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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagacatcaacgctgcttataagattaggatcctccaagataaacaagtttgtggtggcttattttaaattttgttgcttgcagGTATGTTGCACCAGAGTATGCGGGCACTGGCATGTTGAATGAAACTAGCGATGTCTATAGTTTCGGAATTCTTATCATGGAAATAATATCTGGCCGTGTA

Basic information

species Zea mays
transcript GRMZM2G050861_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G050861_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os04g35080.1 (Oryza sativa), 3'ss of exon 4
gttagacatcaacgctgcttataagattaggatcctccaagataaacaagtttgtggtggcttattttaaattttgttgcttgcagGTATGTTGCACCAGAGTATGCGGGCACTGGCATGTTGAATGAAACTAGCGATGTCTATAGTTTCGGAATTCTTATCATGGAAATAATATCTGGCCGTGTA
|||||| || | | |  ||| |||  | |  ||  | ||||| | |  | | | | |   |||||   |  |||||||  ||||||||| || || ||||||||||| || ||||||||||| ||||||||||| |||||||||||||| ||||||||||||||||||||||||||||| || |||
gttagaaattagcacc-cttgtaatgtgataattgtacaagacacatgaatattttg---cttatgc-atcttttgttctttgcagGTACGTAGCTCCAGAGTATGCTGGTACTGGCATGTTAAATGAAACTAGTGATGTCTATAGTTTTGGAATTCTTATCATGGAAATAATATCTGGTCGGGTA

upper sequence: GRMZM2G050861_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA11G05830.1 (Glycine max), 3'ss of exon 4
---------------gttagacatcaacgctgc-ttataagattaggatcctccaagataaacaagtttgtggtggcttattttaaattttgttgctt--gcagGTATGTTGCACCAGAGTATGCGGGCACTGGCATGTTGAATGAAACTAGCGATGTCTATAGTTTCGGAATTCTTATCATGGAAATAATATCTGGCCGTGTA
                ||    ||    ||| | ||    | | |      |    |  |     | ||    |   ||   |||| | || ||  ||  |||| |||||||| || || || ||| | ||||||||||||||||||   || ||||| |||||||| ||||||||||| |||||| ||||  | ||  |    
gtttgtattatcttccttgtctattgttgctccattgcttgctcaaagcattattggtcatgacgggtttccatcaattcccttaattgttcttcttttggcagATATGTTGCTCCTGAATACGCGAGTACTGGCATGTTGAATGAACGGAGTGATGTTTATAGTTTTGGAATTCTTATTATGGAACTAATTACAGGAAGGAAT

upper sequence: GRMZM2G050861_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA01G39420.1 (Glycine max), 3'ss of exon 5
------------------gttagacatcaacgc-tgcttataagattaggatcctccaagataaacaagtttgtggtggcttattttaaattttgttgcttgcagGTATGTTGCACCAGAGTATGCGGGCACTGGCATGTTGAATGAAACTAGCGATGTCTATAGTTTCGGAATTCTTATCATGGAAATAATATCTGGCCGTGTA
                   |      |   | | | | |     |  || |||   ||  ||              || |||| ||    ||||  |  |||||| |||||||| || || || ||  | ||||||||||||||||||   || ||||| |||||||| |||||||| || |||||| ||||  | ||  |    
gtttgtatagtcttccttctctattgttggcccattccttccttacaagtatcggtcattatgggtttccagcaattgccttactt---gtttttctttttgcagATATGTTGCTCCTGAATACGCAAGTACTGGCATGTTGAATGAACGGAGTGATGTTTATAGTTTTGGAATTCTAATTATGGAACTAATTACAGGAAGGAAT

upper sequence: GRMZM2G050861_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv07s0031g00480.t01 (Vitis vinifera), 3'ss of exon 4
----gttaga-catcaacgctgcttataagattaggatcctccaagataaacaagtttgtggtggcttattttaaattttgttgcttgcagGTATGTTGCACCAGAGTATGCGGGCACTGGCATGTTGAATGAAACTAGCGATGTCTATAGTTTCGGAATTCTTATCATGGAAATAATATCTGGCCGTGTA
    ||  || | |   |  | | | |     |    | |||     | || |||   |||||| ||  || |   || ||||  ||| || ||||| || || || |||||  | || ||||||||||||||||  || ||||| |||||||| || |||||||||||||||||||| |||||  |    
gtatgtatgatctttctccttccctcttccccttcccttctctcctgtgaagaagag-gtggtgactatttgt---ttctgtt-tttgtagCTATGTAGCTCCTGAATATGCAAGTACAGGCATGTTGAATGAAAGAAGTGATGTGTATAGTTTTGGGATTCTTATCATGGAAATAATTTCTGGGAGGAAT

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|26557376|gb|CA829611.1|CA829611
EST:     TTGGGTTCAGAAAGGAGTTATGTCACAACCAGGGTCATGGGGACGTTTGG                         GTATGTTGCACCAGAGTATGCGGGCACTGGCATGTTGAATGA
genomic: TTGGGTTCAGAAAGGAGTTATGTCACAACCAGGGTCATGGGGACGTTTGGgttagacatc ... ttgcttgcagGTATGTTGCACCAGAGTATGCGGGCACTGGCATGTTGAATGA
EST: gi|6760613|gb|AW324712.1|AW324712
EST:     TTGGGTTCAGAAAGGAGTTATGTCACAACCAGGGTCATGGGGACATTTGG                         GTATGTTGCGCCAGAGTATGCGGGCACTGGCATGTTGAATGAAACTAGCGA
genomic: TTGGGTTCAGAAAGGAGTTATGTCACAACCAGGGTCATGGGGACGTTTGGgttagacatc ... ttgcttgcagGTATGTTGCACCAGAGTATGCGGGCACTGGCATGTTGAATGAAACTAGCGA
EST: gi|71762004|gb|DR959941.1|DR959941
EST:     GGGTCATGGGGACGTTTGG                         GTATGTTGCACCAGAGTATGCGGGCACTGGCATGTTGAATGAAACTAGCGA
genomic: GGGTCATGGGGACGTTTGGgttagacatc ... ttgcttgcagGTATGTTGCACCAGAGTATGCGGGCACTGGCATGTTGAATGAAACTAGCGA
EST: gi|6742388|gb|AW313203.1|AW313203
EST:     TTGGGTTCAGAAAGGAGTTATGTCACAACCAGGGTCATGGGGACATTTGG                         GTATGTTGCGCCAGAGTATGCGGGCACTGGCATGTTGAATGAAACTAGCGA
genomic: TTGGGTTCAGAAAGGAGTTATGTCACAACCAGGGTCATGGGGACGTTTGGgttagacatc ... ttgcttgcagGTATGTTGCACCAGAGTATGCGGGCACTGGCATGTTGAATGAAACTAGCGA
EST: gi|28931348|gb|CB334709.1|CB334709
EST:     TTGGGTTCAGAAAGGAGTTATGTCACAACCAGGGTCATGGGGACGTTTGG                         GTATGTTGCACCAGAGTATGCGGGCACTGGCATGGTGAATGAAACTA
genomic: TTGGGTTCAGAAAGGAGTTATGTCACAACCAGGGTCATGGGGACGTTTGGgttagacatc ... ttgcttgcagGTATGTTGCACCAGAGTATGCGGGCACTGGCATGTTGAATGAAACTA
EST: gi|5555472|gb|AI881423.1|AI881423
EST:     TTGGGTTCAGAAAGGAGTTATGTCACAACCAGGGTCATGGGGACGTTTGG                         GTATGTTGCACCAGAGTATGCGGGCACTGGCATGTTGAATGAAACTAGCGA
genomic: TTGGGTTCAGAAAGGAGTTATGTCACAACCAGGGTCATGGGGACGTTTGGgttagacatc ... ttgcttgcagGTATGTTGCACCAGAGTATGCGGGCACTGGCATGTTGAATGAAACTAGCGA
EST: gi|78179542|gb|DV549915.1|DV549915
EST:     TTGGGTTCAGAAAGGAGTTATGTCACAACCAGGGTCATGGGGACATTTGG                         GTATGTTGCGCCAGAGTATGCGGGCACTGGCATGTTGAATGAAACTAGCGA
genomic: TTGGGTTCAGAAAGGAGTTATGTCACAACCAGGGTCATGGGGACGTTTGGgttagacatc ... ttgcttgcagGTATGTTGCACCAGAGTATGCGGGCACTGGCATGTTGAATGAAACTAGCGA
EST: gi|78087662|gb|DV516055.1|DV516055
EST:     TGGGTTCAGAAAGGAGTTATGTCACAACCAGGGTCATGGGGACGTTTGG                         GTATGTTGCACCAGAGTATGCGGGCACTGGCATGTTGAATGAAACTAGCGA
genomic: TGGGTTCAGAAAGGAGTTATGTCACAACCAGGGTCATGGGGACGTTTGGgttagacatc ... ttgcttgcagGTATGTTGCACCAGAGTATGCGGGCACTGGCATGTTGAATGAAACTAGCGA
EST: gi|67010388|gb|CO439137.1|CO439137
EST:     TTGGGTTCAGAAAGGAGTTATGTCACAACCAGGGTCATGGGGACGTTTGG                         GTATGTTGCACCAGAGTATGCGGGCACTGGCATGTTGAATGAAACTAGCGA
genomic: TTGGGTTCAGAAAGGAGTTATGTCACAACCAGGGTCATGGGGACGTTTGGgttagacatc ... ttgcttgcagGTATGTTGCACCAGAGTATGCGGGCACTGGCATGTTGAATGAAACTAGCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcctccaagataaacaagtttgtggtggcttattttaaattttgttgcttgcagGTATGTTGCACCAGAGTATGCGGGCACTGGCATGTTGAATGAAACTAGCGATGTCTATAGTTTCGGAATTCTTATCATGGAAATAATATCTGGCCGTGTA
                                        ttttgtt  CT-rich tract
                              ttattttaaattttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagacatcaacgctgcttataagattaggatcctccaagataaacaagtttgtggtggcttattttaaattttgttgcttgcagGTATGTTGCACCAGAGTATGCGGGCACTGGCATGTTGAATGAAACTAGCGATGTCTATAGTTTCGGAATTCTTATCATGGAAATAATATCTGGCCGTGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA