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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagattctttactctttaagttcttgggtctcatatgtgacattttcttctcttgtcgttgatcagGGACGGCTCCGCTCACTGCTGTGCAGCTACTGTGGGTGAATCTGATCATGGACACGTTGGGTGCTCTTGCTCTGGCAACCGAGCCACCGACGGATGATCT

Basic information

species Selaginella moellendorffii
transcript EFJ37088
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ37088 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: LOC_Os11g04460.1 (Oryza sativa), 3'ss of exon 5
-------------------------------gtaagattctttactctttaagttcttg-ggtctcatatgtgacatt--ttcttctcttgtcgttgatcagGGACGGCTCCGCTCACTGCTGTGCAGCTACTGTGGGTGAATCTGATCATGGACACGTTGGGTGCTCTTGCTCTGGCAACCGAGCCACCGACGGATGATCT
                                 | |  | |  | |   |   | |    | ||||  |      | |  |  ||||||  ||  | | ||||||  ||||| |||||||||||||||||| ||||||| ||| |||||||||| ||  |||| ||| | || || ||||| ||||| || |  |||||  |
gtgagggcaacattatagtattcatctgataccatgtatttccattaagtggttccccatgatctccaacacagtactaatgtttctctcttccgtca-cagGGAGCGCTCCTCTCACTGCTGTGCAGCTATTGTGGGTCAATATGATCATGGATACACTGGGAGCTTTAGCACTAGCAACAGAGCCTCCAAATGATGAAAT

upper sequence: EFJ37088 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: LOC_Os12g04220.1 (Oryza sativa), 3'ss of exon 5
-------------------------gtaagattctttact--ctttaagt-----tcttgggtctcatatgtgacatt--ttcttctcttgtcgttgatcagGGACGGCTCCGCTCACTGCTGTGCAGCTACTGTGGGTGAATCTGATCATGGACACGTTGGGTGCTCTTGCTCTGGCAACCGAGCCACCGACGGATGATCT
                          | |   | | || |  | ||||||     ||   | ||||  |      | |  |  ||  ||  ||  | | ||||||  ||||| |||||||||||||||||  ||||||| ||| |||||||||| || ||||| ||| | || || ||||| ||||| || |  |||||  |
gtgagggcaacattatagtattcatctgatgctatgtatttccattaagtggttctccatgatctccaagacagtactaatgttttgctcttccgtca-cagGGAGCGCTCCTCTCACTGCTGTGCAGCTGTTGTGGGTTAATATGATCATGGATACATTGGGAGCTTTAGCACTAGCAACAGAGCCTCCAAATGATGAAAT

upper sequence: EFJ37088 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: LOC_Os01g71240.1 (Oryza sativa), 3'ss of exon 5
-------------------------------------------------gtaagattctttactctttaagttcttgggtctcatatgtgacattttcttctcttgtcgttgat-cagGGACGGCTCCGCTCACTGCTGTGCAGCTACTGTGGGTGAATCTGATCATGGACACGTTGGGTGCTCTTGCTCTGGCAACCGAGCCACCGACGGATGATCT
                                                      ||  |    | |   | ||||  |||      |  ||  | |  |    |||| |  ||| ||||||  || ||||| ||   ||||||||| ||||||||||| ||||||||||||||  |||| || || || ||||| || ||||| ||||  || |   |
gtattaagaatttgaaatttttcgtacaaaaagttgacaaaatttcttctggtcatggtcaggtataagaattctctggttcttgttccgatttatgatgaatttgttggcgattcagGGAGTGCGCCGCTGACGATTGTGCAGCTGCTGTGGGTGAACCTGATCATGGACACACTGGGGGCGCTGGCGCTGGCGACAGAGCCGCCGAACGACGCGAT

upper sequence: EFJ37088 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GRMZM2G104730_T02 (Zea mays), 3'ss of exon 6
--------------------------------------------------------------------------gtaagattctttact-ctttaagttcttgggtctca-tatgtgacattttcttctcttgt--cgttg-atcagGGACGGCTCCGCTCACTGCTGTGCAGCTACTGTGGGTGAATCTGATCATGGACACGTTGGGTGCTCTTGCTCTGGCAACCGAGCCACCGACGGATGATCT
                                                                           |  |  | | | || || |    ||| | ||  || |   |    |  | | ||  |||   | |    ||||||  ||||| ||||| || |||||||| |||||||| ||  |||||||||||||| |||| ||||| ||||| || || ||||| || |  || ||  |
gtttggggccatttacctatgacattcctcttgcaatataatggccatgggccatggctgttcagttagtggttcttggtatatctgctgctatgccatctggagtaacagtgctttgagtgctgtactactgtactgctacgacagGGAGCGCTCCTCTCACGGCGGTGCAGCTGCTGTGGGTCAACATGATCATGGACACGCTGGGAGCTCTGGCTCTAGCCACGGAGCCTCCCAACGACGACAT

upper sequence: EFJ37088 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GRMZM2G028812_T01 (Zea mays), 3'ss of exon 5
------------gtaa-gattctttactcttta-------agttcttgggtctca---tatg----tgacattttcttctcttgtcgttga-----tcagGGACGGCTCCGCTCACTGCTGTGCAGCTACTGTGGGTGAATCTGATCATGGACACGTTGGGTGCTCTTGCTCTGGCAACCGAGCCACCGACGGATGATCT
            | ||  |||| | | | | |        || | |  || ||||   | ||    |||||   ||    ||  |   |||     ||||| |  || || || ||    |||||||| ||||||||||| ||||||||||||||  |||| || || || ||||| || ||||| || |  || |   |
gtgtgcacgcatgcaacaattcctcattttcttgtcagatagctatcaggactcaggatgtgggggtgacacagtcacgactgatgaatgaatggttcagGAAGCGCCCCCCTGACCATCGTGCAGCTGCTGTGGGTGAACCTGATCATGGACACCCTGGGCGCCCTGGCGCTGGCGACGGAGCCCCCCAACGACGCCAT

upper sequence: EFJ37088 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GRMZM2G317270_T01 (Zea mays), 3'ss of exon 3
-------------------gtaagattctttactctttaagttcttgggtctcatatgtgacattttcttctcttgtcgttgatc-agGGACGGCTCCGCTCACTGCTGTGCAGCTACTGTGGGTGAATCTGATCATGGACACGTTGGGTGCTCTTGCTCTGGCAACCGAGCCACCGACGGATGATCT
                   || | |    |   ||   | |       |  | || ||   |   | || ||  ||| || |||| |||||  ||||| || || || |||||||| |||||||||||  |||||||||||||| |||| || || || ||||| || ||||| ||||  || || ||
gtaagcttccaaagaactggtgaaagcaatctgtcgccatgcatgcttgcttgatctgctgctgctgctgcttgtgttgtggatccagGGAGCGCTCCCCTGACAGCCGTGCAGCTGCTGTGGGTGAACATGATCATGGACACGCTGGGAGCGCTGGCGCTGGCCACGGAGCCTCCGAACGACGAGCT

upper sequence: EFJ37088 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GRMZM2G118919_T01 (Zea mays), 3'ss of exon 3
----------------------------------------------------gtaagattctttactctttaagttc--ttgggtctcatatgtga---cattttcttctcttgtcg-ttgatcagGGACGGCTCCGCTCACTGCTGTGCAGCTACTGTGGGTGAATCTGATCATGGACACGTTGGGTGCTCTTGCTCTGGCAACCGAGCCACCGACGGATGATCT
                                                    ||  || |||  | |  |  |  |    |||  | | ||    |   |||    |   ||||||| || ||||||||  || || || ||||| |||||||| || ||||||||  |||||||||||||| |||| ||||| ||  |||| || ||||| || |  || || ||
gtaaaaaaaaaaacctcacgctgctgcgttcatctgtaggtgactgattccagtctgaatctgaaataatagacattgactggagcccgtaaacaaactcataaaatgtgcttgtcgattcatcagGGAGCGCGCCCCTGACTGCGGTGCAGCTGCTCTGGGTGAACATGATCATGGACACGCTGGGAGCTCTGGCGTTGGCCACGGAGCCCCCCAACGACGAGCT

upper sequence: EFJ37088 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: Vv07s0129g00110.t01 (Vitis vinifera), 3'ss of exon 4
--------------------------------------------------------gtaagattctttactctttaagttcttgggtctcatatgtgacattttcttctcttgtcgttgatcagGGACGGCTCCGCTCACTGCTGTGCAGCTACTGTGGGTGAATCTGATCATGGACACGTTGGGTGCTCTTGCTCTGGCAACCGAGCCACCGACGGATGATCT
                                                         |||  |||||   | ||    | | |   | |  | | |  | |||| || ||      || |   || |  ||||| ||||| ||||| ||||| |||||||| ||  |||||||||| ||  |||| ||||||||  | |||||||||||||| || |||||  |
gtaagaagaccccatcttgcttcttccatttcaaagttacttccttgttttgtcaaataaacttcttcttttttc---tccctacattttttttattccttttttttttcaaacacttaa---gGAAATGCTCCCCTCACGGCTGTTCAGCTTCTGTGGGTCAACATGATCATGGATACACTGGGAGCTCTTGCATTAGCAACCGAGCCACCTACTGATGACTT

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), 32 (downstream exon)
Score: 45

GGCCGCTCGGTCTACACAAACATCCAAAAGTTTGTCCAGTTCCAGCTTACAGTGAACCTTGTGGCCCTCGTGTTGAATTTTACATCTGCTTGCATCACAGgtaagattct ... cgttgatcagGGACGGCTCCGCTCACTGCTGTGCAGCTACTGTGGGTGAATCTGATCATGGACACGTTGGGTGCTCTTGCTCTGGCAACCGAGCCACCGACGGATGATCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctttaagttcttgggtctcatatgtgacattttcttctcttgtcgttgatcagGGACGGCTCCGCTCACTGCTGTGCAGCTACTGTGGGTGAATCTGATCATGGACACGTTGGGTGCTCTTGCTCTGGCAACCGAGCCACCGACGGATGATCT
                               ttttcttctcttgtcg  CT-rich tract
                              attttctt  TA-rich tract