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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatttccttgataagtgtgcattgtgtctttcatgttggcaccagctgcaataacatataaaacttgtacctattcttgtagTTTTGTGTCAGTGAGCCATCTTTTTATTGGAGTACTATACTGCCTTATTGGCTGGAGCTTCGGCATCCCAAAGCGCGCG

Basic information

species Zea mays
transcript GRMZM2G083344_T03
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G083344_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g15160.1 (Oryza sativa), 3'ss of exon 3
gtatatttccttgataagtgtgca--------ttgtgtctttcatgttggcaccagctgcaataacatataaaacttgtacct-attcttgtagTTTTGTGTCAGTGAGCCATCTTTTTATTGGAGTACTATACTGCCTTATTGGCTGGAGCTTCGGCATCCCAAAGCGCGCG
|||  ||| ||| ||| ||||||         || |  |||||||||    ||  ||  |   |  || |||||| | |  ||  ||  | |||||||||||| ||||||||||||||  | |||||  | ||||||||| | |||||||| || ||  ||||||||||||||
gtacgtttgctttatatgtgtgcctccttttctttttcctttcatgtgacaacatgcatcttcatgatctaaaacctctttcttgttaatatagTTTTGTGTCGGTGAGCCATCTTTTGGTAGGAGTCTTGTACTGCCTTGTCGGCTGGAGTTTTGGTCTCCCAAAGCGCGCG
















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|78105001|gb|DV523419.1|DV523419
EST:     ATATTTAACATCCTCAACAAGAAGATCTTCGACTACTTCCCCTATCCATA                         TTTTGTGTCAGTGAGCCATCTTTTTATTGGAGTACTATACTGCCTTATTGG
genomic: ATATTTAACATCCTCAACAAGAAGATCTTCGACTACTTCCCCTATCCATAgtatatttcc ... attcttgtagTTTTGTGTCAGTGAGCCATCTTTTTATTGGAGTACTATACTGCCTTATTGG
EST: gi|78104083|gb|DV522501.1|DV522501
EST:     ATATTTAACATCCTCAACAAGAAGATCTTCGACTACTTCCCCTATCCATA                         TTTTGTGTCAGTGAGCCATCTTTTTATTGGAGTACTATACTGCCTTATTGG
genomic: ATATTTAACATCCTCAACAAGAAGATCTTCGACTACTTCCCCTATCCATAgtatatttcc ... attcttgtagTTTTGTGTCAGTGAGCCATCTTTTTATTGGAGTACTATACTGCCTTATTGG
EST: gi|149009525|gb|EE041508.2|EE041508
EST:     ATATTTAACATCCTCAACAAGAAGATCTTCGACTACTTCCCCTATCCATA                         TTTTGTGTCAGTGAGCCATCTTTTTATTGGAGTACTATACTGCCTTATTGG
genomic: ATATTTAACATCCTCAACAAGAAGATCTTCGACTACTTCCCCTATCCATAgtatatttcc ... attcttgtagTTTTGTGTCAGTGAGCCATCTTTTTATTGGAGTACTATACTGCCTTATTGG
EST: gi|71439302|gb|DR820352.1|DR820352
EST:     ATATTTAACATCCTCAACAAGAAGATCTTCGACTACTTCCCCTATCCATA                         TTTTGTGTCAGTGAGCCATCTTTTTATTGGAGTACTATACTGCCTTATTGG
genomic: ATATTTAACATCCTCAACAAGAAGATCTTCGACTACTTCCCCTATCCATAgtatatttcc ... attcttgtagTTTTGTGTCAGTGAGCCATCTTTTTATTGGAGTACTATACTGCCTTATTGG
EST: gi|78087779|gb|DV516172.1|DV516172
EST:     ATATTTAACATCCTCAACAAGAAGATCTTCGACTACTTCCCCTATCCATA                         TTTTGTGTCAGTGAGCCATCTTTTTATTGGAGTACTATACTGCCTTATTGG
genomic: ATATTTAACATCCTCAACAAGAAGATCTTCGACTACTTCCCCTATCCATAgtatatttcc ... attcttgtagTTTTGTGTCAGTGAGCCATCTTTTTATTGGAGTACTATACTGCCTTATTGG
EST: gi|148961156|gb|EE011865.2|EE011865
EST:     ATATTTAACATCCTCAACAAGAAGATCTTCGACTACTTCCCCTATCCATA                         TTTTGTGTCAGTGAGCCATCTTTTTATTGGAGTACTATACTGCCTTATTGG
genomic: ATATTTAACATCCTCAACAAGAAGATCTTCGACTACTTCCCCTATCCATAgtatatttcc ... attcttgtagTTTTGTGTCAGTGAGCCATCTTTTTATTGGAGTACTATACTGCCTTATTGG
EST: gi|31909719|gb|CD651060.1|CD651060
EST:     ATATTTAACATCCTCAACAAGAAGATCTTCGACTACTTCCCCTATCCATA                         TTTTGTGTCCAGTGAGCCATCTTTTTATTGGGAGTACTATACTGCCTTATT
genomic: ATATTTAACATCCTCAACAAGAAGATCTTCGACTACTTCCCCTATCCATAgtatatttcc ... attcttgtagTTTTGTGTC-AGTGAGCCATCTTTTTATTGG-AGTACTATACTGCCTTATT
EST: gi|28931223|gb|CB334584.1|CB334584
EST:     ATATTTAACATCCTCAACAAGAAGATCTTCGACTACTTCCCCTATCCATA                         TTTTGTGTCAGTGAGCCATCTTTTTATTGGAGTACTATACTGGCTTATTGG
genomic: ATATTTAACATCCTCAACAAGAAGATCTTCGACTACTTCCCCTATCCATAgtatatttcc ... attcttgtagTTTTGTGTCAGTGAGCCATCTTTTTATTGGAGTACTATACTGCCTTATTGG
EST: gi|71768356|gb|DR966293.1|DR966293
EST:     ATATTTAACATCCTCAACAAGAAGATCTTCGACTACTTCCCCTATCCATA                         TTTTGTGTCAGTGAGCCATCTTTTTATTGGAGTACTATACTGCCTTATTGG
genomic: ATATTTAACATCCTCAACAAGAAGATCTTCGACTACTTCCCCTATCCATAgtatatttcc ... attcttgtagTTTTGTGTCAGTGAGCCATCTTTTTATTGGAGTACTATACTGCCTTATTGG
EST: gi|211525181|gb|FL202007.1|FL202007
EST:     ATATTTAACATCCTCAACAAGAAGATCTTCGACTACTTCCCCTATCCATA                         TTTTGTGTCAGTGAGCCATCTTTTTATTGGAGTACTATACTGCCTTATTGG
genomic: ATATTTAACATCCTCAACAAGAAGATCTTCGACTACTTCCCCTATCCATAgtatatttcc ... attcttgtagTTTTGTGTCAGTGAGCCATCTTTTTATTGGAGTACTATACTGCCTTATTGG
EST: gi|61119701|gb|DN560662.1|DN560662
EST:     ATATTTAACATCCTCAACAAGAAGATCTTCGACTACTTCCCCTATCCATA                         TTTTGTGTCAGTGAGCCATCTTTTTATTGGAGTACTATACTGCCTTATTGG
genomic: ATATTTAACATCCTCAACAAGAAGATCTTCGACTACTTCCCCTATCCATAgtatatttcc ... attcttgtagTTTTGTGTCAGTGAGCCATCTTTTTATTGGAGTACTATACTGCCTTATTGG
EST: gi|91055754|gb|EB166172.1|EB166172
EST:     ATATTTAACATCCTCAACAAGAAGATCTTCGACTACTTCCCCTATCCATA                         TTTTGTGTCAGTGAGCCATCTTTTTATTGGAGTACTATACTGCCTTATTGG
genomic: ATATTTAACATCCTCAACAAGAAGATCTTCGACTACTTCCCCTATCCATAgtatatttcc ... attcttgtagTTTTGTGTCAGTGAGCCATCTTTTTATTGGAGTACTATACTGCCTTATTGG
EST: gi|76930051|gb|DV172256.1|DV172256
EST:     ATATTTAACATCCTCAACAAGAAGATCTTCGACTACTTCCCCTATCCATA                         TTTTGTGTCAGTGAGCCATCTTTTTATTGGAGTACTATACTGCCTTATTGG
genomic: ATATTTAACATCCTCAACAAGAAGATCTTCGACTACTTCCCCTATCCATAgtatatttcc ... attcttgtagTTTTGTGTCAGTGAGCCATCTTTTTATTGGAGTACTATACTGCCTTATTGG
EST: gi|94477389|gb|EB706347.1|EB706347
EST:     ATATTTAACATCCTCAACAAGAAGATCTTCGACTACTTCCCCTATCCATA                         TTTTGTGTCAGTGAGCCATCTTTTTATTGGAGTACTATACTGCCTTATTGG
genomic: ATATTTAACATCCTCAACAAGAAGATCTTCGACTACTTCCCCTATCCATAgtatatttcc ... attcttgtagTTTTGTGTCAGTGAGCCATCTTTTTATTGGAGTACTATACTGCCTTATTGG
EST: gi|149095075|gb|EE180680.2|EE180680
EST:     ATATTTAACATCCTCAACAAGAAGATCTTCGACTACTTCCCCTATCCATA                         TTTTGTGTCAGTGAGCCATCTTTTTATTGGAGTACTATACTGCCTTATTGG
genomic: ATATTTAACATCCTCAACAAGAAGATCTTCGACTACTTCCCCTATCCATAgtatatttcc ... attcttgtagTTTTGTGTCAGTGAGCCATCTTTTTATTGGAGTACTATACTGCCTTATTGG
EST: gi|28390338|gb|CB250166.1|CB250166
EST:     ATATTTAACATCCTCAACAAGAAGATCTTCGACTACTTCCCCTATCCATA                         TTTTGTGTCAGTGAGCCATCTTTTTATTGGAGTACTATACTGCCTTATTGG
genomic: ATATTTAACATCCTCAACAAGAAGATCTTCGACTACTTCCCCTATCCATAgtatatttcc ... attcttgtagTTTTGTGTCAGTGAGCCATCTTTTTATTGGAGTACTATACTGCCTTATTGG
EST: gi|148962629|gb|EE013519.2|EE013519
EST:     ATATTTAACATCCTCAACAAGAAGATCTTCGACTACTTCCCCTATCCATA                         TTTTGTGTCAGTGAGCCATCTTTTTATTGGAGTACTATACTGCCTTATTGG
genomic: ATATTTAACATCCTCAACAAGAAGATCTTCGACTACTTCCCCTATCCATAgtatatttcc ... attcttgtagTTTTGTGTCAGTGAGCCATCTTTTTATTGGAGTACTATACTGCCTTATTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttcatgttggcaccagctgcaataacatataaaacttgtacctattcttgtagTTTTGTGTCAGTGAGCCATCTTTTTATTGGAGTACTATACTGCCTTATTGGCTGGAGCTTCGGCATCCCAAAGCGCGCG
                     caataac  putative branch site (score: 2)
                                          cctattctt  putative PPT
                      aataacatataaaact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatttccttgataagtgtgcattgtgtctttcatgttggcaccagctgcaataacatataaaacttgtacctattcttgtagTTTTGTGTCAGTGAGCCATCTTTTTATTGGAGTACTATACTGCCTTATTGGCTGGAGCTTCGGCATCCCAAAGCGCGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT