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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcttgtgttttactgaatttctcaataaccatctccgtgcagAGAATGGGAAAATCGGTCATGTAAATCAAGGCAACAATATGTACCTTTTCCCAGG

Basic information

species Selaginella moellendorffii
transcript EFJ21048
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ21048 (Selaginella moellendorffii), 3'ss of exon 14
lower sequence: GLYMA09G39870.1 (Glycine max), 3'ss of exon 14
---------------------------------------------------------------------------------------------------------------------------gtaatcttgtgttttactg-aatttctcaataaccatctccgtgcagAGAATGGGAAAATCGGTCATGTAAATCAAGGCAACAATATGTACCTTTTCCCAGG
                                                                                                                             ||| || |||||||    ||  ||  ||| |  || |  || |||  |||||  || | || ||||||||||||| |||||| |||||||| ||||||||
gtaattgccacttcgtaatatgattcattggttttgaagtatcctgtctagttcgaactttcttcagctatggaggctttattataggatgaatcttgttgctatatagtttcattgttcatttcaatattatgttttaacacaacctccaaatga--atttttgtacagGAAATGGAGAAGTTGGCCATGTAAATCAAGCCAACAACATGTACCTGTTCCCAGG

upper sequence: EFJ21048 (Selaginella moellendorffii), 3'ss of exon 14
lower sequence: GLYMA07G08110.1 (Glycine max), 3'ss of exon 14
------------------------------------------------gtaatcttgtgttttactgaatttctcaataaccatctccgtgcagAGAATGGGAAAATCGGTCATGTAAATCAAGGCAACAATATGTACCTTTTCCCAGG
                                                 |   ||   |||||   |||| | |  ||    || |  ||||||  ||||| |   | ||||||||||||||||  ||||| |||||||| ||||||||
gtaactattaccactttctttggttttgaagtatcttctataattctattttcctcaggttttgaagaatctattgatttaaatttt-gtgcagGTAATGGAATTGTGGGTCATGTAAATCAAGCAAACAACATGTACCTCTTCCCAGG

upper sequence: EFJ21048 (Selaginella moellendorffii), 3'ss of exon 14
lower sequence: GLYMA03G01680.1 (Glycine max), 3'ss of exon 14
--------------------------------------------gtaatcttgtgttttactgaatttctcaataacc----------atctccgtgcagAGAATGGGAAAATCGGTCATGTAAATCAAGGCAACAATATGTACCTTTTCCCAGG
                                            |||   || | |||| || | ||| | || || |          |  |  ||||||  ||||| ||| | ||||||||||||||||  ||||| |||||||| ||||||||
taactaattaccatttaccactttctttggttttgaagtatcttgtataattctattttcctcagtttttgaagaatctattgatttaaattttgtgcagGTAATGGAAAAGTGGGTCATGTAAATCAAGCAAACAACATGTACCTCTTCCCAGG

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|169073337|gb|FE481101.1|FE481101
EST:     AGATCACATTATCTTTGCAAGTGGAAGTCCTTTTGATGACGTGAAACTTG                         AGAATGGGAAAATCGGTCATGTAAATCAAGGCAACAATATGTACCTTTTCC
genomic: AGATCACATTATCTTTGCAAGTGGAAGTCCTTTTGATGACGTGAAACTTGgtaatcttgt ... ctccgtgcagAGAATGGGAAAATCGGTCATGTAAATCAAGGCAACAATATGTACCTTTTCC
EST: gi|169094681|gb|FE492494.1|FE492494
EST:     CAAGTGAAAGTCCTTTTGATGACGTGAAACTTG                         AGAATGGGAAAATCGGTCATGTAAATCAAGGCAACAATATGTACCTTTTCC
genomic: CAAGTGGAAGTCCTTTTGATGACGTGAAACTTGgtaatcttgt ... ctccgtgcagAGAATGGGAAAATCGGTCATGTAAATCAAGGCAACAATATGTACCTTTTCC
EST: gi|169056283|gb|FE464106.1|FE464106
EST:     AGATCACATTATCTTTGCAAGTGGAAGTCCTTTTGATGACGTGAAACTTG                         AGAATGGGAAAATCGGTCATGTAAATCAAGGCAACAATATGTACCTTTTCC
genomic: AGATCACATTATCTTTGCAAGTGGAAGTCCTTTTGATGACGTGAAACTTGgtaatcttgt ... ctccgtgcagAGAATGGGAAAATCGGTCATGTAAATCAAGGCAACAATATGTACCTTTTCC
EST: gi|169088830|gb|FE494394.1|FE494394
EST:     AGATCACATTATCTTTGCAAGTGGAAGTCCTTTTGATGACGTGAAACTTG                         AGAATGGGAAAATCGGTCATGTAAATCAAGGCAACAATATGTACCTTTTCC
genomic: AGATCACATTATCTTTGCAAGTGGAAGTCCTTTTGATGACGTGAAACTTGgtaatcttgt ... ctccgtgcagAGAATGGGAAAATCGGTCATGTAAATCAAGGCAACAATATGTACCTTTTCC
EST: gi|169022197|gb|FE431806.1|FE431806
EST:     AGATCACATTATCTTTGCAAGTGGAAGTCCTTTTGATGACGTGAAACTTG                         AGAATGGGAAAATCGGTCATGTAAATCAAGGCAACAATATGTACCTTTTCC
genomic: AGATCACATTATCTTTGCAAGTGGAAGTCCTTTTGATGACGTGAAACTTGgtaatcttgt ... ctccgtgcagAGAATGGGAAAATCGGTCATGTAAATCAAGGCAACAATATGTACCTTTTCC
EST: gi|169026051|gb|FE434468.1|FE434468
EST:     AGATCACATTATCTTTGCAAGTGGAAGTCCTTTTGATGACGTGAAACTTG                         AGAATGGGAAAATCGGTCATGTAAATCAAGGCAACAATATGTACCTTTTCC
genomic: AGATCACATTATCTTTGCAAGTGGAAGTCCTTTTGATGACGTGAAACTTGgtaatcttgt ... ctccgtgcagAGAATGGGAAAATCGGTCATGTAAATCAAGGCAACAATATGTACCTTTTCC

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: 28 (upstream exon), 34 (downstream exon)
Score: 19

CTGAATGCACAGCAGAAGAAGCATTTAAGCATGTGGGAGATCACATTATCTTTGCAAGTGGAAGTCCTTTTGATGACGTGAAACTTGgtaatcttgt ... ctccgtgcagAGAATGGGAAAATCGGTCATGTAAATCAAGGCAACAATATGTACCTTTTCCCAGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaatcttgtgttttactgaatttctcaataaccatctccgtgcagAGAATGGGAAAATCGGTCATGTAAATCAAGGCAACAATATGTACCTTTTCCCAGG
                                   caataac  putative branch site (score: 19)
                                         ccatctcc  CT-rich tract
          taatctt  TA-rich tract