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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatctaccagtgccctgcaatacaaattcttgaatactgcatgctatttaatctgatcctctaaacatcttggtttgtagGGTTCAGTTTATGCTCCATCATTTGATCATGGTGTTGGCGACCCAGTTGAGAATGACATATTTGTAAAGCCACA

Basic information

species Zea mays
transcript GRMZM2G035338_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G035338_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os12g40880.2 (Oryza sativa), 3'ss of exon 7
gtatctaccagtgcc-ctgcaatacaaattcttgaatactgcatgctatttaatctgatcctctaaacatcttggtttgtagGGTTCAGTTTATGCTCCATCATTTGATCATGGTGTTGGCGACCCAGTTGAGAATGACATATTTGTAAAGCCACA--------------------------
|| | |||||||  | |||  |   |   | ||  | |   |||  | |||   ||||||    ||||||||| || || |||||||||||||||||||||||||||||||||||||||| || |||||||| |||||||||||||||||||| ||                          
gtgt-taccagtttcactgtcaagtattctattacacataacattgtgttttgactgatcgctgaaacatctttgtctgcagGGTTCAGTTTATGCTCCATCATTTGATCATGGTGTTGGTGATCCAGTTGAAAATGACATATTTGTAAAGCCGCAGTGAGTTATCATTGCAGATCCAGAAT

upper sequence: GRMZM2G035338_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os12g40880.1 (Oryza sativa), 3'ss of exon 7
gtatctaccagtgcc-ctgcaatacaaattcttgaatactgcatgctatttaatctgatcctctaaacatcttggtttgtagGGTTCAGTTTATGCTCCATCATTTGATCATGGTGTTGGCGACCCAGTTGAGAATGACATATTTGTAAAGCCACA
|| | |||||||  | |||  |   |   | ||  | |   |||  | |||   ||||||    ||||||||| || || |||||||||||||||||||||||||||||||||||||||| || |||||||| |||||||||||||||||||| ||
gtgt-taccagtttcactgtcaagtattctattacacataacattgtgttttgactgatcgctgaaacatctttgtctgcagGGTTCAGTTTATGCTCCATCATTTGATCATGGTGTTGGTGATCCAGTTGAAAATGACATATTTGTAAAGCCGCA

upper sequence: GRMZM2G035338_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA03G31550.1 (Glycine max), 3'ss of exon 6
-----------------------gtatctaccagtgccctgcaatac--aaattcttgaatactgcatgctatttaatctgatcctctaaacatcttggtttgtagGGTTCAGTTTATGCTCCATCATTTGATCATGGTGTTGGCGACCCAGTTGAGA-ATGACATATTTGTAAA-GCCACA------------------------
                       |||   | | ||||  ||  ||     |||||||   | ||   | || ||  || |       | ||  | ||  |||  |||| ||||||||||  ||||||||||| ||||||||||| ||||||||| |||  ||    | |  | |       |                        
agctggggtgcacagaaagagcagtaagcatccgtgcattgacatgacggaattcttatctgctttgttctgttgcattttgg----tgaaattttt--ttttcagGGATCAGTTTATGTACCATCATTTGACCATGGTGTTGGGGACCCAGTTAAGATGTGGTCCACTCATCAGCATTTTATAAATTTCTGACACAAATTATGAT

upper sequence: GRMZM2G035338_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA19G34390.1 (Glycine max), 3'ss of exon 7
-----------------------gtatctaccagtgccctgcaatac--aaattcttgaatactgcatgctatttaatctgatcctctaaacatcttggtttgtagGGTTCAGTTTATGCTCCATCATTTGATCATGGTGTTGGCGACCCAGTTGAGAATGACATATTTGTAAAGCCACA
                       |||   | | |||| |||  ||     | |||||   | ||   | || ||  || |        |||||  ||    |  |||| ||||||||||  ||||||||||| ||||||||||| |||||||||||  |||| || ||||| || |  ||
agctgggatgcacagaaagaacagtaagcatctgtgcactgacatgatggagttcttatctgctttgttctgttgcattttggt---gaaacaaatt---cttcagGGATCAGTTTATGTACCATCATTTGACCATGGTGTTGGGGACCCAGTTGAAGATGATATCTTTGTGAACCTTCA

upper sequence: GRMZM2G035338_T01 (Zea mays), 3'ss of exon 7
lower sequence: AT1G03030.1 (Arabidopsis thaliana), 3'ss of exon 7
--------gtatctaccagtgccctgcaatac-aaattcttgaatactgcatgctatttaatctgatcctctaaacatcttgg-tttgtagGGTTCAGTTTATGCTCCATCATTTGATCATGGTGTTGGCGACCCAGTTGAGAATGACATATTTGTAAAGCCACA
        ||   ||| |   |      |    |   |||||||   ||   |   |  |||    ||   | |   |    | |||  |||| ||||||||||  ||||||||||||||||| ||||| || ||||||||  |||| || ||||| |  |  ||
gtaaagaggtggttacaaaatcttgttgaccttaggatcttgaa-gttgggagacttacaatagactctgattagttttcaagctttccagGGCTCAGTTTATGTGCCATCATTTGATCATGGAGTTGGGGATCCAGTTGAAGATGATATCTTTGTTAGCCTCCA

upper sequence: GRMZM2G035338_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv07s0141g00310.t01 (Vitis vinifera), 3'ss of exon 7
-----------------------------------------------------------------------------------gtatctaccagtgccctgcaatacaaattcttgaatac-tgcatgctatt----taatctgatcctctaaacatcttggtttgtagGGTTCAGTTTATGCTCCATCATTTGATCATGGTGTTGGCGACCCAGTTGAGAATGACATATTTGTAAAGCCACA
                                                                                    | | |  ||         |||| ||| | |    ||| ||  | || ||    || |    |    | | ||   |  | ||||||| ||||||||||| ||||| ||||||||||||||||| || ||||||||  |||| |||||| | |  |  ||
gtgagtagctattgatgttggctgcgtcattttattcttgttgagactttagaactggttggtgcataaacttatctttttttttttttttcaaaaataaaaaataaaaaatttgtggtacatgagtacttttctcatattgcattatgatgagcaatattttctgtagGGGTCAGTTTATGCACCATCGTTTGATCATGGTGTTGGAGATCCAGTTGAAGATGATATATTTATCAGCCTCCA

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 4 RNA-Seq libraries.


Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 38

CACCCTGGACATTCAATCCATCACTGTTTCTGAAATGTCTACATACACTAAGAACAGAGgtatctacca ... tggtttgtagGGTTCAGTTTATGCTCCATCATTTGATCATGGTGTTGGCGACCCAGTTGAGAATGACATATTTGTAAAGCCACA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 41

CACCCTGGACATTCAATCCATCACTGTTTCTGAAATGTCTACATACACTAAGAACAGAGgtatctacca ... tggtttgtagGGTTCAGTTTATGCTCCATCATTTGATCATGGTGTTGGCGACCCAGTTGAGAATGACATATTTGTAAAGCCACA


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 32

CACCCTGGACATTCAATCCATCACTGTTTCTGAAATGTCTACATACACTAAGAACAGAGgtatctacca ... tggtttgtagGGTTCAGTTTATGCTCCATCATTTGATCATGGTGTTGGCGACCCAGTTGAGAATGACATATTTGTAAAGCCACA


Block sizes: 43 (upstream exon), 46 (downstream exon)
Score: 29

CACCCTGGACATTCAATCCATCACTGTTTCTGAAATGTCTACATACACTAAGAACAGAGgtatctacca ... tggtttgtagGGTTCAGTTTATGCTCCATCATTTGATCATGGTGTTGGCGACCCAGTTGAGAATGACATATTTGTAAAGCCACA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcttgaatactgcatgctatttaatctgatcctctaaacatcttggtttgtagGGTTCAGTTTATGCTCCATCATTTGATCATGGTGTTGGCGACCCAGTTGAGAATGACATATTTGTAAAGCCACA
                                 ctctaaa  putative branch site (score: 29)
                   tatttaatct  TA-rich tract