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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttctggtcaatatatcacaaagtttatgatttattatgcttatcattattaatttattatattctcatgcccctttggtccatccatatgaataaaatatttttggttttcatctgcttcttgaaacttacttatcatgtacatgttggtattctgatttctgatgacagCTCCAAATGGATACACTGCAAAGCCGACTTGATGCAGAGTTCCTTCTAGCTCATATGTGTTCAGTCAAGTTTAAGGAATGGATCGTGGTGCTAGCTACTT

Basic information

species Zea mays
transcript GRMZM2G475867_T01
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G475867_T01 (Zea mays), 3'ss of exon 19
lower sequence: LOC_Os02g54500.1 (Oryza sativa), 3'ss of exon 19
gttctggtcaatatatcacaaagtttatgatttattatgcttatcattattaatttattatattctcatgcccctttggtccatccatatgaataaaatatttttggttttcatctgcttcttgaaacttacttatcatgtacatgttggtattctgatttctgatgacagCTCCAAATGGATACACTGCAAAGCCGACTTGATGCAGAGTTCCTTCTAGCTCATATGTGTTCAGTCAAGTTTAAGGAATGGATCGTGGTGCTAGCTACTT
                                                             | ||  || ||        | ||  |   ||| ||  |   |    || | ||||||  |||| | |||  || |||| || |  ||| |||||||||       ||||||| |||||||| || || ||||| || |||||||| ||||||||||| ||||| |||||||| |||||||||||||||||||| || |||||||| ||||
------------------------------------------------------------cactca-atacctgagcaaccaatataccagaacaatctcgctgatattattatctgc--cttggatctttgttctcatttata-attgatattctgat-------gacagCTTCAAATGGACACTCTTCAAAGTCGGCTTGATGCTGAGTTCCTTCTTGCTCACATGTGTTCTGTCAAGTTTAAGGAATGGATTGTTGTGCTAGCAACTT

upper sequence: GRMZM2G475867_T01 (Zea mays), 3'ss of exon 19
lower sequence: GLYMA18G47050.1 (Glycine max), 3'ss of exon 20
gttctggtcaatatatcacaaagtttatgatttattatgcttatcattattaatttattatattctcatgcccctttggtccatccatatgaataaaatatttttggttttcatctgcttcttgaaacttacttatcatgtacatgttggtattctgatttctgatgacagCTCCAAATGGATACACTGCAAAGCCGACTTGATGCAGAGTTCCTTCTAGCTCATATGTGTTCAGTCAAGTTTAAGGAATGGATCGTGGTGCTAGCTACTT
                                                          |||| | | | | |       |  |  ||| ||     |   |     || | ||| ||  |  ||| | || ||| |        | |||  |  ||  ||| || |  ||||| |||||||  ||| | || |||||  | ||||| || || || ||| |||||||||| || |||||||||||||||||||| || || || |||||| 
--------------------------------------------------------gctataatgtaaagtc-------ttaaatcatttggcaggagctt-----gtctacatttg--tgctgatattttctttttgctcctttattga-acactattttttgttatcagCTTCAAATGGGAACATTACAGAGCCGTTTGGATGCTGACTTTCTCCTATCTCATATGTGCTCTGTCAAGTTTAAGGAATGGATAGTTGTCCTGGCTACTC

upper sequence: GRMZM2G475867_T01 (Zea mays), 3'ss of exon 19
lower sequence: Vv15s0046g01890.t01 (Vitis vinifera), 3'ss of exon 20
gttctggtcaatatatcacaaagtttatgatttattatgcttatcattattaatttattatattctcatgcccctttggtccatccatatgaataaaatatttttggttttcatctgcttcttgaaacttacttatcatgtacatgttggtattctgatttctgatgacagCTCCAAATGGATACACTGCAAAGCCGACTTGATGCAGAGTTCCTTCTAGCTCATATGTGTTCAGTCAAGTTTAAGGAATGGATCGTGGTGCTAGCTACTT
                                                           | ||| |        |||||   ||  |    |  |  |    | |   |||| | |  || ||||   ||| ||            ||| | |  || ||  |  |  |||||  |||||| ||| ||||| ||||| || ||||||||||||||| | ||||||||||| || || |||||||| || ||||| || || || |||||| 
-----------------------------------------------------------agatttttgataaattttggagtattgaggcaagcatga---ctgttaatttctttttttttttgacctttatttgat---------ttgatttattgtttcatattttcagCTTGAAATGGGTACGCTGCAGAGCCGGCTGGATGCAGAGTTCCTTTTGGCTCATATGTGCTCTGTTAAGTTTAAAGAGTGGATAGTTGTCCTGGCTACTC

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|32924522|gb|CF029334.1|CF029334
EST:     CTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAG                         CTCCAAATGGATACACTGCAAAGCCGACTTGATGCA
genomic: CTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAGgttctggtca ... ctgatgacagCTCCAAATGGATACACTGCAAAGCCGACTTGATGCA
EST: gi|32924638|gb|CF029450.1|CF029450
EST:     CTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAG                         CTCCAAATGGGTACACTGCAAAGCCGACTTGATGCAGAGTTCCTTCTAGCT
genomic: CTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAGgttctggtca ... ctgatgacagCTCCAAATGGATACACTGCAAAGCCGACTTGATGCAGAGTTCCTTCTAGCT
EST: gi|32924314|gb|CF029126.1|CF029126
EST:     CTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAG                         CTCCAAATGGATACACTGCAAAGCCGACTTGATGCAGAGTTCCTTCTAGCT
genomic: CTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAGgttctggtca ... ctgatgacagCTCCAAATGGATACACTGCAAAGCCGACTTGATGCAGAGTTCCTTCTAGCT
EST: gi|71760706|gb|DR958643.1|DR958643
EST:     ATTTTGCTTCTGCACTCGAACTGATTGGACAAAAG                         CTCCAAATGGATACACTGCAAAGCCGACTTGATGCAGAGTTCCTTCTAGCT
genomic: ATTTTGCTTCTGCACTCGAACTGATTGGACAAAAGgttctggtca ... ctgatgacagCTCCAAATGGATACACTGCAAAGCCGACTTGATGCAGAGTTCCTTCTAGCT
EST: gi|32848274|gb|CD987955.1|CD987955
EST:     CTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAG                         CTCCAAATGGATACACTGCAAAGCCGACTTGATGCAGAGTTCCTTCTAGCT
genomic: CTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAGgttctggtca ... ctgatgacagCTCCAAATGGATACACTGCAAAGCCGACTTGATGCAGAGTTCCTTCTAGCT
EST: gi|32924177|gb|CF028989.1|CF028989
EST:     CTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAACAG                         CTCCAAATGGATACACTGCAAAGCCGACTTGATG
genomic: CTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAGgttctggtca ... ctgatgacagCTCCAAATGGATACACTGCAAAGCCGACTTGATG
EST: gi|32924022|gb|CF028834.1|CF028834
EST:     CTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAG                         CTCCAAATGGATACACTGCAAAGCCGACTTGATGCAGAGTTCCTTCTAGCT
genomic: CTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAGgttctggtca ... ctgatgacagCTCCAAATGGATACACTGCAAAGCCGACTTGATGCAGAGTTCCTTCTAGCT
EST: gi|32924179|gb|CF028991.1|CF028991
EST:     CTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAG                         CTCCAAATGGATACACTGCAAAGCCGACTTGATGCAGAGTTCCTTCTAGCT
genomic: CTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAGgttctggtca ... ctgatgacagCTCCAAATGGATACACTGCAAAGCCGACTTGATGCAGAGTTCCTTCTAGCT
EST: gi|32924558|gb|CF029370.1|CF029370
EST:     CTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAG                         CTCCAAATGGGTACACTGCAAAGCCGACTTGATGCAGAGTTCCTTCTAGCT
genomic: CTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAGgttctggtca ... ctgatgacagCTCCAAATGGATACACTGCAAAGCCGACTTGATGCAGAGTTCCTTCTAGCT
EST: gi|78024464|gb|DV492851.1|DV492851
EST:     CTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAGATGACAG                   
genomic: CTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGAC---A-A--A-AGgttctggtca ... ctga
EST: gi|32923896|gb|CF028708.1|CF028708
EST:     CTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAG                         CTCCAAATGGATACACTGCAAAGCCGACTTGATGCAGAGTTCCTTCTAGCT
genomic: CTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAGgttctggtca ... ctgatgacagCTCCAAATGGATACACTGCAAAGCCGACTTGATGCAGAGTTCCTTCTAGCT
EST: gi|32923795|gb|CF028607.1|CF028607
EST:     CTGCTCGTCTGGAGAATTTTGCTTCTACACTCGAACTGATTGGACAAAAG                         CTCCAAATGGATACACTGCAAAGCCGACTTGATGCAGAGTTCCTTCTAGCT
genomic: CTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAGgttctggtca ... ctgatgacagCTCCAAATGGATACACTGCAAAGCCGACTTGATGCAGAGTTCCTTCTAGCT
EST: gi|32924605|gb|CF029417.1|CF029417
EST:     CTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAG                         CTCCAAATGGATACACTGCAAAGCCGACTTGATGCAGAGTTCCTTCTAGCT
genomic: CTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAGgttctggtca ... ctgatgacagCTCCAAATGGATACACTGCAAAGCCGACTTGATGCAGAGTTCCTTCTAGCT
EST: gi|32924330|gb|CF029142.1|CF029142
EST:     CTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAG                         CTCCAAATGGATACACTGCAAAGCCGACTTGATGCAGAGTTCCTTCTAGCT
genomic: CTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAGgttctggtca ... ctgatgacagCTCCAAATGGATACACTGCAAAGCCGACTTGATGCAGAGTTCCTTCTAGCT
EST: gi|9952965|gb|BE639548.1|BE639548
EST:     CTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAG                         CTCCAAATGGATACACTGCAAAGCCGACTTGATGCAGAGTTCCTTCTAGCT
genomic: CTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAGgttctggtca ... ctgatgacagCTCCAAATGGATACACTGCAAAGCCGACTTGATGCAGAGTTCCTTCTAGCT
EST: gi|32923682|gb|CF028494.1|CF028494
EST:     CTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAG                         CTCCAAATGGATACACTGCAAAGCCGACTTGATGCAGAGTTCCTTCTAGCT
genomic: CTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAGgttctggtca ... ctgatgacagCTCCAAATGGATACACTGCAAAGCCGACTTGATGCAGAGTTCCTTCTAGCT
EST: gi|32924338|gb|CF029150.1|CF029150
EST:     CTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAG                         CTCCAAATGGATACACTGCAAAGCCGACTTGATGCAGAGTTCCTTCTAGCT
genomic: CTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAGgttctggtca ... ctgatgacagCTCCAAATGGATACACTGCAAAGCCGACTTGATGCAGAGTTCCTTCTAGCT
EST: gi|9952966|gb|BE639549.1|BE639549
EST:     CTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAG                         CTCCAAATGGATACACTGCAAAGCCGACTTGATGCAGAGTTCCTTCTAGCT
genomic: CTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAGgttctggtca ... ctgatgacagCTCCAAATGGATACACTGCAAAGCCGACTTGATGCAGAGTTCCTTCTAGCT
EST: gi|32924097|gb|CF028909.1|CF028909
EST:     CTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAG                         CTCCAAATGGATACACTGCAAAGCCGACTTGATGCAGAGTTCCTTCTAGCT
genomic: CTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAGgttctggtca ... ctgatgacagCTCCAAATGGATACACTGCAAAGCCGACTTGATGCAGAGTTCCTTCTAGCT
EST: gi|32923641|gb|CF028453.1|CF028453
EST:     CTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAG                         CTCCAAATGGGTACACTGCAAAGCCGACTTGATGCAGAGTTCCTTCTAGCT
genomic: CTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAGgttctggtca ... ctgatgacagCTCCAAATGGATACACTGCAAAGCCGACTTGATGCAGAGTTCCTTCTAGCT
EST: gi|32924376|gb|CF029188.1|CF029188
EST:     CTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAG                         CTCCAAATGGATACACTGCAAAGCCGACTTGATGCAGAGTTCCTTCTAGCT
genomic: CTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAGgttctggtca ... ctgatgacagCTCCAAATGGATACACTGCAAAGCCGACTTGATGCAGAGTTCCTTCTAGCT
EST: gi|32924146|gb|CF028958.1|CF028958
EST:     CTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAG                         CTCCAAATGGATACACTGCAAAGCCGACTTGATGCAGAGTTCCTTCTAGCT
genomic: CTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAGgttctggtca ... ctgatgacagCTCCAAATGGATACACTGCAAAGCCGACTTGATGCAGAGTTCCTTCTAGCT
EST: gi|32923916|gb|CF028728.1|CF028728
EST:     CTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAG                         CTCCAAATGGATACACCGCAAAGCCGACTTGATGCAGAGTTCCTTCTAGCT
genomic: CTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAGgttctggtca ... ctgatgacagCTCCAAATGGATACACTGCAAAGCCGACTTGATGCAGAGTTCCTTCTAGCT
EST: gi|32923936|gb|CF028748.1|CF028748
EST:     CTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAG                         CTCCAAATGGGTACACTGCAAAGCCGACTTGATGCAGAGTTCCTTCTAGCT
genomic: CTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAGgttctggtca ... ctgatgacagCTCCAAATGGATACACTGCAAAGCCGACTTGATGCAGAGTTCCTTCTAGCT
EST: gi|56462016|gb|CK986314.1|CK986314
EST:     CTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAG                         CTCCAAATGGATACACTGCAAAGCCGACTTGATGCAGAGTTCCTTCTAGCT
genomic: CTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAGgttctggtca ... ctgatgacagCTCCAAATGGATACACTGCAAAGCCGACTTGATGCAGAGTTCCTTCTAGCT
EST: gi|32923696|gb|CF028508.1|CF028508
EST:     CTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAG                         CTCCAAATGGATACACTGCAAAGCCGACTTGATGCAGAGTTCCTTCTAGCT
genomic: CTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAGgttctggtca ... ctgatgacagCTCCAAATGGATACACTGCAAAGCCGACTTGATGCAGAGTTCCTTCTAGCT
EST: gi|32924087|gb|CF028899.1|CF028899
EST:     CTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAG                         CTCCAAATGGATACACTGCAAAGCCGACTTGATGCAGAGTTCCTTCTAGCT
genomic: CTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAGgttctggtca ... ctgatgacagCTCCAAATGGATACACTGCAAAGCCGACTTGATGCAGAGTTCCTTCTAGCT

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), 31 (downstream exon)
Score: 15

GAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAGgttctggtca ... ctgatgacagCTCCAAATGGATACACTGCAAAGCCGACTTGATGCAGAGTTCCTTCTAGCTCATATGTGTTCAGTCAAGTTTAAGGAATGGATCGTGGTGCTAGCTACTT


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 15

GAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAGgttctggtca ... ctgatgacagCTCCAAATGGATACACTGCAAAGCCGACTTGATGCAGAGTTCCTTCTAGCTCATATGTGTTCAGTCAAGTTTAAGGAATGGATCGTGGTGCTAGCTACTT


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 22

GAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAGgttctggtca ... ctgatgacagCTCCAAATGGATACACTGCAAAGCCGACTTGATGCAGAGTTCCTTCTAGCTCATATGTGTTCAGTCAAGTTTAAGGAATGGATCGTGGTGCTAGCTACTT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 39

GAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAGgttctggtca ... ctgatgacagCTCCAAATGGATACACTGCAAAGCCGACTTGATGCAGAGTTCCTTCTAGCTCATATGTGTTCAGTCAAGTTTAAGGAATGGATCGTGGTGCTAGCTACTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttcttgaaacttacttatcatgtacatgttggtattctgatttctgatgacagCTCCAAATGGATACACTGCAAAGCCGACTTGATGCAGAGTTCCTTCTAGCTCATATGTGTTCAGTCAAGTTTAAGGAATGGATCGTGGTGCTAGCTACTT
                                          tttct  CT-rich tract
            ttacttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttctggtcaatatatcacaaagtttatgatttattatgcttatcattattaatttattatattctcatgcccctttggtccatccatatgaataaaatatttttggttttcatctgcttcttgaaacttacttatcatgtacatgttggtattctgatttctgatgacagCTCCAAATGGATACACTGCAAAGCCGACTTGATGCAGAGTTCCTTCTAGCTCATATGTGTTCAGTCAAGTTTAAGGAATGGATCGTGGTGCTAGCTACTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA