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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtacttttttttatcagtttaactgtctgtagattatttacttctattcttgtttaaagagacagacacatacatcttcatgcggtagtgcctaacaagtgtcttttgtaatggtaactccaatttgcagTTTGATATTACTTTTCCGAGCATTCCTTGCACACTCCTCAGCGTTGATACAACGGATATTAGTGGAGAGCAGCATCATGACATT

Basic information

species Zea mays
transcript GRMZM2G161019_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G161019_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os05g41120.1 (Oryza sativa), 3'ss of exon 2
gttagtactttttt--ttatcagtttaactgtctgt-agattatttacttctattcttgtttaaagagacagacacatacatcttcatgcggtagtgcctaacaa---------------------gtgtcttttgt--------aatggtaactccaatttgcagTTTGATATTACTTTTCCGAGCATTCCTTGCACACTCCTCAGCGTTGATACAACGGATATTAGTGGAGAGCAGCATCATGACATT
||||||| || |||  || | |   ||  |   ||| | ||  | ||||||||||   ||||  ||    | |  |||||   ||  |  | || |  || ||||                      | | |  |||        |||| |||  |   ||||||||||||  | |||||||||||  |||| ||||| || ||||| |||||||| | |||||||||||||||||||||||||||||||
gttagtatttatttgattgttaaactagattcatgtcatatgttgtacttctatt---gtttctagtataaaatgcatactcttttgtatgctattcacttacaatctgttgggaactaggtgtgaatatttcctgttaacttctaatgctaaaactgttttgcagTTTGACGTAACTTTTCCGAGTGTTCCCTGCACCCTTCTCAGTGTTGATACCATGGATATTAGTGGAGAGCAGCATCATGACATT
















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|71331223|gb|DR802438.1|DR802438
EST:     AGACTAAGTTAGTCGTGGACACATCAAGAGGGGAAAGGCTACGAGTAAAT                         TTTGATATTACTTTTCCGAGCATTCCTTGCACACTCCTCAGCGTTGATACA
genomic: AGACTAAGTTAGTCGTGGACACATCAAGAGGGGAAAGGCTACGAGTAAATgttagtactt ... caatttgcagTTTGATATTACTTTTCCGAGCATTCCTTGCACACTCCTCAGCGTTGATACA
EST: gi|148972613|gb|EE023572.2|EE023572
EST:     AGACTAAGTTAGTCGTGGACACATCAAGAGGGGAAAGGCTACGAGTAAAT                         TTTGATATTACTTTTCCGAGCATTCCTTGCA
genomic: AGACTAAGTTAGTCGTGGACACATCAAGAGGGGAAAGGCTACGAGTAAATgttagtactt ... caatttgcagTTTGATATTACTTTTCCGAGCATTCCTTGCA
EST: gi|30306484|gb|CD001157.1|CD001157
EST:     AGACTAAGTTAGTCGTGGACACATCAAGAGGGGAAAGGCTACGAGTAAAT                         TTTGATATTACTTTTCCGAGCATTCCTTGCACACTCCTCAGCGTTGATACA
genomic: AGACTAAGTTAGTCGTGGACACATCAAGAGGGGAAAGGCTACGAGTAAATgttagtactt ... caatttgcagTTTGATATTACTTTTCCGAGCATTCCTTGCACACTCCTCAGCGTTGATACA
EST: gi|149112736|gb|EE295558.2|EE295558
EST:     AGACTAAGTTAGTCGTGGACACATCAAGAGGGGAAAGGCTACGAGTAAAT                         TTTGATATTACTTTTCCGAGCATTCCTTGCACACTCCTCAGCGTTGATACA
genomic: AGACTAAGTTAGTCGTGGACACATCAAGAGGGGAAAGGCTACGAGTAAATgttagtactt ... caatttgcagTTTGATATTACTTTTCCGAGCATTCCTTGCACACTCCTCAGCGTTGATACA
EST: gi|149015010|gb|EE044754.2|EE044754
EST:     AGACTAAGTTAGTCGTGGACACATCAAGAGGGGAAAGGCTACGAGTAAAT                         TTTGATATTACTTTTCCGAGCATTCCTTGCACACTCCTCAGCGTTGATACA
genomic: AGACTAAGTTAGTCGTGGACACATCAAGAGGGGAAAGGCTACGAGTAAATgttagtactt ... caatttgcagTTTGATATTACTTTTCCGAGCATTCCTTGCACACTCCTCAGCGTTGATACA
EST: gi|71772297|gb|DR970233.1|DR970233
EST:     AGACTAAGTTAGTCGTGGACACATCAAGAGGGGAAAGGCTACGAGTAAAT                         TTTGATATTACTTTTCCGAGCATTCCTTGCACACTCCTCAGCGTTGATACA
genomic: AGACTAAGTTAGTCGTGGACACATCAAGAGGGGAAAGGCTACGAGTAAATgttagtactt ... caatttgcagTTTGATATTACTTTTCCGAGCATTCCTTGCACACTCCTCAGCGTTGATACA
EST: gi|149089164|gb|EE178352.2|EE178352
EST:     AGACTAAGTTAGTCGTGGACACATCAAGAGGGGAAAGGCTACGAGTAAAT                         TTTGATATTACTTTTCCGAGCATTCCTTGCACACTCCTCAGCGTTGATACA
genomic: AGACTAAGTTAGTCGTGGACACATCAAGAGGGGAAAGGCTACGAGTAAATgttagtactt ... caatttgcagTTTGATATTACTTTTCCGAGCATTCCTTGCACACTCCTCAGCGTTGATACA
EST: gi|74232610|gb|DT640524.1|DT640524
EST:     AGACTAAGTTAGTCGTGGACACATCAAGAGGGGAAAGGCTACGAGTAAAT                         TTTGATATTACTTTTCCGAGCATTCCTTGCACACTCCTCAGCGTTGATACA
genomic: AGACTAAGTTAGTCGTGGACACATCAAGAGGGGAAAGGCTACGAGTAAATgttagtactt ... caatttgcagTTTGATATTACTTTTCCGAGCATTCCTTGCACACTCCTCAGCGTTGATACA
EST: gi|74034984|gb|DT535474.1|DT535474
EST:     AGACTAAGTTAGTCGTGGACACATCAAGAGGGGAAAGGCTACGAGTAAAT                         TTTGATATTACTTTTCCGAGCATTCCTTGCACACTCCTCAGCGTTGATACA
genomic: AGACTAAGTTAGTCGTGGACACATCAAGAGGGGAAAGGCTACGAGTAAATgttagtactt ... caatttgcagTTTGATATTACTTTTCCGAGCATTCCTTGCACACTCCTCAGCGTTGATACA
EST: gi|71328273|gb|DR800766.1|DR800766
EST:     AGACTAAGTTAGTCGTGGACACATCAAGAGGGGAAAGGCTACGAGTAAAT                         TTTGATATTACTTTTCCGAGCATTCCTTGCACACTCCTCAGCGTTGATACA
genomic: AGACTAAGTTAGTCGTGGACACATCAAGAGGGGAAAGGCTACGAGTAAATgttagtactt ... caatttgcagTTTGATATTACTTTTCCGAGCATTCCTTGCACACTCCTCAGCGTTGATACA
EST: gi|149104647|gb|EE290096.2|EE290096
EST:     AGACTAAGTTAGTCGTGGACACATCAAGAGGGGAAAGGCTACGAGTAAAT                         TTTGATATTACTTTTCCGAGCATTCCTTGCACACTCCTCAGCGTTGATACA
genomic: AGACTAAGTTAGTCGTGGACACATCAAGAGGGGAAAGGCTACGAGTAAATgttagtactt ... caatttgcagTTTGATATTACTTTTCCGAGCATTCCTTGCACACTCCTCAGCGTTGATACA
EST: gi|148948260|gb|EC893776.2|EC893776
EST:     AGACTAAGTTAGTCGTGGACACATCAAGAGGGGAAAGGCTACGAGTAAAT                         TTTGATATTACTTTTCCGAGCATTCCTTGCACACTCCTCAGCGTTGATACA
genomic: AGACTAAGTTAGTCGTGGACACATCAAGAGGGGAAAGGCTACGAGTAAATgttagtactt ... caatttgcagTTTGATATTACTTTTCCGAGCATTCCTTGCACACTCCTCAGCGTTGATACA
EST: gi|149071871|gb|EE160258.2|EE160258
EST:     AGACTAAGTTAGTCGTGGACACATCAAGAGGGGAAAGGCTACGAGTAAAT                         TTTGATATTACTTTTCCGAGCATTCCTTGCACACTCCTCAGCGTTGATACA
genomic: AGACTAAGTTAGTCGTGGACACATCAAGAGGGGAAAGGCTACGAGTAAATgttagtactt ... caatttgcagTTTGATATTACTTTTCCGAGCATTCCTTGCACACTCCTCAGCGTTGATACA
EST: gi|86465733|gb|DY232106.1|DY232106
EST:     AGACTAAGTTAGTCGTGGACACATCAAGAGGGGAAAGGCTACGAGTAAAT                         TTTGATATTACTTTTCAGAGCATTCCTTGCACACTCCTCAGCGTTGATACA
genomic: AGACTAAGTTAGTCGTGGACACATCAAGAGGGGAAAGGCTACGAGTAAATgttagtactt ... caatttgcagTTTGATATTACTTTTCCGAGCATTCCTTGCACACTCCTCAGCGTTGATACA
EST: gi|74242178|gb|DT650092.1|DT650092
EST:     AGACTAAGTTAGTCGTGGACACATCAAGAGGGGAAAGGCTACGAGTAAAT                         TTTGATATTACTTTTCCGAGCATTCCTTGCACACTCCTCAGCGTTGATACA
genomic: AGACTAAGTTAGTCGTGGACACATCAAGAGGGGAAAGGCTACGAGTAAATgttagtactt ... caatttgcagTTTGATATTACTTTTCCGAGCATTCCTTGCACACTCCTCAGCGTTGATACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcatgcggtagtgcctaacaagtgtcttttgtaatggtaactccaatttgcagTTTGATATTACTTTTCCGAGCATTCCTTGCACACTCCTCAGCGTTGATACAACGGATATTAGTGGAGAGCAGCATCATGACATT
                                    tggtaac  putative branch site (score: 2)
                            ttttgtaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtacttttttttatcagtttaactgtctgtagattatttacttctattcttgtttaaagagacagacacatacatcttcatgcggtagtgcctaacaagtgtcttttgtaatggtaactccaatttgcagTTTGATATTACTTTTCCGAGCATTCCTTGCACACTCCTCAGCGTTGATACAACGGATATTAGTGGAGAGCAGCATCATGACATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG