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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggtggtacttgtactatgttatttggttttttcacagtatattatatttcaaatgcatgatttttactgctacggcatcaactatgtatccatttggattttctttaattgtctacacttaattgtccaccatagGTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCTGATGCAGAGAAGGCTTATTACTTGGAGAGAGGCATCACGCCCCCGAATT

Basic information

species Zea mays
transcript GRMZM2G006507_T03
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006507_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g19510.1 (Oryza sativa), 3'ss of exon 14
gtaaggtggtacttgtactatgttatttggttttttcacagtatattatatttcaaatgcatgatttttactgctacggcatcaactatgtatc-catttggattttctttaattgtctacacttaattgtccaccatagGTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCTGATGCAGAGAAGGCTTATTACTTGGAGAGAGGCATCACGCCCCCGAATT
|| | | | | | | | || | ||| ||||| | | || | | | |||| |||| |||| || | ||| ||| ||| || |||| |||||||||||||||| || |||||||||| ||||||||| || |||||||| ||||| |||||||| || ||||| ||| ||||| || || || |
-----------------gtaagcaaatacatatccttatgtaatctgcagttttaaatg--ttgtagatattcccaacgcatgaactctgtacagcacataaattcctcttacgatggtacgttt---tgtct----cagGTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGAGGCTGGCCGATGCCGAGAAGGCATACTACTTATCACAAGGAATCACACCACCCAACT
















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|78106684|gb|DV525102.1|DV525102
EST:     CACTTGGGAACCAGGGCAAGTCAGATAATGGAAGAGCACCATGGGAAGGG                         GTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCT
genomic: CACTTGGGAACCAGGGCAAGTCAGATAATGGAAGAGCACCATGGGAAGGGgtaaggtggt ... tccaccatagGTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCT
EST: gi|74235735|gb|DT643649.1|DT643649
EST:     CACTTGGGAACCAGGGCAAGTCAGATAATGGAAGAGCACCATGGGAAGGG                         GTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCT
genomic: CACTTGGGAACCAGGGCAAGTCAGATAATGGAAGAGCACCATGGGAAGGGgtaaggtggt ... tccaccatagGTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCT
EST: gi|32928781|gb|CF033593.1|CF033593
EST:     CACTTGGGAACCAGGGCAAGTCAGATAATGGAAGAGCCCCATGGGAAGGG                         GTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCT
genomic: CACTTGGGAACCAGGGCAAGTCAGATAATGGAAGAGCACCATGGGAAGGGgtaaggtggt ... tccaccatagGTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCT
EST: gi|31348516|gb|CD432873.1|CD432873
EST:     CACTTGGGAACCAGGGCAAGTCAGATAATGGAAGAGCACCATGGGAAGGG                         GTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCT
genomic: CACTTGGGAACCAGGGCAAGTCAGATAATGGAAGAGCACCATGGGAAGGGgtaaggtggt ... tccaccatagGTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCT
EST: gi|24763232|gb|CA398411.1|CA398411
EST:     CACTTGGGAACCAGGGCAAGTCAGATAATGGAAGAGCACCATGGGAAGGG                         GTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCT
genomic: CACTTGGGAACCAGGGCAAGTCAGATAATGGAAGAGCACCATGGGAAGGGgtaaggtggt ... tccaccatagGTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCT
EST: gi|74237173|gb|DT645087.1|DT645087
EST:     CACTTGGGAACCAGGGCAAGTCAGATAATGGAAGAGCACCATGGGAAGGG                         GTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCT
genomic: CACTTGGGAACCAGGGCAAGTCAGATAATGGAAGAGCACCATGGGAAGGGgtaaggtggt ... tccaccatagGTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCT
EST: gi|32928833|gb|CF033645.1|CF033645
EST:     CACTTGGGAACCAGGGCAAGTCAGATAATGGAAGAGCACCATGGGAAGGG                         GTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCT
genomic: CACTTGGGAACCAGGGCAAGTCAGATAATGGAAGAGCACCATGGGAAGGGgtaaggtggt ... tccaccatagGTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCT
EST: gi|88751496|gb|DY535637.1|DY535637
EST:     CACTTGGGAACCAGGGCAAGTCAGATAATGGAAGAGCACCATGGGAAGGG                         GTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGGT
genomic: CACTTGGGAACCAGGGCAAGTCAGATAATGGAAGAGCACCATGGGAAGGGgtaaggtggt ... tccaccatagGTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCT
EST: gi|116824427|gb|EC868047.1|EC868047
EST:     CACTTGGGAACCAGGGCAAGTCAGATAATGGAAGAGCACCATGGGAAGGG                         GTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAATGCTGGCT
genomic: CACTTGGGAACCAGGGCAAGTCAGATAATGGAAGAGCACCATGGGAAGGGgtaaggtggt ... tccaccatagGTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCT
EST: gi|78544004|gb|DV621502.1|DV621502
EST:     CACTTGGGAACCAGGGCAAGTCAGATAATGGAAGAGCACCATGGGAAGGG                         GTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCT
genomic: CACTTGGGAACCAGGGCAAGTCAGATAATGGAAGAGCACCATGGGAAGGGgtaaggtggt ... tccaccatagGTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actatgtatccatttggattttctttaattgtctacacttaattgtccaccatagGTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCTGATGCAGAGAAGGCTTATTACTTGGAGAGAGGCATCACGCCCCCGAATT
                                    acttaat  putative branch site (score: 4)
 attttctttaattgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggtggtacttgtactatgttatttggttttttcacagtatattatatttcaaatgcatgatttttactgctacggcatcaactatgtatccatttggattttctttaattgtctacacttaattgtccaccatagGTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCTGATGCAGAGAAGGCTTATTACTTGGAGAGAGGCATCACGCCCCCGAATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG