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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catctaagtactttaagatatagactgaacaatggtgctcctcattttgtcatgttggttatcttggaaccattatataatgtctgaggtggcctttcagGGAGAGGATTTAATTCGGGAAAGCGGTATTCCGTACACTATTGTAAGGCCATGTGCATTAACTGAGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGG

Basic information

species Zea mays
transcript GRMZM2G019358_T06
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G019358_T03 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os02g13970.2 (Oryza sativa), 3'ss of exon 13
catctaagtactttaagatatagactgaacaatggtgctcctcattttgt-catgt-tggttatc--ttggaaccattatataatgtctgagg--tggcctttcagGGAGAGGATTTAATTCGGGAAAGCGGTATTCCGTACACTATTGTAAGGCCATGTGCATTAACTGAGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGG
                      |  ||  | ||  | |   |  | |||| ||| | || ||||   ||   | |||     ||||  |   |  || |||||||||| ||||||||||| |||||||| || ||||| || ||||||||  ||||||||||  |||| ||||||||||||||||| || ||||| ||||||||||
----------------------gtatgcgccatttttcctttattattgtgcatttgtgcttattgattcacatcatgtctaaatgcttatcgcatgtcctttcagGGTGAGGATTTAATCCGGGAAAGTGGCATTCCATATACTATTGTGCGGCCATGTGCTCTAACAGAGGAACCAGCTGGAGCTGACCTCATATTTGACCAGG

upper sequence: GRMZM2G019358_T03 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA05G29330.2 (Glycine max), 3'ss of exon 13
--catctaagtactttaagatatagactgaacaatggtgctcctcattttgtcatgttggttatcttggaaccattatataatgtctgaggtggcctttcagGGAGAGGATTTAATTCGGGAAAGCGGTATTCCGTACACTATTGTAAGGCCATGTGCATTAACTGAGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGG
   | ||   || |    |  |||| ||    | |  |||   |||| ||  | ||     ||  |    |       | | ||  | | || ||    ||||| ||||||||| || | ||||| || ||||| ||    || || ||||| ||||||||||||||||| || ||||| |||||||| || ||||| || |
ggaacctccttattgcttgccatagcctatttagttatgcaattcatatttccctgccacatacttgttcatttgctaaaagtggtttatgttgca--acagGGCGAGGATTTACTTAGAGAAAGTGGCATTCCCTATGTAATCGTGAGGCCTTGTGCATTAACTGAGGAGCCTGCTGGTGCCGATCTTATTTTTGATCAAG

upper sequence: GRMZM2G019358_T03 (Zea mays), 3'ss of exon 11
lower sequence: Vv10s0003g01640.t01 (Vitis vinifera), 3'ss of exon 13
catctaa-gtactttaagatatagactgaacaatggtg-ctcctcattttgtcatgttggttatcttggaaccattatataatgtctgaggtggcctttcagGGAGAGGATTTAATTCGGGAAAGCGGTATTCCGTACACTATTGTAAGGCCATGTGCATTAACTGAGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGG
  |||   ||     ||       |||    | ||    ||||   |     |   ||  |||| ||   |   || |     |       |  |    |||||||||||||| || |||||||| ||  | || ||  | ||||| ||||| ||||||||||||||||| || |||||||| |||||||| ||||| || |
tgtcttttgttggccaactagctaactaggaagtgaaaactccatgtggcagctctttatttattttttcatttttcttagccggtcacttttaca--acagGGAGAGGATTTGATACGGGAAAGTGGAGTGCCTTATGCAATTGTGAGGCCTTGTGCATTAACTGAGGAGCCTGCTGGAGCTGATCTCATTTTTGATCAAG

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|13125927|gb|BG316602.1|BG316602
EST:     CTGTTCGATTGAACAAAGAGCTTGGCTCCATTTTAACTTTTAAGTTGAAG                         GGAGAGGATTTAATTCGGGAAAGCGGTATTCCGTACACTATTGTAAGGCCA
genomic: CTGTTCGATTGAACAAAGAGCTTGGCTCCATTTTAACTTTTAAGTTGAAGgcatgctcat ... ggcctttcagGGAGAGGATTTAATTCGGGAAAGCGGTATTCCGTACACTATTGTAAGGCCA
EST: gi|211503640|gb|FL133352.1|FL133352
EST:     CTGTTCGATTGAACAAAGAGCTTGGCTCCATTTTAACTTTTAAGTTGAAG                         GGAGAGGATTTAATTCGGGAAAGCGGTATTCCGTACACTATTGTAAGGCCA
genomic: CTGTTCGATTGAACAAAGAGCTTGGCTCCATTTTAACTTTTAAGTTGAAGgcatgctcat ... ggcctttcagGGAGAGGATTTAATTCGGGAAAGCGGTATTCCGTACACTATTGTAAGGCCA
EST: gi|16377470|gb|BI991944.1|BI991944
EST:     CTGTTCGATTGAACAAAGAGCTTGGCTCCATTTTAACTTTTAAGTTGAAG                         GGAGAGGATTTAATTCGGGAAAGCGGTATTCCGTACACTATTGTAAGGCCA
genomic: CTGTTCGATTGAACAAAGAGCTTGGCTCCATTTTAACTTTTAAGTTGAAGgcatgctcat ... ggcctttcagGGAGAGGATTTAATTCGGGAAAGCGGTATTCCGTACACTATTGTAAGGCCA
EST: gi|211503639|gb|FL133351.1|FL133351
EST:     CTGTTCGATTGAACAAAGAGCTTGGCTCCATTTTAACTTTTAAGTTGAAG                         GGAGAGGATTTAATTCGGGAAAGCGGTATTCCGTACACTATTGTAAGGCCA
genomic: CTGTTCGATTGAACAAAGAGCTTGGCTCCATTTTAACTTTTAAGTTGAAGgcatgctcat ... ggcctttcagGGAGAGGATTTAATTCGGGAAAGCGGTATTCCGTACACTATTGTAAGGCCA
EST: gi|211501308|gb|FL133349.1|FL133349
EST:     CTGTTCGATTGAACAAAGAGCTTGGCTCCATTTTAACTTTTAAGTTGAAG                         GGAGAGGATTTAATTCGGGAAAGCGGTATTCCGTACACTATTGTAAGGCCA
genomic: CTGTTCGATTGAACAAAGAGCTTGGCTCCATTTTAACTTTTAAGTTGAAGgcatgctcat ... ggcctttcagGGAGAGGATTTAATTCGGGAAAGCGGTATTCCGTACACTATTGTAAGGCCA
EST: gi|60352340|gb|DN219313.1|DN219313
EST:     CTGTTCGATTGAACAAAGAGCTTGGCTCCATTTTAACTTTTAAGTTGAAG                         GGAGAGGATTTAATTCGGGAAAGCGGTATTCCGTACACTATTGTAAGGCCA
genomic: CTGTTCGATTGAACAAAGAGCTTGGCTCCATTTTAACTTTTAAGTTGAAGgcatgctcat ... ggcctttcagGGAGAGGATTTAATTCGGGAAAGCGGTATTCCGTACACTATTGTAAGGCCA
EST: gi|211501307|gb|FL133348.1|FL133348
EST:     CTGTTCGATTGAACAAAGAGCTTGGCTCCATTTTAACTTTTATGTTGAAG                         GGAGAGGATTTAATTCGGGAAAGCGGTATTCCGTACACTATTGTAAGGCCA
genomic: CTGTTCGATTGAACAAAGAGCTTGGCTCCATTTTAACTTTTAAGTTGAAGgcatgctcat ... ggcctttcagGGAGAGGATTTAATTCGGGAAAGCGGTATTCCGTACACTATTGTAAGGCCA
EST: gi|12968100|gb|BG265047.1|BG265047
EST:     TTAAGTTGAAG                         GGAGAGGATTTAATTCGGGAAAGCGGTATTCCGTACACTATTGTAAGGCCA
genomic: TTAAGTTGAAGgcatgctcat ... ggcctttcagGGAGAGGATTTAATTCGGGAAAGCGGTATTCCGTACACTATTGTAAGGCCA
EST: gi|71760712|gb|DR958649.1|DR958649
EST:     CTGTTCGATTGAACAAAGAGCTTGGCTCCATTTTAACTTTTAAGTTGAAG                         GGAGAGGATTTAATTCGGGAAAGCGGTATTCCGTACACTATTGTAAGGCCA
genomic: CTGTTCGATTGAACAAAGAGCTTGGCTCCATTTTAACTTTTAAGTTGAAGgcatgctcat ... ggcctttcagGGAGAGGATTTAATTCGGGAAAGCGGTATTCCGTACACTATTGTAAGGCCA
EST: gi|16378431|gb|BI992443.1|BI992443
EST:     CTGTTCGATTGAACAAAGAGCTTGGCTCCATTTTAACTTTTAAGTTGAAG                         GGAGAGGATTTAATTCGGGAAAGCGGTATTCCGTACACTATTGTAAGGCCA
genomic: CTGTTCGATTGAACAAAGAGCTTGGCTCCATTTTAACTTTTAAGTTGAAGgcatgctcat ... ggcctttcagGGAGAGGATTTAATTCGGGAAAGCGGTATTCCGTACACTATTGTAAGGCCA
EST: gi|148936819|gb|EC880960.2|EC880960
EST:     CTGTTGGATTGAACAAAGAGCTTGGCTCCATTTTAACTTTTAAGTTGAAG                         GGAGAGGATTTAATTCGGGAAAGCGGTATTCCGTACACTATTGTAAGGCCA
genomic: CTGTTCGATTGAACAAAGAGCTTGGCTCCATTTTAACTTTTAAGTTGAAGgcatgctcat ... ggcctttcagGGAGAGGATTTAATTCGGGAAAGCGGTATTCCGTACACTATTGTAAGGCCA
EST: gi|12967873|gb|BG264820.1|BG264820
EST:     CTGTTCGATTGAACAAAGAGCTTGGCTCCATTTTAACTTTTAAGTTGAAG                         GGAGAGGATTTAATTCGGGAAAGCGGTATTCCGTACACTATTGTAAGGCCA
genomic: CTGTTCGATTGAACAAAGAGCTTGGCTCCATTTTAACTTTTAAGTTGAAGgcatgctcat ... ggcctttcagGGAGAGGATTTAATTCGGGAAAGCGGTATTCCGTACACTATTGTAAGGCCA
EST: gi|211503638|gb|FL133350.1|FL133350
EST:     CTGTTCGATTGAACAAAGAGCTTGGCTCCATTTTAACTTTTAAGTTGAAG                         GGAGAGGATTTAATTCGGGAAAGCGGTATTCCTTACACTATTGTAAGGCCA
genomic: CTGTTCGATTGAACAAAGAGCTTGGCTCCATTTTAACTTTTAAGTTGAAGgcatgctcat ... ggcctttcagGGAGAGGATTTAATTCGGGAAAGCGGTATTCCGTACACTATTGTAAGGCCA

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: 48 (upstream exon), 46 (downstream exon)
Score: 58

AGTTACAAGACCTGAAAGACCGGGGTTAGATTTAAGCAAGCAGCCACCTGCTGTTCGATTGAACAAAGAGCTTGGCTCCATTTTAACTTTTAAGTTGAAGgcatgctcat ... ggcctttcagGGAGAGGATTTAATTCGGGAAAGCGGTATTCCGTACACTATTGTAAGGCCATGTGCATTAACTGAGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 93

AGTTACAAGACCTGAAAGACCGGGGTTAGATTTAAGCAAGCAGCCACCTGCTGTTCGATTGAACAAAGAGCTTGGCTCCATTTTAACTTTTAAGTTGAAGgcatgctcat ... ggcctttcagGGAGAGGATTTAATTCGGGAAAGCGGTATTCCGTACACTATTGTAAGGCCATGTGCATTAACTGAGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 11

AGTTACAAGACCTGAAAGACCGGGGTTAGATTTAAGCAAGCAGCCACCTGCTGTTCGATTGAACAAAGAGCTTGGCTCCATTTTAACTTTTAAGTTGAAGgcatgctcat ... ggcctttcagGGAGAGGATTTAATTCGGGAAAGCGGTATTCCGTACACTATTGTAAGGCCATGTGCATTAACTGAGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 62

AGTTACAAGACCTGAAAGACCGGGGTTAGATTTAAGCAAGCAGCCACCTGCTGTTCGATTGAACAAAGAGCTTGGCTCCATTTTAACTTTTAAGTTGAAGgcatgctcat ... ggcctttcagGGAGAGGATTTAATTCGGGAAAGCGGTATTCCGTACACTATTGTAAGGCCATGTGCATTAACTGAGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtcatgttggttatcttggaaccattatataatgtctgaggtggcctttcagGGAGAGGATTTAATTCGGGAAAGCGGTATTCCGTACACTATTGTAAGGCCATGTGCATTAACTGAGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGG
                                               cctttc  CT-rich tract
                      aaccattatataat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catctaagtactttaagatatagactgaacaatggtgctcctcattttgtcatgttggttatcttggaaccattatataatgtctgaggtggcctttcagGGAGAGGATTTAATTCGGGAAAGCGGTATTCCGTACACTATTGTAAGGCCATGTGCATTAACTGAGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - ctgaaca
- - - - - - - - - - - - - - - - tggtgct
- - - - - - - - - - - - - - - - - - - - - - - - - - tgttggt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgtctg