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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCACCTTTACTCTTTCGAATCTTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACTgtaagatggacaatttattttattctccatttctattttaatgcaattctgcataccctactgaaatatccgggttactgaaaacag

Basic information

species Zea mays
transcript GRMZM2G036534_T02
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G036534_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os12g08170.1 (Oryza sativa), 5'ss of exon 4
GCACCTTTACTCTTTCGAATCTTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACTgtaagatggacaattta--ttttattctccatttctattttaatgcaatt--ctgcataccctactgaaatatccgggttactgaaaacag
||||||||||| |||| || |||||||||||||||||||| || || ||||||||  |||||||||||||||||||| | |   |  |  ||||| | || |||   |||  |||||   |  ||||||    ||    | ||||    || ||||||||||
GCACCTTTACTATTTCAAACCTTGGTATGTTTGGAGTTGACAGATTTGATGCAATCTTGCCACCTGGAACTgtaagacgaaatttccatcttttaatttctattatcattc-aatgctgcttgctgcatgatttatgttattatctttattgctgaaaacag

upper sequence: GRMZM2G036534_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA10G35960.1 (Glycine max), 5'ss of exon 5
GCACCTTTACTCTTTCGAATCTTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACTgtaagatggacaatttattttattctccatttctattttaat--gcaattctgcataccctactgaaatatc--cgggttac-tgaaaacag-------------------------
| || || ||||| || ||||| || |||||||| |||||| | || ||||| || ||||||||||||||||| || ||    | |  |  |    |        |  || |   |   |||    ||      |  || |     |||  ||  ||| |                            
GTACTTTCACTCTGTCCAATCTGGGAATGTTTGGTGTTGATCGCTTTGATGCTATTCTGCCACCTGGAACTgtgag-tgttttactcgtgctcaaatatggcaagagattgactagttgttccaattagaagtttagaacagtgatgggaaacacgaatatgatccttctctggatatatttctgtag

upper sequence: GRMZM2G036534_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA20G31630.1 (Glycine max), 5'ss of exon 5
GCACCTTTACTCTTTCGAATCTTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACTgtaagatggacaatttattttattctccatttctattttaatgcaattctgcataccctactgaaatatc--cgggttac-tgaaaacag-------------------------
| || || ||||| || ||||| || |||||||| |||||| | || ||||| || ||||||||||||||||| ||        |||   || |  || | |        |     | |     |  || | |  || |     |||| ||  |||||                            
GTACTTTCACTCTGTCCAATCTGGGAATGTTTGGCGTTGATCGCTTTGATGCTATTCTGCCACCTGGAACTgtgagt------gttttacttgtgttcaaatatggcaagagattgactagttgt-tccaattagaacagtgatgggtcacacgaaaatgatcattctatggatttatttgtgtag

upper sequence: GRMZM2G036534_T02 (Zea mays), 5'ss of exon 5
lower sequence: Vv18s0072g01000.t01 (Vitis vinifera), 5'ss of exon 4
GCACCTTTACTCTTTCGAATCTTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACTgtaag-------atggacaattta-----ttttattctcca---tttctattttaatgcaattctgcat---accctactgaa--atatccgggttactgaaaacag-------------------------
| || || |||||||| || ||||| |||||||| || ||| |||| || ||||| ||||||||||||||||||||       |   | |||||       |  | ||| ||   ||  ||  ||   |||  | || |         ||| ||   |||| || | |    ||  |                          
GTACTTTCACTCTTTCAAACCTTGGAATGTTTGGTGTGGATCGGTTTGACGCAATTCTGCCACCTGGAACTgtaagtatttaaactcagaatttgaacctctccactctgcaaaattcatagcttggggcagatatggaatgagggggactaaattgtatcaggataaacataattatgttgatttgcatgttttttctgcag

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|6539042|gb|AW225181.1|AW225181
EST:     TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACT                         GGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
genomic: TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACTgtaagatgga ... ctgaaaacagGGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
EST: gi|6865176|gb|AW360526.1|AW360526
EST:     TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACT                         GGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
genomic: TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACTgtaagatgga ... ctgaaaacagGGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
EST: gi|78106198|gb|DV524616.1|DV524616
EST:     TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACT                         GGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
genomic: TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACTgtaagatgga ... ctgaaaacagGGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
EST: gi|23357491|gb|BU645140.1|BU645140
EST:     TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACT                         GGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
genomic: TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACTgtaagatgga ... ctgaaaacagGGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
EST: gi|24768304|gb|CA403433.1|CA403433
EST:     TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACT                         GGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
genomic: TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACTgtaagatgga ... ctgaaaacagGGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
EST: gi|6448387|gb|AW181153.1|AW181153
EST:     AATACTGCCACCTGGAACT                         GGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
genomic: AATACTGCCACCTGGAACTgtaagatgga ... ctgaaaacagGGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
EST: gi|211440164|gb|FL434174.1|FL434174
EST:     TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACT                         GGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
genomic: TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACTgtaagatgga ... ctgaaaacagGGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
EST: gi|6022391|gb|AW067319.1|AW067319
EST:     TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACT                         GGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
genomic: TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACTgtaagatgga ... ctgaaaacagGGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
EST: gi|71765103|gb|DR963040.1|DR963040
EST:     TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACT                         GGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
genomic: TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACTgtaagatgga ... ctgaaaacagGGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
EST: gi|60344293|gb|DN211266.1|DN211266
EST:     TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACT                         GGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
genomic: TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACTgtaagatgga ... ctgaaaacagGGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
EST: gi|78088435|gb|DV516828.1|DV516828
EST:     TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACT                         GGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
genomic: TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACTgtaagatgga ... ctgaaaacagGGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
EST: gi|149027250|gb|EE046447.2|EE046447
EST:     TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACT                         GGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
genomic: TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACTgtaagatgga ... ctgaaaacagGGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
EST: gi|93013412|gb|EB638932.1|EB638932
EST:     TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACT                         GGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
genomic: TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACTgtaagatgga ... ctgaaaacagGGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
EST: gi|71444183|gb|DR825233.1|DR825233
EST:     TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACT                         GGCGCAATCATGGCCGTCGGTGCATCAGACCCGACAGTTGTTGGTACAAAA
genomic: TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACTgtaagatgga ... ctgaaaacagGGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
EST: gi|93284411|gb|EB676675.1|EB676675
EST:     TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACT                         GGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
genomic: TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACTgtaagatgga ... ctgaaaacagGGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
EST: gi|83279414|gb|DV943422.1|DV943422
EST:     TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACT                         GGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
genomic: TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACTgtaagatgga ... ctgaaaacagGGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
EST: gi|74246257|gb|DT654171.1|DT654171
EST:     TTGGTATGTTTGGAGTTGATAGGTTGGATGCAATACTGCCCCCTGGAACT                         GGGGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
genomic: TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACTgtaagatgga ... ctgaaaacagGGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
EST: gi|78074314|gb|DV502748.1|DV502748
EST:     TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACT                         GGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
genomic: TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACTgtaagatgga ... ctgaaaacagGGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
EST: gi|71759734|gb|DR957671.1|DR957671
EST:     TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACT                         GGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTAC-AAA
genomic: TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACTgtaagatgga ... ctgaaaacagGGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
EST: gi|74236968|gb|DT644882.1|DT644882
EST:     TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACT                         GGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
genomic: TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACTgtaagatgga ... ctgaaaacagGGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
EST: gi|149035803|gb|EE155127.2|EE155127
EST:     TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACT                         GGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
genomic: TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACTgtaagatgga ... ctgaaaacagGGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCACCTTTACTCTTTCGAATCTTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACTgtaagatggacaatttattttattctccatttctattttaatgcaattctgcataccctactgaaatatccgggttactgaaaacag

- - - - - - - - - - - - - - - TTGGAG