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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcgtaatgtccatattctatcctagtatagttacgtttttctgtgttttcttagAGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTCGTCCCGTATGGAGTCTGGCAATGGCAACGGGGACAGTGAAGTGCAGAGA

Basic information

species Selaginella moellendorffii
transcript EFJ20576
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ04162 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GLYMA08G24000.1 (Glycine max), 3'ss of exon 5
-----------------------------------------gtatcgtaatgtccatattctatcctagtatagttacgtt-tttctgtgtt-ttcttagAGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTCGTCCCGTATGGAGTCTGGCAATGGCAACGGGGACAGTGAAGTGCAGAGA
                                         |  | |      |  |||| |||   | |||  ||| |       ||| || |||  || || ||||||||||| |||||||| |||||||| |||||||| ||||| ||  | || ||||| ||||| | |||||| || || ||||| || ||| | 
ttgcttaactttttgattcattaattttcatgttatttggagacttgcctaaccattattatatatgaatattattatggaacacttgtcttcttcccagGGAACATGCTCCATCAATTATCTTCATGGACGAAATTGACAGTATTGGATCTGCTCGGATGGAATCTGGAAGTGGCAATGGTGATAGTGAGGTACAGCGT

upper sequence: EFJ04162 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 5
-----------------------------------------gtatcgtaatgtccatattctatcctagtatagttacgtttttctgtgttttctt---agAGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTCGTCCCGTATGGAGTCTGGCAATGGCAACGGGGACAGTGAAGTGCAGAGA
                                         |  | |      |  |||| |||   | |||  | | |     || ||| |||||   || || ||||||||||| |||||||| ||||| || |||||||| ||||| ||  | || ||||| ||||| | ||||||||| || ||||| || ||| | 
aactttttgattcattaattttcatgtttatgttatttggagccttgcctaaccattattatatatgaatattatcatggaacact-tgtcttcttcacagGGAACATGCTCCATCAATTATCTTCATGGATGAAATTGACAGTATTGGATCTGCTCGGATGGAATCTGGAAGTGGCAACGGTGATAGTGAGGTACAGCGT

upper sequence: EFJ04162 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 5
--------------------------------------gtatcgtaatgtccatatt-ctatcctagtatagttacgttttt---ctgtgttttct-tagAGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTCGTCCCGTATGGAGTCTGGCAATGGCAACGGGGACAGTGAAGTGCAGAGA
                                        ||  |  | ||  | || || |     || | ||   |||||   || | |||  |  || |||||||| ||||| || ||||||||||| ||||||||||| ||||| ||  | |||||||| || || | |||||| || || |||||||| ||| | 
gtagagcccatcatcaacaataacaaaaaggaaaaaaaaaatgttgctttctttgttgctgtttgtttaaactttactttttgaactatctttcttacagGGAGCATGCACCATCAATAATCTTTATGGATGAGATTGACAGTATTGGATCTGCTCGTATGGAATCAGGAAGTGGCAATGGTGATAGTGAAGTCCAGCGG

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|169037547|gb|FE446288.1|FE446288
EST:     TACATCGGAGAAGGGTCGAGGATGGTGCGAGAGCTTTTCGTCATGGCAAG                         AGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTC
genomic: TACATCGGAGAAGGGTCGAGGATGGTGCGAGAGCTTTTCGTCATGGCAAGgtatcgtaat ... gttttcttagAGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTC
EST: gi|169065602|gb|FE475882.1|FE475882
EST:     TACATCGGAGAAGGGTCGAGGATGGTGCGAGAGCTTTTCGTCATGGCAAG                         AGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTC
genomic: TACATCGGAGAAGGGTCGAGGATGGTGCGAGAGCTTTTCGTCATGGCAAGgtatcgtaat ... gttttcttagAGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTC
EST: gi|169094801|gb|FE492952.1|FE492952
EST:     TACATCGGAGAAGGGTCGAGAATGGTGCGAGAGCTNTTCGTCATGGCAAG                         AGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTC
genomic: TACATCGGAGAAGGGTCGAGGATGGTGCGAGAGCTTTTCGTCATGGCAAGgtatcgtaat ... gttttcttagAGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTC
EST: gi|169071822|gb|FE478109.1|FE478109
EST:     TACATCGGAGAAGGGTCGAGAATGGTGCGAGAGCTTTTCGTCATGGCAAG                         AGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTC
genomic: TACATCGGAGAAGGGTCGAGGATGGTGCGAGAGCTTTTCGTCATGGCAAGgtatcgtaat ... gttttcttagAGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTC
EST: gi|169062819|gb|FE472348.1|FE472348
EST:     TACATCGGAGAAGGGTCGAGAATGGTGCGAGAGCTTTTCGTCATGGCAAG                         AGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTC
genomic: TACATCGGAGAAGGGTCGAGGATGGTGCGAGAGCTTTTCGTCATGGCAAGgtatcgtaat ... gttttcttagAGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTC
EST: gi|169113190|gb|FE514436.1|FE514436
EST:     TACATCGGAGAAGGGTCGAGAATGGTGCGAGAGCTTTTCGTCATGGCAAG                         AGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTC
genomic: TACATCGGAGAAGGGTCGAGGATGGTGCGAGAGCTTTTCGTCATGGCAAGgtatcgtaat ... gttttcttagAGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTC
EST: gi|169062833|gb|FE472349.1|FE472349
EST:     TACATCGGAGAAGGGTCGAGAATGGTGCGAGAGCTTTTCGTCATGGCAAG                         AGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTC
genomic: TACATCGGAGAAGGGTCGAGGATGGTGCGAGAGCTTTTCGTCATGGCAAGgtatcgtaat ... gttttcttagAGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTC
EST: gi|169039782|gb|FE449444.1|FE449444
EST:     TACATCGGAGAAGGGTCGAGAATGGTGCGAGAGCTTTTCGTCATGGCAAG                         AGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTC
genomic: TACATCGGAGAAGGGTCGAGGATGGTGCGAGAGCTTTTCGTCATGGCAAGgtatcgtaat ... gttttcttagAGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTC
EST: gi|169065603|gb|FE475883.1|FE475883
EST:     TACATCGGAGAAGGGTCGAGGATGGTGCGAGAGCTTTTCGTCATGGCAAG                         AGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTC
genomic: TACATCGGAGAAGGGTCGAGGATGGTGCGAGAGCTTTTCGTCATGGCAAGgtatcgtaat ... gttttcttagAGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTC
EST: gi|169094802|gb|FE492953.1|FE492953
EST:     TACATCGGAGAAGGGTCGAGAATGGTGCGAGAGCTTTTCGTCATGGCAAG                         AGAGCATGCTCCATCCATTATNCTT-ATGGACGAGATTGACAGCATTGGCT
genomic: TACATCGGAGAAGGGTCGAGGATGGTGCGAGAGCTTTTCGTCATGGCAAGgtatcgtaat ... gttttcttagAGAGCATGCTCCATCCATTAT-CTTTATGGACGAGATTGACAGCATTGGCT
EST: gi|169113973|gb|FE516444.1|FE516444
EST:     TACATCGGAGAAGGGTCGAGAATGGTGCGAGAGCTTTTCGTCATGGCAAG                         AGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTC
genomic: TACATCGGAGAAGGGTCGAGGATGGTGCGAGAGCTTTTCGTCATGGCAAGgtatcgtaat ... gttttcttagAGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTC
EST: gi|169038427|gb|FE446128.1|FE446128
EST:     TACATCGGAGAAGGGTCGAGGATGGTGCGAGAGCTTTTCGTCATGGCAAG                         AGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTC
genomic: TACATCGGAGAAGGGTCGAGGATGGTGCGAGAGCTTTTCGTCATGGCAAGgtatcgtaat ... gttttcttagAGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTC
EST: gi|169055186|gb|FE461060.1|FE461060
EST:     TACATCGGAGAAGGGTCGAGAATGGTGCGAGAGCTNTTCGTCATGGCAAG                         AGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTC
genomic: TACATCGGAGAAGGGTCGAGGATGGTGCGAGAGCTTTTCGTCATGGCAAGgtatcgtaat ... gttttcttagAGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTC
EST: gi|169071823|gb|FE478110.1|FE478110
EST:     TACATCGGAGAAGGGTCGAGAATGGTGCGAGAGCTTTTCGTCATGGCAAG                         AGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTC
genomic: TACATCGGAGAAGGGTCGAGGATGGTGCGAGAGCTTTTCGTCATGGCAAGgtatcgtaat ... gttttcttagAGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTC
EST: gi|169037548|gb|FE446289.1|FE446289
EST:     TACATCGGAGAAGGGTCGAGGATGGTGCGAGAGCTTTTCGTCATGGCAAG                         AGAGCATGCTCCATCCATTATCTTTAT
genomic: TACATCGGAGAAGGGTCGAGGATGGTGCGAGAGCTTTTCGTCATGGCAAGgtatcgtaat ... gttttcttagAGAGCATGCTCCATCCATTATCTTTAT
EST: gi|169113189|gb|FE514435.1|FE514435
EST:     TACATCGGAGAAGGGTCGAGAATGGTGCGAGAGCTTTTCGTCATGGCAAG                         AGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTC
genomic: TACATCGGAGAAGGGTCGAGGATGGTGCGAGAGCTTTTCGTCATGGCAAGgtatcgtaat ... gttttcttagAGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTC

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), 31 (downstream exon)
Score: 23

ATACTGACTGTACATTCATAAGAGTTTCAGGGTCCGAGCTAGTCCAGAAATACATCGGAGAAGGGTCGAGGATGGTGCGAGAGCTTTTCGTCATGGCAAGgtatcgtaat ... gttttcttagAGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTCGTCCCGTATGGAGTCTGGCAATGGCAACGGGGACAGTGAAGTGCAGAGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcgtaatgtccatattctatcctagtatagttacgtttttctgtgttttcttagAGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTCGTCCCGTATGGAGTCTGGCAATGGCAACGGGGACAGTGAAGTGCAGAGA
                                    tttttctgtgttttct  CT-rich tract
            atattctat  TA-rich tract