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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtttaagagcgcatggtatccaacggactcggaaacagtacatgccttgtttgcttacagttttcccttaccataaaatccatcgcctgttgatacatagGATGCCAGATTGGGCCGATATAGCGTCCTCACTCAACCAGCTCTCGGACTCCGAAGTCCTGCTGCGGTGCTCCACCTCTCCAGCCGCAGAACCACCTCAC

Basic information

species Zea mays
transcript GRMZM2G144362_T04
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G144362_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os06g41390.2 (Oryza sativa), 3'ss of exon 7
gtttaagagcgcatggtatccaacggactcggaaaca-gtacatgccttgtttgcttacagttttcccttaccataaaatccatcg----cctgttga---tacatagGATGCCAGATTGGGCCGATATAGCGTCCTCACTCAACCAGCTCTCGGACTCCGAAGTCCTGCTGCGGTGCTCCACCTCTCCAGCCGCAGAACCACCTCAC
         |   |   || |||   ||| | | |    ||| |  || | |          ||     | | |||   || ||||    | ||||        |||||||||| |||||||| || || || || ||||| |||||||| |||||||| || ||| || ||| |||||||||||||||||| || || ||||| || 
--------actattacaattcaaaatactagcacatgcatacttttctgggtaatcacttaattgatgatcctatatgctctatcgatatcttgttctgctcgtatagGATGCCGGATTGGGCTGAAATGGCATCATCACTTAACCAGCTATCGGACTCTGAGGTCTTGTTGCAGTGCTCCACCTCTCCAGCTGCCGAGCCACCACAT
















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|149014215|gb|EE043769.2|EE043769
EST:     GAGACTTACGATACTCAGGACGATGTTTTCCAAATTGCACCTGCCTGCTG                         GATGCCAGATTGGGCCGATATAGCGTCCTCACTCAACCAGCTCTCGGACTC
genomic: GAGACTTACGATACTCAGGACGATGTTTTCCAAATTGCACCTGCCTGCTGgtatctaaaa ... tgatacatagGATGCCAGATTGGGCCGATATAGCGTCCTCACTCAACCAGCTCTCGGACTC
EST: gi|148933495|gb|EC877204.2|EC877204
EST:     GAGACTTACGATACTCAGGACGATGTTTTCCAAATTGCACCTGCCTGCTG                         GATGCCAGATTGGGCCGATATAGCGTCCTCACTCAACCAGCTCTCGGACTC
genomic: GAGACTTACGATACTCAGGACGATGTTTTCCAAATTGCACCTGCCTGCTGgtatctaaaa ... tgatacatagGATGCCAGATTGGGCCGATATAGCGTCCTCACTCAACCAGCTCTCGGACTC
EST: gi|13237097|gb|BG355111.1|BG355111
EST:     GAGACTTACGATACTCAGGACGATGTTTTCCAAATTGCACCTGCCTGCTG                         GATGCCAGATTGGGCCGATATAGCGTCCTCACTCAACCAGCTCTCGGACTC
genomic: GAGACTTACGATACTCAGGACGATGTTTTCCAAATTGCACCTGCCTGCTGgtatctaaaa ... tgatacatagGATGCCAGATTGGGCCGATATAGCGTCCTCACTCAACCAGCTCTCGGACTC
EST: gi|211211873|gb|FL151948.1|FL151948
EST:     GAGACTTACGATACTCAGGACGATGTTTTCCAAATTGCACCTGCCTGCTG                         GATGCCAGATTGGGCCGATATAGCGTCCTCACTCAACCAGCTCTCGGACTC
genomic: GAGACTTACGATACTCAGGACGATGTTTTCCAAATTGCACCTGCCTGCTGgtatctaaaa ... tgatacatagGATGCCAGATTGGGCCGATATAGCGTCCTCACTCAACCAGCTCTCGGACTC
EST: gi|78123130|gb|DV541514.1|DV541514
EST:     GAGACTTACGATACTCAGGACGATGTTTTCCAAATTGCACCTGCCTGCTG                         GATGCCAGATTGGGCCGATATAGCGTCCTCACTCAACCAGCTCTCGGACTC
genomic: GAGACTTACGATACTCAGGACGATGTTTTCCAAATTGCACCTGCCTGCTGgtatctaaaa ... tgatacatagGATGCCAGATTGGGCCGATATAGCGTCCTCACTCAACCAGCTCTCGGACTC
EST: gi|78079634|gb|DV508046.1|DV508046
EST:     GAGACTTACGATACTCAGGACGATGTTTTCCAAATTGCACCTGCCTGCTG                         GATGCCAGATTGGGCCGATATAGCGTCCTCACTCAACCAGCTCTCGGACTC
genomic: GAGACTTACGATACTCAGGACGATGTTTTCCAAATTGCACCTGCCTGCTGgtatctaaaa ... tgatacatagGATGCCAGATTGGGCCGATATAGCGTCCTCACTCAACCAGCTCTCGGACTC
EST: gi|76291843|gb|DV031411.1|DV031411
EST:     GAGACTTACGATACTCAGGACGATGTTTTCCAAATTGCACCTGCCTGCTG                         GATGCCAGATTGGGCCGATATAGCGTCCTCACTCAACCAGCTCTCGGACTC
genomic: GAGACTTACGATACTCAGGACGATGTTTTCCAAATTGCACCTGCCTGCTGgtatctaaaa ... tgatacatagGATGCCAGATTGGGCCGATATAGCGTCCTCACTCAACCAGCTCTCGGACTC
EST: gi|71430540|gb|DR811590.1|DR811590
EST:     GAGACTTACGATACTCAGGACGATGTTTTCCAAATTGCACCTGCCTGCTG                         GATGCCAGATTGGGCCGATATAGCGTCCTCACTCAACCAGCTCTCGGACTC
genomic: GAGACTTACGATACTCAGGACGATGTTTTCCAAATTGCACCTGCCTGCTGgtatctaaaa ... tgatacatagGATGCCAGATTGGGCCGATATAGCGTCCTCACTCAACCAGCTCTCGGACTC
EST: gi|78088518|gb|DV516911.1|DV516911
EST:     GAGACTTACGATACTCAGGACGATGTTTTCCAAATTGCACCTGCCTGCTG                         GATGCCAGATTGGGCCGATATAGCGTCCTCACTCAACCAGCTCTCGGACTC
genomic: GAGACTTACGATACTCAGGACGATGTTTTCCAAATTGCACCTGCCTGCTGgtatctaaaa ... tgatacatagGATGCCAGATTGGGCCGATATAGCGTCCTCACTCAACCAGCTCTCGGACTC
EST: gi|211356743|gb|FL440510.1|FL440510
EST:     GAGACTTACGATACTCAGGACGATGTTTTCCAAATTGCACCTGCCTGCTG                         GATGCCAGATTGGGCCGATATAGCGTCCTCACTCAACCAGCTCTCGGACTC
genomic: GAGACTTACGATACTCAGGACGATGTTTTCCAAATTGCACCTGCCTGCTGgtatctaaaa ... tgatacatagGATGCCAGATTGGGCCGATATAGCGTCCTCACTCAACCAGCTCTCGGACTC
EST: gi|93281087|gb|EB673351.1|EB673351
EST:     AAATTGCACCTGCCTGCTG                         GATGCCAGATTGGGCCGATATAGCGTCCTCACTCAACCAGCTCTCGGACTC
genomic: AAATTGCACCTGCCTGCTGgtatctaaaa ... tgatacatagGATGCCAGATTGGGCCGATATAGCGTCCTCACTCAACCAGCTCTCGGACTC
EST: gi|93282997|gb|EB675261.1|EB675261
EST:     GAGACTTACGATACTCAGGACGATGTTTTCCAAATTGCACCTGCCTGCTG                         GATGCCAGATTGGGCCGATATAGCGTCCTCACTCAACCAGCTCTCGGACTC
genomic: GAGACTTACGATACTCAGGACGATGTTTTCCAAATTGCACCTGCCTGCTGgtatctaaaa ... tgatacatagGATGCCAGATTGGGCCGATATAGCGTCCTCACTCAACCAGCTCTCGGACTC
EST: gi|86468332|gb|DY234702.1|DY234702
EST:     GAGACTTACGATACTCAGGACGATGTTTTCCAAATTGCACCTCCCTGCTG                         GATGCCAGATTGGGCCGATATAGCGTCCTCACTCAACCAGCTCTCGGACTC
genomic: GAGACTTACGATACTCAGGACGATGTTTTCCAAATTGCACCTGCCTGCTGgtatctaaaa ... tgatacatagGATGCCAGATTGGGCCGATATAGCGTCCTCACTCAACCAGCTCTCGGACTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgtttgcttacagttttcccttaccataaaatccatcgcctgttgatacatagGATGCCAGATTGGGCCGATATAGCGTCCTCACTCAACCAGCTCTCGGACTCCGAAGTCCTGCTGCGGTGCTCCACCTCTCCAGCCGCAGAACCACCTCAC
                           ataaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttaagagcgcatggtatccaacggactcggaaacagtacatgccttgtttgcttacagttttcccttaccataaaatccatcgcctgttgatacatagGATGCCAGATTGGGCCGATATAGCGTCCTCACTCAACCAGCTCTCGGACTCCGAAGTCCTGCTGCGGTGCTCCACCTCTCCAGCCGCAGAACCACCTCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC