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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtttgaaccttgatatttgagaatcatttgcttgaaacatatcacatcagaactttaatgctcaacgttaagctcaaaagttaattatctggttatgtagGAAGGTCATCCATACTGTGGGCCCAAAATATGCTGTAAAGTATCACACAGCTGCAGAGAATGCGCTTAGCCACTGCTACAGGTCTTGTCTAGAACTGCTC

Basic information

species Zea mays
transcript GRMZM2G100707_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G100707_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g05660.1 (Oryza sativa), 3'ss of exon 3
----gtttgaaccttgatatttgagaatcatttgcttgaaacatatcacatcagaactttaatgctcaacgttaagctcaaaagttaattatctggttatgtagGAAGGTCATCCATACTGTGGGCCCAAAATATGCTGTAAAGTATCACACAGCTGCAGAGAATGCGCTTAGCCACTGCTACAGGTCTTGTCTAGAACTGCTC
     |  | |  ||  | | |   | | || || ||   | ||   |||     |     ||||||  |  | | ||  || | | || |  ||||   | |||||||| || |||||||||||||| ||||||||||| |||||||||||||||||||||||||| |||||||||||||||||||||||| | ||||| |||
ctacctgaggatgttagtttatttca-tgatatggttttgagatgatacactgatatac--atgctcttcactgacctataatgcttatgaa-tggtctggcagGAAGGTAATTCATACTGTGGGCCCTAAATATGCTGTCAAGTATCACACAGCTGCAGAGAATGCACTTAGCCACTGCTACAGGTCTTGTTTGGAACTTCTC

upper sequence: GRMZM2G100707_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA02G12670.1 (Glycine max), 3'ss of exon 4
gtttgaaccttgatatttgagaatcatttgcttgaaacatatcacatcagaactttaatgctcaacgttaagctcaaaagttaattatctggttat-----gtagGAAGGTCATCCATACTGTGGGCCCAAAATATGCTGTAAAGTATCACACAGCTGCAGAGAATGCGCTTAGCCACTGCTACAGGTCTTGTCTAGAACTGCTC
    |   |   ||||||     | | |||| || ||  | ||    |  ||  |||     | || |        ||| |||    |    | ||     | ||||| || ||||||||||| |||||||| ||||||   ||||| || || ||||||||||||||  | ||||| |||||  | ||||| ||||||||  | 
----gctgccctatatttcttttttagttgcatgtaat-tctcttggctaaaagttagattcctacctagcatctgaaatttatgccttcaataatttcttgcagGAAAGTTATCCATACTGTTGGCCCAAAGTATGCTTCGAAGTACCAAACTGCTGCAGAGAATGCTTTAAGCCATTGCTATCGTTCTTGCCTAGAACTTTTA

upper sequence: GRMZM2G100707_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA01G06730.1 (Glycine max), 3'ss of exon 4
-gtttgaaccttgatatttgagaatcatttgcttgaaacatatcacatcagaactttaatgctcaacgtt--aagctcaaaagttaattatctggttatgtagGAAGGTCATCCATACTGTGGGCCCAAAATATGCTGTAAAGTATCACACAGCTGCAGAGAATGCGCTTAGCCACTGCTACAGGTCTTGTCTAGAACTGCTC
 |||    || | ||||||     | | |||| |  ||           | || ||  || |  | | |   ||  | |    || | ||  |  |  || ||||| || ||||||||||| |||||||| ||||||   ||||| || || ||||||||||||||  | ||||| |||||  | ||||| ||||||||  | 
tgttgctgccct-atatttcctccttagttgcatataattctcttggctaaaagttagattcctagcatatgaaatttatgccttcaataatt--tcgtgcagGAAAGTTATCCATACTGTTGGCCCAAAGTATGCTTCGAAGTACCAAACTGCTGCAGAGAATGCCTTAAGCCATTGCTATCGTTCTTGCCTAGAACTTTTA

upper sequence: GRMZM2G100707_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT1G69340.1 (Arabidopsis thaliana), 3'ss of exon 4
gtttgaaccttgatatttgagaatcatttgcttgaaacat--atcacatcagaactttaatgctcaacgttaagctcaaaagttaattatctgg---ttatgtagGAAGGTCATCCATACTGTGGGCCCAAAATATGCTGTAAAGTATCACACAGCTGCAGAGAATGCGCTTAGCCACTGCTACAGGTCTTGTCTAGAACTGCTC
      |||  |   | || |   | ||    || |   |  |  | ||  |  | ||| | | |||| | ||    |   |||  || | ||    || |  |||| ||| |||||||| || || || || ||||| ||||||||||| |||||||| |||||||| || || |||||||| || |||||||| ||||| |||
----ataccaagcattctgtgcgactttaatatggactgtgaaatagatttgtgccttagtccccaac-tcaaaaaaatgtgttttttgtttgtcttttgttcagGAGGGTTATCCATACAGTAGGACCCAAGTATGCAGTAAAGTATCATACAGCTGCTGAGAATGCTCTAAGTCACTGCTATAGATCTTGTCTGGAACTTCTC

upper sequence: GRMZM2G100707_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv01s0011g00870.t01 (Vitis vinifera), 3'ss of exon 3
-gtttgaacct-tgatatttgagaatcatttgcttgaaacatatcacatcagaactttaatgctcaacgttaagct-caaaagttaattatctggttatg-tagGAAGGTCATCCATACTGTGGGCCCAAAATATGCTGTAAAGTATCACACAGCTGCAGAGAATGCGCTTAGCCACTGCTACAGGTCTTGTCTAGAACTGCTC
  | | |||       ||        |||||| || |    | | |   ||    |||| | || || | | |         |||  ||      ||||| ||||| ||| || ||||||||||| || || ||||| ||||| ||||| || ||||||||||||||  | || ||||||||  ||||||| || ||||| || 
catatcaacaaacagcatacatactccatttgtttaa----ttttagggcatgtgtttattacttaaagctgattgattcttgtttcttgctatcttatggtagGAGGGTTATTCATACTGTGGGTCCCAAGTATGCAGTAAAATATCATACTGCTGCAGAGAATGCTTTGAGTCACTGCTATCGGTCTTGCCTTGAACTTCTT

upper sequence: GRMZM2G100707_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ24833 (Selaginella moellendorffii), 3'ss of exon 3
gtttgaaccttgatatttgagaatcatttgcttgaaacatatcacatcagaactttaatgctcaacgttaagctcaaaagttaattatctggttatgtagGAAGGTCATCCATACTGTGGGCCCAAAATATGCTGTAAAGTATCACACAGCTGCAGAGAATGCGCTTAGCCACTGCTACAGGTCTTGTCTAGAACTGCTC
                            | |||| ||   |||||||||    |||  |||   |        |||     || |   ||  || | ||||   ||||| || |||||||| ||   ||| ||||| ||||||||||||||||| || ||||| || || || ||||| ||||||||||| || || || 
---------------------------gtacttggaa---atcacatca----ttttgtgcatga--------tca-----tagtacgctttttctctagGCGTGTCATTCACACTGTGGGTCCTCGATACGCTGTGAAGTATCACACAGCTGCTGAAAATGCCCTGAGTCATTGCTATAGGTCTTGTCTTGAGCTCCTA

upper sequence: GRMZM2G100707_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ30302 (Selaginella moellendorffii), 3'ss of exon 3
gtttgaaccttgatatttgagaatcatttgcttgaaacatatcacatcagaactttaatgctcaacgttaagctcaaaagttaattatctggttatgtagGAAGGTCATCCATACTGTGGGCCCAAAATATGCTGTAAAGTATCACACAGCTGCAGAGAATGCGCTTAGCCACTGCTACAGGTCTTGTCTAGAACTGCTC
                            | |||| ||   |||||||||    |||  |||   |        |||     || |   ||  || | ||||   ||||| || |||||||| ||   ||| ||||| ||||||||||||||||| || ||||| ||||| || ||||| ||||||||||| || || || 
---------------------------gtacttggaa---atcacatca----ttttgtgcatga--------tca-----tagtacgctttttctctagGCGTGTCATTCACACTGTGGGTCCTCGATACGCTGTGAAGTATCACACAGCTGCTGAAAATGCCCTTAGTCATTGCTATAGGTCTTGTCTTGAGCTCCTA

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|149097071|gb|EE182878.2|EE182878
EST:     TGCCGCACTGGGATGGCTAAGATGACAAATGCTTATGATTTGCCTGCCAG                         GAAGGTCATCCATACTGTGGGCCCAAAATATGCTGTAAAGTATCACACAGC
genomic: TGCCGCACTGGGATGGCTAAGATGACAAATGCTTATGATTTGCCTGCCAGgtatgtcatt ... ggttatgtagGAAGGTCATCCATACTGTGGGCCCAAAATATGCTGTAAAGTATCACACAGC
EST: gi|93015869|gb|EB641389.1|EB641389
EST:     TGCCGCACTGGGATGGCTAAGATGACAAATGCTTATGATTTGCCTGCCAG                         GAAGGTCATCCATACTGTGGGCCCAAAATATGCTGTAAAGTATCACACAGC
genomic: TGCCGCACTGGGATGGCTAAGATGACAAATGCTTATGATTTGCCTGCCAGgtatgtcatt ... ggttatgtagGAAGGTCATCCATACTGTGGGCCCAAAATATGCTGTAAAGTATCACACAGC
EST: gi|71763741|gb|DR961678.1|DR961678
EST:     TGCCGCACTGGGATGGCTAAGATGACAAATGCTTATGATTTGCCTGCCAG                         GAAGGTCATCCATACTGTGGGCCCAAAATATGCTGTAAAGTATCACACAGC
genomic: TGCCGCACTGGGATGGCTAAGATGACAAATGCTTATGATTTGCCTGCCAGgtatgtcatt ... ggttatgtagGAAGGTCATCCATACTGTGGGCCCAAAATATGCTGTAAAGTATCACACAGC
EST: gi|148965131|gb|EE015945.2|EE015945
EST:     TGCCGCACTGGGATGGCTAAGATGACAAATGCTTATGATTTGCCTGCCAG                         GAAGGTCATCCATACTGTGGGCCCAAAATATGCTGTAAAGTATCACACAGC
genomic: TGCCGCACTGGGATGGCTAAGATGACAAATGCTTATGATTTGCCTGCCAGgtatgtcatt ... ggttatgtagGAAGGTCATCCATACTGTGGGCCCAAAATATGCTGTAAAGTATCACACAGC
EST: gi|60342456|gb|DN209429.1|DN209429
EST:     TGCCGCACTGGGATGGCTAAGATGACAAATGCTTATGATTTGCCTGCCAG                         GAAGGTCATCCATACTGTGGGCCCAAAATATGCTGTAAAGTATCACACAGC
genomic: TGCCGCACTGGGATGGCTAAGATGACAAATGCTTATGATTTGCCTGCCAGgtatgtcatt ... ggttatgtagGAAGGTCATCCATACTGTGGGCCCAAAATATGCTGTAAAGTATCACACAGC
EST: gi|149110834|gb|EE294332.2|EE294332
EST:     TGCCGCACTGGGATGGCTAAGATGACAAATGCTTATGATTTGCCTGCCAG                         GAAGGTCATCCATACTGTGGGCCCAAAATATGCTGTAAAGTATCACACAGC
genomic: TGCCGCACTGGGATGGCTAAGATGACAAATGCTTATGATTTGCCTGCCAGgtatgtcatt ... ggttatgtagGAAGGTCATCCATACTGTGGGCCCAAAATATGCTGTAAAGTATCACACAGC
EST: gi|31351359|gb|CD435716.1|CD435716
EST:     TGCCGCACTGGGATGGCTAAGATGACAAATGCTTATGATTTGCCTGCCAG                         GAAGGTCATCCATACTGTGGGCCCAAAATATGCTGTAAAGTATCACACAGC
genomic: TGCCGCACTGGGATGGCTAAGATGACAAATGCTTATGATTTGCCTGCCAGgtatgtcatt ... ggttatgtagGAAGGTCATCCATACTGTGGGCCCAAAATATGCTGTAAAGTATCACACAGC
EST: gi|88754428|gb|DY538569.1|DY538569
EST:     TGCCGCACTGGGATGGCTAAGATGACAAATGCTTATGATTTGCCTGCCAG                         GAAGGTCATCCATACTGTGGGCCCAAAATATGCTGTAAAGTATCACACAGC
genomic: TGCCGCACTGGGATGGCTAAGATGACAAATGCTTATGATTTGCCTGCCAGgtatgtcatt ... ggttatgtagGAAGGTCATCCATACTGTGGGCCCAAAATATGCTGTAAAGTATCACACAGC

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), 49 (downstream exon)
Score: 97

GGTGGCTGCCGCACTGGGATGGCTAAGATGACAAATGCTTATGATTTGCCTGCCAGgtatgtcatt ... ggttatgtagGAAGGTCATCCATACTGTGGGCCCAAAATATGCTGTAAAGTATCACACAGCTGCAGAGAATGCGCTTAGCCACTGCTACAGGTCTTGTCTAGAACTGCTC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 98

GGTGGCTGCCGCACTGGGATGGCTAAGATGACAAATGCTTATGATTTGCCTGCCAGgtatgtcatt ... ggttatgtagGAAGGTCATCCATACTGTGGGCCCAAAATATGCTGTAAAGTATCACACAGCTGCAGAGAATGCGCTTAGCCACTGCTACAGGTCTTGTCTAGAACTGCTC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 122

GGTGGCTGCCGCACTGGGATGGCTAAGATGACAAATGCTTATGATTTGCCTGCCAGgtatgtcatt ... ggttatgtagGAAGGTCATCCATACTGTGGGCCCAAAATATGCTGTAAAGTATCACACAGCTGCAGAGAATGCGCTTAGCCACTGCTACAGGTCTTGTCTAGAACTGCTC


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 90

GGTGGCTGCCGCACTGGGATGGCTAAGATGACAAATGCTTATGATTTGCCTGCCAGgtatgtcatt ... ggttatgtagGAAGGTCATCCATACTGTGGGCCCAAAATATGCTGTAAAGTATCACACAGCTGCAGAGAATGCGCTTAGCCACTGCTACAGGTCTTGTCTAGAACTGCTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcagaactttaatgctcaacgttaagctcaaaagttaattatctggttatgtagGAAGGTCATCCATACTGTGGGCCCAAAATATGCTGTAAAGTATCACACAGCTGCAGAGAATGCGCTTAGCCACTGCTACAGGTCTTGTCTAGAACTGCTC
                                 agttaat  putative branch site (score: 90)
                            tcaaaagttaattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgaaccttgatatttgagaatcatttgcttgaaacatatcacatcagaactttaatgctcaacgttaagctcaaaagttaattatctggttatgtagGAAGGTCATCCATACTGTGGGCCCAAAATATGCTGTAAAGTATCACACAGCTGCAGAGAATGCGCTTAGCCACTGCTACAGGTCTTGTCTAGAACTGCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - tgcttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - aatgctc