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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggtacctaccaggatagaagacaatttctggaactaagattgcattagcttttctcagtagcatgataatactggtgttgtttttttctccagGGATGACTACTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAAGGGGTGGT

Basic information

species Zea mays
transcript GRMZM2G164562_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G164562_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g14990.1 (Oryza sativa), 3'ss of exon 3
gtatggtacctaccaggatagaagacaatttctggaa--------ctaagatt---gcattagcttttctcagtagcatgataatactggtgttgtttttttctccagGGATGACTACTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAAGGGGTGGT
|||||||  ||  ||||| |   || ||  |  | ||         | |  ||   | |||||||| |||||    || ||||  | || ||      |||||| |||| ||||| ||||| ||||||||||| || |||||||| ||||||||||| || || |||
gtatggtgtctttcaggacatgggataaacttggaaaaaatatttttgaatttagagtattagcttgtctcatattcacgatagcattgatggg----ttttctgcagGAATGACCACTGGGACACCAATTCATGTTTTTGTCCCGAACACAGATCAGAGAGGGGGT
















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|211165636|gb|FL126855.1|FL126855
EST:     CCCAAGAAAGGAGACTGATACATGCAAAATTCTATCAGGGACACATGATG                         GGATGACTACTGGTACACCAA
genomic: CCCAAGAAAGGAGACTGATACATGCAAAATTCTATCAGGGACACATGATGgtatggtacc ... ttttctccagGGATGACTACTGGTACACCAA
EST: gi|149088514|gb|EE177624.2|EE177624
EST:     CCCAAGAAAGGAGACTGATACATGCAAAATTCTATCAGGGACACATGATG                         GGATGACTACTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAA
genomic: CCCAAGAAAGGAGACTGATACATGCAAAATTCTATCAGGGACACATGATGgtatggtacc ... ttttctccagGGATGACTACTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAA
EST: gi|28361588|gb|CB239944.1|CB239944
EST:     CCCAAGAAAGGAGACTGATACATGCAAAATTCTATCAGGGACACATGATG                         GGATGACTACTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAA
genomic: CCCAAGAAAGGAGACTGATACATGCAAAATTCTATCAGGGACACATGATGgtatggtacc ... ttttctccagGGATGACTACTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAA
EST: gi|211165635|gb|FL126854.1|FL126854
EST:     CCCAAGAAAGGAGACTGATACATGCAAAATTCTATCAGGGACACATGATG                         GGATGACTACTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAA
genomic: CCCAAGAAAGGAGACTGATACATGCAAAATTCTATCAGGGACACATGATGgtatggtacc ... ttttctccagGGATGACTACTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAA
EST: gi|149070137|gb|EE158538.2|EE158538
EST:     CCCAAGAAAGGAGACTGATACATGCAAAATTCTATCAGGGACACATGATG                         GGATGACTACTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAA
genomic: CCCAAGAAAGGAGACTGATACATGCAAAATTCTATCAGGGACACATGATGgtatggtacc ... ttttctccagGGATGACTACTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAA
EST: gi|211165641|gb|FL126860.1|FL126860
EST:     CCCAAGAAAGGAGACTGATACATGCAAAATTCTATCAGGGACACATGATG                         GGATGACTACTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAA
genomic: CCCAAGAAAGGAGACTGATACATGCAAAATTCTATCAGGGACACATGATGgtatggtacc ... ttttctccagGGATGACTACTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAA
EST: gi|211165634|gb|FL126853.1|FL126853
EST:     CCCAAGAAAGGAGACTGATACATGCAAAATTCTATCAGGGACACATGATG                         GGATGACTACTGGTAMAC-AATTCACGTCTTTGTCCCAAACACAGATCAAA
genomic: CCCAAGAAAGGAGACTGATACATGCAAAATTCTATCAGGGACACATGATGgtatggtacc ... ttttctccagGGATGACTACTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAA
EST: gi|211062099|gb|FL126842.1|FL126842
EST:     CCCAAGAAAGGAGACTGATACATGCAAAATTCTATCAGGGACACATGATG                         GGATGACTACTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCANA
genomic: CCCAAGAAAGGAGACTGATACATGCAAAATTCTATCAGGGACACATGATGgtatggtacc ... ttttctccagGGATGACTACTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAA
EST: gi|76020355|gb|DT947525.1|DT947525
EST:     CCCAAGAAAGGAGACTGATACATGCAAAATTCTATCAGGGACACATGATG                         GGATGACTACTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAA
genomic: CCCAAGAAAGGAGACTGATACATGCAAAATTCTATCAGGGACACATGATGgtatggtacc ... ttttctccagGGATGACTACTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAA
EST: gi|211165637|gb|FL126856.1|FL126856
EST:     CCCAAGAAAGGAGACTGATACATGCAAAATTCTATCAGGGACACATGATG                         GGATGACTACTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAA
genomic: CCCAAGAAAGGAGACTGATACATGCAAAATTCTATCAGGGACACATGATGgtatggtacc ... ttttctccagGGATGACTACTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAA
EST: gi|211062105|gb|FL126848.1|FL126848
EST:     CCCAAGAAAGGAGACTGATACATGCAAAATTCTATCAGGGACACATSATG                         GGATGACTACTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAA
genomic: CCCAAGAAAGGAGACTGATACATGCAAAATTCTATCAGGGACACATGATGgtatggtacc ... ttttctccagGGATGACTACTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAA
EST: gi|149015775|gb|EE045474.2|EE045474
EST:     CCCAAGAAAGGAGACTGATACATGCAAAATTCTATCAGGGACACATGATG                         GGATGACTACTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAA
genomic: CCCAAGAAAGGAGACTGATACATGCAAAATTCTATCAGGGACACATGATGgtatggtacc ... ttttctccagGGATGACTACTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAA
EST: gi|71442663|gb|DR823713.1|DR823713
EST:     CCCAAGAAAGGAGACTGATACATGCAAAATTCTATCAGGGACACATGATG                         GGATGACTACTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAA
genomic: CCCAAGAAAGGAGACTGATACATGCAAAATTCTATCAGGGACACATGATGgtatggtacc ... ttttctccagGGATGACTACTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAA
EST: gi|37424877|gb|CF650172.1|CF650172
EST:     CCCAAGAAAGGAGACTGATACATGCAAAATTCTATCAGGGACACATGATG                         GGATGACTACTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCA
genomic: CCCAAGAAAGGAGACTGATACATGCAAAATTCTATCAGGGACACATGATGgtatggtacc ... ttttctccagGGATGACTACTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCA
EST: gi|211062107|gb|FL126850.1|FL126850
EST:     CCCAAGAAAGGAGACTGATACATGCAAAATTCTATCAGGGACACATGATG                         GGATGACTACTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAA
genomic: CCCAAGAAAGGAGACTGATACATGCAAAATTCTATCAGGGACACATGATGgtatggtacc ... ttttctccagGGATGACTACTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAA
EST: gi|148963945|gb|EE015067.2|EE015067
EST:     CCCAAGAAAGGAGACTGATACATGCAAAATTCTATCAGGGACACATGATG                         GGATGACTACTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAA
genomic: CCCAAGAAAGGAGACTGATACATGCAAAATTCTATCAGGGACACATGATGgtatggtacc ... ttttctccagGGATGACTACTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAA
EST: gi|211062101|gb|FL126844.1|FL126844
EST:     CCCAAGAAAGGAGACTGATACATGCAAAATTCTATCAGGGACACATGATG                         GGATGACTACTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAA
genomic: CCCAAGAAAGGAGACTGATACATGCAAAATTCTATCAGGGACACATGATGgtatggtacc ... ttttctccagGGATGACTACTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAA
EST: gi|28390366|gb|CB250180.1|CB250180
EST:     CCCAAGAAAGGAGACTGATACATGCAAAATTCTATCAGGGACACATGATG                         GGATGACTACTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAA
genomic: CCCAAGAAAGGAGACTGATACATGCAAAATTCTATCAGGGACACATGATGgtatggtacc ... ttttctccagGGATGACTACTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAA
EST: gi|78089034|gb|DV517427.1|DV517427
EST:     CCCAAGAAAGGAGACTGATACATGCAAAATTCTATCAGGGACACATGATG                         GGATGACTACTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAA
genomic: CCCAAGAAAGGAGACTGATACATGCAAAATTCTATCAGGGACACATGATGgtatggtacc ... ttttctccagGGATGACTACTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAA
EST: gi|211165640|gb|FL126859.1|FL126859
EST:     CCCAAGAWAGGAGACTGATACATGCAAAATTCTATCAGGGACACATGATG                         GGATGACTACTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCA
genomic: CCCAAGAAAGGAGACTGATACATGCAAAATTCTATCAGGGACACATGATGgtatggtacc ... ttttctccagGGATGACTACTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCA
EST: gi|149100015|gb|EE186068.2|EE186068
EST:     CCCAAGAAAGGAGACTGATACATGCAAAATTCTATCAGGGACACATGATG                         GGATGACTACTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAA
genomic: CCCAAGAAAGGAGACTGATACATGCAAAATTCTATCAGGGACACATGATGgtatggtacc ... ttttctccagGGATGACTACTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAA
EST: gi|148966882|gb|EE018003.2|EE018003
EST:     CCCAAGAAAGGAGACTGATACATGCAAAATTCTATCAGGGACACATGATG                         GGATGACTACTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAA
genomic: CCCAAGAAAGGAGACTGATACATGCAAAATTCTATCAGGGACACATGATGgtatggtacc ... ttttctccagGGATGACTACTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAA
EST: gi|211165639|gb|FL126858.1|FL126858
EST:     CCCAAGAAAGGAGACTGATACATGCAAAATTCTATCAGGGACACATGATG                         GGATGACTACTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAA
genomic: CCCAAGAAAGGAGACTGATACATGCAAAATTCTATCAGGGACACATGATGgtatggtacc ... ttttctccagGGATGACTACTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAA

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: 48 (upstream exon), 49 (downstream exon)
Score: 168

ACGTCCGGGTCAAAGTAGAATTACAACCCCAAGAAAGGAGACTGATACATGCAAAATTCTATCAGGGACACATGATGgtatggtacc ... ttttctccagGGATGACTACTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAAGGGGTGGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 487

ACGTCCGGGTCAAAGTAGAATTACAACCCCAAGAAAGGAGACTGATACATGCAAAATTCTATCAGGGACACATGATGgtatggtacc ... ttttctccagGGATGACTACTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAAGGGGTGGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 574

ACGTCCGGGTCAAAGTAGAATTACAACCCCAAGAAAGGAGACTGATACATGCAAAATTCTATCAGGGACACATGATGgtatggtacc ... ttttctccagGGATGACTACTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAAGGGGTGGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 503

ACGTCCGGGTCAAAGTAGAATTACAACCCCAAGAAAGGAGACTGATACATGCAAAATTCTATCAGGGACACATGATGgtatggtacc ... ttttctccagGGATGACTACTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAAGGGGTGGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgcattagcttttctcagtagcatgataatactggtgttgtttttttctccagGGATGACTACTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAAGGGGTGGT
                                     tgttgtttttttctcc  CT-rich tract
                                       ttgttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggtacctaccaggatagaagacaatttctggaactaagattgcattagcttttctcagtagcatgataatactggtgttgtttttttctccagGGATGACTACTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAAGGGGTGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA