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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgggcaatgaaccttcttatatttgtttcacttgttatgcacatgttaatatagatattagataggcagatggtattggtgcaaatcttcttttggtcctctttcgttgacaactattaacaaacttggttcttgttaatccgatttggtttgcatgtagGTTATGGATATTTTGGGACCAAGCCTATGGGATGTTTGGAATAATAATTCCCACTC

Basic information

species Zea mays
transcript GRMZM2G045259_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G045259_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g10150.1 (Oryza sativa), 3'ss of exon 4
gtttgggcaatgaaccttcttatatttgtttcacttgttatgcacatgttaatatagatattagataggcagatggtattggtgcaaatcttcttttggtcctctttcgttgacaactattaacaaacttggttcttgttaatccgatttggtttgcatgtagGTTATGGATATTTTGGGACCAAGCCTATGGGATGTTTGGAATAATAATTCCCACTC
                                    || ||| |    | ||  ||||| ||   |          |   |||  |    ||  || | | || ||||  | |  |  |||| ||| ||  ||| ||  ||| |  |     ||| |||| ||||||||||||| |||||||| ||||| ||||||||||||||||| |||||||||||
------------------------------------gtaatgga-gcatgaac-tagatttttttttttttttgctttccggtttatggtttgattggtttctttttctcttaaga--attatcaa-ctacgttttttctaaccatacacatttttcatgcagGTTATGGATATGTTGGGACCGAGCCTGTGGGATGTTTGGAATAACAATTCCCACTC

upper sequence: GRMZM2G045259_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA07G01890.1 (Glycine max), 3'ss of exon 4
gtttgggcaatgaaccttcttatatttgtttcacttgttatgcacatgttaatatagatattagataggcagatggtattggtgcaaatcttcttttggtcctctttcgttgacaactattaacaaacttggttcttgttaatccgatttggtttgcatgtagGTTATGGATATTTTGGGACCAAGCCTATGGGATGTTTGGAATAATAATTCCCACTC
                                                                            | ||| ||    |  |  ||  || |   ||| || |  |||| ||  |   |   |  |  || |    ||||  ||||  || |||||||||||||  ||||||| ||||| ||||| |||||||||||||     ||   
-------------------------------------------------------------------------gtatgttgttgagtcttattcttgagtgcatgttcatt-attactactattattttgaatgatgattcact--atttcctttg--tgcagGTTATGGATATGCTGGGACCTAGCCTCTGGGACGTTTGGAATAATAGCAATCATCA

upper sequence: GRMZM2G045259_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA08G21570.1 (Glycine max), 3'ss of exon 4
gtttgggcaatgaaccttcttatatttgtttcacttgttatgcacatgttaatatagatattagataggcagatggtattggtgcaaatcttcttttggtcctctttcgttgacaactattaacaaacttggttcttgttaatccgatttggtttgcatgtagGTTATGGATATTTTGGGACCAAGCCTATGGGATGTTTGGAATAATAATTCCCACTC
                                                                        ||| | |||   |  ||  |    || |  |   |  || |  |||||||      |||     || | || | || |    |   || |||||||||||||  ||||||| ||||| ||||| |||||||||||||     ||   
----------------------------------------------------------------------gtatgttgttgagtcttattcttgagtgtttgttcattatt-atgactattatt----ttgaa---tgatgattccatatttcctttgtgcagGTTATGGATATGCTGGGACCTAGCCTCTGGGACGTTTGGAATAATAGCAATCATCA

upper sequence: GRMZM2G045259_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv09s0002g03680.t01 (Vitis vinifera), 3'ss of exon 4
gtttgggcaatgaaccttcttatatttgtttcacttgttatgcacatgttaat-atagatattagataggcagatggtattggtgcaaatcttcttttggtcctctttcgttgacaactattaacaaacttggttcttgttaatccgatttggtttgcatgtagGTTATGGATATTTTGGGACCAAGCCTATGGGATGTTTGGAATAATAATTCCCACTC
                      |||   | ||| ||| | |   | ||||  | ||  || |  | | | ||           ||   |  |||||| |    | | || || |      |||  |    ||  |  |   || ||    |||||     | |||||||||| ||  | ||||||||| | |||||||||||||||||||| || ||| |
---------------------gtatgc-tatcatttgctgt---cttgttggttatgaatttatggtggtcaa---------ctgtggagtttctttagtctgtttctccttaat-----ttagaatgtctgtgtgatagaaaacctgaatggtt-----gcagGTTATGGACATGCTTGGACCAAGCTTGTGGGATGTTTGGAATAATAACTCTCACAC

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: 49 (upstream exon), 49 (downstream exon)
Score: 136

CACTCTTAGTGGGAACCATGGTGTCCCACGGGTACACTACAAAGGAAAGCAGGGAGAGTTTTACATCATGgtttgggcaa ... ttgcatgtagGTTATGGATATTTTGGGACCAAGCCTATGGGATGTTTGGAATAATAATTCCCACTC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 119

CACTCTTAGTGGGAACCATGGTGTCCCACGGGTACACTACAAAGGAAAGCAGGGAGAGTTTTACATCATGgtttgggcaa ... ttgcatgtagGTTATGGATATTTTGGGACCAAGCCTATGGGATGTTTGGAATAATAATTCCCACTC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 152

CACTCTTAGTGGGAACCATGGTGTCCCACGGGTACACTACAAAGGAAAGCAGGGAGAGTTTTACATCATGgtttgggcaa ... ttgcatgtagGTTATGGATATTTTGGGACCAAGCCTATGGGATGTTTGGAATAATAATTCCCACTC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 141

CACTCTTAGTGGGAACCATGGTGTCCCACGGGTACACTACAAAGGAAAGCAGGGAGAGTTTTACATCATGgtttgggcaa ... ttgcatgtagGTTATGGATATTTTGGGACCAAGCCTATGGGATGTTTGGAATAATAATTCCCACTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgacaactattaacaaacttggttcttgttaatccgatttggtttgcatgtagGTTATGGATATTTTGGGACCAAGCCTATGGGATGTTTGGAATAATAATTCCCACTC
         tattaacaaa  TA-rich tract