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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaacatgctgcttaggaaattatctgttatacttgttagtttaacttagtgcattatcatttgatatcaaaattagtttcctgcttagaagtacttgccaacctgttaacttttgaactctgtcgagtctgaaaaactttgtttattctctagAGTTTGATCCTGATGATTGCCCACTGGATTGCTCAAAGCCATGTGAGAAAGTTTGCCCAGCTGATGCAATATCACTAAAGCATTCCATGGTTGATGGAGA

Basic information

species Zea mays
transcript GRMZM5G864166_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G864166_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g06510.1 (Oryza sativa), 3'ss of exon 3
gtaagaacatgctgcttaggaaattatctgttatacttgttagtttaacttagtgcattatcatttgatatcaaaattagtttcctgcttagaagtacttgccaacctgttaacttttgaactctgtcgagtctgaaaaactttgtttattctctagAGTTTGATCCTGATGATTGCCCACTGGATTGCTCAAAGCCATGTGAGAAAGTTTGCCCAGCTGATGCAATATCACTAAAGCATTCCATGGTTGATGGAGA
                                                             | ||   || ||| |   ||| | || |||    |   ||   |||| |    | ||    |||   |  |   |    |||| | | ||||||||| ||||||||||| ||||||||||  |||||||||||||||||||||||||| || || |||||||||||||   || ||      ||| |||| | |||
-------------------------------------------------------ttcctgctttcactagcaagacctgttgcatgtttatggatttctgaataccttt--gttctttgcttctaaaggtttccacttcctttctcttttctctagAATTTGATCCTGAGGATTGCCCACCAGATTGCTCAAAGCCATGTGAGAAAGTCTGTCCTGCTGATGCAATATTGTTAGAGAGGGTTATGATTGAGGAAGA
















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|211305789|gb|FL318625.1|FL318625
EST:     GATGATTAGTGTTAATGATGATTGCAGAGATCTTCATTTCCGTAAAGCTG                         AGTTTGATCCTGATGATTGCCCACTGGATTGCTCAAAGCCATGTGAGAAAG
genomic: GATGATTAGTGTTAATGATGATTGCAGAGATCTTCATTTCCGTAAAGCTGgtaagaacat ... tattctctagAGTTTGATCCTGATGATTGCCCACTGGATTGCTCAAAGCCATGTGAGAAAG
EST: gi|50326457|gb|CO521583.1|CO521583
EST:     GATGATTAGTGTTAATGATGATTGCAGAGATCTTCATTTCCGTAAAGCTG                         AGTTTGATCCTGATGATTGCCCACTGGATTGCTCAAAGCCATGTGAGAAAG
genomic: GATGATTAGTGTTAATGATGATTGCAGAGATCTTCATTTCCGTAAAGCTGgtaagaacat ... tattctctagAGTTTGATCCTGATGATTGCCCACTGGATTGCTCAAAGCCATGTGAGAAAG
EST: gi|50329289|gb|CO524415.1|CO524415
EST:     GATGATTAGTGTTAATGATGATTGCAGAGATCTTCATTTCCGTAAAGCTG                         AGTTTGATCCTGATGATTGCCCACTGGATTGCTCAAAGCCATGTGAGAAAG
genomic: GATGATTAGTGTTAATGATGATTGCAGAGATCTTCATTTCCGTAAAGCTGgtaagaacat ... tattctctagAGTTTGATCCTGATGATTGCCCACTGGATTGCTCAAAGCCATGTGAGAAAG
EST: gi|76293255|gb|DV032823.1|DV032823
EST:     GATGATTAGTGTTAATGATGATTGCAGAGATCTTCATTTCCGTAAAGCTG                         AGTTTGATCCTGATGATTGCCCACTGGATTGCTCAAAGCCATGTGAGAAAG
genomic: GATGATTAGTGTTAATGATGATTGCAGAGATCTTCATTTCCGTAAAGCTGgtaagaacat ... tattctctagAGTTTGATCCTGATGATTGCCCACTGGATTGCTCAAAGCCATGTGAGAAAG
EST: gi|71772666|gb|DR970593.1|DR970593
EST:     GATGATTAGTGTTAATGATGATTGCAGAGATCTTCATTTCCGTAAAGCTG                         AGTTTGATCCTGATGATTGCCCACTGGATTGCTCAAAGCCATGTGAGAAAG
genomic: GATGATTAGTGTTAATGATGATTGCAGAGATCTTCATTTCCGTAAAGCTGgtaagaacat ... tattctctagAGTTTGATCCTGATGATTGCCCACTGGATTGCTCAAAGCCATGTGAGAAAG
EST: gi|211290993|gb|FL323352.1|FL323352
EST:     GATGATTAGTGTTAATGATGATTGCAGAGATCTTCATTTCCGTAAAGCTG                         AGTTTGATCCTGATGATTGCCCACTGGATTGCTCAAAGCCATGTGAGAAAG
genomic: GATGATTAGTGTTAATGATGATTGCAGAGATCTTCATTTCCGTAAAGCTGgtaagaacat ... tattctctagAGTTTGATCCTGATGATTGCCCACTGGATTGCTCAAAGCCATGTGAGAAAG
EST: gi|91057203|gb|EB167621.1|EB167621
EST:     GATGATTAGTGTTAATGATGATTGCAGAGATCTTCATTTCCGTAAAGCTG                         AGTTTGATCCTGATGATTGCCCACTGGATTGCTCAAAGCCATGTGAAAAAG
genomic: GATGATTAGTGTTAATGATGATTGCAGAGATCTTCATTTCCGTAAAGCTGgtaagaacat ... tattctctagAGTTTGATCCTGATGATTGCCCACTGGATTGCTCAAAGCCATGTGAGAAAG
EST: gi|32864298|gb|CF003980.1|CF003980
EST:     GATGATTAGTGTTAATGATGATTGCAGAGATCTTCATTTCCGTAAAGCTG                         AGTTTGATCCTGATGATTGCCCACTGGATTGCTCAAAGCCATGTGAGAAAG
genomic: GATGATTAGTGTTAATGATGATTGCAGAGATCTTCATTTCCGTAAAGCTGgtaagaacat ... tattctctagAGTTTGATCCTGATGATTGCCCACTGGATTGCTCAAAGCCATGTGAGAAAG
EST: gi|74243604|gb|DT651518.1|DT651518
EST:     GATGATTAGTGTTAATGATGATTGCAGAGATCTTCATTTCCGTAAAGCTG                         AGTTTGATCCTGATGATTGCCCACTGGATTGCTCAAAGCCATGTGAGAAAG
genomic: GATGATTAGTGTTAATGATGATTGCAGAGATCTTCATTTCCGTAAAGCTGgtaagaacat ... tattctctagAGTTTGATCCTGATGATTGCCCACTGGATTGCTCAAAGCCATGTGAGAAAG
EST: gi|78088237|gb|DV516630.1|DV516630
EST:     GATGATTAGTGTTAATGATGATTGCAGAGATCTTCATTTCCGTAAAGCTG                         AGTTTGATCCTGATGATTGCCCACTGGATTGCTCAAAGCCATGTGAGAAAG
genomic: GATGATTAGTGTTAATGATGATTGCAGAGATCTTCATTTCCGTAAAGCTGgtaagaacat ... tattctctagAGTTTGATCCTGATGATTGCCCACTGGATTGCTCAAAGCCATGTGAGAAAG
EST: gi|50335836|gb|CO530962.1|CO530962
EST:     GATGATTAGTGTTAATGATGATTGCAGAGATCTTCATTTCCGTAAAGCTG                         AGTTTGATCCTGATGATTGCCCACTGGATTGCTCAAAGCCATGTGAGAAAG
genomic: GATGATTAGTGTTAATGATGATTGCAGAGATCTTCATTTCCGTAAAGCTGgtaagaacat ... tattctctagAGTTTGATCCTGATGATTGCCCACTGGATTGCTCAAAGCCATGTGAGAAAG
EST: gi|211353992|gb|FL313760.1|FL313760
EST:     GATGATTAGTGTTAATGATGATTGCAGAGATCTTCATTTCCGTAAAGCTG                         AGTTTGATCCTGATGATTGCCCACTGGATTGCTCAAAGCCATGTGAGAAAG
genomic: GATGATTAGTGTTAATGATGATTGCAGAGATCTTCATTTCCGTAAAGCTGgtaagaacat ... tattctctagAGTTTGATCCTGATGATTGCCCACTGGATTGCTCAAAGCCATGTGAGAAAG

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), 47 (downstream exon)
Score: 93

GGTATTGAAGTAGCAGCATCAATTGTACCAACAGTTCAAAGGCCTTGGCTGATGATTAGTGTTAATGATGATTGCAGAGATCTTCATTTCCGTAAAGCTGgtaagaacat ... tattctctagAGTTTGATCCTGATGATTGCCCACTGGATTGCTCAAAGCCATGTGAGAAAGTTTGCCCAGCTGATGCAATATCACTAAAGCATTCCATGGTTGATGGAGA


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 60

GGTATTGAAGTAGCAGCATCAATTGTACCAACAGTTCAAAGGCCTTGGCTGATGATTAGTGTTAATGATGATTGCAGAGATCTTCATTTCCGTAAAGCTGgtaagaacat ... tattctctagAGTTTGATCCTGATGATTGCCCACTGGATTGCTCAAAGCCATGTGAGAAAGTTTGCCCAGCTGATGCAATATCACTAAAGCATTCCATGGTTGATGGAGA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 13

GGTATTGAAGTAGCAGCATCAATTGTACCAACAGTTCAAAGGCCTTGGCTGATGATTAGTGTTAATGATGATTGCAGAGATCTTCATTTCCGTAAAGCTGgtaagaacat ... tattctctagAGTTTGATCCTGATGATTGCCCACTGGATTGCTCAAAGCCATGTGAGAAAGTTTGCCCAGCTGATGCAATATCACTAAAGCATTCCATGGTTGATGGAGA


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 12

GGTATTGAAGTAGCAGCATCAATTGTACCAACAGTTCAAAGGCCTTGGCTGATGATTAGTGTTAATGATGATTGCAGAGATCTTCATTTCCGTAAAGCTGgtaagaacat ... tattctctagAGTTTGATCCTGATGATTGCCCACTGGATTGCTCAAAGCCATGTGAGAAAGTTTGCCCAGCTGATGCAATATCACTAAAGCATTCCATGGTTGATGGAGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caacctgttaacttttgaactctgtcgagtctgaaaaactttgtttattctctagAGTTTGATCCTGATGATTGCCCACTGGATTGCTCAAAGCCATGTGAGAAAGTTTGCCCAGCTGATGCAATATCACTAAAGCATTCCATGGTTGATGGAGA
     tgttaac  putative branch site (score: 12)
                                      ctttgtttattctct  putative PPT
                                 aaaaactttgtttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaacatgctgcttaggaaattatctgttatacttgttagtttaacttagtgcattatcatttgatatcaaaattagtttcctgcttagaagtacttgccaacctgttaacttttgaactctgtcgagtctgaaaaactttgtttattctctagAGTTTGATCCTGATGATTGCCCACTGGATTGCTCAAAGCCATGTGAGAAAGTTTGCCCAGCTGATGCAATATCACTAAAGCATTCCATGGTTGATGGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA