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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagctcacgattctttgctcacttctactaaatttttctctccagATTGTTACTTCGCTTTGAAGGTTTGGAACGCACAAAACGCTGGAGCGGCTGCTGTACTGGTTGCGGATGATAGAACCGAGCCTCTGATCACCATGGACTC

Basic information

species Selaginella moellendorffii
transcript EFJ22768
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ22768 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA20G27000.1 (Glycine max), 3'ss of exon 1
--------------------------------------------------gtgagct-cacgattctttgctcact-tctactaaatttttctctc-cagATTGTTACTTCGCTTTGAAGGTTTGGAACGCACAAAACGCTGGAGCGGCTGCTGTACTGGTTGCGGATGATAGAACCGAGCCTCTGATCACCATGGACTC
                                                   |  | | |  |  | | | || | | | |  ||  | || || |  ||||||| | ||| ||||||||||| ||||| ||||| || ||||||||  ||||||| || |||||||||||||     ||     |||| ||||||||| |
tgtggtgtgcttttgcacaagtgacatgctgtaagtatgaacaggtctcaatatgttgcttgggtgtattctaagtgttttttatgtgttccttttgcagATTGCTTCTTTGCTTTGAAGGTATGGAATGCACAGAAGGCTGGAGCTTCTGCTGTTCTTGTTGCGGATGATATTGTGGAAAAGTTGATAACCATGGACAC

upper sequence: EFJ22768 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA10G40340.1 (Glycine max), 3'ss of exon 1
----------------------------------------------------gtgagctcacgattctttgctcacttctactaaatttttctctc-cagATTGTTACTTCGCTTTGAAGGTTTGGAACGCACAAAACGCTGGAGCGGCTGCTGTACTGGTTGCGGATGATAGAACCGAGCCTCTGATCACCATGGACTC
                                                     ||       | | | ||         |  ||  | || || |  ||||||| | ||| ||||||||||| ||||| ||||| || ||||||||  ||||||| || ||| |||||||||     ||     |||| ||||||||| |
tgtgatttgcttttacacaagtgtcatgctgtaagtatgaccaagtcttgatatgttgcttgggtgcattctaagtggtttttatgtgttccttttgcagATTGCTTCTTTGCTTTGAAGGTATGGAATGCACAGAAGGCTGGAGCTTCTGCTGTTCTTGTTTCGGATGATATTGAGGAAAAGTTGATAACCATGGACAC

upper sequence: EFJ22768 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: AT2G14720.2 (Arabidopsis thaliana), 3'ss of exon 2
-----------------------------gtgagctcacgattctttgctcacttctact---aaatttttctctccagATTGTTACTTCGCTTTGAAGGTTTGGAACGCACAAAACGCTGGAGCGGCTGCTGTACTGGTTGCGGATGATAGAACCGAGCCTCTGATCACCATGGACTC
                             || || |     | ||| |     || ||||      | ||  | |  |||||||| ||||||||||||||| ||||||||||| || || || ||  ||||||| || || || ||| ||      |||||| |||| || |||||  |
gtactttcatcttttcttcaatcgatttcgttagattcgattccttagggtttttatacttgtggttgttattgtgtagATTGTTTCTTCGCTTTGAAGGTATGGAACGCACAGAAAGCAGGTGCTTCTGCTGTTCTTGTAGCTGATAATGTTGATGAGCCTTTGATTACAATGGATAC

upper sequence: EFJ22768 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: AT2G14740.2 (Arabidopsis thaliana), 3'ss of exon 1
--------------------------------------------------gtgagctcacgattctttgctcacttctactaaatttttctctccagATTGTTACTTCGCTTTGAAGGTTTGGAACGCACAAAACGCTGGAGCGGCTGCTGTACTGGTTGCGGATGATAGAACCGAGCCTCTGATCACCATGGACTC
                                                    | | | |  | | ||   |   |  |  |   | ||  | |  |||||||| ||||||||||||||| ||||||||||| || || || ||  ||||||| || || || ||| ||      || ||| |||| || |||||  |
gtacttcaatctcttactcaatcgatttgattcgattcgattcgattccttagggtttataagtgttg--ttgttgttgttgt-tgttgttgtgtagATTGTTTCTTCGCTTTGAAGGTATGGAACGCACAGAAAGCAGGTGCTTCTGCTGTTCTTGTAGCTGATAATGTTGATGAACCTTTGATTACAATGGATAC

upper sequence: EFJ22768 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: Vv08s0040g00700.t01 (Vitis vinifera), 3'ss of exon 2
-----------------------------------------------gtgagctcacgattctttgctcac----ttctactaaatt--tttctctccagATTGTTACTTCGCTTTGAAGGTTTGGAACGCACAAAACGCTGGAGCGGCTGCTGTACTGGTTGCGGATGATAGAACCGAGCC---TCTGATCACCATGGACTC
                                               |||  | ||  |   |   | ||     ||     ||||   ||  | | ||||||||||||| ||  ||||||| |||| |||||| ||||| ||||| |||||||| ||| |||| ||  | | | | ||| |    | | | | ||   |   
aatgaagaaaaataggagctcaatggacagttatgtcctcctctaatgtgtacccattaacatggacccagggtattaagggaaataaattattttgcagATTGTTACTTTGCGCTGAAGGTATGGAGCGCACAGAACGCGGGAGCTGCTGCTGTTCTGATTGCAGACAACATAGCTGAGACATTCCCGGTGAGCAGACA---

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|169114822|gb|FE516083.1|FE516083
EST:     CAGGAGGAAATCCGGTGGGCTTCCCAACGTGGTGCTTGTCGATCGAGGAG                         ATTGTTACTTCGCTTTGAAGGTTTGGAACGCACAAAACGCTGGAGCGGCTG
genomic: CAGGAGGAAATCCGGTGGGCTTCCCAACGTGGTGCTTGTCGATCGAGGAGgtgagctcac ... ttctctccagATTGTTACTTCGCTTTGAAGGTTTGGAACGCACAAAACGCTGGAGCGGCTG
EST: gi|169075667|gb|FE482053.1|FE482053
EST:     CAGGAGGAAATCCGGTGGGCTTCCCAACGTGGTGCTTGTCGATCGAGGAG                         ATTGTTACTTCGCTTTGAAGGTTTGGAACGCACAAAACGCTGGAGCGGCTG
genomic: CAGGAGGAAATCCGGTGGGCTTCCCAACGTGGTGCTTGTCGATCGAGGAGgtgagctcac ... ttctctccagATTGTTACTTCGCTTTGAAGGTTTGGAACGCACAAAACGCTGGAGCGGCTG
EST: gi|169102389|gb|FE507081.1|FE507081
EST:     CAGGAGGAAATCCGGTGGGCTTCCCAACGTGGTGCTTGTCGATCGAGGAG                         ATTGTTACTTCGCTTTGAAGGTTTGGAACGCACAAAACGCTGGAGCGGCTG
genomic: CAGGAGGAAATCCGGTGGGCTTCCCAACGTGGTGCTTGTCGATCGAGGAGgtgagctcac ... ttctctccagATTGTTACTTCGCTTTGAAGGTTTGGAACGCACAAAACGCTGGAGCGGCTG
EST: gi|169082428|gb|FE488990.1|FE488990
EST:     CAGGAGGAAATCCGGTGGGCTTCCCAACGTGGTGCTTGTCGATCGAGGAG                         ATTGTTACTTCGCTTTGAAGGTTTGGAACGCACAAAACGCTGGAGCGGCTG
genomic: CAGGAGGAAATCCGGTGGGCTTCCCAACGTGGTGCTTGTCGATCGAGGAGgtgagctcac ... ttctctccagATTGTTACTTCGCTTTGAAGGTTTGGAACGCACAAAACGCTGGAGCGGCTG
EST: gi|169080759|gb|FE487228.1|FE487228
EST:     TGCTTGTCGATCGAGGAG                         ATTGTTACTTCGCTTTGAAGGTTTGGAACGCACAAAACGCTGGAGCGGCTG
genomic: TGCTTGTCGATCGAGGAGgtgagctcac ... ttctctccagATTGTTACTTCGCTTTGAAGGTTTGGAACGCACAAAACGCTGGAGCGGCTG
EST: gi|169080941|gb|FE486110.1|FE486110
EST:     CAGGAGGAAATCCGGTGGGCTTCCCAACGTGGTGCTTGTCGATCGAGGAG                         ATTGTTACTTCGCTTTGAAGGTTTGGAACGCACAAAACGCTGGAGCGGCTG
genomic: CAGGAGGAAATCCGGTGGGCTTCCCAACGTGGTGCTTGTCGATCGAGGAGgtgagctcac ... ttctctccagATTGTTACTTCGCTTTGAAGGTTTGGAACGCACAAAACGCTGGAGCGGCTG
EST: gi|169038899|gb|FE449616.1|FE449616
EST:     CAGGAGGAAATCCGGTGGGCTTCCCAACGTGGTGCTTGTCGATCGAGGAG                         ATTGTTACTTCGCTTTGAAGGTTTGGAACGCACAAAACGCTGGAGCGGCTG
genomic: CAGGAGGAAATCCGGTGGGCTTCCCAACGTGGTGCTTGTCGATCGAGGAGgtgagctcac ... ttctctccagATTGTTACTTCGCTTTGAAGGTTTGGAACGCACAAAACGCTGGAGCGGCTG
EST: gi|169107251|gb|FE508250.1|FE508250
EST:     CAGGAGGAAATCCGGTGGGCTTCCCAACGTGGTGCTTGTCGATCGAGGAG                         ATTGTTACTTCGCTTTGAAGGTTTGGAACGCACAAAACGCTGGAGCGGCTG
genomic: CAGGAGGAAATCCGGTGGGCTTCCCAACGTGGTGCTTGTCGATCGAGGAGgtgagctcac ... ttctctccagATTGTTACTTCGCTTTGAAGGTTTGGAACGCACAAAACGCTGGAGCGGCTG
EST: gi|169115683|gb|FE517269.1|FE517269
EST:     CAGGAGGAAATCCGGTGGGCTTCCCAACGTGGTGCTTGTCGATCGAGGAG                         ATTGTTACTTCGCTTTGAAGGTTTGGAACGCACAAAACGCTGGAGCGGCTG
genomic: CAGGAGGAAATCCGGTGGGCTTCCCAACGTGGTGCTTGTCGATCGAGGAGgtgagctcac ... ttctctccagATTGTTACTTCGCTTTGAAGGTTTGGAACGCACAAAACGCTGGAGCGGCTG
EST: gi|169031592|gb|FE439057.1|FE439057
EST:     CAGGAGGAAATCCGGTGGGCTTCCCAACGTGGTGCTTGTCGATCGAGGAG                         ATTGTTACTTCGCTTTGAAGGTTTGGAACGCACAAAACGCTGGAGCGGCTG
genomic: CAGGAGGAAATCCGGTGGGCTTCCCAACGTGGTGCTTGTCGATCGAGGAGgtgagctcac ... ttctctccagATTGTTACTTCGCTTTGAAGGTTTGGAACGCACAAAACGCTGGAGCGGCTG
EST: gi|169080526|gb|FE488464.1|FE488464
EST:     CAGGAGGAAATCCGGTGGGCTTCCCAACGTGGTGCTTGTCGATCGAGGAG                         ATTGTTACTTCGCTTTGAAGGTTTGGAACGCACAAAACGCTGGAGCGGCTG
genomic: CAGGAGGAAATCCGGTGGGCTTCCCAACGTGGTGCTTGTCGATCGAGGAGgtgagctcac ... ttctctccagATTGTTACTTCGCTTTGAAGGTTTGGAACGCACAAAACGCTGGAGCGGCTG
EST: gi|169026483|gb|FE434770.1|FE434770
EST:     CAGGAGGAAATCCGGTGGGCTTCCCAACGTGGTGCTTGTCGATCGAGGAG                         ATTGTTACTTCGCTTTGAAGGTTTGGAACGCACAAAACGCTGGAGCGGCTG
genomic: CAGGAGGAAATCCGGTGGGCTTCCCAACGTGGTGCTTGTCGATCGAGGAGgtgagctcac ... ttctctccagATTGTTACTTCGCTTTGAAGGTTTGGAACGCACAAAACGCTGGAGCGGCTG
EST: gi|169083004|gb|FE488526.1|FE488526
EST:     CAGGAGGAAATCCGGTGGGCTTCCCAACGTGGTGCTTGTCGATCGAGGAG                         ATTGTTACTTCGCTTTGAAGGTTTGGAACGCACAAAACGCTGGAGCGGCTG
genomic: CAGGAGGAAATCCGGTGGGCTTCCCAACGTGGTGCTTGTCGATCGAGGAGgtgagctcac ... ttctctccagATTGTTACTTCGCTTTGAAGGTTTGGAACGCACAAAACGCTGGAGCGGCTG
EST: gi|169092914|gb|FE495208.1|FE495208
EST:     ATCCGGTGGGCTTCCCAACGTGGTGCTTGTCGATCGAGGAG                         ATTGTTACTTCGCTTTGAAGGTTTGGAACGCACAAAACGCTGGAGCGGCTG
genomic: ATCCGGTGGGCTTCCCAACGTGGTGCTTGTCGATCGAGGAGgtgagctcac ... ttctctccagATTGTTACTTCGCTTTGAAGGTTTGGAACGCACAAAACGCTGGAGCGGCTG
EST: gi|169019881|gb|FE426968.1|FE426968
EST:     CAGGAGGAAATCCGGTGGGCTTCCCAACGTGGTGCTTGTCGATCGAGGAG                         ATTGTTACTTCGCTTTGAAGGTTTGGAACGCACAAAACGCTGGAGCGGCTG
genomic: CAGGAGGAAATCCGGTGGGCTTCCCAACGTGGTGCTTGTCGATCGAGGAGgtgagctcac ... ttctctccagATTGTTACTTCGCTTTGAAGGTTTGGAACGCACAAAACGCTGGAGCGGCTG

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: 76

CCGAAGGATTCGAGGATGGCATGCAAACCGTACAGTGATTCCGATACTTTCAGGAGGAAATCCGGTGGGCTTCCCAACGTGGTGCTTGTCGATCGAGGAGgtgagctcac ... ttctctccagATTGTTACTTCGCTTTGAAGGTTTGGAACGCACAAAACGCTGGAGCGGCTGCTGTACTGGTTGCGGATGATAGAACCGAGCCTCTGATCACCATGGACTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgagctcacgattctttgctcacttctactaaatttttctctccagATTGTTACTTCGCTTTGAAGGTTTGGAACGCACAAAACGCTGGAGCGGCTGCTGTACTGGTTGCGGATGATAGAACCGAGCCTCTGATCACCATGGACTC
                                   tactaaa  putative branch site (score: 76)
                                          tttttctctcc  CT-rich tract
                                ttctactaaattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagctcacgattctttgctcacttctactaaatttttctctccagATTGTTACTTCGCTTTGAAGGTTTGGAACGCACAAAACGCTGGAGCGGCTGCTGTACTGGTTGCGGATGATAGAACCGAGCCTCTGATCACCATGGACTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA