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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacgatttggattcttggagcttgaaatttcacatttctcttcgcttcatagAGGGCAAGACCGATTATCGGGCTCGGGTGCGCTTGACGAATCAGGACAAGAACAAATACAACACACCGAAGTACCGATTCGTCGTTCGCTTT

Basic information

species Selaginella moellendorffii
transcript EFJ17161
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ17161 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: LOC_Os01g67134.1 (Oryza sativa), 3'ss of exon 2
--------------------------------gtaacgatttggattcttggagcttgaaatttcacatttctcttcgcttcatagAGGGCAAGACCGATTATCGGGCTCGGGTGCGCTTGACGAATCAGGACAAGAACAAATACAACACACCGAAGTACCGATTCGTCGTTCGCTTT
                                    | | |     | |||  |     ||| |||  ||| || | | ||   |||||||||||| || ||  ||||  || |  |  | || || || || |||||||| |||||||||||||||||||| ||||| ||  | |||
gtaagtcaagttcaagagaccgaggcgtttccaagtcaagtcaaggttttgacgtacttaatctca--tttgtcattgttt-gcagAGGGCAAGACTGACTACAGGGCCAGGATTAGGCTCACCAACCAAGATAAGAACAAGTACAACACACCGAAGTACCGCTTCGTTGTGAGATTT

upper sequence: EFJ17161 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: LOC_Os01g67126.1 (Oryza sativa), 3'ss of exon 2
----------------------------------------------gtaacgatttggattcttggagcttgaaatttcacatttctcttcgcttcatagAGGGCAAGACCGATTATCGGGCTCGGGTGCGCTTGACGAATCAGGACAAGAACAAATACAACACACCGAAGTACCGATTCGTCGTTCGCTTT
                                              ||||          | |||  |     ||| |||  ||| |  | | ||   |||||||||||| || ||  ||||  || |  |  | || || || || |||||||| |||||||||||||||||||| |||||          
gtaagttcaatataatcctttcatgtggctcatgcattctgtgcttgtaatatagctaggttttgatgtacttaatctca--tttgttattgttt-gcagAGGGCAAGACTGACTACAGGGCCAGGATTAGGCTCACCAACCAAGATAAGAACAAGTACAACACACCGAAGTACCGCTTCGTT---------

upper sequence: EFJ17161 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA07G06580.1 (Glycine max), 3'ss of exon 2
----------------gtaacgatttggattcttggagcttgaaatttc--------acattt-ctcttcgcttcatagAGGGCAAGACCGATTATCGGGCTCGGGTGCGCTTGACGAATCAGGACAAGAACAAATACAACACACCGAAGTACCGATTCGTCGTTCGCTTT
                 |   | ||||   | ||  |  |||||   ||        ||  |   |||         |||||| || |||||||| || ||  || | || ||||  |||||||||||||||||||| ||||| ||||| |||||||| || |||||||||
gttatcatattcgcctattttgttttgtcatgttcaatgttgaatactctgttagtaacggtgattctgttacctgcagAGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGAACAAATATAACACTCCGAAATACCGATTTGTTGTTCGCTTT

upper sequence: EFJ17161 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA13G35580.2 (Glycine max), 3'ss of exon 2
-----------------gtaacgatttggattcttggagcttgaa----at-ttcacatt--tctcttcgct--tcatagAGGGCAAGACCGATTATCGGGCTCGGGTGCGCTTGACGAATCAGGACAAGAACAAATACAACACACCGAAGTACCGATTCGTCGTTCGCTTT
                  |  || || |   | ||| |  |||||    || || | | |  |   || | |      |||||| || |||||||| || ||  || | || ||||  |||||||||||||||||||| ||||| ||||| |||||||| || |||||||||
gttttcattttctacttttttcgtttcgtcgtgttgaatgttgaatacgatgtttataatggtgattttgttatctgcagAGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGAACAAATATAACACTCCGAAATACCGATTTGTGGTTCGCTTT

upper sequence: EFJ17161 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S364_3V6.1 (Physcomitrella patens), 3'ss of exon 2
-----------------------------------------------------------------------------------------------------gtaacgatttggattct----tggagcttgaaatttcacatttctcttcgctt-catagAG---------GGCAAGACCGATTATCGGGCTCGGGTGCGCTTGACGAATCAGGACAAGAACAAATACAACACACCGAAGTACCGATTCGTCGTTCGCTTT
                                                                                                      |  || ||| | || |    |||   ||    || |  || |    | |  | ||| ||          || || |||||||| |||||  || | || ||||| | ||||||||||||||| |||||||| ||||||||||| ||||||||||| || 
gtgcggatttttttgtggcatttgtcaccctcactgtcgaagatccttgatcttgaatcttttctgtgtgtcgttggtacagagggttgtatcgctggggtttctcgttttaggttttctgctggtatttcttgttgcggatctgagattgtgtgcatggattatgcagCTGGTAAAACCGATTACCGGGCGAGGATCCGTTTGACCACTCAGGACAAGAACAAGTACAACACCCCGAAGTACCGTTTCGTCGTTCGTTTC

upper sequence: EFJ17161 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S97_115V6.1 (Physcomitrella patens), 3'ss of exon 2
-------------------------------------------------------------------------------------------gtaacgatttggattcttggagcttgaaatttcacatttctcttcgctt-catagAGGGCAAGACCGATTATCGGGCTCGGGTGCGCTTGACGAATCAGGACAAGAACAAATACAACACACCGAAGTACCGATTCGTCGTTCGCTTT
                                                                                            | | | ||||      | |  | || |  |         |    | ||  | ||  || |||||||| || || ||| || | ||| |||| |  ||||||||||||||||||||||| ||||||||||| || ||||| || |||
gtaaggtttttattgtcccggactagtttgtgatttcgtcagggttgtagtgttttacactactgtgtcgaatttttagttgttgatgaggattagggtttgatggactagtccatggagctgactgcgagtggctgtttatacagCTGGAAAGACCGACTACCGAGCTAGGATTCGCCTGACCACCCAGGACAAGAACAAATACAACACCCCGAAGTACCGTTTGGTCGTGCGATTT

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|169079163|gb|FE490910.1|FE490910
EST:     ATCCAAATCCTACTACAAGAGGTACCAGGTCAAGTACCGCCGCCGAAGAG                         AGGGCAAGACCGATTATCGGGCTCGGGTGCGCTTGACGAATCAGGACAAGA
genomic: ATCCAAATCCTACTACAAGAGGTACCAGGTCAAGTACCGCCGCCGAAGAGgtaacgattt ... cgcttcatagAGGGCAAGACCGATTATCGGGCTCGGGTGCGCTTGACGAATCAGGACAAGA
EST: gi|169051355|gb|FE459213.1|FE459213
EST:     ATCCAAATCCTACTACAAGAGGTACCAGGTCAAGTACCGCCGCCGAAGAG                         AGGGCAAGACCGATTATCGGGCTCGGGTGCGCTTGACGAATCAGGACAAGA
genomic: ATCCAAATCCTACTACAAGAGGTACCAGGTCAAGTACCGCCGCCGAAGAGgtaacgattt ... cgcttcatagAGGGCAAGACCGATTATCGGGCTCGGGTGCGCTTGACGAATCAGGACAAGA
EST: gi|169110842|gb|FE509325.1|FE509325
EST:     ATCCAAATCCTACTACAAGAGGTACCAGGTCAAGTACCGCCGCCGAAGAG                         AGGGCAAGACCGATTATCGGGCTCGGGTGCGCTTGACGAATCAGGACAAGA
genomic: ATCCAAATCCTACTACAAGAGGTACCAGGTCAAGTACCGCCGCCGAAGAGgtaacgattt ... cgcttcatagAGGGCAAGACCGATTATCGGGCTCGGGTGCGCTTGACGAATCAGGACAAGA
EST: gi|169039069|gb|FE448785.1|FE448785
EST:     ATCCAAATCCTACTACAAGAGGTACCAGGTCAAGTACCGCCGCCGAAGAG                         AGGGCAAGACCGATTATCGGGCTCGGGTGCGCTTGACGAATCAGGACAAGA
genomic: ATCCAAATCCTACTACAAGAGGTACCAGGTCAAGTACCGCCGCCGAAGAGgtaacgattt ... cgcttcatagAGGGCAAGACCGATTATCGGGCTCGGGTGCGCTTGACGAATCAGGACAAGA
EST: gi|70670052|gb|DN838629.1|DN838629
EST:     ATCCAAATCCTACTACAAGAGGTACCAGGTCAAGTACCGCCGCCGAAGAG                         AGGGCAAGACCGATTATCGGGCTCGGGTGCGCTTGACGAATCAGGACAAGA
genomic: ATCCAAATCCTACTACAAGAGGTACCAGGTCAAGTACCGCCGCCGAAGAGgtaacgattt ... cgcttcatagAGGGCAAGACCGATTATCGGGCTCGGGTGCGCTTGACGAATCAGGACAAGA
EST: gi|169106956|gb|FE508839.1|FE508839
EST:     ATCCAAATCCTACTACAAGAGGTACCAGGTCAAGTACCGCCGCCGAAGAG                         AGGGCAAGACCGATTATCGGGCTCGGGTGCGCTTGACGAATCAGGACAAGA
genomic: ATCCAAATCCTACTACAAGAGGTACCAGGTCAAGTACCGCCGCCGAAGAGgtaacgattt ... cgcttcatagAGGGCAAGACCGATTATCGGGCTCGGGTGCGCTTGACGAATCAGGACAAGA
EST: gi|169041727|gb|FE449298.1|FE449298
EST:     ATCCAAATCCTACTACAAGAGGTACCAGGTCAAGTACCGCCGCCGAAGAG                         AGGGCAAGACCGATTATCGGGCTCGGGTGCGCTTGACGAATCAGGACAAGA
genomic: ATCCAAATCCTACTACAAGAGGTACCAGGTCAAGTACCGCCGCCGAAGAGgtaacgattt ... cgcttcatagAGGGCAAGACCGATTATCGGGCTCGGGTGCGCTTGACGAATCAGGACAAGA
EST: gi|169033527|gb|FE442079.1|FE442079
EST:     ATCCAAATCCTACTACAAGAGGTACCAGGTCAAGTACCGCCGCCGAAGAG                         AGGGCAAGACCGATTATCGGGCTCGGGTGCGCTTGACGAATCAGGACAAGA
genomic: ATCCAAATCCTACTACAAGAGGTACCAGGTCAAGTACCGCCGCCGAAGAGgtaacgattt ... cgcttcatagAGGGCAAGACCGATTATCGGGCTCGGGTGCGCTTGACGAATCAGGACAAGA

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: 65

GCAGTCGCCAGGGCGCAGAAATCCAAATCCTACTACAAGAGGTACCAGGTCAAGTACCGCCGCCGAAGAGgtaacgattt ... cgcttcatagAGGGCAAGACCGATTATCGGGCTCGGGTGCGCTTGACGAATCAGGACAAGAACAAATACAACACACCGAAGTACCGATTCGTCGTTCGCTTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaacgatttggattcttggagcttgaaatttcacatttctcttcgcttcatagAGGGCAAGACCGATTATCGGGCTCGGGTGCGCTTGACGAATCAGGACAAGAACAAATACAACACACCGAAGTACCGATTCGTCGTTCGCTTT
                              tttcacatttctcttc  CT-rich tract
                        ttgaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacgatttggattcttggagcttgaaatttcacatttctcttcgcttcatagAGGGCAAGACCGATTATCGGGCTCGGGTGCGCTTGACGAATCAGGACAAGAACAAATACAACACACCGAAGTACCGATTCGTCGTTCGCTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC