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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATGCACGACTTCCTGATAATATCATGGCATATGACAATGCTGTTTCGGCGCTTGGAAAAATATGCCAATTTCATCGGGATGGTATTGATGCAGCTCAGgtatcagcatcttttccttatgatgtcgccaatattttctagtaatgtgcctttgacaacttgcttgagatgattgtgttgttgtgatatgataaaaaaa...

Basic information

species Zea mays
transcript GRMZM5G887631_T01
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G887631_T01 (Zea mays), 5'ss of exon 16
lower sequence: LOC_Os07g38760.1 (Oryza sativa), 5'ss of exon 17
TGATGCACGACTTCCTGATAATATCATGGCATATGACAATGCTGTTTCGGCGCTTGGAAAAATATGCCAATTTCATCGGGATGGTATTGATGCAGCTCAGgtatcagcatcttttcctta-tgatgtc--gccaatattttctagtaatgtgcctttgacaacttgcttgagatgattgtgttgttgtgatatgataaaaaaa
||| |||   | | | || ||||| ||||||||||||||||||||||| |||||||| |||||||||||||| ||||| |||||||| |||||||||||||||  ||||| | |  | || | |  |   | || |     | | |    |   ||||  |  |   ||  |     ||| ||  | |   |  |||  || |
TGAAGCAAAGCATGCAGACAATATAATGGCATATGACAATGCTGTTTCAGCGCTTGGTAAAATATGCCAATTCCATCGTGATGGTATCGATGCAGCTCAGgta--agcatatctcacatagtcacattcagtcagttaaaacaactgtcattgttttgttatatatattctgtcttctgtttt-ctatccaaccatattaaca

upper sequence: GRMZM5G887631_T01 (Zea mays), 5'ss of exon 16
lower sequence: GLYMA05G28950.1 (Glycine max), 5'ss of exon 19
TGATGCACGACTTCCTGATAATATCATGGCATATGACAATGCTGTTTCGGCGCTTGGAAAAATATGCCAATTTCATCGGGATGGTATTGATGCAGCTCAGgtatcagcatcttttcc--ttatga--tgtcgccaatatttt-----ctagtaatgt--gcctttg--acaacttgcttgagatgattgtg--ttgttgtgatatgataaaaaaa--------------------------------------
| |||| |  | | | |||||| | ||||||||||||||||||||||| ||  | |||||||| |||||||||||||| ||  |||||||| | || |||||     ||| ||||||  |||| |  || |       ||||      |  | ||||  | | ||   |  |     |     ||| | ||  |||||||  |  | |  | |                                        
TAATGCTCTTCATTCAGATAATGTAATGGCATATGACAATGCTGTTTCCGCTTTGGGAAAAATTTGCCAATTTCATCGTGACAGTATTGATTCTGCCCAGgtcagtacatattttccgtttataacttgcctttgtggttttggttcttgattatgtttgtcattattatgatcaattctttctgagtctgatttgttgtttttaggttgagatgatggttaatatttttgtaatgttctgtcatgtttgcag

upper sequence: GRMZM5G887631_T01 (Zea mays), 5'ss of exon 16
lower sequence: GLYMA08G12120.1 (Glycine max), 5'ss of exon 17
TGATGCACGACTTCCTGATAATATCATGGCATATGACAATGCTGTTTCGGCGCTTGGAAAAATATGCCAATTTCATCGGGATGGTATTGATGCAGCTCAGgtatcagcatcttttcc----ttatga--------tgtcgccaatattttctagta-atgtgccttt-----gacaacttgcttgagatgattgtgttgttgtgatatgataaaaaaa-----------------------------------
| |||| |  | | | |||||| | ||||||||||||||||| ||||| || || |||||||| |||||||||||||| ||  |||||||| | || |||||     ||| ||||||    |||| |        ||| |     ||| |  | ||  | || | ||     ||  | ||  |||||    || ||||||| | |  |    |  | |                                   
TAATGCTCTTCATTCAGATAATGTAATGGCATATGACAATGCCGTTTCCGCTCTGGGAAAAATTTGCCAATTTCATCGTGACAGTATTGATTCTGCCCAGgtcagtacatattttccctgtttataacttgcttttgtggttttgattcttcattatgtttgtcattattatgatcaattctttgagtctgttttgttgtttttaggttgagatgatagttaatatttttgtaatgttctgttatgtttgcag

upper sequence: GRMZM5G887631_T01 (Zea mays), 5'ss of exon 16
lower sequence: GLYMA19G29010.1 (Glycine max), 5'ss of exon 17
TGATGCACGACTTCCTGATAATATCATGGCATATGACAATGCTGTTTCGGCGCTTGGAAAAATATGCCAATTTCATCGGGATGGTATTGATGCAGCTCAGgtatcagcatcttttccttatgatgtcgccaatattttctagtaatgtgcctttgacaacttgcttgagatgattgtgttgttgtgatatgataaaaaaa
  |||||| || | ||||||| || ||||||||||||||||| || || || |||||||||||||||||||| ||||| ||| | ||  ||||||| |||||||       |||        ||||| ||    | || ||  |   ||   |||   ||||  |   | |  |  |     ||| || ||| |||  | 
AAATGCACTACATGCTGATAACATAATGGCATATGACAATGCCGTCTCAGCTCTTGGAAAAATATGCCAATTCCATCGTGATAGCATAAATGCAGCACAGgtattttacaatttggtgctccatgtctccgcagtcttttaaaatgctgttcttgtttacttaatcttgcttgtgatcccaatgtcatttgaaaaagtat

upper sequence: GRMZM5G887631_T01 (Zea mays), 5'ss of exon 16
lower sequence: GLYMA16G04400.1 (Glycine max), 5'ss of exon 17
TGATGCACGACTTCCTGATAATATCATGGCATATGACAATGCTGTTTCGGCGCTTGGAAAAATATGCCAATTTCATCGGGATGGTATTGATGCAGCTCAGgtatcagcatcttttccttatgatgtcgccaatattttctagtaatgtgcct-ttgacaacttgcttgagatgattgtgttgttgtgatatgataaaaaaa
  |||||| || | ||||||| || ||||||||||||||||||||||| || |||||||||||||||||||| ||||| ||| | ||  ||||||| |||||||    |  |||        ||||| |   | |||   | |  ||| | | |||   ||||  |   | |  |  |  |  |   || ||| | |  | 
AAATGCACTACATTCTGATAACATAATGGCATATGACAATGCTGTTTCAGCTCTTGGAAAAATATGCCAATTCCATCGTGATAGCATAAATGCAGCACAGgtattt-tacatttggtgccccatgtctctgctgtttgaaaatgctgttcttgttgtttacttaatcttgcttgtgatcctaataccatttgaaacagtat

upper sequence: GRMZM5G887631_T01 (Zea mays), 5'ss of exon 16
lower sequence: Vv08s0007g07240.t01 (Vitis vinifera), 5'ss of exon 17
TGATGCACGACTTCCTGATAATATCATGGCATATGACAATGCTGTTTCGGCGCTTGGAAAAATATGCCAATTTCATCGGGATGGTATTGATGCAGCTCAGgtatcagcatcttttccttatgatgtcgccaatattttctagtaatgtgcctttgacaacttgcttgagatgattgtgttgttgtg-atatgataaaaaaa
| |||||||   | | |||||| | ||||| ||||| ||||||||||| || ||||||||||||||||| || ||||| ||| |||| ||||| |  |||||||    ||||  || ||    ||       |   ||||    ||    | || | |  | ||||    |       || ||  |    |  |||  |  
TAATGCACGGGATTCAGATAATGTAATGGCTTATGATAATGCTGTTTCCGCACTTGGAAAAATATGCCAGTTCCATCGCGATAGTATAGATGCCGTGCAGgtatatatatctcatcattcct-tgctttgggttgcttctgtgtatactacctttatacgtagcttcccctcccctcttttttaggcgcttcctaatcatg

upper sequence: GRMZM5G887631_T01 (Zea mays), 5'ss of exon 16
lower sequence: Vv06s0004g00500.t01 (Vitis vinifera), 5'ss of exon 17
TGATGCACGACTTCCTGATAATATCATGGCATATGACAATGCTGTTTCGGCGCTTGGAAAAATATGCCAATTTCATCGGGATGGTATTGATGCAGCTCAGgtatcagcatcttttccttatgatgtcgccaatattttctagtaatgtgcctttgacaacttgcttgagatgattgtgttgttgtgatatgataaaaaaa---
| ||||||  |  || |||||| | ||||||||||| ||||||||||| || || |||||||| ||||| |||||||| ||  |||||||| |||||||||||    || ||||||   |  || ||     ||    |  ||    |   |||    |    ||    |||  | |         ||    |||||||    
TAATGCACTGCAACCAGATAATGTAATGGCATATGATAATGCTGTTTCTGCTCTAGGAAAAATTTGCCAGTTTCATCGTGACAGTATTGATTCAGCTCAGgtagtttca-cttttctcaaccatatcatatctaagcacaggttgattatattttgtcatcatctactcatg--tattccaacaaaattgcctaaaaaattgg

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|211018174|gb|FL213619.1|FL213619
EST:     CGCTTGGAAAAATATGCCAATTTCATCGGGATGGTATTGATGCAGCTCAG                         GTTGTTCCAGCCTGGCTTAGCTGCTTGCCTATAAAAGACGACAAGGTTGAA
genomic: CGCTTGGAAAAATATGCCAATTTCATCGGGATGGTATTGATGCAGCTCAGgtatcagcat ... tgtttctcagGTTGTTCCAGCCTGGCTTAGCTGCTTGCCTATAAAAGACGACAAGGTTGAA
EST: gi|37377906|gb|CF625599.1|CF625599
EST:     CGCTTGGAAAAATATGCCAATTTCATCGGGATGGTATTGATGCAGCTCAG                         GTTGTTCCAGCCTGGCTTAGCTGCTTGCCTATAAAAGACGACAAGGTTGAA
genomic: CGCTTGGAAAAATATGCCAATTTCATCGGGATGGTATTGATGCAGCTCAGgtatcagcat ... tgtttctcagGTTGTTCCAGCCTGGCTTAGCTGCTTGCCTATAAAAGACGACAAGGTTGAA
EST: gi|60352763|gb|DN219736.1|DN219736
EST:     CGCTTGGAAAAATATGCCAATTTCATCGGGATGGTATTGATGCAGCTCAG                         GTTGTTCCAGCCTGGCTTAGCTGCTTGCCTATAAAAGACGACAAGGTTGAA
genomic: CGCTTGGAAAAATATGCCAATTTCATCGGGATGGTATTGATGCAGCTCAGgtatcagcat ... tgtttctcagGTTGTTCCAGCCTGGCTTAGCTGCTTGCCTATAAAAGACGACAAGGTTGAA
EST: gi|211015404|gb|FL213618.1|FL213618
EST:     CGCTTGGAAAAATATGCCAATTTCATCGGGATGGTATTGATGCAGCTCAG                         GTTGTTCCAGCCTGGCTTAGCTGCTTGCCTATAAAAGACGACAAGGTTGAA
genomic: CGCTTGGAAAAATATGCCAATTTCATCGGGATGGTATTGATGCAGCTCAGgtatcagcat ... tgtttctcagGTTGTTCCAGCCTGGCTTAGCTGCTTGCCTATAAAAGACGACAAGGTTGAA
EST: gi|61119517|gb|DN560478.1|DN560478
EST:     CGCTTGGAAAAATATGCCAATTTCATCGGGATGGTATTGATGCAGCTCAG                         GTTGTTCCAGCCTGGCTTAGCTGCTTGCCTATAAAAGACGACAAGGTTGAA
genomic: CGCTTGGAAAAATATGCCAATTTCATCGGGATGGTATTGATGCAGCTCAGgtatcagcat ... tgtttctcagGTTGTTCCAGCCTGGCTTAGCTGCTTGCCTATAAAAGACGACAAGGTTGAA
EST: gi|5018426|gb|AI714619.1|AI714619
EST:     TCATCGGGATGGTATTGATGCAGCTCAG                         GTTGTTCCAGCCTGGCTTAGCTGCTTGCCTATAAAAGACNNCAAGGTTGAA
genomic: TCATCGGGATGGTATTGATGCAGCTCAGgtatcagcat ... tgtttctcagGTTGTTCCAGCCTGGCTTAGCTGCTTGCCTATAAAAGACGACAAGGTTGAA
EST: gi|33094008|gb|CF054002.1|CF054002
EST:     CGCTTGGAAAAACATGCCAATTTCATCGGGATGGTATTGACGCAGCTCAG                         GTTGTTCCAGCCTGGCTTAGCTGCTTGCCTATAAAAGACGACAAGGTTGAA
genomic: CGCTTGGAAAAATATGCCAATTTCATCGGGATGGTATTGATGCAGCTCAGgtatcagcat ... tgtttctcagGTTGTTCCAGCCTGGCTTAGCTGCTTGCCTATAAAAGACGACAAGGTTGAA
EST: gi|9028748|gb|BE238788.1|BE238788
EST:     CGCTTGGAAAA-TATGCCAATTTCATCGGGATGGTATTGATGCAGCTCAG                         GTTGTTCCAGCCTGGCTTAGCTGCTTGCCTATAAAAGACGACAAGGTTGAA
genomic: CGCTTGGAAAAATATGCCAATTTCATCGGGATGGTATTGATGCAGCTCAGgtatcagcat ... tgtttctcagGTTGTTCCAGCCTGGCTTAGCTGCTTGCCTATAAAAGACGACAAGGTTGAA
EST: gi|9028539|gb|BE238534.1|BE238534
EST:     CGCTTGGAAAA-TATGCCAATTTCATCGGGATGGTATTGATGCAGCTCAG                         GTTGTTCCAGCCTGGCTTAGCTGCTTGCCTATAAAAGACGACAAGGTTGAA
genomic: CGCTTGGAAAAATATGCCAATTTCATCGGGATGGTATTGATGCAGCTCAGgtatcagcat ... tgtttctcagGTTGTTCCAGCCTGGCTTAGCTGCTTGCCTATAAAAGACGACAAGGTTGAA
EST: gi|71770781|gb|DR968718.1|DR968718
EST:     CGCTTGGAAAAATATGCCAATTTCATCGGGATGGTATTGATGCAGCTCAG                         GTTGTTCCAGCCTGGCTTAGCTGCTTGCCTATAAAAGACGACAAGGTTGAA
genomic: CGCTTGGAAAAATATGCCAATTTCATCGGGATGGTATTGATGCAGCTCAGgtatcagcat ... tgtttctcagGTTGTTCCAGCCTGGCTTAGCTGCTTGCCTATAAAAGACGACAAGGTTGAA
EST: gi|60396898|gb|DN229717.1|DN229717
EST:     CGCTTGGAAAAATATGCCAATTTCATCGGGATGGTATTGATGCAGCTCAG                         GTTGTTCCAGCCTGGCTTAGCTGCTTGCCTATAAAAGACGACAAGGTTGAA
genomic: CGCTTGGAAAAATATGCCAATTTCATCGGGATGGTATTGATGCAGCTCAGgtatcagcat ... tgtttctcagGTTGTTCCAGCCTGGCTTAGCTGCTTGCCTATAAAAGACGACAAGGTTGAA
EST: gi|33091899|gb|CF051893.1|CF051893
EST:     CGCTTGGAAAAATATGCCAATTTCATCGGGATGGTATTGACGCAGCTCAG                         GTTGTTCCAGCCTGGCTTAGCTGCTTGCCTATAAAAGACGACAAGGTTGAA
genomic: CGCTTGGAAAAATATGCCAATTTCATCGGGATGGTATTGATGCAGCTCAGgtatcagcat ... tgtttctcagGTTGTTCCAGCCTGGCTTAGCTGCTTGCCTATAAAAGACGACAAGGTTGAA
EST: gi|211015403|gb|FL213617.1|FL213617
EST:     CGCTTGGAAAAATATGCCAATTTCATCGGGATGGTATTGATGCAGCTCAG                         GTTGTTCCAGCCTGGCTTAGCTGCTTGCCTATAAAAGACGACAAGGTTGAA
genomic: CGCTTGGAAAAATATGCCAATTTCATCGGGATGGTATTGATGCAGCTCAGgtatcagcat ... tgtttctcagGTTGTTCCAGCCTGGCTTAGCTGCTTGCCTATAAAAGACGACAAGGTTGAA
EST: gi|60401162|gb|DN233969.1|DN233969
EST:     CGCTTGGAAAAATATGCCAATTTCATCGGGATGGTATTGATGCAGCTCAG                         GTTGTTCCAGCCTGGCTTAGCTGCTTGCCTATAAAAGACGACAAGGTTGAA
genomic: CGCTTGGAAAAATATGCCAATTTCATCGGGATGGTATTGATGCAGCTCAGgtatcagcat ... tgtttctcagGTTGTTCCAGCCTGGCTTAGCTGCTTGCCTATAAAAGACGACAAGGTTGAA
EST: gi|9953899|gb|BE640482.1|BE640482
EST:     CGCTTGGAAAA-TATGCCAATTTCATCGGGATGGTATTGATGCAGCTCAG                         GTTGTTCCAGCCTGGCTTAGCTGCTTGCCTATAAAAGACGACAAGGTTGAA
genomic: CGCTTGGAAAAATATGCCAATTTCATCGGGATGGTATTGATGCAGCTCAGgtatcagcat ... tgtttctcagGTTGTTCCAGCCTGGCTTAGCTGCTTGCCTATAAAAGACGACAAGGTTGAA
EST: gi|37382036|gb|CF627936.1|CF627936
EST:     GCTTGG-AAAATATNGCCAATTTCATCGGGATGGTATTGATGCAGCTCAG                         GTTGTTCCAGCCTGGCTTAGCTGCTTGCCTATAAAAGACGACAAGGTTGAA
genomic: GCTTGGAAAAATAT-GCCAATTTCATCGGGATGGTATTGATGCAGCTCAGgtatcagcat ... tgtttctcagGTTGTTCCAGCCTGGCTTAGCTGCTTGCCTATAAAAGACGACAAGGTTGAA
EST: gi|13149409|gb|BG319731.1|BG319731
EST:     CGCTTGGAAAAATATGCCAATTTCATCGGGATGGTATTGATGCAGCTCAG                         GTTGTTCCAGCCTGGCTTAGCTGCTTGCCTATAAAAGACGACAAGGTTGAA
genomic: CGCTTGGAAAAATATGCCAATTTCATCGGGATGGTATTGATGCAGCTCAGgtatcagcat ... tgtttctcagGTTGTTCCAGCCTGGCTTAGCTGCTTGCCTATAAAAGACGACAAGGTTGAA

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: 228

TGATGCACGACTTCCTGATAATATCATGGCATATGACAATGCTGTTTCGGCGCTTGGAAAAATATGCCAATTTCATCGGGATGGTATTGATGCAGCTCAGgtatcagcat ... tgtttctcagGTTGTTCCAGCCTGGCTTAGCTGCTTGCCTATAAAAGACGACAAGGTTGAAGCTAAAGTTGTACATGGACAGCTTTGCTCCATGGTGGAGAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 395

TGATGCACGACTTCCTGATAATATCATGGCATATGACAATGCTGTTTCGGCGCTTGGAAAAATATGCCAATTTCATCGGGATGGTATTGATGCAGCTCAGgtatcagcat ... tgtttctcagGTTGTTCCAGCCTGGCTTAGCTGCTTGCCTATAAAAGACGACAAGGTTGAAGCTAAAGTTGTACATGGACAGCTTTGCTCCATGGTGGAGAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 261

TGATGCACGACTTCCTGATAATATCATGGCATATGACAATGCTGTTTCGGCGCTTGGAAAAATATGCCAATTTCATCGGGATGGTATTGATGCAGCTCAGgtatcagcat ... tgtttctcagGTTGTTCCAGCCTGGCTTAGCTGCTTGCCTATAAAAGACGACAAGGTTGAAGCTAAAGTTGTACATGGACAGCTTTGCTCCATGGTGGAGAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 167

TGATGCACGACTTCCTGATAATATCATGGCATATGACAATGCTGTTTCGGCGCTTGGAAAAATATGCCAATTTCATCGGGATGGTATTGATGCAGCTCAGgtatcagcat ... tgtttctcagGTTGTTCCAGCCTGGCTTAGCTGCTTGCCTATAAAAGACGACAAGGTTGAAGCTAAAGTTGTACATGGACAGCTTTGCTCCATGGTGGAGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATGCACGACTTCCTGATAATATCATGGCATATGACAATGCTGTTTCGGCGCTTGGAAAAATATGCCAATTTCATCGGGATGGTATTGATGCAGCTCAGgtatcagcatcttttccttatgatgtcgccaatattttctagtaatgtgcctttgacaacttgcttgagatgattgtgttgttgtgatatgataaaaaaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ataaaaaa