Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaacctagaacttccttgtaccgagtggcaaatgttttgagtctttaagatgactaattttcttattttcctcttggcctttttcacatatcaaatgcagGGCAGAAAAGGGAAATCTTGGTGTGCCACTACTGCCAGGCCAAGGTTGTTCGTTTTATAGCTTCAAGACAAACACATACAAACTGAACTTTACGGAGAGC

Basic information

species Zea mays
transcript GRMZM2G010146_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G010146_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g33020.1 (Oryza sativa), 3'ss of exon 1
gaacctagaacttccttgtaccgagtggcaaatgttttgagtct---ttaagatgactaattttcttattttcctcttggcctttttcacatatcaa-atgcagGGCAGAAAAGGGAAATCTTGGTGTGCCACTACTGCCAGGCCAAGGTTGTTCGTTTTATAGCTTCAAGACAAACACATACAAACTGAACTTTACGGAGAGC
   || |  |  |  ||   |    ||   |||    ||| |||   || || | |  ||| || | | | | ||| ||  |  | |  || ||||  |||||| ||||||||||| |||||||| |||||||||||||| ||||| ||||| || ||||| |||||||||||||||||||||||| |||||||    ||||||
-tgcccacgagattgttac-cattttgatgaattaggtgaatctaaattgagcttaa-aatgttatcagtgttctcatgatcactct-gcacatcactatgcagAGCAGAAAAGGGGAATCTTGGGGTGCCACTACTGCCGGGCCAGGGTTGCTCATTTTACAGCTTCAAGACAAACACATACAAATTGAACTTCCTAGAGAGC
















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|94477699|gb|EB706657.1|EB706657
EST:     GGGCTCCTCTTCTCCCTTCGCTCCTTCACCGCCAAGATCGACCCAACCAC                         ---A-AAA-GGGAAATCTTGGTGTGCCACTACTGCCAGGCCAAGGTTGTTC
genomic: GGGCTCCTCTTCTCCCTTCGCTCCTTCACCGCCAAGATCGACCCAACCACgtacgtccta ... tcaaatgcagGGCAGAAAAGGGAAATCTTGGTGTGCCACTACTGCCAGGCCAAGGTTGTTC
EST: gi|71425314|gb|DR806606.1|DR806606
EST:     GGGCTCCTCTTCTCCCTTCGCTCCTTCACCGCCAAGATCGACCCAACCAC                         GGCAGAAAAGGGAAATCTTGGTGTGCCACTACTGCCAGGCCAAGGTTGTTC
genomic: GGGCTCCTCTTCTCCCTTCGCTCCTTCACCGCCAAGATCGACCCAACCACgtacgtccta ... tcaaatgcagGGCAGAAAAGGGAAATCTTGGTGTGCCACTACTGCCAGGCCAAGGTTGTTC
EST: gi|148944695|gb|EC889832.2|EC889832
EST:     GGGCTCCTCTTCTCCCTTCGCTCCTTCACCGCCAAGATCGACCCAACCAC                         GGCAGAAAAGGGAAATCTTGGTGTGCCACTACTGCCAGGCCAAGGTTGTTC
genomic: GGGCTCCTCTTCTCCCTTCGCTCCTTCACCGCCAAGATCGACCCAACCACgtacgtccta ... tcaaatgcagGGCAGAAAAGGGAAATCTTGGTGTGCCACTACTGCCAGGCCAAGGTTGTTC
EST: gi|78083968|gb|DV512361.1|DV512361
EST:     GGGCTCCTCTTCTCCCTTCGCTCCTTCACCGCCAAGATCGACCCAACCAC                         GGCAGAAAAGGGAAATCTTGGTGTGCCACTACTGCCAGGCCAAGGTTGTTC
genomic: GGGCTCCTCTTCTCCCTTCGCTCCTTCACCGCCAAGATCGACCCAACCACgtacgtccta ... tcaaatgcagGGCAGAAAAGGGAAATCTTGGTGTGCCACTACTGCCAGGCCAAGGTTGTTC
EST: gi|71436637|gb|DR817687.1|DR817687
EST:     GGGCTCCTCTTCTCCCTTCGCTCCTTCACCGCCAAGATCGACCCAACCAC                         GGCAGAAAAGGGAAATCTTGGTGTGCCACTACTGCCAGGCCAAGGTTGTTC
genomic: GGGCTCCTCTTCTCCCTTCGCTCCTTCACCGCCAAGATCGACCCAACCACgtacgtccta ... tcaaatgcagGGCAGAAAAGGGAAATCTTGGTGTGCCACTACTGCCAGGCCAAGGTTGTTC
EST: gi|71757992|gb|DR955929.1|DR955929
EST:     GGGCTCCTCTTCTCCCTTCGCTCCTTCACCGCCAAGATCGACCCAACCAC                         GGCAGAAAAGGGAAATCTTGGTGTGCCACTACTGCCAGGCCAAGGTTGTTC
genomic: GGGCTCCTCTTCTCCCTTCGCTCCTTCACCGCCAAGATCGACCCAACCACgtacgtccta ... tcaaatgcagGGCAGAAAAGGGAAATCTTGGTGTGCCACTACTGCCAGGCCAAGGTTGTTC
EST: gi|93284352|gb|EB676616.1|EB676616
EST:     GGGCTCCTCTTCTCCCTTCGCTCCTTCACCGCCAAGATCGACCCAACCAC                         GGCAGAAAAGGGAAATCTTGGTGTGCCACTACTGCCAGGCCAAGGTTGTTC
genomic: GGGCTCCTCTTCTCCCTTCGCTCCTTCACCGCCAAGATCGACCCAACCACgtacgtccta ... tcaaatgcagGGCAGAAAAGGGAAATCTTGGTGTGCCACTACTGCCAGGCCAAGGTTGTTC
EST: gi|71316463|gb|DR794909.1|DR794909
EST:     GGCTCCTCTTCTCCCTTCGCTCCTTCACCCGCCA-GATCGACCCAACCAC                         GGCAGAAAAGGGAA
genomic: GGCTCCTCTTCTCCCTTCGCTCCTTCACC-GCCAAGATCGACCCAACCACgtacgtccta ... tcaaatgcagGGCAGAAAAGGGAA
EST: gi|74238223|gb|DT646137.1|DT646137
EST:     GGGCTCCTCTTCTCCCTTCGCTCCTTCACCGCCAAGATCGACCCAACCAC                         GGCAGAAAAGGGAAATCTTGGTGTGCCACTACTGCCAGGCCAAGGTTGTTC
genomic: GGGCTCCTCTTCTCCCTTCGCTCCTTCACCGCCAAGATCGACCCAACCACgtacgtccta ... tcaaatgcagGGCAGAAAAGGGAAATCTTGGTGTGCCACTACTGCCAGGCCAAGGTTGTTC
EST: gi|148932965|gb|EE285816.2|EE285816
EST:     GGGCTCCTCTTCTCCCTTCGCTCCTTCACCGCCAAGATCGACCCAACCAC                         GGCAGAAAAGGGAAATCTTGGTGTGCCACTACTGCCAGGCCAAGGTTGTTC
genomic: GGGCTCCTCTTCTCCCTTCGCTCCTTCACCGCCAAGATCGACCCAACCACgtacgtccta ... tcaaatgcagGGCAGAAAAGGGAAATCTTGGTGTGCCACTACTGCCAGGCCAAGGTTGTTC
EST: gi|76292672|gb|DV032240.1|DV032240
EST:     GGGCTCCTCTTCTCCCTTCGCTCCTTCACCGCCAAGATCGACCCAACCAC                         GGCAGAAAAGGGAAATCTTGGTGTGCCACTACTGCC
genomic: GGGCTCCTCTTCTCCCTTCGCTCCTTCACCGCCAAGATCGACCCAACCACgtacgtccta ... tcaaatgcagGGCAGAAAAGGGAAATCTTGGTGTGCCACTACTGCC
EST: gi|91872814|gb|EB402771.1|EB402771
EST:     GGGCTCCTCTTCTCCCTTCGCTCCTTCACCGCCAAGATCGACCCAACCAC                         GGCAGAAAAGGGAAATCTTGGTGTGCCACTACTGCCAGGCCAAGGTTGTTC
genomic: GGGCTCCTCTTCTCCCTTCGCTCCTTCACCGCCAAGATCGACCCAACCACgtacgtccta ... tcaaatgcagGGCAGAAAAGGGAAATCTTGGTGTGCCACTACTGCCAGGCCAAGGTTGTTC
EST: gi|71434336|gb|DR815386.1|DR815386
EST:     GGGCTCCTCTTCTCCCTTCGCTCCTTCACCGCCAAGATCGACCCAACCAC                         GGCAGAAAAGGGAAATCTTGGTGTGCCACTACTGCCAGGCCAAGGTTGTTC
genomic: GGGCTCCTCTTCTCCCTTCGCTCCTTCACCGCCAAGATCGACCCAACCACgtacgtccta ... tcaaatgcagGGCAGAAAAGGGAAATCTTGGTGTGCCACTACTGCCAGGCCAAGGTTGTTC
EST: gi|71443624|gb|DR824674.1|DR824674
EST:     GGGCTCCTCTTCTCCCTTCGCTCCTTCACCGCCAAGATCGACCCAACCAC                         GGCAGAAAAGGGAAATCTTGGTGTGCCACTACTGCCAGGCCAAGGTTGTTC
genomic: GGGCTCCTCTTCTCCCTTCGCTCCTTCACCGCCAAGATCGACCCAACCACgtacgtccta ... tcaaatgcagGGCAGAAAAGGGAAATCTTGGTGTGCCACTACTGCCAGGCCAAGGTTGTTC
EST: gi|71302504|gb|DR787370.1|DR787370
EST:     GGGCTCCTCTTCTCCCTTCGCTCCTTCACCGCCAAGATCGACCCAACCAC                         GGCAGAAAAGGGAAATCTTGGTGTGCCACTACTGCCAGGCCAAGGTTGTTC
genomic: GGGCTCCTCTTCTCCCTTCGCTCCTTCACCGCCAAGATCGACCCAACCACgtacgtccta ... tcaaatgcagGGCAGAAAAGGGAAATCTTGGTGTGCCACTACTGCCAGGCCAAGGTTGTTC
EST: gi|148930227|gb|EC872669.2|EC872669
EST:     GGGCTCCTCTTCTCCCTTCGCTCCTTCACCGCCAAGATCGACCCAACCAC                         GGCAGAAAAGGGAAATCTTGGTGTGCCACTACTGCCAGGCCAAGGTTGTTC
genomic: GGGCTCCTCTTCTCCCTTCGCTCCTTCACCGCCAAGATCGACCCAACCACgtacgtccta ... tcaaatgcagGGCAGAAAAGGGAAATCTTGGTGTGCCACTACTGCCAGGCCAAGGTTGTTC
EST: gi|211038846|gb|FL245342.1|FL245342
EST:     GGGCTCCTCTTCTCCCTTCGCTCCTTCACCGCCAAGATCGACCCAACCAC                         GGCAGAAAAGGGAAATCTTGGTGTGCCACTACTGCCAGGCCAAGGTTGTTC
genomic: GGGCTCCTCTTCTCCCTTCGCTCCTTCACCGCCAAGATCGACCCAACCACgtacgtccta ... tcaaatgcagGGCAGAAAAGGGAAATCTTGGTGTGCCACTACTGCCAGGCCAAGGTTGTTC
EST: gi|101393644|gb|EB818754.1|EB818754
EST:     GGGCTCCTCTTCTCCCTTCGCTCCTTCACCGCCAAGATCGACCCAACCAC                         GGCAGAAAAGGGAAATCTTGGTGTGCCACTACTGCCAGGCCAAGGTTGTTC
genomic: GGGCTCCTCTTCTCCCTTCGCTCCTTCACCGCCAAGATCGACCCAACCACgtacgtccta ... tcaaatgcagGGCAGAAAAGGGAAATCTTGGTGTGCCACTACTGCCAGGCCAAGGTTGTTC
EST: gi|71436489|gb|DR817539.1|DR817539
EST:     GGGCTCCTCTTCTCCCTTCGCTCCTTCACCGCCAAGATCGACCCAACCAC                         GGCAGAAAAGGGAAATCTTGGTGTGCCACTACTGCCAGGCCAAGGTTGTTC
genomic: GGGCTCCTCTTCTCCCTTCGCTCCTTCACCGCCAAGATCGACCCAACCACgtacgtccta ... tcaaatgcagGGCAGAAAAGGGAAATCTTGGTGTGCCACTACTGCCAGGCCAAGGTTGTTC

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: 32

ACCGCCCCCTCCGCACGCTCGACCCCACCCAGGATCACAAGCTCATGTTCGGGCTCCTCTTCTCCCTTCGCTCCTTCACCGCCAAGATCGACCCAACCACgtacgtccta ... tcaaatgcagGGCAGAAAAGGGAAATCTTGGTGTGCCACTACTGCCAGGCCAAGGTTGTTCGTTTTATAGCTTCAAGACAAACACATACAAACTGAACTTTACGGAGAGC


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 28

ACCGCCCCCTCCGCACGCTCGACCCCACCCAGGATCACAAGCTCATGTTCGGGCTCCTCTTCTCCCTTCGCTCCTTCACCGCCAAGATCGACCCAACCACgtacgtccta ... tcaaatgcagGGCAGAAAAGGGAAATCTTGGTGTGCCACTACTGCCAGGCCAAGGTTGTTCGTTTTATAGCTTCAAGACAAACACATACAAACTGAACTTTACGGAGAGC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 39

ACCGCCCCCTCCGCACGCTCGACCCCACCCAGGATCACAAGCTCATGTTCGGGCTCCTCTTCTCCCTTCGCTCCTTCACCGCCAAGATCGACCCAACCACgtacgtccta ... tcaaatgcagGGCAGAAAAGGGAAATCTTGGTGTGCCACTACTGCCAGGCCAAGGTTGTTCGTTTTATAGCTTCAAGACAAACACATACAAACTGAACTTTACGGAGAGC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 46

ACCGCCCCCTCCGCACGCTCGACCCCACCCAGGATCACAAGCTCATGTTCGGGCTCCTCTTCTCCCTTCGCTCCTTCACCGCCAAGATCGACCCAACCACgtacgtccta ... tcaaatgcagGGCAGAAAAGGGAAATCTTGGTGTGCCACTACTGCCAGGCCAAGGTTGTTCGTTTTATAGCTTCAAGACAAACACATACAAACTGAACTTTACGGAGAGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taagatgactaattttcttattttcctcttggcctttttcacatatcaaatgcagGGCAGAAAAGGGAAATCTTGGTGTGCCACTACTGCCAGGCCAAGGTTGTTCGTTTTATAGCTTCAAGACAAACACATACAAACTGAACTTTACGGAGAGC
      gactaat  putative branch site (score: 46)
       actaattttcttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaacctagaacttccttgtaccgagtggcaaatgttttgagtctttaagatgactaattttcttattttcctcttggcctttttcacatatcaaatgcagGGCAGAAAAGGGAAATCTTGGTGTGCCACTACTGCCAGGCCAAGGTTGTTCGTTTTATAGCTTCAAGACAAACACATACAAACTGAACTTTACGGAGAGC

- - - - - - - - - - - - - - - - tgttttg