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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaagtggtgtttccattgatcgcttgaaaatgctgattctgatctcttcccttgcagGATTCTGGGACATGTATGACCCCGAGGGATACTCCCTGTGGTTCTGCGACTACAAGTACAACGATGAGAACACGGTGCCTTTCGTGACGATGAACAAGGT

Basic information

species Selaginella moellendorffii
transcript EFJ26267
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ26267 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: LOC_Os06g37440.1 (Oryza sativa), 3'ss of exon 7
------------------------------------------gtacaagtggtgtttccattgatcgcttgaaaatgctgattctgatctcttcccttgcagGATTCTGGGACATGTATGACCCCGAGGGATACTCCCTGTGGTTCTGCGACTACAAGTACAACGATGAGAACACGGTGCCTTTCGTGACGATGAACAAGGT
                                           |  |     | ||    ||  |   || | |  |   ||| | |  |||    || |||| |||||||||||||||||||| ||||| ||||| ||||||||||| |||||||||||||||||||||||||| ||  | || |||||||||||||||||
cttcttgttacaattttagcaatatatttaggcatgaacttaatttattccattttcttgtttttgaattaacagagac-attatcacgtctattttt-cagGTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACTACAAGTACAACGATGAGAACACCGTATCGTTTGTGACGATGAACAAGGT

upper sequence: EFJ26267 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: LOC_Os02g12800.1 (Oryza sativa), 3'ss of exon 7
----------------------------------gtac-aagtggtgtttccattgatcgcttgaaaatgctgattctgatctcttccc-----ttgcagGATTCTGGGACATGTATGACCCCGAGGGATACTCCCTGTGGTTCTGCGACTACAAGTACAACGATGAGAACACGGTGCCTTTCGTGACGATGAACAAGGT
                                    || || |  ||||    |||| |   ||  |||  |  |   | | ||||| |     ||||||| |||||||| ||||||||||| || || |||||||||||||||||||||||||| ||||| ||||||||||| ||| | |||||||| |||||||||||
ttagttctctcttctacaccattatttctcatctacaccaacttctgttgagtttgaactgctgtgaattgtactcaagttatcttctcatgtattgcagGTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTCTGCGACTACAAATACAATGATGAGAACACCGTGTCCTTCGTGACCATGAACAAGGT

upper sequence: EFJ26267 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: LOC_Os02g12794.3 (Oryza sativa), 3'ss of exon 6
-----------------------------------gtacaagtggtgtttccattgatcgcttgaaaatgctgattctgatctcttccc-----ttgcagGATTCTGGGACATGTATGACCCCGAGGGATACTCCCTGTGGTTCTGCGACTACAAGTACAACGATGAGAACACGGTGCCTTTCGTGACGATGAACAAGGT
                                      ||| |  ||||     |||     ||  |||     |    || ||||| |     ||||||| |||||||| ||||||||||| || || |||||||||||||| || |||||||| ||||| || |||||||| ||| | |||||||| |||||||||||
ttatatctctttgattaccattatttgtcatctgctcccaacttctgttgtgtatgaagttctgtgaattgaactcaacatgtcttctcacttattgcagGTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTTTGTGACTACAAATACAATGACGAGAACACTGTGTCCTTCGTGACCATGAACAAGGT

upper sequence: EFJ26267 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GRMZM2G029559_T02 (Zea mays), 3'ss of exon 7
-----------------------gtacaagtggtgtttccattgatcgcttgaaaatgctgatt---------ctgatctc--ttcccttg------cagGATTCTGGGACATGTATGACCCCGAGGGATACTCCCTGTGGTTCTGCGACTACAAGTACAACGATGAGAACACGGTGCCTTTCGTGACGATGAACAAGGT
                       || |     || ||    ||||||  ||   | ||||             |||| |||   |||| ||      |||| |||||||||||||||||||| ||||| ||||||||||||||||| |||||||||||||| || |||||||| ||| | || ||||| |||||||||||
gcatttaaacaccccattaagcggttctcaaagttttgtttttgatctgttagtagtgctatgcacaagtcaactgaactcaactcccatgtattttcagGTTTCTGGGACATGTATGACCCAGAGGGCTACTCCCTGTGGTTCTGTGACTACAAGTACAATGACGAGAACACAGTGTCGTTTGTGACTATGAACAAGGT

upper sequence: EFJ26267 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GRMZM2G134582_T01 (Zea mays), 3'ss of exon 7
--------------------------------gtacaagt---ggtgtttccattg---atcgcttgaaaatgctgattctga--tctcttcccttgcagGATTCTGGGACATGTATGACCCCGAGGGATACTCCCTGTGGTTCTGCGACTACAAGTACAACGATGAGAACACGGTGCCTTTCGTGACGATGAACAAGGT
                                    ||||   | | | ||  | |   |  |   |||    ||||     |  |||| |   ||  ||| |||||||| ||||| ||||| ||||| ||||||||||||||||| |||||||||||||| ||||||||||| ||| | || ||||| |||||||||||
gtttggtatatctttttggtgttttaagcagttcctaagttttgatctgtcagtagtgcaatgtacgaaccaactgaactcaaactctcatgtattttagGTTTCTGGGATATGTACGACCCAGAGGGCTACTCCCTGTGGTTCTGTGACTACAAGTACAATGATGAGAACACAGTGTCGTTTGTGACCATGAACAAGGT

upper sequence: EFJ26267 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GRMZM2G059580_T03 (Zea mays), 3'ss of exon 5
------------------------------------gtacaagtggtgtttccattgat-cgcttg-aaaatgctgattc-tgatctcttccc-ttgcagGATTCTGGGACATGTATGACCCCGAGGGATACTCCCTGTGGTTCTGCGACTACAAGTACAACGATGAGAACACGGTGCCTTTCGTGACGATGAACAAGGT
                                    |     ||    ||||| ||     | |||   | |  |||    | |||  |     || |||| |||||||||||||||||||| ||||| ||||| ||||||||||| |||||||||||||| || |||||||| ||  | || |||||  ||||||||||
agagggagtactgcttgtaaattaattagctggatggcttgggtttcctttccttttccatgtttgtggagtcttgaccaataatccgtctatgtttcagGTTTCTGGGACATGTATGACCCAGAGGGCTACTCTCTGTGGTTCTGTGACTACAAGTACAATGACGAGAACACCGTCTCCTTTGTGACCCTGAACAAGGT

upper sequence: EFJ26267 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GRMZM2G122871_T02 (Zea mays), 3'ss of exon 6
------------------------------gtacaagtggtgtttccattgatcgcttgaaaatgctgattct-gatct---------cttcccttgcagGATTCTGGGACATGTATGACCCCGAGGGATACTCCCTGTGGTTCTGCGACTACAAGTACAACGATGAGAACACGGTGCCTTTCGTGACGATGAACAAGGT
                              | |    | |  ||||| ||    | |      ||  || ||| || ||           |   || |||| |||||||||||||| ||||| ||||| |||||  |||||||||| |||||||||||||| ||||||||||| ||  | || |||||  ||||||||||
ggcgtactgcaagcaaattaattgttagatgaattgcttggatttcctttccctgttcatgtttgtggactcttgacctagtaatccgtgtgtgtttcagGTTTCTGGGACATGTACGACCCAGAGGGCTACTCTTTGTGGTTCTGTGACTACAAGTACAATGATGAGAACACCGTCTCCTTTGTGACCCTGAACAAGGT

upper sequence: EFJ26267 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GRMZM2G122871_T03 (Zea mays), 3'ss of exon 6
-----------------------------------------------gtacaagtggtgtttccattgatcgcttgaaaatgctgattctgatctcttcccttgcagGATTCTGGGACATGTATGACCCCGAGG-GATACTCCCTGTGGTTCTGCGACTACAAGTACAACGATGAGAACACGGTGCCTTTCGTGACGATGAACAAGGT
                                                |   |     || ||| |||    | |||| | | |   |    ||      |     |   | ||   || ||| | |   | |  ||| |||    | |        | ||   |  | |     |  |   |   ||| |||| | | |        
cgacccagagggctactctttgtggttctgtgactacaagtacaatgatgagaacaccgtctcctttgtgaccctgaacaaggttggtggattcctgcagCGGATGGACCTGTGCCGCAAGTACGCCTTTGGGAAGATGCTCGTGATAGGCTCTGAGCCACCCTTCAAGCTGAAGGGCCTTTGGCTCTTCCGTGGCCAGG--------

upper sequence: EFJ26267 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GLYMA17G00470.4 (Glycine max), 3'ss of exon 6
--------------------------------------------------------------------------------------------------------------------gtacaagtggtgtttccattgatcgcttgaaaatgctgattctgatctcttcccttgcagGATTCTGGGACATGTATGACCCCGAGGGATACTCCCTGTGGTTCTGCGACTACAAGTACAACGATGAGAACACGGTGCCTTTCGTGACGATGAACAAGGT
                                                                                                                     |  ||    |  |  ||   |  | |   |  |  |       |  | ||  ||||||||||| |||||||||||||| |||||||||||||| || ||||| || || ||||| |||||||| ||||| || ||  |||| |||||  ||||||||||
gtattgtttttgtgtcccccctgtgggttcattgttttaaatgtttcctaaattaggattgtgattatagcctataatcattgcaaaattagttatgatgaatcttctctcagaattttaaaaaaattatgacacccagagttgagatctttttgaatccactttttatcttgcagGATTTTGGGACATGTATGATCCCGAGGGATACTCTCTCTGGTTTTGTGATTACAAATACAACGACGAGAATACTGTTTCTTTTGTGACATTGAACAAGGT

upper sequence: EFJ26267 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GLYMA16G00360.1 (Glycine max), 3'ss of exon 6
-------------------gtacaagtggtgtttccattgatcgcttgaaaatg---ctgattctgatctcttc--ccttgcagGATTCTGGGACATGTATGACCCCGAGGGATACTCCCTGTGGTTCTGCGACTACAAGTACAACGATGAGAACACGGTGCCTTTCGTGACGATGAACAAGGT
                    |   | || ||  |    ||||    || | ||     | || ||  ||  ||     |||||||||| ||||||||||| || || |||||||| || ||||||||||| || ||||| ||||| ||||||||||| ||  | || || ||| | ||||||||
gtataactattctattatgatggcaatgatggatatgatgatgagatgcacatcattttaatccttttccttttaattttgcagGATTTTGGGACATGTACGATCCAGAGGGATATTCTCTGTGGTTCTGTGATTACAAATACAATGATGAGAACACAGTTTCCTTTGTTACGTTAAACAAGGT

upper sequence: EFJ26267 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GLYMA12G28670.1 (Glycine max), 3'ss of exon 6
-----------------gtacaagtggtgtttccattgatcgcttgaaa-----atgctgattctgatctcttcccttgcagGATTCTGGGACATGTATGACCCCGAGGGATACTCCCTGTGGTTCTGCGACTACAAGTACAACGATGAGAACACGGTGCCTTTCGTGACGATGAACAAGGT
                  |     |||  |    ||     || ||  |     || ||  || | |  | |    |||||||||| ||||||||||| || || |||||||| || ||||||||||| || ||||| ||||| ||||||||| | ||  | || || ||  | ||||||||
gtatagctattcattctattatgatggcatggatatgagatgcatgtcattttaatcctccttttaaattttaattttgcagGATTTTGGGACATGTACGATCCAGAGGGATATTCTCTGTGGTTCTGTGATTACAAATACAATGATGAGAACTCAGTTTCCTTTGTTACATTAAACAAGGT

upper sequence: EFJ26267 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GLYMA07G40330.1 (Glycine max), 3'ss of exon 7
-------------------------------------------------------------------------------------------------------------------gtacaagtggtgtttccattgatcgcttgaaa--atgctgattctgatctcttcccttgcagGATTCTGGGACATGTATGACCCCGAGGGATACTCCCTGTGGTTCTGCGACTACAAGTACAACGATGAGAACACGGTGCCTTTCGTGACGATGAACAAGGT
                                                                                                                    |  ||    | | |  ||    |  |||| |   |  ||| ||  |  | ||  ||||||||||| |||||||||||||| |||||||||||||| || ||||| || || ||||| |||||  | ||||| || ||  |||| |||||  ||||||||||
gtattgtttttgtggcccctcgggctcgttgttttacatgtttcctaaattaggaatatgattatatgactataatcattgcaaaattagttattatgaatcttgcctcaaagaattttaaaaaatatat--atgacacagttgacatccttttgaatcc-actttttatcttgcagGATTTTGGGACATGTATGATCCCGAGGGATACTCTCTCTGGTTTTGTGATTACAAATACAATCAGGAGAATACTGTTTCTTTTGTGACATTGAACAAGGT

upper sequence: EFJ26267 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: AT1G09640.1 (Arabidopsis thaliana), 3'ss of exon 7
-------------------------------------------gtacaagtggtgttt--ccattg--atcgcttgaaaatgctgat-tctgatctcttccct----tgcagGATTCTGGGACATGTATGACCCCGAGGGATACTCCCTGTGGTTCTGCGACTACAAGTACAACGATGAGAACACGGTGCCTTTCGTGACGATGAACAAGGT
                                            |    |   | |||  | ||||  |||  |||    |  | || ||| || |  |  ||    ||||||||||||||||||||||||||| ||||||||||| || |||||||| ||||||||||||||||||||||||| |||| | || || ||| | ||||||||
gtgtgtggtgatatcttcctctacctagtttttcagctttgctatcagggaattatttagctattggaatcaattgttttttatcatgtctaatattgtggctcaaatgcagGATTCTGGGACATGTATGACCCAGAGGGATACTCACTATGGTTCTGTGACTACAAGTACAACGATGAGAACATGGTGTCATTTGTCACGCTCAACAAGGT

upper sequence: EFJ26267 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: AT1G57720.1 (Arabidopsis thaliana), 3'ss of exon 7
---------------------------------------------gtacaagtggtgtttccattgatcgcttgaaaatgctgattctgatctcttcccttgcagGATTCTGGGACATGTATGACCCCGAGGGATACTCCCTGTGGTTCTGCGACTACAAGTACAACGATGAGAACACGGTGCCTTTCGTGACGATGAACAAGGT
                                             ||   |  |    ||| ||| | | |     |||||      || | |  | | |||||||||||||||||||||||||||| ||||| ||||| || |||||||| ||||| ||||||||||||||||||| |||  | || || ||  | ||||||||
ttagaggggtactcactatggtttatgggacatgtatggcccagagtctgaaagtacattctattaagctc-----aatgccttgaatgtttttcttcattgcagGATTCTGGGACATGTATGACCCGGAGGGGTACTCACTATGGTTCTGTGACTATAAGTACAACGATGAGAACATGGTCTCCTTTGTTACACTCAACAAGGT

upper sequence: EFJ26267 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: Vv18s0041g01900.t01 (Vitis vinifera), 3'ss of exon 7
----------------------------gtacaagtggtgtttcca--ttgatcgcttgaaaatgctgattct---------gatctcttccc-ttgcagGATTCTGGGACATGTATGACCCCGAGGGATACTCCCTGTGGTTCTGCGACTACAAGTACAACGATGAGAACACGGTGCCTTTCGTGACGATGAACAAGGT
                             |  | || | || | ||  ||      ||  | |||||| ||           | ||||||    | |||||||| |||||||||||||| || ||||| ||||| || ||||||||||| ||||||||||| |||||||| || ||  | || |||||  ||||||||||
gcctgaagttcattcacaatttgaatgttttgatgtagggtattcagttttgcatgttccatatgctgttttcttcatcctcgttctctttttatggcagGATTTTGGGACATGTATGATCCTGAGGGCTACTCTCTCTGGTTCTGCGATTACAAGTACAATGATGAGAATACTGTCTCATTTGTGACTTTGAACAAGGT

upper sequence: EFJ26267 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: Vv12s0035g01130.t01 (Vitis vinifera), 3'ss of exon 7
-----------------------------------gtacaagtggtgtttcca---ttgatcgcttgaaa---atgctgattctgatctcttcccttgcagGATTCTGGGACATGTATGACCCCGAGGGATACTCCCTGTGGTTCTGCGACTACAAGTACAACGATGAGAACACGGTGCCTTTCGTGACGATGAACAAGGT
                                    |||   |  |  ||| |   || |    |||||    |   ||| | || ||  |     ||||||||||||||||||||| || |||||||||||||| || |||||||| || ||||| ||||| || ||||| || ||  | ||||| ||  ||||||||||
gcctagttgataagttgctatggttgctctgttttctacttctcattcttcaaggtttaaaactttgaagttcacaatgaatatgttca-tgattatgcagGATTCTGGGACATGTACGATCCCGAGGGATACTCTCTTTGGTTCTGTGATTACAAATACAATGACGAGAATACCGTCTCATTCGTAACTCTGAACAAGGT

upper sequence: EFJ26267 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: Vv12s0035g01120.t01 (Vitis vinifera), 3'ss of exon 3
-----------------------------------gtacaagtggtgtttcca---ttgatcgcttgaaa---atgctgattctgatctcttcccttgcagGATTCTGGGACATGTATGACCCCGAGGGATACTCCCTGTGGTTCTGCGACTACAAGTACAACGATGAGAACACGGTGCCTTTCGTGACGATGAACAAGGT
                                    |||   |  |  ||| |   || |    |||||    |   ||| | || ||  |     ||||||||||||||||||||| || |||||||||||||| || |||||||| || ||||| ||||| |  ||||| || ||  | ||||| ||  ||| ||||||
gcctagttgataagttgctatggttgctctgtttactacttctcattcttcaaggtttaaaactttgaagttcacaatgaatatgttca-tgattatgcagGATTCTGGGACATGTACGATCCCGAGGGATACTCTCTTTGGTTCTGTGATTACAAATACAATGCCGAGAATACCGTCTCATTCGTAACTCTGATCAAGGT

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|169109795|gb|FE513842.1|FE513842
EST:     GCTCTACTCCAACACCAAGGCCAAGGACTTCGCAGAAGTTGCTCTCAAAG                         GATTCTGGGACATGTATGACCCCGAGGGATACTCCCTGTGGTTCTGCGACT
genomic: GCTCTACTCCAACACCAAGGCCAAGGACTTCGCAGAAGTTGCTCTCAAAGgtacaagtgg ... tcccttgcagGATTCTGGGACATGTATGACCCCGAGGGATACTCCCTGTGGTTCTGCGACT




















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: 127

CCTCTCGACTTGCTGCCACCGAGTCCCATGGTTTTGGACGACTGGAAGAGGCTCTACTCCAACACCAAGGCCAAGGACTTCGCAGAAGTTGCTCTCAAAGgtacaagtgg ... tcccttgcagGATTCTGGGACATGTATGACCCCGAGGGATACTCCCTGTGGTTCTGCGACTACAAGTACAACGATGAGAACACGGTGCCTTTCGTGACGATGAACAAGGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtggtgtttccattgatcgcttgaaaatgctgattctgatctcttcccttgcagGATTCTGGGACATGTATGACCCCGAGGGATACTCCCTGTGGTTCTGCGACTACAAGTACAACGATGAGAACACGGTGCCTTTCGTGACGATGAACAAGGT
                                  ttctgat  putative branch site (score: 127)
                                  ttctgatctcttccct  CT-rich tract
                     ttgaaaat  TA-rich tract