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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacctgcatatgtcattatgacactgacatttgccctataaggatatttactgactaaaatattttttcctccgaaacttcagATTTAGGTCAGGTGTGGGGTTGGGGATATGGAGGAGAAGGGCAACTAGGTTTGGGTTCTAGAATCCGAACTGTTTCTTCTCCCCATCCTGTACCGTGCAT

Basic information

species Zea mays
transcript GRMZM2G337819_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G337819_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g62810.3 (Oryza sativa), 3'ss of exon 2
gtaacctgcata------tgtcattatgacactgacatttgcccta-taaggatatttactgactaaaat--attttttcctccgaaacttcagATTTAGGTCAGGTGTGGGGTTGGGGATATGGAGGAGAAGGGCAACTAGGTTTGGGTTCTAGAATCCGAACTGTTTCTTCTCCCCATCCTGTACCGTGCAT
||| ||| |||       |  || |||| |||| ||||||||     || |||  ||| |||| |||||   | | ||| |||  || ||||||||||||| || || ||||||||||| |||||||||||||||||||||||  |||||||||||||||| |||||||| ||||| |||||| | ||||||||
gtagcctacattttgcactaacactatggcact-acatttgctgggctagggaactttgctgattaaaactaaatgttttctcgaaagcttcagATTTAGGCCAAGTATGGGGTTGGGGCTATGGAGGAGAAGGGCAACTAGGCCTGGGTTCTAGAATCCGGACTGTTTCCTCTCCACATCCTATCCCGTGCAT

upper sequence: GRMZM2G337819_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g62810.4 (Oryza sativa), 3'ss of exon 4
gtaacctgcat------atgtcattatgacactgacatttgcccta-taaggatatttactgactaaaat--attttttcctccgaaacttcagATTTAGGTCAGGTGTGGGGTTGGGGATATGGAGGAGAAGGGCAACTAGGTTTGGGTTCTAGAATCCGAACTGTTTCTTCTCCCCATCCTGTACCGTGCAT
||| ||| |||       |  || |||| |||| ||||||||     || |||  ||| |||| |||||   | | ||| |||  || ||||||||||||| || || ||||||||||| |||||||||||||||||||||||  |||||||||||||||| |||||||| ||||| |||||| | ||      
gtagcctacattttgcactaacactatggcact-acatttgctgggctagggaactttgctgattaaaactaaatgttttctcgaaagCTTCAGATTTAGGCCAAGTATGGGGTTGGGGCTATGGAGGAGAAGGGCAACTAGGCCTGGGTTCTAGAATCCGGACTGTTTCCTCTCCACATCCTATCCC------

upper sequence: GRMZM2G337819_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA18G40600.1 (Glycine max), 3'ss of exon 7
-------------------------------gtaacctgcatatgtcattatgacactgaca-tttgccctataaggatatttactgactaaaatattttttcctccgaaacttcagATTTAGGTCAGGTGTGGGGTTGGGGATATGGAGGAGAAGGGCAACTAGGTTTGGGTTCTAGAATCCGAACTGTTTCTTCTCCCCATCCTGTACCGTGCAT
                               |||   |  ||     || | || |  ||   |||    | ||| |  |   ||    |  |  || ||||   |  |   ||||||| | || ||||| ||||||||||| |||||||| ||||| || ||||| ||||||||| |  |    |  || || || || |||| | |||       
gttggctcttgtggttacattatgtagttttgtaggttcaatgaagtatgaagatatggaaggtttttgatgtaaagcaagacacctgatgcatcatatttttaccgaagTTTTCAGATGTGGGACAGGTCTGGGGTTGGGGCTATGGAGGTGAAGGACAGCTAGGATTGGGTTCTCGGGTAAAGATGGTATCATCCCCTCATCTTATAC-------

upper sequence: GRMZM2G337819_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA07G16400.1 (Glycine max), 3'ss of exon 6
-------------------------------gtaacctgcatatgtcattatgacactgaca-tttgccctataaggatatttactgactaaaatattttttcctccgaaacttcagATTTAGGTCAGGTGTGGGGTTGGGGATATGGAGGAGAAGGGCAACTAGGTTTGGGTTCTAGAATCCGAACTGTTTCTTCTCCCCATCCTGTACCGTGCAT
                               |||   |  ||     || | || |  ||   |||    | ||| |  |   ||    |  |  || ||||   |  |   ||||||| | || ||||| ||||||||||| |||||||| ||||| || ||||| ||||||||| || |    |  || || || || |||| | |||       
gttgcctcttgtggttacattatatagttttgtaggttcaatgaagtatgaagataaggatggtttttgatgtaaagcaagacacctgatgcatcatatttttaccaaagTTTTCAGATGTGGGACAGGTCTGGGGTTGGGGTTATGGAGGTGAAGGACAGCTAGGATTGGGTTCTCGAGTAAAGATGGTATCATCCCCTCATCTTATAC-------

upper sequence: GRMZM2G337819_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA11G34470.1 (Glycine max), 3'ss of exon 5
------------------------------------------------------------------gtaacctgcatatgtc---attatgacactgacatttgccctat--aaggatatttactgact--aaaatatttt-----------ttcctccgaaacttcagATTTAGGTCAGGTGTGGGGTTGGGGATATGGAGGAGAAGGGCAACTAGGTTTGGGTTCTAGAATCCGAACTGTTTCTTCTCCCCATCCTGTACCGTGCAT
                                                                   |||  ||   || |     ||    ||      ||||  ||||  |||   | |||   | |  || | || |            ||     |||  ||||||| |||| ||||||||||||||||| ||||| || |||||||| || ||||||||||||||||| ||||  || || ||||| ||||  || || || ||
gtattgactttattatgggctatttgtcaacctaggtctaaaattttatctatgctattttcgtatataatatgataatcttttggttgaagcataactttttgtgctatggaagatcagttatgcattcgaagacatgtcattgattgtaattttctggaagtttcagATATAGGACAGGTGTGGGGTTGGGGCTATGGTGGTGAAGGGCAGCTTGGTTTGGGTTCTAGAATACGAATGGTGTCCTCTCCTCATCTAGTTCCTTGTAT

upper sequence: GRMZM2G337819_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA18G03870.1 (Glycine max), 3'ss of exon 5
-----------------------------------------------------------------------------------------gta-acctgcatatgtcattatgacactgacatttgccctataaggatatttactgactaaaatattttttcctccgaaacttcagATTTAGGTCAGGTGTGGGGTTGGGGATATGGAGGAGAAGGGCAACTAGGTTTGGGTTCTAGAATCCGAACTGTTTCTTCTCCCCATCCTGTACCGTGCAT
                                                                                         | | | ||   | ||| ||   ||   | |  | |||  | ||||     | | ||| |  ||| || | |       |  ||||||| |||| ||||||||||||||||| ||||| || |||||||| || ||||||||||||||||| ||||  || || ||||| ||||  || || || ||
gtattgactttattatgaactatttgtcaacctaggtctaaaattttatctgttattttcgtatatgatgtgataatcttttggttgaagcagaactttttgtgttat--ggaagatcagttatgcaatctaagacatgtcattgattgtaattttctgt------gagtttcagATATAGGACAGGTGTGGGGTTGGGGCTATGGTGGTGAAGGGCAGCTTGGTTTGGGTTCTAGAATACGAATGGTGTCCTCTCCTCATCTAGTTCCTTGTAT

upper sequence: GRMZM2G337819_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA14G07160.1 (Glycine max), 3'ss of exon 5
------------------------------------------------------------gtaacctgcatatgtcattatgacactgacatttgccctataaggatatttactgactaaaatattttttcctccgaaa-cttcagATTTAGGTCAGGTGTGGGGTTGGGGATATGGAGGAGAAGGGCAACTAGGTTTGGGTTCTAGAATCCGAACTGTTTCTTCTCCCCATCCTGTACCGTGCAT
                                                             |  ||    | |  | |  |     |||    |   |||| | |      ||| |  |     | |  |  || || |  |||||||  ||| | |||||||| |||||| |||||||| |||||||| || ||||||||||| ||||| || |  |||||  |||| |||| ||| || || ||
gtacaggacctttttatggagtatttttacacataaatctaagattttatgtatgttactcttcccattgtgtagcgtggtttggttgaagcatcaactatgatgtctaagacttatcattgattctagttttctgagagtttcagATACAGGACTGGTGTGGGCTTGGGGCTATGGAGGTGAAGGGCAGCTTGGTTTGGGTTCCAGAATACGCATGGTTTCCACTCCTCATCTTGTTCCTTGTAT

upper sequence: GRMZM2G337819_T02 (Zea mays), 3'ss of exon 5
lower sequence: AT3G55580.1 (Arabidopsis thaliana), 3'ss of exon 5
---------------------------------------------------------------------gtaacctgcatatgtcattatgacactga-catttgccctataaggatatttactgactaaaa--tattttttcctccgaaacttcagATTTAGGTCAGGTGTGGGGTTGGGGATATGGAGGAGAAGGGCAACTAGGTTTGGGTTCTAGAATCCGAACTGTTTCTTCTCCCCATCCTGTACCGTGCAT
                                                                      | |   ||      ||||| |  |  || | ||||   |   |  ||| | |||   |  |   || |||||  || |||  | ||||| | || ||||||||||||||||| |||||||||||||| || || || ||||| ||| |  | ||    || || ||||| |||||| | || |||||
gtgagatttttagcttttcacacaccatgtcactaatgaggtacattggttatcaattatgaaaaaaatatcagtggcggtatccattaagctaaagagcttttggtgtgctataataatcacttgatgcatcctaattttttttctgaag-tccagATATTGGACAGGTGTGGGGTTGGGGTTATGGAGGAGAAGGACAGCTTGGATTGGGCTCTCGTGTACGTCTAGTCTCCTCTCCTCATCCTATTCCATGCAT

upper sequence: GRMZM2G337819_T02 (Zea mays), 3'ss of exon 5
lower sequence: AT3G53830.1 (Arabidopsis thaliana), 3'ss of exon 5
-----gtaacctgcatatgtcattatgacactgacat-------ttgccctataa--ggatatttact-gactaaaatattttttcctccgaaacttcagATTTAGGTCAGGTGTGGGGTTGGGGATATGGAGGAGAAGGGCAACTAGGTTTGGGTTCTAGAATCCGAACTGTTTCTTCTCCCCATCCTGTACCGTGCAT
     ||    |  |    |  |||  |  | || ||        | || | ||   | | ||| | | ||  |  ||  | |||   | |||  |||||||||||| ||| | |||||||||||||||||||| ||||| |||||||| ||||||||  | ||   ||  || || ||||| ||||   |||| ||| |
gtgaagttgaataaacgactttttacaaatccgagatgaagctgctaccttgtagttgaagattcatttgaggatgatcatgtttttacggaagtttcagATTTAGGACAGATTTGGGGTTGGGGATATGGAGGCGAAGGTCAACTAGGATTGGGTTCCCGGATTAAAATGGTGTCATCTCCTCATCTAATACCTTGCCT

upper sequence: GRMZM2G337819_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv13s0019g02280.t01 (Vitis vinifera), 3'ss of exon 5
----------------------------------------------------------------------------------------gtaacctgcatatgtcattatgacactgacatt-tgccctataaggatatttactgactaaaatattttttcctccgaaacttcagATTTAGGTCAGGTGTGGGGTTGGGGATATGGAGGAGAAGGGCAACTAGGTTTGGGTTCTAGAATCCGAACTGTTTCTTCTCCCCATCCTGTACCGTGCAT
                                                                                        |||  ||   |||| |   | | ||  ||  || |    | ||| |  |   ||| | |    | | || | | || ||  ||||||| | || ||||||||||||||||| ||||| || || ||||||||||||||||||||  | || || |  || || ||||| |||||||| || ||  |
gtaaatccatgaaatcttggattgttgtccctaagcctcagttttaattcatagttctttttctgttgtggttatgcaacataggctggta--ctcagtatgactagaagccatggaagttctattttgtaaagcaacaaacttaatgttttctattgttcccccaagtttcagATGTTGGACAGGTGTGGGGTTGGGGCTATGGGGGTGAGGGGCAACTAGGTTTGGGTTCCCGGATACGTATGGTATCCTCTCCTCATCCTGTGCCTTGTGT

upper sequence: GRMZM2G337819_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv08s0007g00930.t01 (Vitis vinifera), 3'ss of exon 5
---------------------------------------------------------------------------gtaac-ctgcatatgtcattatgacact-gacatttgcc-ctata-aggatatttactg---actaaaatattttttcctccgaaa-cttcagATTTAGGTCAGGTGTGGGGTTGGGGATATGGAGGAGAAGGGCAACTAGGTTTGGGTTCTAGAATCCGAACTGTTTCTTCTCCCCATCCTGTACCGTGCAT
                                                                           || || ||  |||  |   || | || | ||  |  |   ||||  | ||| |||| ||   |  || | |  |  |    | |||  ||||||| | || ||||||||||||||||| |||||||| |||||||| ||||||||||||||| | |        || |||||||| ||||   |||| ||| |
gtaaattctccatcccctgggtcactgcagcccacacaagccacagttttcaggtgtagcaatttcttctttgtggttacactatatagttttgtaggtcatttgaagtacgaagctatggaagatctttaatgtaaagcaagacacctaatttaacaaaagtttcagATATGGGACAGGTGTGGGGTTGGGGCTATGGAGGCGAAGGGCAGCTAGGTTTGGGTTCTCGGACAAAGCTGGTGTCTTCTCCTCATCTCATACCTTGCTT

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), 44 (downstream exon)
Score: 97

GATGAAAGTCTTTCAGCACCCCCTTGTGTTGTGACATTTAGTACAGGAGTGAAAATAGTGGCTGTAGCCGCTGGTGGTCGTCATACATTAGCACTATCAGgtaacctgca ... gaaacttcagATTTAGGTCAGGTGTGGGGTTGGGGATATGGAGGAGAAGGGCAACTAGGTTTGGGTTCTAGAATCCGAACTGTTTCTTCTCCCCATCCTGTACCGTGCAT


Block sizes: 37 (upstream exon), 44 (downstream exon)
Score: 12

GATGAAAGTCTTTCAGCACCCCCTTGTGTTGTGACATTTAGTACAGGAGTGAAAATAGTGGCTGTAGCCGCTGGTGGTCGTCATACATTAGCACTATCAGgtaacctgca ... gaaacttcagATTTAGGTCAGGTGTGGGGTTGGGGATATGGAGGAGAAGGGCAACTAGGTTTGGGTTCTAGAATCCGAACTGTTTCTTCTCCCCATCCTGTACCGTGCAT


Block sizes: 43 (upstream exon), 43 (downstream exon)
Score: 9

GATGAAAGTCTTTCAGCACCCCCTTGTGTTGTGACATTTAGTACAGGAGTGAAAATAGTGGCTGTAGCCGCTGGTGGTCGTCATACATTAGCACTATCAGgtaacctgca ... gaaacttcagATTTAGGTCAGGTGTGGGGTTGGGGATATGGAGGAGAAGGGCAACTAGGTTTGGGTTCTAGAATCCGAACTGTTTCTTCTCCCCATCCTGTACCGTGCAT


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 67

GATGAAAGTCTTTCAGCACCCCCTTGTGTTGTGACATTTAGTACAGGAGTGAAAATAGTGGCTGTAGCCGCTGGTGGTCGTCATACATTAGCACTATCAGgtaacctgca ... gaaacttcagATTTAGGTCAGGTGTGGGGTTGGGGATATGGAGGAGAAGGGCAACTAGGTTTGGGTTCTAGAATCCGAACTGTTTCTTCTCCCCATCCTGTACCGTGCAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttgccctataaggatatttactgactaaaatattttttcctccgaaacttcagATTTAGGTCAGGTGTGGGGTTGGGGATATGGAGGAGAAGGGCAACTAGGTTTGGGTTCTAGAATCCGAACTGTTTCTTCTCCCCATCCTGTACCGTGCAT
                                tattttttcctccg  CT-rich tract
               atatttactgactaaa  TA-rich tract