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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttttttttcacttttttttgttctttcttttatttttcatttttttgtttcttttacaaagttggatttttatttttttggtttcttcacagACCATGGCTTGGATTCTGGATGAGTACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTT

Basic information

species Selaginella moellendorffii
transcript EFJ36430
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ36430 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: LOC_Os04g45970.1 (Oryza sativa), 3'ss of exon 3
gtttttttttcacttttttttgttctttcttttatttttcatttttttgtttcttttacaaagttggatttttatttttttggtttcttcacagACCATGGCTTGGATTCTGGATGAGTACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTT----
             | | || || | | |||  ||||||||   |  |  || | || |  | ||   ||         | |  |||   |||||||||||||||||||| ||||||||||||| || || |||||  | || || ||||| |||||||| |||||| |     
------------gtatattctgctttctctagtatttttc---tactacttcccttcatcatgtaacatcccc-----tgtaattttgacacagACCATGGCTTGGATTTTGGATGAGTACTCGAAATTCCATGGTCATTCACCGGCAGTTGTCACTGGGAAGCCAATAGTAA

upper sequence: EFJ36430 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: LOC_Os04g45970.2 (Oryza sativa), 3'ss of exon 3
gtttttttttcacttttttttgttctttcttttatttttcatttttttgtttcttttacaaagttggatttttatttttttggtttcttcacagACCATGGCTTGGATTCTGGATGAGTACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTT
             | | || || | | |||  ||||||||   |  |  || | || |  | ||   ||         | |  |||   |||||||||||||||||||| ||||||||||||| || || |||||  | || || ||||| |||||||| |||||| | 
------------gtatattctgctttctctagtatttttc---tactacttcccttcatcatgtaacatcccc-----tgtaattttgacacagACCATGGCTTGGATTTTGGATGAGTACTCGAAATTCCATGGTCATTCACCGGCAGTTGTCACTGGGAAGCCAATA

upper sequence: EFJ36430 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: LOC_Os02g43470.1 (Oryza sativa), 3'ss of exon 3
------------gtttttttttcacttttttttgttctttcttttatttttcatttttttgtttcttttacaaagttggatttttatttttttggtttcttcacagACCATGGCTTGGATTCTGGATGAGTACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTT
             ||   | | |  | |  ||| |  | |  | | ||  |  | |  || ||  ||  |      || |  ||| | ||||    |   |||||||||||||| ||||| || ||||| ||||| ||||| |||||  |||| ||||| || ||||| ||||||||| ||
gtgagtcatccaattccatctgccttataatttatcatctgctgtcttcatactctgcttcttctttacatgtttctgaaaattt-tattttcaactg--tcacagACCATGGCATGGATACTAGATGAATACTCAAAGTTCCATGGCCACTCCCCAGCTGTTGTCACGGGAAAGCCAATT

upper sequence: EFJ36430 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GRMZM2G427097_T01 (Zea mays), 3'ss of exon 3
gtttttttttcacttttttttgttctttcttttatttttcatttttttgtttcttttacaaagttggatttttatttttt-tggtttcttcacagACCATGGCTTGGATTCTGGATGAGTACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTT
        |   | |    ||| | ||  | || |||||  | |  |    | | ||      ||  |||| ||  |||| ||   |  | |||||||||||| ||||| |||||||||||||| || ||||||||  |||| |||||||| |||||||| |||||| | 
-------gtaggcctaacattgcttttgttatttttttttgtatgctcagctatcttgtt---tttcatttgtaccttttatgcaattgtgacagACCATGGCATGGATGCTGGATGAGTACTCGAAATTTCATGGTCACTCCCCAGCAGTCGTCACTGGGAAGCCAATA

upper sequence: EFJ36430 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GRMZM2G427097_T02 (Zea mays), 3'ss of exon 3
gtttttttttcacttttttttgttctttcttttatttttcatttttttgtttcttttacaaagttggatttttatttttt-tggtttcttcacagACCATGGCTTGGATTCTGGATGAGTACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTT-------------------------
        |   | |    ||| | ||  | || |||||  | |  |    | | ||      ||  |||| ||  |||| ||   |  | |||||||||||| ||||| |||||||||||||| || ||||||||  |||| |||||||| |||||||| |||||| |                          
-------gtaggcctaacattgcttttgttatttttttttgtatgctcagctatcttgtt---tttcatttgtaccttttatgcaattgtgacagACCATGGCATGGATGCTGGATGAGTACTCGAAATTTCATGGTCACTCCCCAGCAGTCGTCACTGGGAAGCCAATAGTAAGTGAAAAAATGTGGCAGCAAG

upper sequence: EFJ36430 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA02G07940.1 (Glycine max), 3'ss of exon 4
----------------------------------gtttttttttcacttt-tttttgttctttcttttatttttcatttttttgtttcttttacaaagttggatt-tttatttttttggtttcttcacagACCATGGCTTGGATTCTGGATGAGTACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTT
                                   |  || ||   |||      |||| |    | | || ||||| ||    ||| || || ||   |   |   ||| |  || | | |     ||||| ||||| |||||||| |||||||| ||||| ||||||||  |||||||||||||||| ||||| || ||  | 
gtcagtacaacaactaagctttgtgaatttgctgatgattgttatgcttgacaaatgttatgctctcttttcttcatattggactttattataaaacactcactaacttactagttggttgtgaatgcagACTATGGCATGGATTCTAGATGAGTATTCCAAATTTCATGGCCACTCTCCAGCAGTAGTGACTGGGAAACCTATA

upper sequence: EFJ36430 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA05G05460.1 (Glycine max), 3'ss of exon 3
gtttttttttcacttttttttgttctttcttttatttttcatttttttgtttcttttacaaagttggatttttatttttttg----------gtttcttcacagACCATGGCTTGGATTCTGGATGAGTACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTT
||  |  ||||||    |  |  | |    |  |||| |  | |   |  |    ||  | ||||  || | |  ||| |            |||  ||||||||||||||| |||||||| |||||||| || |||||||||||| | || || ||||| || || || |||||  ||
gtactgatttcacaacatagtactttcctgtccatttattttataaataatagcattcaatagtttcatatatcctttctcattggtccactgttgtttcacagACCATGGCATGGATTCTCGATGAGTATTCAAAGTTTCATGGGCATTCACCTGCAGTTGTGACAGGGAAGCCTATT

upper sequence: EFJ36430 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA01G41310.1 (Glycine max), 3'ss of exon 3
-------------------------gtttttttttcacttttttttgttctttcttttatttttcatttttttgtttcttttacaaagttgg-atttttatt---tttttggtttcttcacagACCATGGCTTGGATTCTGGATGAGTACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTT
                          ||  ||| |   || |     ||  || | | |     ||| |    ||||| || || |   |   ||||| |||   ||  |  ||  ||||||||| |||||||||||||| |||||||| || |||||||||||  | || |||||||| || ||||| || ||  | 
gttctgatttaattatattcccttacttaatttctggtttgtgcccatttcttatgtaaaccaacatctagcagtttcattcactattctatcattttcattcgtttactatttatttcacagACAATGGCTTGGATTCTTGATGAGTATTCTAAGTTTCATGGACATTCACCAGCAGTTGTGACTGGGAAACCTATA

upper sequence: EFJ36430 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA11G04090.1 (Glycine max), 3'ss of exon 3
gtttttttttcacttttttttgttctttcttttat-ttttcatttttttgtttcttt-tacaaagttggatttttatttttttggtttcttcacagACCATGGCTTGGATTCTGGATGAGTACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTT
                      |  |    ||||  ||| |||||  |  | | |   |||   |||    | | |||  |||  | | ||||| ||| |||||||||||||| |||||||| || |||||||||||  | || |||||||| || ||||| |||||  ||
-------------------caatcgtagaatttacatttgcatttgctaatgtatccctactttgttttcctatcattcgtttactat-ttcactgacaatggcttggattcttgatgagTATTCAAAGTTTCATGGACATTCACCAGCAGTTGTGACTGGGAAGCCTTTT

upper sequence: EFJ36430 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA17G15740.1 (Glycine max), 3'ss of exon 4
gtttttttttcacttttttttgttctttcttttatt--tttcatttttttgtttcttttacaaagttggat---ttttatttttttggt----ttcttcacagACCATGGCTTGGATTCTGGATGAGTACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTT
||  |  ||||||       |    ||   |  |||  ||| || |      |    ||  | ||||  ||   |  | | || |||||    |  || |||||||||||| |||||||| ||||| || || |||||||||||| | || || ||||| || || || |||||  ||
gtactgatttcacaacacagtacatttctgtccatttattttatctaaaaaatagcattcaatagtttcatatatcctttcttattggtccactgtttgacagACCATGGCATGGATTCTTGATGAATATTCAAAGTTTCATGGGCATTCACCTGCAGTTGTGACAGGGAAGCCTATT

upper sequence: EFJ36430 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: AT5G18170.1 (Arabidopsis thaliana), 3'ss of exon 3
gtttttttttcacttttttttgttctttcttttatttttcatttttttgtttcttttacaaagttggatttttatttttttggtttcttcacagACCATGGCTTGGATTCTGGATGAGTACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTT
    || ||  ||| | ||  |  | ||     | | |||  | |||| ||| |   || |  ||  |  ||| |   || |     ||  ||||| |||||||||||||| ||||| ||||| ||||||||||| ||||| || ||||| || |||||||| ||  ||
---gttcttaaactctcttcagaacgtttccaaaatgttctgtgtttt-tttttgaaaccatctttcaactttttcccttggtggaatttgcagACAATGGCTTGGATTCTTGATGAATACTCTAAGTTTCATGGATACTCGCCTGCAGTTGTGACTGGAAAACCCATT

upper sequence: EFJ36430 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: Vv00s1491g00010.t01 (Vitis vinifera), 3'ss of exon 1
gtttttttttc---acttttttttgt--tctttctttt-----------atttttcatttttttgtttcttttacaaagttggatttttatttttttggtttc----ttcacagACCATGGCTTGGATTCTGGATGAGTACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTT
|||||   |||   | | |  | |||  | | || |||           | | || | | |||    | | ||   || ||| |||||  |||  ||  | ||    |  |||||| ||||| |||||||||||||| ||||| |||||||||||| | || || ||||| || || ||||||||| ||
gttttccattcctgaatctaatatgtagtgtgtcctttccaggaaaaaaaatattgactctttgacctttcttt--aacttgaattttactttccttactctcgatttggacagACGATGGCATGGATTCTGGATGAATACTCAAAGTTTCATGGGCATTCACCTGCAGTTGTTACAGGAAAGCCAATT

upper sequence: EFJ36430 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: Vv08s0007g07400.t01 (Vitis vinifera), 3'ss of exon 5
----------------gtttttttttcacttttttttgttctttcttttatttttcatttttttgtttcttttacaaagttggatttttatttttttggtttcttcacagACCATGGCTTGGATTCTGGATGAGTACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTT
                   || |  |  ||||  ||||    |||    || ||| |  |   |||  |||||           ||| |  || ||  |||  |  |||||||||||| ||||| || ||||||||||| || |||||||| ||||| || || || || |||||||||||  ||
agaaggaaaaaaaaaaaagttatggtatctttggtttgaatgttcaaccatatttgaactaactgtggcttttg----------tttctggttcttgtgttgttgaacagACCATGGCATGGATACTAGATGAGTACTCGAAATTTCATGGCTACTCACCTGCTGTGGTGACTGGAAAGCCTATT

upper sequence: EFJ36430 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: PP1S62_236V6.1 (Physcomitrella patens), 3'ss of exon 4
-----------------------gtttttttttcacttttttttgttctttcttttatttttcatttttttgtttcttttacaaagttggatttttattttt------ttggtttcttcacagACCATGGCTTGGATTCTGGATGAGTACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTT
                         |  | || ||||    |    | || ||  |   | ||||  |   | |   |  | | |      | | |  | |       || |||| |  |||||| |||||||||||| |||| |||||||| || |||||||||||  |||| || || || ||||| || ||  | 
gtatgttccgtatattgaagctctctcgtgttccactaacatgccgtattgctgatgcgtctcatcat---gctcagtgcagagaaacccctctctgatctcaacgactttgtttttgtacagACTATGGCTTGGATTTTGGACGAGTACTCGAAATTTCATGGGTATACTCCGGCCGTCGTAACTGGTAAACCGGTG

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

CGAGCTAGAGCGGCTCACTCGAGTTTTTACGCAAAAGATCCACGACGTCATTGGTGTTCGTACGGATATTCCAGCACCTGACATGGGAACGAATGCTCAGgttttttttt ... ttcttcacagACCATGGCTTGGATTCTGGATGAGTACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttttttgtttcttttacaaagttggatttttatttttttggtttcttcacagACCATGGCTTGGATTCTGGATGAGTACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTT
                             tttttatttttttggt  CT-rich tract
              ttttacaaagttggat  TA-rich tract