGAATCGGATGCTTGGCCAGCAGAG                         CCTCAAGATGCTTATGGACTAGAGAAGCTCTGCAGTGAAGAGCTGTGCAAG
genomic: AACTTGAAACGAACGTGAGTCTCAAGGAATCGGATGCTTGGCCAGCAGAGgtatgctgtc ... ctctttctagCCTCAAGATGCTTATGGACTAGAGAAGCTCTGCAGTGAAGAGCTGTGCAAG
EST: gi|169102736|gb|FE508091.1|FE508091
EST:     AACTGGAAACGAACGTGAGTCTCAAGGAATCGGATGCTTGGCCAGCAGAG                         CCTCAAGATGCTTATGGACTAGAGAAGCTCTGCAGTGAAGAGCTGTGCAAG
genomic: AACTTGAAACGAACGTGAGTCTCAAGGAATCGGATGCTTGGCCAGCAGAGgtatgctgtc ... ctctttctagCCTCAAGATGCTTATGGACTAGAGAAGCTCTGCAGTGAAGAGCTGTGCAAG
EST: gi|169081289|gb|FE489279.1|FE489279
EST:     AACTTGAAACGAACGTGAGTCTCAAGGAATCGGATGCTTGGCCAGCAGAG                         CCTCAAGATGCTTATGGACTAGAGAAGCTCTGCAGTGAAGAGCTGTGCAAG
genomic: AACTTGAAACGAACGTGAGTCTCAAGGAATCGGATGCTTGGCCAGCAGAGgtatgctgtc ... ctctttctagCCTCAAGATGCTTATGGACTAGAGAAGCTCTGCAGTGAAGAGCTGTGCAAG
EST: gi|169045727|gb|FE451700.1|FE451700
EST:     CTTGAAACGAACGTGAGTCTCAAGGAATCGGATGCTTGGCCAGCAGAG                         CCTCAAGATGCTTATGGACTAGAGAAGCTCTGCAGTGAAGAGCTGTGCAAG
genomic: CTTGAAACGAACGTGAGTCTCAAGGAATCGGATGCTTGGCCAGCAGAGgtatgctgtc ... ctctttctagCCTCAAGATGCTTATGGACTAGAGAAGCTCTGCAGTGAAGAGCTGTGCAAG
EST: gi|169102737|gb|FE508092.1|FE508092
EST:     AACTTGAAACGAACGTGAGTCTCAAGGAATCGGATGCTTGGCCAGCAGAG                         CCTCAAGATGCTTATGGACTAGAGAAGCTCTGCAGTGAAGAGCTGTGCAAG
genomic: AACTTGAAACGAACGTGAGTCTCAAGGAATCGGATGCTTGGCCAGCAGAGgtatgctgtc ... ctctttctagCCTCAAGATGCTTATGGACTAGAGAAGCTCTGCAGTGAAGAGCTGTGCAAG
EST: gi|169066577|gb|FE474137.1|FE474137
EST:     AACTTGAAACGAACGTGAGTCTCAAGGAATCGGATGCTTGGCCAGCAGAG                         CCTCAAGATGCTTATGGACTAGAGAAGCTCTGCAGTGAAGAGCTGTGCAAG
genomic: AACTTGAAACGAACGTGAGTCTCAAGGAATCGGATGCTTGGCCAGCAGAGgtatgctgtc ... ctctttctagCCTCAAGATGCTTATGGACTAGAGAAGCTCTGCAGTGAAGAGCTGTGCAAG
EST: gi|169115073|gb|FE516646.1|FE516646
EST:     AACTTGAAACGAACGTGAGTCTCAAGGAATCGGATGCTTGGCCAGCAGAG                         CCTCAAGATGCTTATGGACTAGAGAAGCTCTGCAGTGAAGAGCTGTGCAAG
genomic: AACTTGAAACGAACGTGAGTCTCAAGGAATCGGATGCTTGGCCAGCAGAGgtatgctgtc ... ctctttctagCCTCAAGATGCTTATGGACTAGAGAAGCTCTGCAGTGAAGAGCTGTGCAAG
EST: gi|169113665|gb|FE515291.1|FE515291
EST:     AACTTGAAACGAACGTGAGTCTCAAGGAATCGGATGCTTGGCCAGCAGAG                         CCTCAAGATGCTTATGGACTAGAGAAGCTCTGCAGTGAAGAGCTGTGCAAG
genomic: AACTTGAAACGAACGTGAGTCTCAAGGAATCGGATGCTTGGCCAGCAGAGgtatgctgtc ... ctctttctagCCTCAAGATGCTTATGGACTAGAGAAGCTCTGCAGTGAAGAGCTGTGCAAG
EST: gi|169074849|gb|FE482743.1|FE482743
EST:     AACTTGAAACGAACGTGAGTCTCAAGGAATCGGATGCTTGGCCAGCAGAG                         CCTCAAGATGCTTATGGACTAGAGAAGCTCTGCAGTGAAGAGCTGTGCAAG
genomic: AACTTGAAACGAACGTGAGTCTCAAGGAATCGGATGCTTGGCCAGCAGAGgtatgctgtc ... ctctttctagCCTCAAGATGCTTATGGACTAGAGAAGCTCTGCAGTGAAGAGCTGTGCAAG
EST: gi|169045726|gb|FE451699.1|FE451699
EST:     CTTGAAACGAACGTGAGTCTCAAGGAATCGGATGCTTGGCCAGCAGAG                         CCTCAAGATGCTTATGGACTAGAGAAGCTCTGCAGTGAAGAGCTGTGCAAG
genomic: CTTGAAACGAACGTGAGTCTCAAGGAATCGGATGCTTGGCCAGCAGAGgtatgctgtc ... ctctttctagCCTCAAGATGCTTATGGACTAGAGAAGCTCTGCAGTGAAGAGCTGTGCAAG
EST: gi|169078885|gb|FE489657.1|FE489657
EST:     AACTTGAAACGAACGTGAGTCTCAAGGAATCGGATGCTTGGCCAGCAGAG                         CCTCAAGATGCTTATGGACTAGAGAAGCTCTGCAGTGAAGAGCTGTGCAAG
genomic: AACTTGAAACGAACGTGAGTCTCAAGGAATCGGATGCTTGGCCAGCAGAGgtatgctgtc ... ctctttctagCCTCAAGATGCTTATGGACTAGAGAAGCTCTGCAGTGAAGAGCTGTGCAAG
EST: gi|169099895|gb|FE503383.1|FE503383
EST:     AACTTGAAACGAACGTGAGTCTCAAGGAATCGGATGCTTGGCCAGCAGAG                         CCTCAAGATGCTTATGGACTAGAGAAGCTCTGCAGTGAAGAGCTGTGCAAG
genomic: AACTTGAAACGAACGTGAGTCTCAAGGAATCGGATGCTTGGCCAGCAGAGgtatgctgtc ... ctctttctagCCTCAAGATGCTTATGGACTAGAGAAGCTCTGCAGTGAAGAGCTGTGCAAG

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), 32 (downstream exon)
Score: 7

ATTTTTCTATGCATCCAGCGCATGCATTTACCCAGAATTCAAGCAACTTGAAACGAACGTGAGTCTCAAGGAATCGGATGCTTGGCCAGCAGAGgtatgctgtc ... ctctttctagCCTCAAGATGCTTATGGACTAGAGAAGCTCTGCAGTGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGAATCGAGTGCCGGATTGGAAGATTTCACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagaaaaaaacaacttgtttctcaaactttttgtttttcatgttgctctttctagCCTCAAGATGCTTATGGACTAGAGAAGCTCTGCAGTGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGAATCGAGTGCCGGATTGGAAGATTTCACA
                          ctttttgtttttcatg  CT-rich tract
                       aaactttttgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctgtcttccaagaaaaaaacaacttgtttctcaaactttttgtttttcatgttgctctttctagCCTCAAGATGCTTATGGACTAGAGAAGCTCTGCAGTGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGAATCGAGTGCCGGATTGGAAGATTTCACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA