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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaacatgccttaatagttagagaaacattttcactagattttgctggcttctgcactccattgttgcttaagttatgatatattgatattacctttttagGAGAGAGATGTTAATGAGGAATCAGGATGGAAGCTTGTCCATGGCGATGTATTTCGGCCTCCCCAAAGTTTGATGTTTCTTTCTGCACTTGTTGGTATCG

Basic information

species Zea mays
transcript GRMZM2G420310_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G420310_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os12g07670.1 (Oryza sativa), 3'ss of exon 7
--------aaacatgccttaatagttagagaaacattttca-ctagattttgctggcttctgcactccattgtt-gcttaagttatgatatattgatattaccttt-ttagGAGAGAGATGTTAATGAGGAATCAGGATGGAAGCTTGTCCATGGCGATGTATTTCGGCCTCCCCAAAGTTTGATGTTTCTTTCTGCACTTGTTGGTATCG
        |    |   ||||| ||      | |  |  || |||  ||    | | ||   |          | | ||  |   | |  | |||||||| | ||| ||||||||||||||||||||||||||| |||||||||||||| ||||| ||||||||||| ||||| | |||||||   |||||||||||| ||||||| ||||
gtatatctaccttttgtttaattgtattcttagctctagcatctaagttggatttgttttcacctagtgccactcgattgggacctcaagtcttgatattccttttgttagGAGAGAGATGTTAATGAGGAATCTGGATGGAAGCTTGTTCATGGTGATGTATTTCGCCCTCCTCGAAGTTTGGCCTTTCTTTCTGCAGTTGTTGGCATCG

upper sequence: GRMZM2G420310_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 7
---------------------------aaacatgccttaatagttagagaaacattttcac------tagattttgctggcttctgcactccattgttgcttaagttatgatatattgat--attacc-----tttttagGAGAGAGATGTTAATGAGGAATCAGGATGGAAGCTTGTCCATGGCGATGTATTTCGGCCTCCCCAAAGTTTGATGTTTCTTTCTGCACTTGTTGGTATCG
                           |    |    | ||  ||    |||  | |          |||||| || |  | |    | | |||||| | |    || | |  | ||| |  |   ||     |||  |||| |||||||||| ||| ||||| || ||||| ||||| ||||| ||||| ||||||||||| |  |||||| |  ||||||| ||  |||||||||  |
gttaggctttcttgatgtttgtctgttactattattattattatttttaaaatttatgtgtggaacatagattctgttttcctggaaagttcattgtggttctgattgtcaattcttgttcaacccccaaatatttccagGAAAGAGATGTTAGTGAAGAATCTGGCTGGAAACTTGTGCATGGTGATGTTTTTCGGCCTCCTCGCAGTTTGGTTATTCTTTCAGCTGTTGTTGGTACAG

upper sequence: GRMZM2G420310_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA08G13370.1 (Glycine max), 3'ss of exon 7
--------------aaacatgcctt-aatagttagagaaacattttcactagattttgctggcttc--tgcactccattgttgcttaagttatgatatattgatattacctttttagGAGAGAGATGTTAATGAGGAATCAGGATGGAAGCTTGTCCATGGCGATGTATTTCGGCCTCCCCAAAGTTTGATGTTTCTTTCTGCACTTGTTGGTATCG
              |    |  ||| |||| || | | || ||   |  |   |  |   |   ||  ||   | | |  |||   ||  | || |  |||  |   |   ||  ||||||||||||||| ||| ||||| || ||||| ||||| ||||| ||||| ||||| || || |  |  ||  |  ||||||| ||  ||||||| |  |
gtgatggtttcatgacttttatctttaataatttgtggaatatgaacctttcttcctagagaaatcattgtggttc-taattgtcgaatatttggt-catttcttccatgcttacagGAGAGAGATGTTAGTGAAGAATCTGGCTGGAAACTTGTGCATGGTGATGTTTTTCGACCGCCTCGCAACTTAGTTATTCTTTCAGCTGTTGTTGGCACAG

upper sequence: GRMZM2G420310_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA12G29120.1 (Glycine max), 3'ss of exon 7
-----------------------------------aaacatgccttaatagtta-gagaaacattttcactagattttgctggcttctgcactccattgttgctta--agttatgatatattgatattacctttttagGAGAGAGATGTTAATGAGGAATCAGGATGGAAGCTTGTCCATGGCGATGTATTTCGGCCTCCCCAAAGTTTGATGTTTCTTTCTGCACTTGTTGGTATCG
                                    |  ||   |||| | ||| | |    |  |  | |  | ||| ||||    | || |    |  || ||   | || |  |  |       ||| |||  |||| |||||||||| ||| ||||| || ||||| ||||| ||||| ||||| ||||||||||| |  |||||| |  ||||||| ||  |||||||||  |
gtgaggctttcttgatgtttgtctgttactattattactattttttaaaatttatgtgtggaacatagattctactttcctggaaaattcattgtggttctgattgtcaattcttgttcaacccccatacatttccagGAAAGAGATGTTAGTGAAGAATCTGGCTGGAAACTTGTGCATGGTGATGTTTTTCGGCCTCCTCGCAGTTTGGTTATTCTTTCAGCTATTGTTGGTACAG

upper sequence: GRMZM2G420310_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA05G30210.1 (Glycine max), 3'ss of exon 7
--------------aaacatgccttaatagttagagaaacattttcactagattttgctggcttctgcactccatt----gttgcttaagttatgatatattgatattacctttttagGAGAGAGATGTTAATGAGGAATCAGGATGGAAGCTTGTCCATGGCGATGTATTTCGGCCTCCCCAAAGTTTGATGTTTCTTTCTGCACTTGTTGGTATCG
              |    |  ||||||  || | | || ||     ||   | || || | |   ||| |    |     ||| | ||  | || |  |||  |   |   ||  ||||||||||||||| ||| ||||| || ||||| ||||| ||||| ||||| ||||||||||| |  |  ||  |  ||||||| ||  ||||||| |  |
gtgatggtttcgtgacttttatcttaattatttgtggaatatgaatcct--ttcttactagataaagcattgtggttctaattgttgaatatttggt-catttcttccatgcttacagGAGAGAGATGTTAGTGAAGAATCTGGCTGGAAACTTGTGCATGGTGATGTTTTTCGGCCTCCTCGCAACTTAGTTATTCTTTCAGCTGTTGTTGGCACTG

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|67012575|gb|CO441324.1|CO441324
EST:     GAAACGATTATGCCAAATATGCTCGTGAAGATGATGATCTAGAGTCCCTG                         GAGAGAGATGTTAATGAGGAATCAGGATGGAAGCTTGTCCATGGCGATGTA
genomic: GAAACGATTATGCCAAATATGCTCGTGAAGATGATGATCTAGAGTCCCTGgtgaggatct ... acctttttagGAGAGAGATGTTAATGAGGAATCAGGATGGAAGCTTGTCCATGGCGATGTA
EST: gi|78079181|gb|DV507593.1|DV507593
EST:     AAGATGATGATCTAGAGTCCCTG                         GAGAGAGATG-TAATGAGGGAATCAGGATGGAAGCTTGTCCATGGCGATGT
genomic: AAGATGATGATCTAGAGTCCCTGgtgaggatct ... acctttttagGAGAGAGATGTTAATGA-GGAATCAGGATGGAAGCTTGTCCATGGCGATGT
EST: gi|21891548|gb|BQ744761.1|BQ744761
EST:     GAAACGATTATGCCAAATATGCTCGTGAAGATGATGATCTAGAGTCCCTG                         GAGAGAGATGTTAATGAGGAATCAGGATGGAAGCTTGTCCATGGCGATGTA
genomic: GAAACGATTATGCCAAATATGCTCGTGAAGATGATGATCTAGAGTCCCTGgtgaggatct ... acctttttagGAGAGAGATGTTAATGAGGAATCAGGATGGAAGCTTGTCCATGGCGATGTA
EST: gi|160481321|gb|EY254485.1|EY254485
EST:     GAAACGATTATGCCAAATATGCTCGTGAAGATGATGATCTAGAGTCCCTG                         GAGAGAGATGTTAATGAGGAATCAGGATG
genomic: GAAACGATTATGCCAAATATGCTCGTGAAGATGATGATCTAGAGTCCCTGgtgaggatct ... acctttttagGAGAGAGATGTTAATGAGGAATCAGGATG
EST: gi|71766500|gb|DR964437.1|DR964437
EST:     GAAACGATTATGCCCAATATGCTCGTGAAGATGATGATCTAGAGTCCCTG                         CAGAGAGATGTTAATGAGGAATCA
genomic: GAAACGATTATGCCAAATATGCTCGTGAAGATGATGATCTAGAGTCCCTGgtgaggatct ... acctttttagGAGAGAGATGTTAATGAGGAATCA
EST: gi|13516079|gb|BG518355.1|BG518355
EST:     GAAACGATTATGCCAAATATGCTCGTGAAGATGATGATCTAGAGTCCCTG                         GAGAGAGATGTTAATGAGGAATCAGGATGGAAGCTTGTCCATGGCGATGTA
genomic: GAAACGATTATGCCAAATATGCTCGTGAAGATGATGATCTAGAGTCCCTGgtgaggatct ... acctttttagGAGAGAGATGTTAATGAGGAATCAGGATGGAAGCTTGTCCATGGCGATGTA
EST: gi|71327794|gb|DR800533.1|DR800533
EST:     GAAACGATTATGCCAAATATGCTCGTGAAGATGATGATCTAGAGTCCCTG                         GAGAGAGATGTTAATGAGGAATCAGGATGGAAGCTTGTCCATGGCGATGTA
genomic: GAAACGATTATGCCAAATATGCTCGTGAAGATGATGATCTAGAGTCCCTGgtgaggatct ... acctttttagGAGAGAGATGTTAATGAGGAATCAGGATGGAAGCTTGTCCATGGCGATGTA
EST: gi|32931030|gb|CF035842.1|CF035842
EST:     GAAACGATTATGCCAAATATGCTCGTGAAGATGATGATCTAGAGTCCCTG                         GAGAGAGATGTTAATGAGGAATCAGGATGGAAGCTTGTCCATGGCGATGTA
genomic: GAAACGATTATGCCAAATATGCTCGTGAAGATGATGATCTAGAGTCCCTGgtgaggatct ... acctttttagGAGAGAGATGTTAATGAGGAATCAGGATGGAAGCTTGTCCATGGCGATGTA
EST: gi|67018280|gb|CO447029.1|CO447029
EST:     G-AACGATTATGCCAAATATGCTCGTGAAGATGATGATCTAGAGTCCCTG                         GAGAGAGATGTTAATGAGGAATCAGGATGGAAGCTTGTCCATGGCGATGTA
genomic: GAAACGATTATGCCAAATATGCTCGTGAAGATGATGATCTAGAGTCCCTGgtgaggatct ... acctttttagGAGAGAGATGTTAATGAGGAATCAGGATGGAAGCTTGTCCATGGCGATGTA
EST: gi|94476145|gb|EB705103.1|EB705103
EST:     GAAACGATTATGCCAAATATGCTCGTGAAGATGATGATCTAGAGTCCCTG                         GAGAGAGATGTTAATGAGGAATCAGGATGGAAGCTTGTCCATGGCGATGTA
genomic: GAAACGATTATGCCAAATATGCTCGTGAAGATGATGATCTAGAGTCCCTGgtgaggatct ... acctttttagGAGAGAGATGTTAATGAGGAATCAGGATGGAAGCTTGTCCATGGCGATGTA

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), 48 (downstream exon)
Score: 363

GGTTATTTTCCTAACTGGTTTGGTTTCGATGATATTGATGCGGACTTTGAGAAACGATTATGCCAAATATGCTCGTGAAGATGATGATCTAGAGTCCCTGgtgaggatct ... acctttttagGAGAGAGATGTTAATGAGGAATCAGGATGGAAGCTTGTCCATGGCGATGTATTTCGGCCTCCCCAAAGTTTGATGTTTCTTTCTGCACTTGTTGGTATCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 427

GGTTATTTTCCTAACTGGTTTGGTTTCGATGATATTGATGCGGACTTTGAGAAACGATTATGCCAAATATGCTCGTGAAGATGATGATCTAGAGTCCCTGgtgaggatct ... acctttttagGAGAGAGATGTTAATGAGGAATCAGGATGGAAGCTTGTCCATGGCGATGTATTTCGGCCTCCCCAAAGTTTGATGTTTCTTTCTGCACTTGTTGGTATCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 448

GGTTATTTTCCTAACTGGTTTGGTTTCGATGATATTGATGCGGACTTTGAGAAACGATTATGCCAAATATGCTCGTGAAGATGATGATCTAGAGTCCCTGgtgaggatct ... acctttttagGAGAGAGATGTTAATGAGGAATCAGGATGGAAGCTTGTCCATGGCGATGTATTTCGGCCTCCCCAAAGTTTGATGTTTCTTTCTGCACTTGTTGGTATCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 638

GGTTATTTTCCTAACTGGTTTGGTTTCGATGATATTGATGCGGACTTTGAGAAACGATTATGCCAAATATGCTCGTGAAGATGATGATCTAGAGTCCCTGgtgaggatct ... acctttttagGAGAGAGATGTTAATGAGGAATCAGGATGGAAGCTTGTCCATGGCGATGTATTTCGGCCTCCCCAAAGTTTGATGTTTCTTTCTGCACTTGTTGGTATCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggcttctgcactccattgttgcttaagttatgatatattgatattacctttttagGAGAGAGATGTTAATGAGGAATCAGGATGGAAGCTTGTCCATGGCGATGTATTTCGGCCTCCCCAAAGTTTGATGTTTCTTTCTGCACTTGTTGGTATCG
                                   tattgat  putative branch site (score: 638)
                                           ttaccttttt  CT-rich tract
                           ttatgatatattgata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaacatgccttaatagttagagaaacattttcactagattttgctggcttctgcactccattgttgcttaagttatgatatattgatattacctttttagGAGAGAGATGTTAATGAGGAATCAGGATGGAAGCTTGTCCATGGCGATGTATTTCGGCCTCCCCAAAGTTTGATGTTTCTTTCTGCACTTGTTGGTATCG

- acatgcc
- - - - - - - - - -gagaaaca
- - - - - - - - - - - - - - - - - - - -tttgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgct