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'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagctgaattcctgttggttatataaaagcaatttgcaatagttatctctttacgttatttatggtttgtgcgggatgttccttgctattcttatctcagGCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACTTCAGTCTATGGTGAAAATTATGACCAAGAGGAGGCAGAAGCGGCAGCAGGGAAAGCTTCCCGT

Basic information

species Zea mays
transcript GRMZM2G414496_T07
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G414496_T07 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os07g08729.1 (Oryza sativa), 3'ss of exon 17
-------------aagctgaattcctgttggttatataaaagcaatttgcaatagttatctctttacgttatttatggtttgtgcgggatgttccttgctattcttatctcagGCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACTTCAGTCTATGGTGAAAATTATGACCAAGAGGAGGCAGAAGCGGCAGCAGGGAAAGCTTCCCGT
              |  | | ||    ||  ||  |||| | |||  | ||| ||| | |||||             | || || ||| |||| | | | | ||||||||||||||||  ||||  || ||| | |||||||| ||| ||||||||||||||||||||||||| |||||||| || || || ||||||| ||| |||     |
tctactacatattcaattcagttttacttttttgcataacaacaacgtacaacagtcacctctt-------------gcttatgtgggttgtttcctaccactcttatctcagGCCAGTAGTAGTTAAAGCTGTCGAGGAATTTAAGGCTTCAGTCTATGGTGAAAATTATGATCAAGAGGAAGCCGAGGCAGCAGCAGCGAAGGCTGGGGCT
















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|37377775|gb|CF625524.1|CF625524
EST:     ATGCCTGATATAAAGGACGAGACCCTGCCTGACGAAGAAGGCTT-TCTAA                         GCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACTTCAGTCTATGGTGA
genomic: ATGCCTGATATAAAGGATGAGACCCTGCCTGACGAAGAAGGCTTGTCTAAgtacttcttt ... cttatctcagGCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACTTCAGTCTATGGTGA
EST: gi|71312125|gb|DR792591.1|DR792591
EST:     ATGCCTGATATAAAGGATGAGACCCTGCCTGACGAAGAAGGCTTGTTTAA                         GCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACTTCAGTCTATGGTGA
genomic: ATGCCTGATATAAAGGATGAGACCCTGCCTGACGAAGAAGGCTTGTCTAAgtacttcttt ... cttatctcagGCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACTTCAGTCTATGGTGA
EST: gi|14245465|gb|BG874047.1|BG874047
EST:     ATGCCTGATATAAAGGATGAGACCCTGCCTGACGAAGAAGGCTTGTCTAA                         GCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACTTCAGTCTATGGTGA
genomic: ATGCCTGATATAAAGGATGAGACCCTGCCTGACGAAGAAGGCTTGTCTAAgtacttcttt ... cttatctcagGCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACTTCAGTCTATGGTGA
EST: gi|60400302|gb|DN233109.1|DN233109
EST:     ATGCTTGATATAAAGGATGAGACCCTGCCTGACGAAGAAGGCTTGTCTAA                         GCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACTTCAGTCTATGGTGA
genomic: ATGCCTGATATAAAGGATGAGACCCTGCCTGACGAAGAAGGCTTGTCTAAgtacttcttt ... cttatctcagGCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACTTCAGTCTATGGTGA
EST: gi|71312126|gb|DR792592.1|DR792592
EST:     ATGCCTGATATAAAGGATGAGACCCTGCCTGACGAAGAAGGCTTGTCTAA                         GCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACTTCAGTCTATGGTGA
genomic: ATGCCTGATATAAAGGATGAGACCCTGCCTGACGAAGAAGGCTTGTCTAAgtacttcttt ... cttatctcagGCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACTTCAGTCTATGGTGA
EST: gi|32937939|gb|CF042758.1|CF042758
EST:     ATGCCTGATATAAAGGATGAGACCCTGCCTGACGAAGAAGGCTTGTCTAA                         GCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACTTCAGTCTATGGTGA
genomic: ATGCCTGATATAAAGGATGAGACCCTGCCTGACGAAGAAGGCTTGTCTAAgtacttcttt ... cttatctcagGCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACTTCAGTCTATGGTGA
EST: gi|76285513|gb|DV025081.1|DV025081
EST:     ATGCCTGATATAAAGGATGAGACCCTGCCTGACGAAGAAGGCTTGTCTAA                         GCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACTTCAGTCTATGGTGA
genomic: ATGCCTGATATAAAGGATGAGACCCTGCCTGACGAAGAAGGCTTGTCTAAgtacttcttt ... cttatctcagGCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACTTCAGTCTATGGTGA
EST: gi|211402618|gb|FL252146.1|FL252146
EST:     ATGCCTGATATAAAGGATGAGACCCTGCCTGACGAAGAAGGCTTGTCTAA                         GCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACTTCAGTCTATGGTGA
genomic: ATGCCTGATATAAAGGATGAGACCCTGCCTGACGAAGAAGGCTTGTCTAAgtacttcttt ... cttatctcagGCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACTTCAGTCTATGGTGA
EST: gi|78544440|gb|DV621938.1|DV621938
EST:     ATGCCTGATATAAAGGATGAGACCCTGCCTGACGAAGAAGGCTTGTCTAA                         GCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACTTCAGTCTATGGTGA
genomic: ATGCCTGATATAAAGGATGAGACCCTGCCTGACGAAGAAGGCTTGTCTAAgtacttcttt ... cttatctcagGCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACTTCAGTCTATGGTGA
EST: gi|40334316|gb|CK368386.1|CK368386
EST:     ATGCCTGATATAAAGGACGAGACCCTGCCTGACGAAGAAGGCTTGTCTAA                         GCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACTTCAGTCTATGGTGA
genomic: ATGCCTGATATAAAGGATGAGACCCTGCCTGACGAAGAAGGCTTGTCTAAgtacttcttt ... cttatctcagGCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACTTCAGTCTATGGTGA
EST: gi|71446738|gb|DR827788.1|DR827788
EST:     ATGCCTGATATAAAGGATGAGACCCTGCCTGACGAAGAAGGCTTGTCTAA                         GCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACTTCAGTCTATGGTGA
genomic: ATGCCTGATATAAAGGATGAGACCCTGCCTGACGAAGAAGGCTTGTCTAAgtacttcttt ... cttatctcagGCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACTTCAGTCTATGGTGA
EST: gi|37383098|gb|CF628530.1|CF628530
EST:     ATGCCTGATATAAAGGACGAGACCCTGCCTGACGAAGAAGGCTTGTCTAA                         GCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACTTCAGTCTATGGTGA
genomic: ATGCCTGATATAAAGGATGAGACCCTGCCTGACGAAGAAGGCTTGTCTAAgtacttcttt ... cttatctcagGCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACTTCAGTCTATGGTGA
EST: gi|60338376|gb|DN205349.1|DN205349
EST:     ATGCCTGATATAAAGGATGAGACCCTGCCTGACGAAGAAGGCTTGTCTAA                         GCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACTTCAGTCTATGGTGA
genomic: ATGCCTGATATAAAGGATGAGACCCTGCCTGACGAAGAAGGCTTGTCTAAgtacttcttt ... cttatctcagGCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACTTCAGTCTATGGTGA
EST: gi|60347385|gb|DN214358.1|DN214358
EST:     ATGCCTGATATAAAGGATGAGACCCTGCCTGACGAAGAAGGCTTGTCTAA                         GCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACTTCAGTCTATGGTGA
genomic: ATGCCTGATATAAAGGATGAGACCCTGCCTGACGAAGAAGGCTTGTCTAAgtacttcttt ... cttatctcagGCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACTTCAGTCTATGGTGA
EST: gi|101382023|gb|EB813067.1|EB813067
EST:     ATGCCTGATATAAAGGATGAGACCCTGCCTGACGAAGAAGGCTTGTCTAA                         GCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACTTCAGTCTATGGTGA
genomic: ATGCCTGATATAAAGGATGAGACCCTGCCTGACGAAGAAGGCTTGTCTAAgtacttcttt ... cttatctcagGCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACTTCAGTCTATGGTGA
EST: gi|33097000|gb|CF056960.1|CF056960
EST:     ATGCCTGATATAAAGGATGAGACCCTGCCTGACGAAGAAGGCTTGTCTAA                         GCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACCTCAGTCTATGGTGA
genomic: ATGCCTGATATAAAGGATGAGACCCTGCCTGACGAAGAAGGCTTGTCTAAgtacttcttt ... cttatctcagGCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACTTCAGTCTATGGTGA
EST: gi|71761431|gb|DR959368.1|DR959368
EST:     ATGCCTGATATAAAGGATGAGACCCTGCCTGACGAAGAAGGCTTGTCTAA                         GCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACTTCAGTCTATGGTGA
genomic: ATGCCTGATATAAAGGATGAGACCCTGCCTGACGAAGAAGGCTTGTCTAAgtacttcttt ... cttatctcagGCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACTTCAGTCTATGGTGA
EST: gi|24768047|gb|CA403179.1|CA403179
EST:     ATGCCTGATATAAAGGATGAGACCCTGCCTGACGAAGAAGGCTTGTCTAA                         GCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACTTCAGTCTATGGTGA
genomic: ATGCCTGATATAAAGGATGAGACCCTGCCTGACGAAGAAGGCTTGTCTAAgtacttcttt ... cttatctcagGCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACTTCAGTCTATGGTGA
EST: gi|32935327|gb|CF040139.1|CF040139
EST:     ATGCCTGATATAAAGGATGAGACCCTGCCTGACGAAGAAGGCTTGTCTAA                         GCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACTTCAGTCTATGGTGA
genomic: ATGCCTGATATAAAGGATGAGACCCTGCCTGACGAAGAAGGCTTGTCTAAgtacttcttt ... cttatctcagGCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACTTCAGTCTATGGTGA

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), 49 (downstream exon)
Score: 506

TGCAAAGACACTATGGGATCTTGGAGGCCTTAGCTTTAGGCGAAGATGAGATGCCTGATATAAAGGATGAGACCCTGCCTGACGAAGAAGGCTTGTCTAAgtacttcttt ... cttatctcagGCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACTTCAGTCTATGGTGAAAATTATGACCAAGAGGAGGCAGAAGCGGCAGCAGGGAAAGCTTCCCGT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 65

TGCAAAGACACTATGGGATCTTGGAGGCCTTAGCTTTAGGCGAAGATGAGATGCCTGATATAAAGGATGAGACCCTGCCTGACGAAGAAGGCTTGTCTAAgtacttcttt ... cttatctcagGCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACTTCAGTCTATGGTGAAAATTATGACCAAGAGGAGGCAGAAGCGGCAGCAGGGAAAGCTTCCCGT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 76

TGCAAAGACACTATGGGATCTTGGAGGCCTTAGCTTTAGGCGAAGATGAGATGCCTGATATAAAGGATGAGACCCTGCCTGACGAAGAAGGCTTGTCTAAgtacttcttt ... cttatctcagGCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACTTCAGTCTATGGTGAAAATTATGACCAAGAGGAGGCAGAAGCGGCAGCAGGGAAAGCTTCCCGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 91

TGCAAAGACACTATGGGATCTTGGAGGCCTTAGCTTTAGGCGAAGATGAGATGCCTGATATAAAGGATGAGACCCTGCCTGACGAAGAAGGCTTGTCTAAgtacttcttt ... cttatctcagGCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACTTCAGTCTATGGTGAAAATTATGACCAAGAGGAGGCAGAAGCGGCAGCAGGGAAAGCTTCCCGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctctttacgttatttatggtttgtgcgggatgttccttgctattcttatctcagGCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACTTCAGTCTATGGTGAAAATTATGACCAAGAGGAGGCAGAAGCGGCAGCAGGGAAAGCTTCCCGT
                                 ttccttgctattctt  CT-rich tract
          ttatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagctgaattcctgttggttatataaaagcaatttgcaatagttatctctttacgttatttatggtttgtgcgggatgttccttgctattcttatctcagGCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACTTCAGTCTATGGTGAAAATTATGACCAAGAGGAGGCAGAAGCGGCAGCAGGGAAAGCTTCCCGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC