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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttttttctttttcttttgttctttctttcttttctttttttgcaaagttggattttcattttttttgtttcttcacagACCATGGCTTGGATTCTGGATGAGTACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTT

Basic information

species Selaginella moellendorffii
transcript EFJ06181
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ06181 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: LOC_Os04g45970.1 (Oryza sativa), 3'ss of exon 3
gtttttttctttttcttttgttctttctttcttttctttttttgcaaagttggattttcattttttttgtttcttcacagACCATGGCTTGGATTCTGGATGAGTACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTT----
|| | ||    ||||| | ||  |||  | ||  | |   ||    | ||   ||   |  |  |||||      |||||||||||||||||||| ||||||||||||| || || |||||  | || || ||||| |||||||| |||||| |     
gtatattctgctttctctagtatttttctactact-tcccttcatcatgtaacatcccctgtaattttga-----cacagACCATGGCTTGGATTTTGGATGAGTACTCGAAATTCCATGGTCATTCACCGGCAGTTGTCACTGGGAAGCCAATAGTAA

upper sequence: EFJ06181 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: LOC_Os04g45970.2 (Oryza sativa), 3'ss of exon 3
gtttttttctttttcttttgttctttctttcttttctttttttgcaaagttggattttcattttttttgtttcttcacagACCATGGCTTGGATTCTGGATGAGTACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTT
|| | ||    ||||| | ||  |||  | ||  | |   ||    | ||   ||   |  |  |||||      |||||||||||||||||||| ||||||||||||| || || |||||  | || || ||||| |||||||| |||||| | 
gtatattctgctttctctagtatttttctactact-tcccttcatcatgtaacatcccctgtaattttga-----cacagACCATGGCTTGGATTTTGGATGAGTACTCGAAATTCCATGGTCATTCACCGGCAGTTGTCACTGGGAAGCCAATA

upper sequence: EFJ06181 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: LOC_Os02g43470.1 (Oryza sativa), 3'ss of exon 3
---------------------gtttttttctttttcttttgtt-ctttctttcttttctttttttgcaaagttggattttcattttttttgtttct-tcacagACCATGGCTTGGATTCTGGATGAGTACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTT
                     |  || |  ||| || | || |   ||| | || | ||| || |  | |  |   |    ||||| |||    || |||||||||||||| ||||| || ||||| ||||| ||||| |||||  |||| ||||| || ||||| ||||||||| ||
gtgagtcatccaattccatctgccttataatttatcatctgctgtcttcatactctgcttcttctttacatgtttctgaaaattttattttcaactgtcacagACCATGGCATGGATACTAGATGAATACTCAAAGTTCCATGGCCACTCCCCAGCTGTTGTCACGGGAAAGCCAATT

upper sequence: EFJ06181 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GRMZM2G427097_T01 (Zea mays), 3'ss of exon 3
----gtttttttctttttcttttgttctttctttcttttctttttttgcaaagttggattttcattttttttgtt-tcttcacagACCATGGCTTGGATTCTGGATGAGTACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTT
    |  |     |  || | || || ||| ||   |       | |      ||  ||||  |  |||| ||   |  | |||||||||||| ||||| |||||||||||||| || ||||||||  |||| |||||||| |||||||| |||||| | 
gtaggcctaacattgcttttgttatttttttttgtatgctcagctatcttgtttttcatttgtaccttttatgcaattgtgacagACCATGGCATGGATGCTGGATGAGTACTCGAAATTTCATGGTCACTCCCCAGCAGTCGTCACTGGGAAGCCAATA

upper sequence: EFJ06181 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GRMZM2G427097_T02 (Zea mays), 3'ss of exon 3
----gtttttttctttttcttttgttctttctttcttttctttttttgcaaagttggattttcattttttttgtt-tcttcacagACCATGGCTTGGATTCTGGATGAGTACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTT-------------------------
    |  |     |  || | || || ||| ||   |       | |      ||  ||||  |  |||| ||   |  | |||||||||||| ||||| |||||||||||||| || ||||||||  |||| |||||||| |||||||| |||||| |                          
gtaggcctaacattgcttttgttatttttttttgtatgctcagctatcttgtttttcatttgtaccttttatgcaattgtgacagACCATGGCATGGATGCTGGATGAGTACTCGAAATTTCATGGTCACTCCCCAGCAGTCGTCACTGGGAAGCCAATAGTAAGTGAAAAAATGTGGCAGCAAG

upper sequence: EFJ06181 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA02G07940.1 (Glycine max), 3'ss of exon 4
---------------------------------------------gtttttttctttttcttttgttctttctttctttt---ctttttttgcaaagttggattttcattttttttgtttcttca--cagACCATGGCTTGGATTCTGGATGAGTACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTT
                                             | ||      | || |  | |  ||||||  | ||   |||| ||   |||     | |  | |  |  ||| || |  |  ||||| ||||| |||||||| |||||||| ||||| ||||||||  |||||||||||||||| ||||| || ||  | 
gtcagtacaacaactaagctttgtgaatttgctgatgattgttatgcttgacaaatgttatgctctcttttcttcatattggactttattataaaacactcactaacttactagttggttgtgaatgcagACTATGGCATGGATTCTAGATGAGTATTCCAAATTTCATGGCCACTCTCCAGCAGTAGTGACTGGGAAACCTATA

upper sequence: EFJ06181 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA05G05460.1 (Glycine max), 3'ss of exon 3
------------------gtttttttctttttcttttgttctttctttctt----ttctttttttgcaaagttggattttcatt--ttttttgtttcttcacagACCATGGCTTGGATTCTGGATGAGTACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTT
                    |  |||| | | | ||| || | |   |  |    |||  |  || || |  |   || |||||  |    ||||  ||||||||||||||| |||||||| |||||||| || |||||||||||| | || || ||||| || || || |||||  ||
gtactgatttcacaacatagtactttcctgtccatttattttataaataatagcattcaatagtttcatatatcctttctcattggtccactgttgtttcacagACCATGGCATGGATTCTCGATGAGTATTCAAAGTTTCATGGGCATTCACCTGCAGTTGTGACAGGGAAGCCTATT

upper sequence: EFJ06181 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA01G41310.1 (Glycine max), 3'ss of exon 3
------------------------------------gtttttttctttttcttttgt---tctttctttcttttctttttttgcaaagttgg-attttcatt--ttttttgttt-cttcacagACCATGGCTTGGATTCTGGATGAGTACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTT
                                    |||| |  |  |||||| |||    |    | |      ||  ||  | |   |   |||||||||  |||  | |||  ||||||||| |||||||||||||| |||||||| || |||||||||||  | || |||||||| || ||||| || ||  | 
gttctgatttaattatattcccttacttaatttctggtttgtgcccatttcttatgtaaaccaacatctagcagtttcattcactattctatcattttcattcgtttactatttatttcacagACAATGGCTTGGATTCTTGATGAGTATTCTAAGTTTCATGGACATTCACCAGCAGTTGTGACTGGGAAACCTATA

upper sequence: EFJ06181 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA11G04090.1 (Glycine max), 3'ss of exon 3
-gtttttttctttttcttttgttctttctttcttttctttttttgcaaagttggattttcattttttttgtttcttcacagACCATGGCTTGGATTCTGGATGAGTACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTT
   |  |    ||| | ||||   || ||    | ||  |  ||     |||    | |||||  |||   |  ||||| ||| |||||||||||||| |||||||| || |||||||||||  | || |||||||| || ||||| |||||  ||
caatcgtagaatttacatttgcatttgctaatgtatccctacttt----gttttcctatcattcgttt-actatttcactgacaatggcttggattcttgatgagTATTCAAAGTTTCATGGACATTCACCAGCAGTTGTGACTGGGAAGCCTTTT

upper sequence: EFJ06181 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA17G15740.1 (Glycine max), 3'ss of exon 4
------------------gtttttttctttttcttttgttctttctttcttttctttttttgcaaagttggattttcattttttttgtttc-----ttcacagACCATGGCTTGGATTCTGGATGAGTACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTT
                    |   ||  | | | ||| || | |||      |    ||    |   |   || | | || || ||| | |     || |||||||||||| |||||||| ||||| || || |||||||||||| | || || ||||| || || || |||||  ||
gtactgatttcacaacacagtacatttctgtccatttattttatctaaaaaatagcattcaatagtttcatatatcctttcttattggtccactgtttgacagACCATGGCATGGATTCTTGATGAATATTCAAAGTTTCATGGGCATTCACCTGCAGTTGTGACAGGGAAGCCTATT

upper sequence: EFJ06181 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: AT5G18170.1 (Arabidopsis thaliana), 3'ss of exon 3
gtttttttctttttcttttgttctttc-----tttcttttctttttttgcaaagttggattttcattttttttgttt-----cttcacagACCATGGCTTGGATTCTGGATGAGTACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTT
||| ||    | |  |       ||||     | |  | | |||||||   ||      |||  | |||||   ||       ||  ||||| |||||||||||||| ||||| ||||| ||||||||||| ||||| || ||||| || |||||||| ||  ||
gttcttaaactctcttcagaacgtttccaaaatgttctgtgtttttttttgaaaccatctttcaactttttcccttggtggaatttgcagACAATGGCTTGGATTCTTGATGAATACTCTAAGTTTCATGGATACTCGCCTGCAGTTGTGACTGGAAAACCCATT

upper sequence: EFJ06181 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: Vv00s1491g00010.t01 (Vitis vinifera), 3'ss of exon 1
-------------------------------gtttttttctttttcttttgttctttctttcttttctttttttg--caaagttggattttcattttttttgtttcttcacagACCATGGCTTGGATTCTGGATGAGTACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTT
                               ||  ||| |           |  |  || | |   |||| |||      | ||  | |||| ||  | | | || |  |||||| ||||| |||||||||||||| ||||| |||||||||||| | || || ||||| || || ||||||||| ||
gttttccattcctgaatctaatatgtagtgtgtcctttccaggaaaaaaaatattgactctttgacctttctttaacttgaattttactttccttactctcgatt-tggacagACGATGGCATGGATTCTGGATGAATACTCAAAGTTTCATGGGCATTCACCTGCAGTTGTTACAGGAAAGCCAATT

upper sequence: EFJ06181 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: Vv08s0007g07400.t01 (Vitis vinifera), 3'ss of exon 5
------------------gtttttttctttttcttttgttctttctttcttttctttttttgcaaag--ttggattttcattttttttgtttcttcacagACCATGGCTTGGATTCTGGATGAGTACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTT
                  ||| |  | | |||  ||||    |||   | | | |    |  |   |  ||   |||    || || ||||  |  |||||||||||| ||||| || ||||||||||| || |||||||| ||||| || || || || |||||||||||  ||
agaaggaaaaaaaaaaaagttatggtatctttggtttgaatgttcaaccatatttgaactaactgtggcttttgtttctggttcttgtgttgttgaacagACCATGGCATGGATACTAGATGAGTACTCGAAATTTCATGGCTACTCACCTGCTGTGGTGACTGGAAAGCCTATT

upper sequence: EFJ06181 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: PP1S62_236V6.1 (Physcomitrella patens), 3'ss of exon 4
-----------------------------gttttttt--ctttttcttttgttctttc-tttcttttctttttttgcaaag--------ttggattttcattttttttgtttcttcacagACCATGGCTTGGATTCTGGATGAGTACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTT
                             |||    |  | |    | ||| |  | | | || |     |   |||| ||         |    | |||     ||||||| |  |||||| |||||||||||| |||| |||||||| || |||||||||||  |||| || || || ||||| || ||  | 
gtatgttccgtatattgaagctctctcgtgttccactaacatgccgtattgctgatgcgtctcatcatgctcagtgcagagaaacccctctctgatctcaacgactttgtttttgtacagACTATGGCTTGGATTTTGGACGAGTACTCGAAATTTCATGGGTATACTCCGGCCGTCGTAACTGGTAAACCGGTG

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|169067884|gb|FE474755.1|FE474755
EST:     TTGGTGTTCGTACGGATATTCCAGCACCTGACATGGGAACGAACGCTCAG                         ACCATGGCTTGGATTCTGGATGAGTACTCCAAGTTTCATGGGTACTCTCCA
genomic: TTGGTGTTCGTACGGATATTCCAGCACCTGACATGGGAACGAACGCTCAGgtttttttct ... ttcttcacagACCATGGCTTGGATTCTGGATGAGTACTCCAAGTTTCATGGGTACTCTCCA




















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: 34 (upstream exon), 35 (downstream exon)
Score: 79

CGAGCTAGAGCGGCTCACTCGAGTTTTTACGCAAAAGATCCACGACGTCATTGGTGTTCGTACGGATATTCCAGCACCTGACATGGGAACGAACGCTCAGgtttttttct ... ttcttcacagACCATGGCTTGGATTCTGGATGAGTACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttcttttctttttttgcaaagttggattttcattttttttgtttcttcacagACCATGGCTTGGATTCTGGATGAGTACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTT
                             ttttcattttttttgt  CT-rich tract
                            attttcattttttttg  TA-rich tract