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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAGgttctccctcgttttctagcactcaaatgcttgtttttttttgttactcctacgtggctgaatttgcaaaaaaaaaaaaacatttcag

Basic information

species Zea mays
transcript GRMZM2G000718_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G000718_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os07g44350.1 (Oryza sativa), 5'ss of exon 8
ACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAGgttctccctcgttttctagcactc---aaatgcttgt-ttttttttgttactcctacgtggctg-aatttgcaaaaaaaaaaaaacatttcag---------------------------------------------------------------------------
|| |||||||||||||| || |||||||||||||| || || ||||||||||||||||||||||| |||||||||||||||||||| || ||||||||| |||  | |||  | | |   | |  | | | ||  |  | |    || |  |   || |     | |    |||     | |  |                                                                            
ACAGAACAAATGAAGAGAATTGGCAATGAGCTAGACTCGGTTCACTTTTCACTGAAGAAGGCTAGCCAAATGGTGAAAGAGATTGGTCGCCAGgttctctctctctctctccccccctgcacacacgtatgttactcgtttcgtcccaaaataagtgcagccctctagttcaaatttgaactagaaggctgcactcattttgggacagatggagtatatttgaagtggctgtgcctagacttacaagattcattgctgcag
















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|148993115|gb|EE033715.2|EE033715
EST:     ACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAG                         GTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGT
genomic: ACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAGgttctccctc ... aacatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGT
EST: gi|211130915|gb|FL136653.1|FL136653
EST:     ACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAG                         GTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGT
genomic: ACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAGgttctccctc ... aacatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGT
EST: gi|6022470|gb|AW067503.1|AW067503
EST:     ACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAG                         GTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGT
genomic: ACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAGgttctccctc ... aacatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGT
EST: gi|60354623|gb|DN221596.1|DN221596
EST:     ACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAG                         GTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGT
genomic: ACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAGgttctccctc ... aacatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGT
EST: gi|30088412|gb|CB886617.1|CB886617
EST:     ACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAG                         GTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGT
genomic: ACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAGgttctccctc ... aacatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGT
EST: gi|149002889|gb|EE038886.2|EE038886
EST:     ACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAG                         GTTGCTACTGACAAATGCATTATGGCGTTCCTGGTTCTGATTGTCTGTGGT
genomic: ACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAGgttctccctc ... aacatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGT
EST: gi|16926228|gb|BM079296.1|BM079296
EST:     ACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAG                         GTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGT
genomic: ACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAGgttctccctc ... aacatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGT
EST: gi|60346808|gb|DN213781.1|DN213781
EST:     ACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAG                         GTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTATGATTGTCTGTGGT
genomic: ACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAGgttctccctc ... aacatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGT
EST: gi|28982933|gb|BQ538434.2|BQ538434
EST:     TGAAAGAGATTGGCCGTCAG                         GTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGT
genomic: TGAAAGAGATTGGCCGTCAGgttctccctc ... aacatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGT
EST: gi|37420501|gb|CF647941.1|CF647941
EST:     ACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAG                         GTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGT
genomic: ACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAGgttctccctc ... aacatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGT
EST: gi|60398834|gb|DN231650.1|DN231650
EST:     ACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAG                         GTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGT
genomic: ACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAGgttctccctc ... aacatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGT
EST: gi|33466594|gb|CF243643.1|CF243643
EST:     CTTTTCACTGAAGAAGGCTAGTCAAATGGGTGAA-GAGATTGGCCGTCAG                         GTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCT
genomic: CTTTTCACTGAAGAAGGCTAGTCAAATGG-TGAAAGAGATTGGCCGTCAGgttctccctc ... aacatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCT
EST: gi|28985028|gb|BQ539307.2|BQ539307
EST:     ACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAG                         GTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGT
genomic: ACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAGgttctccctc ... aacatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGT
EST: gi|71327359|gb|DR800293.1|DR800293
EST:     ACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAG                         GTTGCTACTGACAAATGCATTATG
genomic: ACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAGgttctccctc ... aacatttcagGTTGCTACTGACAAATGCATTATG
EST: gi|60349330|gb|DN216303.1|DN216303
EST:     ACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAG                         GTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGT
genomic: ACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAGgttctccctc ... aacatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGT
EST: gi|148993116|gb|EE033716.2|EE033716
EST:     ACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAG                         GTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCT
genomic: ACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAGgttctccctc ... aacatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCT
EST: gi|50333643|gb|CO528769.1|CO528769
EST:     CCTTTTCCCTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAG                         GTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGT
genomic: ACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAGgttctccctc ... aacatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGT
EST: gi|60345394|gb|DN212367.1|DN212367
EST:     ACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAG                         GTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGT
genomic: ACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAGgttctccctc ... aacatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGT
EST: gi|60352046|gb|DN219019.1|DN219019
EST:     ACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAG                         GTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGT
genomic: ACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAGgttctccctc ... aacatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGT
EST: gi|149009782|gb|EE041679.2|EE041679
EST:     ACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAG                         GTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGT
genomic: ACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAGgttctccctc ... aacatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGT
EST: gi|211541391|gb|FL468178.1|FL468178
EST:     ACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAG                         GTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGT
genomic: ACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAGgttctccctc ... aacatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGT
EST: gi|78117925|gb|DV536312.1|DV536312
EST:     ACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAG                         GTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGT
genomic: ACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAGgttctccctc ... aacatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGT
EST: gi|149089650|gb|EE178904.2|EE178904
EST:     ACTTTTCACTGAAGAAGGCTAGTCACATGGTGAAAGAGATTGGCCGTCAG                         GTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGT
genomic: ACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAGgttctccctc ... aacatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGT
EST: gi|211386633|gb|FL468002.1|FL468002
EST:     ACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAG                         GTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGT
genomic: ACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAGgttctccctc ... aacatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGT
EST: gi|78083753|gb|DV512146.1|DV512146
EST:     ACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAG                         GTTGCTACTGACAAATGCATTATGGCGTTCCTGTTT
genomic: ACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAGgttctccctc ... aacatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTT
EST: gi|71327358|gb|DR800292.1|DR800292
EST:     ACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAG                         GTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGT
genomic: ACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAGgttctccctc ... aacatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGT
EST: gi|60344730|gb|DN211703.1|DN211703
EST:     ACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAG                         GTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGT
genomic: ACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAGgttctccctc ... aacatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGT
EST: gi|149112850|gb|EE295663.2|EE295663
EST:     TTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATGGGCCGTCAG                         GTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGT
genomic: TTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAGgttctccctc ... aacatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGT
EST: gi|149074291|gb|EE162669.2|EE162669
EST:     ACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAG                         GTTGCTACTGACAAATG
genomic: ACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAGgttctccctc ... aacatttcagGTTGCTACTGACAAATG
EST: gi|33466593|gb|CF243642.1|CF243642
EST:     CCTTTTCCCTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAG                         GTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGT
genomic: ACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAGgttctccctc ... aacatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGT
EST: gi|50333644|gb|CO528770.1|CO528770
EST:     ACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAG                         GTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCT
genomic: ACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAGgttctccctc ... aacatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCT
EST: gi|211130916|gb|FL136654.1|FL136654
EST:     ACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAG                         GTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGT
genomic: ACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAGgttctccctc ... aacatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGT
EST: gi|5804633|gb|AI979603.1|AI979603
EST:     NCTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAG                         GTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGT
genomic: ACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAGgttctccctc ... aacatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGT
EST: gi|60343169|gb|DN210142.1|DN210142
EST:     ACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAG                         GTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGT
genomic: ACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAGgttctccctc ... aacatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGT

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: 45 (upstream exon), 49 (downstream exon)
Score: 280

ACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAGgttctccctc ... aacatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 256

ACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAGgttctccctc ... aacatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 142

ACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAGgttctccctc ... aacatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 246

ACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAGgttctccctc ... aacatttcagGTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAGgttctccctcgttttctagcactcaaatgcttgtttttttttgttactcctacgtggctgaatttgcaaaaaaaaaaaaacatttcag

- - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA