Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtgatcttcctccctgttctctttctagcataccagtttggtggacctcccaatatttcctggcacattcgttattacatgctatggaatatttcattgtcaataaaatttacttgttctctcagGAATTGGGCCTCAGCCCTTCAGTGCCACTGCATGTCGTTCTGCAAGATTGGATCAGGCATACGGATGGGAAATTGAGCTTTCTCGGATTTGTCAAGTTAT

Basic information

species Zea mays
transcript GRMZM2G109843_T02
intron # 10
splice site 3'
intron type U2

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|4314706|gb|AI438618.2|AI438618
EST:     TGTAATAGAT-AA-TAGCTTCT                         GAA-TGGGCNTCAGCCCTTCAGTGCCACTGCATGTCGTTCTGCAAGATTGG
genomic: TGTAATAGATGAATTAGCTTCTgtacgtgatc ... gttctctcagGAATTGGGCCTCAGCCCTTCAGTGCCACTGCATGTCGTTCTGCAAGATTGG
EST: gi|60342659|gb|DN209632.1|DN209632
EST:     ATTTTGAGAAGGAAGGCAACCGAGCTATTGTAATAGATGAATTAGCTTCT                         GAATTGGGCCTCAGCCCTTCAGTGCCACTGCATGTCGTTCTGCAAGATTGG
genomic: ATTTTGAGAAGGAAGGCAACCGAGCTATTGTAATAGATGAATTAGCTTCTgtacgtgatc ... gttctctcagGAATTGGGCCTCAGCCCTTCAGTGCCACTGCATGTCGTTCTGCAAGATTGG
EST: gi|211220514|gb|FL333416.1|FL333416
EST:     ATTTTGAGAAGGAAGGCAACCGAGCTATTGTMATAGATGAATTAGCTTCT                         GAATTGGGCCTCAGCCCTTCAGTGCCACTGCATGTCGTGCTGCAAGATTGG
genomic: ATTTTGAGAAGGAAGGCAACCGAGCTATTGTAATAGATGAATTAGCTTCTgtacgtgatc ... gttctctcagGAATTGGGCCTCAGCCCTTCAGTGCCACTGCATGTCGTTCTGCAAGATTGG
EST: gi|211047725|gb|FL481870.1|FL481870
EST:     ATTTTGAGAAGGAAGGCAACCGAGCTATTGTAATAGATGAATTAGCTTCT                         GAATTGGGCCTCAGCCCTTCAGTGCCACTGCATGTCGTTCTGCAAGATTGG
genomic: ATTTTGAGAAGGAAGGCAACCGAGCTATTGTAATAGATGAATTAGCTTCTgtacgtgatc ... gttctctcagGAATTGGGCCTCAGCCCTTCAGTGCCACTGCATGTCGTTCTGCAAGATTGG
EST: gi|211362656|gb|FL465488.1|FL465488
EST:     ATTTTGAGAAGGAAGGCAACCGAGCTATTGTAATAGATGAATTAGCTTCT                         GAATTGGGCCTCAGCCCTTCAGCGCCACTGCATGTCGTTCTGCAAGATTGG
genomic: ATTTTGAGAAGGAAGGCAACCGAGCTATTGTAATAGATGAATTAGCTTCTgtacgtgatc ... gttctctcagGAATTGGGCCTCAGCCCTTCAGTGCCACTGCATGTCGTTCTGCAAGATTGG
EST: gi|67012906|gb|CO441655.1|CO441655
EST:     ATTTTGAGAAGGAAGGCAACCGAGCTATTGTAATAGATGAATTAGCTTCT                         GAATTGGGCCTCAGCCCTTCAGTGCCACTGCATGTCGTTCTGCAAGATTGG
genomic: ATTTTGAGAAGGAAGGCAACCGAGCTATTGTAATAGATGAATTAGCTTCTgtacgtgatc ... gttctctcagGAATTGGGCCTCAGCCCTTCAGTGCCACTGCATGTCGTTCTGCAAGATTGG
EST: gi|211362655|gb|FL465487.1|FL465487
EST:     ATTTTGAGAAGGAAGGCAACCGAGCTATTGTAATAGATGAATTAGCTTCT                         GAATTGGGCCTCAGCCCTTCAGCGCCACTGCATGTCGTTCTGCAAGATTGG
genomic: ATTTTGAGAAGGAAGGCAACCGAGCTATTGTAATAGATGAATTAGCTTCTgtacgtgatc ... gttctctcagGAATTGGGCCTCAGCCCTTCAGTGCCACTGCATGTCGTTCTGCAAGATTGG
EST: gi|60345920|gb|DN212893.1|DN212893
EST:     ATTTTGAGAAGGAAGGCAACCGAGCTATTGTAATAGATGAATTAGCTTCT                         GAATTGGGCCTCAGCCCTTCAGTGCCACTGCATGTCGTTCTGCAAGATTGG
genomic: ATTTTGAGAAGGAAGGCAACCGAGCTATTGTAATAGATGAATTAGCTTCTgtacgtgatc ... gttctctcagGAATTGGGCCTCAGCCCTTCAGTGCCACTGCATGTCGTTCTGCAAGATTGG
EST: gi|32930297|gb|CF035109.1|CF035109
EST:     ATTTTGAGAAGGAAGGCAACCGAGCTATTGTAATAGATGAATTAGCTTCT                         GAATTGGGCCTCAGCCCTTCAGTGCCACTGCATGTCGTTCTGCAAGATTGG
genomic: ATTTTGAGAAGGAAGGCAACCGAGCTATTGTAATAGATGAATTAGCTTCTgtacgtgatc ... gttctctcagGAATTGGGCCTCAGCCCTTCAGTGCCACTGCATGTCGTTCTGCAAGATTGG
EST: gi|211442907|gb|FL470068.1|FL470068
EST:     ATTTTGAGAAGGAAGGCAACCGAGCTATTGTAATAGATGAATTAGCTTCT                         GAATTGGGCCTCAGCCCTTCAGTGCC
genomic: ATTTTGAGAAGGAAGGCAACCGAGCTATTGTAATAGATGAATTAGCTTCTgtacgtgatc ... gttctctcagGAATTGGGCCTCAGCCCTTCAGTGCC

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: 46 (upstream exon), 45 (downstream exon)
Score: 124

GCTTGAAGCATTGGATAGATGGGAGCAACATGCGAGATCTGCTTATGAACATTTTGAGAAGGAAGGCAACCGAGCTATTGTAATAGATGAATTAGCTTCTgtacgtgatc ... gttctctcagGAATTGGGCCTCAGCCCTTCAGTGCCACTGCATGTCGTTCTGCAAGATTGGATCAGGCATACGGATGGGAAATTGAGCTTTCTCGGATTTGTCAAGTTAT


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

GCTTGAAGCATTGGATAGATGGGAGCAACATGCGAGATCTGCTTATGAACATTTTGAGAAGGAAGGCAACCGAGCTATTGTAATAGATGAATTAGCTTCTgtacgtgatc ... gttctctcagGAATTGGGCCTCAGCCCTTCAGTGCCACTGCATGTCGTTCTGCAAGATTGGATCAGGCATACGGATGGGAAATTGAGCTTTCTCGGATTTGTCAAGTTAT


Block sizes: 45 (upstream exon), 39 (downstream exon)
Score: 32

GCTTGAAGCATTGGATAGATGGGAGCAACATGCGAGATCTGCTTATGAACATTTTGAGAAGGAAGGCAACCGAGCTATTGTAATAGATGAATTAGCTTCTgtacgtgatc ... gttctctcagGAATTGGGCCTCAGCCCTTCAGTGCCACTGCATGTCGTTCTGCAAGATTGGATCAGGCATACGGATGGGAAATTGAGCTTTCTCGGATTTGTCAAGTTAT


Block sizes: 47 (upstream exon), 44 (downstream exon)
Score: 23

GCTTGAAGCATTGGATAGATGGGAGCAACATGCGAGATCTGCTTATGAACATTTTGAGAAGGAAGGCAACCGAGCTATTGTAATAGATGAATTAGCTTCTgtacgtgatc ... gttctctcagGAATTGGGCCTCAGCCCTTCAGTGCCACTGCATGTCGTTCTGCAAGATTGGATCAGGCATACGGATGGGAAATTGAGCTTTCTCGGATTTGTCAAGTTAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttattacatgctatggaatatttcattgtcaataaaatttacttgttctctcagGAATTGGGCCTCAGCCCTTCAGTGCCACTGCATGTCGTTCTGCAAGATTGGATCAGGCATACGGATGGGAAATTGAGCTTTCTCGGATTTGTCAAGTTAT
                                      tttacttgttctctc  CT-rich tract
                 aatatttcattgtcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtgatcttcctccctgttctctttctagcataccagtttggtggacctcccaatatttcctggcacattcgttattacatgctatggaatatttcattgtcaataaaatttacttgttctctcagGAATTGGGCCTCAGCCCTTCAGTGCCACTGCATGTCGTTCTGCAAGATTGGATCAGGCATACGGATGGGAAATTGAGCTTTCTCGGATTTGTCAAGTTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT