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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtgcctacgtgtttttcttgccttttcttttctctcaacttttgattttcagATCCAACGTATATGATCCGAGCAATCCGGAGCAACGCCTCGGACAATGTCTACTGCACTCTACTCGCTCACAGTGCGATCCACGGAGCAATGGCTGGCTA

Basic information

species Selaginella moellendorffii
transcript EFJ21599
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ21599 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: LOC_Os01g53680.1 (Oryza sativa), 3'ss of exon 12
---------------------------------------------------------------------gtcagtgcctacgtgtttttcttgccttttcttttctctcaacttttgatttt------cagATCCAACGTATATGATCCGAGCAATCCGGAGCAACGCCTCGGACAATGTCTACTGCACTCTACTCGCTCACAGTGCGATCCACGGAGCAATGGCTGGCTA
                                                                      |  ||  ||  || | |  ||      |  |    |  || | | | ||||       |||||||||| || |||||||| ||||| |  ||||| || || ||||||||||||||||| || || || |||||||| || || || ||||||||||| ||
gtaaagatcttgtttttatgttcaattctcgatgcacatgcggagtgctagtttgaagtactactttttatatgtatctgagtatctccctatggaatgttgcaataacagcctgttatttctaatggcagATCCAACCTACATGATCCGTGCAATTCCAAGCAATGCATCAGACAATGTCTACTGCACACTGCTGGCGCACAGTGCCATTCATGGGGCAATGGCTGGATA

upper sequence: EFJ21599 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: LOC_Os05g44922.1 (Oryza sativa), 3'ss of exon 12
-------------------------------------gtcagtgcctacgtgtttttcttgccttttctttt----ctctcaacttttgattttcagATCCAACGTATATGATCCGAGCAATCCGGAGCAACGCCTCGGACAATGTCTACTGCACTCTACTCGCTCACAGTGCGATCCACGGAGCAATGGCTGGCTA
                                          |   |||  || | | |||   |   || |     || | | | || |||| ||||||| || || ||||||||||| || |  ||||| || || ||||||||||||||||| || || || |||||||| || || || |||||||| |||||
gtaactatgtttgcttcacacaggataaggttgttacacatcttattactggtctctattgtactaagttgtgaagttccctattatt-atttgcagATCCTACCTACATGATCCGAGCTATTCCAAGCAATGCATCAGACAATGTCTACTGCACGCTGCTGGCCCACAGTGCTATTCATGGTGCAATGGCCGGCTA

upper sequence: EFJ21599 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 12
-------------gtcagtgcc-tacgtgtttttc--------ttgccttt-tcttttctctcaacttttgat------tttcagATCCAACGTATATGATCCGAGCAATCCGGAGCAACGCCTCGGACAATGTCTACTGCACTCTACTCGCTCACAGTGCGATCCACGGAGCAATGGCTGGCTA
                 ||  | | | || ||| |        ||||     ||   | |||||  |  || |       | ||||||||||||| ||||| || || || |  ||||||||||| || |||||||||||||| || || |||||||||| | |||| ||||| |||||||| ||
gtcagtgattttctctggtatcatgcttgctttacggcaagaattgctagcatcaaatatctcagatgctgttatcctactgcagATCCAACGTACATGATACGTGCCATTCCTAGCAACGCCTCTGATAATGTCTACTGCACACTGCTAGCTCACAGTGTGGTCCATGGAGCCATGGCTGGATA

upper sequence: EFJ21599 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: GLYMA01G00870.1 (Glycine max), 3'ss of exon 11
-----------------------------gtcagtgcctacgtgtt-----------tttcttgccttttcttttctctcaacttttgattttcagATCCAACGTATATGATCCGAGCAATCCGGAGCAACGCCTCGGACAATGTCTACTGCACTCTACTCGCTCACAGTGCGATCCACGGAGCAATGGCTGGCTA
                              |  |||   ||    |           |  ||       |  |  ||      || || ||| |||||||||| |||||||||||||| || |  ||||| ||||| ||||| || |||||||| || || ||||| |||||  | || ||||||||||| || ||
gtttgtaaagattaaaagttcatggaattatgtgtgtacacacactgaaaggagcaatggctgaaagagtaatgccttctcttttctgttttacagATCCAACCTATATGATCCGAGCTATTCCAAGCAATGCCTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCAGTTCATGGAGCAATGGCAGGTTA

upper sequence: EFJ21599 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: GLYMA08G03570.1 (Glycine max), 3'ss of exon 11
----------------------------------------------------------------------gt-cagtgcctac------gtgtttttcttgccttttcttttctctcaacttttgattttcagATCCAACGTATATGATCCGAGCAATCCGGAGCAACGCCTCGGACAATGTCTACTGCACTCTACTCGCTCACAGTGCGATCCACGGAGCAATGGCTGGCTA
                                                                      || || ||| |||      | |    ||  || ||   |||| | | |   |||||    |||||||||||||||||||||||||| | |  ||||| || || ||||| || |||||||| || || ||||| |||||  | || ||||| ||||| || ||
gttcgtaaagacaaaaaactatatatttatacgtatgtgtacatgtgtgcatgttcgattacatttatgtgtgcattgcatactgaaaggaggaaatcaagcattgcatttttttttactatttga----cagATCCAACGTATATGATCCGAGCAGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCTGTTCATGGAGCCATGGCAGGTTA

upper sequence: EFJ21599 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: AT5G61580.1 (Arabidopsis thaliana), 3'ss of exon 11
---------------------------------gtcagtgcctacgtgtttttcttgccttttcttttctctcaacttttgattttcagATCCAACGTATATGATCCGAGCAATCCGGAGCAACGCCTCGGACAATGTCTACTGCACTCTACTCGCTCACAGTGCGATCCACGGAGCAATGGCTGGCTA
                                   ||     ||    | ||   ||| |||  ||  |    |  | ||||    |||| ||||||||||||||  ||||||| | ||| ||||| || ||||||||||| |||||||| || || || |||||  | || |||||||||||||| ||
gtatatcttcagactcactgtctctatcttgttaacaacagttaacactcttctgtgcatttcattgacatgtacttgttgaa---cagACCCAACGTATATGATAAGAGCAATACCGAGTAACGCATCAGACAATGTCTATTGCACTCTTCTTGCCCAAAGTGCAGTTCATGGAGCAATGGCTGGGTA

upper sequence: EFJ21599 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: PP1S282_45V6.1 (Physcomitrella patens), 3'ss of exon 12
---------------------------------------------------------------------------------------------------gtcagtgcctacgtgtttttcttgcctttt------cttttctctcaacttttgattttcagATCCAACGTATATGATCCGAGCAATCCGGAGCAACGCCTCGGACAATGTCTACTGCACTCTACTCGCTCACAGTGCGATCCACGGAGCAATGGCTGGCTA
                                                                                                    |     | | | || |  |||||| ||        ||  ||  |   |  | | | | ||||||| ||||||||||| |||||||| |  ||||| || ||||||||||||||||||||  | || ||||| || || ||||| || || ||||| || ||
gtacagtagccgtcaactgttctaactgttgagtgatggtgatccgtcttcctggtctacatctgtcgattttttacactgtggggaattgcttacattctggccacgtccatggtgatcttgcattcgataagactgctcattatgccatagttctgcagATCCGACGTATATGATTCGAGCAATTCCAAGCAATGCTTCGGACAATGTCTACTGCACATTGCTGGCTCATAGCGCCATCCATGGGGCTATGGCAGGGTA

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|169087233|gb|FE495715.1|FE495715
EST:     GACCACTTCACCGAGAAGAAGGAGATCATCAACCTCAAGTACATTG                         ATCCAACGTATATGATCCGAGCAATCCGGAGCAACGCCTCGGACAATGTCT
genomic: GACCACTTCACCGAGAAGAAGGAGATCATCAACCTCAAGTACATTGgtcagtgcct ... tgattttcagATCCAACGTATATGATCCGAGCAATCCGGAGCAACGCCTCGGACAATGTCT
EST: gi|169028987|gb|FE438127.1|FE438127
EST:     GACCACTTCACCGAGAAGAAGGAGATCATCAACCTCAAGTACATTG                         ATCCAACGTATATGATCCGAGCAATCCGGAGCAACGCCTCGGACAATGTTT
genomic: GACCACTTCACCGAGAAGAAGGAGATCATCAACCTCAAGTACATTGgtcagtgcct ... tgattttcagATCCAACGTATATGATCCGAGCAATCCGGAGCAACGCCTCGGACAATGTCT
EST: gi|169018790|gb|FE426767.1|FE426767
EST:     GACCACTTCACCGAGAAGAAGGAGATCATCAACCTCAAGTACATTG                         ATCCAACGTATATGATCCGAGCAATCCGGAGCAACGCCTCGGACAATGTCT
genomic: GACCACTTCACCGAGAAGAAGGAGATCATCAACCTCAAGTACATTGgtcagtgcct ... tgattttcagATCCAACGTATATGATCCGAGCAATCCGGAGCAACGCCTCGGACAATGTCT
EST: gi|169088819|gb|FE492836.1|FE492836
EST:     GACCACTTCACCGAGAAGAAGGAGATCATCAACCTCAAGTACATTG                         ATCCAACGTATATGATCCGAGCAATCCGGAGCAACGCCTCGGACAATGTCT
genomic: GACCACTTCACCGAGAAGAAGGAGATCATCAACCTCAAGTACATTGgtcagtgcct ... tgattttcagATCCAACGTATATGATCCGAGCAATCCGGAGCAACGCCTCGGACAATGTCT
EST: gi|169088818|gb|FE492835.1|FE492835
EST:     GACCACTTCACCGAGAAGAAGGAGATCATCAACCTCAAGTACATTG                         ATCCAACGTATATGATCCGAGCAATCCGGAGCAACGCCTCGGACAATGTCT
genomic: GACCACTTCACCGAGAAGAAGGAGATCATCAACCTCAAGTACATTGgtcagtgcct ... tgattttcagATCCAACGTATATGATCCGAGCAATCCGGAGCAACGCCTCGGACAATGTCT

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), 34 (downstream exon)
Score: 30

GACCACTTCACCGAGAAGAAGGAGATCATCAACCTCAAGTACATTGgtcagtgcct ... tgattttcagATCCAACGTATATGATCCGAGCAATCCGGAGCAACGCCTCGGACAATGTCTACTGCACTCTACTCGCTCACAGTGCGATCCACGGAGCAATGGCTGGCTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcagtgcctacgtgtttttcttgccttttcttttctctcaacttttgattttcagATCCAACGTATATGATCCGAGCAATCCGGAGCAACGCCTCGGACAATGTCTACTGCACTCTACTCGCTCACAGTGCGATCCACGGAGCAATGGCTGGCTA
                                          ttttgat  putative branch site (score: 30)
              tttttcttgccttttc  CT-rich tract
                                          ttttgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtgcctacgtgtttttcttgccttttcttttctctcaacttttgattttcagATCCAACGTATATGATCCGAGCAATCCGGAGCAACGCCTCGGACAATGTCTACTGCACTCTACTCGCTCACAGTGCGATCCACGGAGCAATGGCTGGCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA