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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatacaaactccttatggacaattgtcaggaaactcaagaaagaatctaacatatcatttttaattgcattgtacagCAACTTTTGTTCTTCATCATCCGGAGCATGGTCATGCAGTTGCACATCCAATTCTTTCACGCATCATAGATGGGACGCTGTGCTATGATAGACATGGTCC

Basic information

species Zea mays
transcript GRMZM2G107101_T03
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107101_T05 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g08700.1 (Oryza sativa), 3'ss of exon 5
gtaatacaaactccttatggacaattgt----caggaaactcaagaaagaatctaacatatcatttttaattgcattgtacagCAACTTTTGTTCTTCATCATCCGGAGCATGGTCATGCAGTTGCACATCCAATTCTTTCACGCATCATAGATGGGACGCTGTGCTATGATAGACATGGTCC
|||||   | |   | ||  | |  |||    ||   || | |||||||| | | ||||||  || | |     ||| | ||||||||||||||||||||||||| |||||||| ||||||||||  ||||| ||||| |||||||||||||||||||| ||  | ||||||||| |||||  
gtaatttgatccagtgatcaatacatgttccacaaacaattgaagaaagagtttgacatatttttctca----tatt-tccagCAACTTTTGTTCTTCATCATCCTGAGCATGGCCATGCAGTTGTGCATCCGATTCTGTCACGCATCATAGATGGGACACTCAGTTATGATAGAAATGGTTT

upper sequence: GRMZM2G107101_T05 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA10G36600.1 (Glycine max), 3'ss of exon 4
-------------------------------gtaatacaaactccttatggaca--attgtcagga---aactcaagaaagaatctaacatatcatttttaattgcat-tgta----cagCAACTTTTGTTCTTCATCATCCGGAGCATGGTCATGCAGTTGCACATCCAATTCTTTCACGCATCATAGATGGGACGCTGTGCTATGATAGACATGGTCC
                                ||  |   ||||   ||  | |   ||  || ||   |  || |       | ||| |  |  ||| |  || ||  ||||     ||| || ||||| ||||||||||| |||||||| ||||||||||  | ||||||| ||||| | || || ||||| || ||   ||||||||    | ||||
gtatttatgctctatcccatgtcagtttaacttatgattgactcaacataaatatggttaccatgatttatttctattttatttgtaataacttctttatgttttcacatgtaaatctagCGACATTTGTCCTTCATCATCCAGAGCATGGGCATGCAGTTGTGCTTCCAATTATTTCATGTATTATTGATGGTACACTAGTCTATGATAAGGCTAGTCC

upper sequence: GRMZM2G107101_T05 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA09G07240.1 (Glycine max), 3'ss of exon 4
----------------------gtaatacaaactcc--ttatggacaattgtcaggaaactcaagaaagaatct------aacatatcattt--ttaattgcat---tgtacagCAACTTTTGTTCTTCATCATCCGGAGCATGGTCATGCAGTTGCACATCCAATTCTTTCACGCATCATAGATGGGACGCTGTGCTATGATAGACATGGTCC--------------------------
                       || ||  |  | |  |||||    | |     | |||| | ||     |||      || |  | ||||  | | |  |||     | ||||     |||||||||||||||| ||||| || ||||||||||  | ||||||| ||||| | || || ||||| ||||||  ||||||||    | ||||                          
gtatagggtatttttgctttacttagtattagtttcaattatgatttactcaacagtaacttatgactatttcttgtccaaataactaatttattcattcacatgtacatccagcggtacttgttcttcatcatccagagCACGGGCATGCAGTTGTGCTTCCAATTATTTCATGTATTATTGATGGTACGCTGGACTATGATAAGACTAGTCCTCCATTTGCTTCTTTCATTTCTTTAG

upper sequence: GRMZM2G107101_T05 (Zea mays), 3'ss of exon 5
lower sequence: AT1G22770.1 (Arabidopsis thaliana), 3'ss of exon 3
--gtaatacaaactccttatggacaattgtcaggaaactcaagaaagaatctaacatatcatttttaattgcattgtacagCAACTTTTGTTCTTCATCATCCGGAGCATGGTCATGCAGTTGCACATCCAATTCTTTCACGCATCATAGATGGGACGCTGTGCTATGATAGACATGGTCC
   | ||  | | |  | ||  ||| || ||           ||| |  |||| |  ||  |  ||   || ||   ||||| |  ||||| |||||||||||||||||||||||||||||    | ||||||  ||||| |  | || |||||  || ||   ||    |   | | || 
gtatgatcaacatttatgatccacacttctctttttgtgtgtgaatg--tctatctgattttcgttttctg-atgaaacagCGATGTTTGTCCTTCATCATCCGGAGCATGGTCATGCAGTCATTCTTCCAATCATTTCATGTCTTATTGATGGCTCGTTGGTGTACAGCAAGGAAGCTCA

upper sequence: GRMZM2G107101_T05 (Zea mays), 3'ss of exon 5
lower sequence: Vv18s0157g00020.t01 (Vitis vinifera), 3'ss of exon 5
-----------------------------------gtaatacaaactccttatggacaattgtcaggaaactcaagaaagaatctaacatatcatttttaattg----cattgtacagCAACTTTTGTTCTTCATCATCCGGAGCATGGTCATGCAGTTGCACATCCAATTCTTTCACGCATCATAGATGGGACGCTGTGCTATGATAGACATGGTCC
                                    | ||| ||  |  ||||   | | | |  | |   || |  ||     ||     |   || |||||     || | | ||||||| |||||||||||||||||||| ||||| ||||| || |  | ||||||| ||||  | ||||| ||||| || |||   ||||||||   |  |||
gtattcatgtttttcaatgttgatatacctaaaaattgatataag-ttattattccctaatat--gaattttctatcaactgcatagtgacttccttataattaaaatcaattttcagCAACGTTTGTTCTTCATCATCCGGAACATGGGCATGCTGTCGTTCTTCCAATTATTTCGTGTATCATTGATGGTACACTGGTGTATGATAGGTGTACTCC

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|149079265|gb|EE168237.2|EE168237
EST:     TCAAAGTTCCTATCCATCAAAAGAAAATCGCTTGGTAGATGAAGTATTGG                         CAACTTTTGTTCTTCATCATCCGGAGCATGGTCATGCAGTTGCACATCCAA
genomic: TCAAAGTTCCTATCCATCAAAAGAAAATCGCTTGGTAGATGAAGTATTGGgtaatacaaa ... cattgtacagCAACTTTTGTTCTTCATCATCCGGAGCATGGTCATGCAGTTGCACATCCAA
EST: gi|32942831|gb|CF047650.1|CF047650
EST:     TCAAAGTTCCTATCCATCAAAAGAAAATCGCTTGGTAGATGAAGTATTGG                         CAACTTTTGTTCTTCATCATCCGGAGCATGGTCATGCAGTTGCACATCCAA
genomic: TCAAAGTTCCTATCCATCAAAAGAAAATCGCTTGGTAGATGAAGTATTGGgtaatacaaa ... cattgtacagCAACTTTTGTTCTTCATCATCCGGAGCATGGTCATGCAGTTGCACATCCAA

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: 285

CTCATTCAAAGTTCCTATCCATCAAAAGAAAATCGCTTGGTAGATGAAGTATTGGgtaatacaaa ... cattgtacagCAACTTTTGTTCTTCATCATCCGGAGCATGGTCATGCAGTTGCACATCCAATTCTTTCACGCATCATAGATGGGACGCTGTGCTATGATAGACATGGTCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 232

CTCATTCAAAGTTCCTATCCATCAAAAGAAAATCGCTTGGTAGATGAAGTATTGGgtaatacaaa ... cattgtacagCAACTTTTGTTCTTCATCATCCGGAGCATGGTCATGCAGTTGCACATCCAATTCTTTCACGCATCATAGATGGGACGCTGTGCTATGATAGACATGGTCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 228

CTCATTCAAAGTTCCTATCCATCAAAAGAAAATCGCTTGGTAGATGAAGTATTGGgtaatacaaa ... cattgtacagCAACTTTTGTTCTTCATCATCCGGAGCATGGTCATGCAGTTGCACATCCAATTCTTTCACGCATCATAGATGGGACGCTGTGCTATGATAGACATGGTCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 298

CTCATTCAAAGTTCCTATCCATCAAAAGAAAATCGCTTGGTAGATGAAGTATTGGgtaatacaaa ... cattgtacagCAACTTTTGTTCTTCATCATCCGGAGCATGGTCATGCAGTTGCACATCCAATTCTTTCACGCATCATAGATGGGACGCTGTGCTATGATAGACATGGTCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtcaggaaactcaagaaagaatctaacatatcatttttaattgcattgtacagCAACTTTTGTTCTTCATCATCCGGAGCATGGTCATGCAGTTGCACATCCAATTCTTTCACGCATCATAGATGGGACGCTGTGCTATGATAGACATGGTCC
                 aaagaatctaacatat  TA-rich tract