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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGGCATACCAGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACATGGTGAACAAAgtaagcagcttcatattgcatacttattttgctatgcgttgactgttgacactggcaggaactcattgtatcttaactgttatgatttacctctttcaat...

Basic information

species Zea mays
transcript GRMZM2G126517_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G126517_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os08g39420.1 (Oryza sativa), 5'ss of exon 5
GTTGGCATACCAGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACATGGTGAACAAAgtaagcagcttcatattgcatacttattttgctatgcgttgactgttgacactggcaggaactcat-tgtatcttaactgttatgatttacctctttcaat
|||||||||||| |||| || ||||| || ||||||||||| |||||| |||||||||| |||||| | |||| |  | |  | |  | |    |  |  |  || |   |||       |  | ||   |   | |  | || ||| |||    |      
GTTGGCATACCAATTTTCGTAACTGGAGGGATTGGAGGTGTTCATAGAAATGGTGAACAGAgtaagtaccttcctccttc-caatcgtgtaaggagtcccttgctatctgcacattttacagttgatgcttcaatcagtttttctgagttatgaatggatgc

upper sequence: GRMZM2G126517_T01 (Zea mays), 5'ss of exon 5
lower sequence: Vv06s0009g02380.t01 (Vitis vinifera), 5'ss of exon 6
GTTGGCATACCAGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACATGGTGAACAAAgtaagcagcttcatattgcatacttattttgctatgcgttgactgttgacactggcaggaactcattgtatcttaactgtta--tgatttacctctttcaat
||||||||||| || ||||||||||| || |||||||| || ||||||||||| ||  | ||||||      |   ||| ||| |  |   ||||    |    || ||    ||   ||  ||   | | ||||  ||   |  | || | |   ||| || 
GTTGGCATACCTGTCTTTGTTACTGGAGGAATTGGAGGAGTACATAGACATGGAGAGAATAgtaagtgcaacccatttgtata-tcctgaagctagaaatgagttggtgtttgtgatgggctctgccttt-tcttggctagaaattcatatgcacttttgaag
















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|67038503|gb|CO464823.1|CO464823
EST:     AGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACATGGTGAACAAA                         CTATGGATGTCTCCTCAGACTTAACTGAACTTGGAAAGACTCCTGTAGCTG
genomic: AGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACATGGTGAACAAAgtaagcagct ... ttcgatgcagCTATGGATGTCTCCTCAGACTTAACTGAACTTGGAAAGACTCCTGTAGCTG
EST: gi|211098559|gb|FL329018.1|FL329018
EST:     AGTTTTTGTTACTGGGGGCATTGGANGTGTGCATAGACATGGTGAACAAA                         CTATGGATGTCTCCTCAGACTTAACTGAACTTGGAA
genomic: AGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACATGGTGAACAAAgtaagcagct ... ttcgatgcagCTATGGATGTCTCCTCAGACTTAACTGAACTTGGAA
EST: gi|149082843|gb|EE172069.2|EE172069
EST:     AGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACATGGTGAACAAA                         CTATGGATGTCTCCTCAGACTTAACTGAACTTGGAAAGACTCCTGTAGCTG
genomic: AGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACATGGTGAACAAAgtaagcagct ... ttcgatgcagCTATGGATGTCTCCTCAGACTTAACTGAACTTGGAAAGACTCCTGTAGCTG
EST: gi|211522432|gb|FL327537.1|FL327537
EST:     AGTTTTTGTTACTGGGGGCATTGGANGTGTGCATAGACATGGTGAACAAA                         CTATGGATGTCTCCTCAGACTTAACTG
genomic: AGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACATGGTGAACAAAgtaagcagct ... ttcgatgcagCTATGGATGTCTCCTCAGACTTAACTG
EST: gi|211193875|gb|FL364459.1|FL364459
EST:     AGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACATGGTGAACAAA                         CTATGGATGTCT
genomic: AGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACATGGTGAACAAAgtaagcagct ... ttcgatgcagCTATGGATGTCT
EST: gi|149015839|gb|EE045506.2|EE045506
EST:     AGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACATGGTGAACAAA                         CTATGGATGTCTCCTCAGACTTAACTGAACTTGGAAAGACTCCTGTAGCTG
genomic: AGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACATGGTGAACAAAgtaagcagct ... ttcgatgcagCTATGGATGTCTCCTCAGACTTAACTGAACTTGGAAAGACTCCTGTAGCTG
EST: gi|211152952|gb|FL361222.1|FL361222
EST:     AGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACATGGTGAACAAA                         CTATGGATGTCTCCTCAGACTTNACTGAACTTGGAAAGACTCCTGTAGCTG
genomic: AGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACATGGTGAACAAAgtaagcagct ... ttcgatgcagCTATGGATGTCTCCTCAGACTTAACTGAACTTGGAAAGACTCCTGTAGCTG
EST: gi|211483892|gb|FL352027.1|FL352027
EST:     GTTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACATGGTGAACAAA                         CTATGGATGTCTCCTCAGACTTAACTGAACTTG
genomic: GTTTTT-GTTACTGGGGGCATTGGAGGTGTGCATAGACATGGTGAACAAAgtaagcagct ... ttcgatgcagCTATGGATGTCTCCTCAGACTTAACTGAACTTG
EST: gi|31355893|gb|CD440250.1|CD440250
EST:     AGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACATGGTGAACAAA                         CTATGGATGTCTCCTCAGACTTAACTGAACTTGGAAAGACTCCTGTAGCTG
genomic: AGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACATGGTGAACAAAgtaagcagct ... ttcgatgcagCTATGGATGTCTCCTCAGACTTAACTGAACTTGGAAAGACTCCTGTAGCTG
EST: gi|211385441|gb|FL308637.1|FL308637
EST:     AGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACATGGTGAACAAA                         CTATGGATGTCTCCTCAGACTTAACTGAACTTGGAAAGACTCCTGTAGCTG
genomic: AGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACATGGTGAACAAAgtaagcagct ... ttcgatgcagCTATGGATGTCTCCTCAGACTTAACTGAACTTGGAAAGACTCCTGTAGCTG
EST: gi|78085709|gb|DV514102.1|DV514102
EST:     AGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACATGGTGAACAAA                         CTATGGATGTCTCCTCAGACTTAACTGAACTTGGAAAGACTCCTGTAGCTG
genomic: AGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACATGGTGAACAAAgtaagcagct ... ttcgatgcagCTATGGATGTCTCCTCAGACTTAACTGAACTTGGAAAGACTCCTGTAGCTG
EST: gi|211023235|gb|FL319676.1|FL319676
EST:     AGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACATGGTGAACAAA                         CTATGGATGTCTCCTCAGACTTAACTGAACTTG
genomic: AGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACATGGTGAACAAAgtaagcagct ... ttcgatgcagCTATGGATGTCTCCTCAGACTTAACTGAACTTG
EST: gi|211216455|gb|FL358323.1|FL358323
EST:     AGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACATGGTGAACAAA                         CTATGGATGTCTC
genomic: AGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACATGGTGAACAAAgtaagcagct ... ttcgatgcagCTATGGATGTCTC
EST: gi|211267860|gb|FL346397.1|FL346397
EST:     AGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACATGGTGAACAAA                         CTATGGATGTCTCCTCAGACTTAACTG
genomic: AGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACATGGTGAACAAAgtaagcagct ... ttcgatgcagCTATGGATGTCTCCTCAGACTTAACTG
EST: gi|211404920|gb|FL353800.1|FL353800
EST:     GTTTTTGTTACTGGGGGCATTGGAGGTGTGGCATAGACATGGTGAACAAA                         CTATGGATGTCTCCTCAGACTT
genomic: GTTTTTGTTACTGGGGGCATTGGAGGTGTG-CATAGACATGGTGAACAAAgtaagcagct ... ttcgatgcagCTATGGATGTCTCCTCAGACTT
EST: gi|74236392|gb|DT644306.1|DT644306
EST:     AGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACATGGTGAACAAA                         CTATGGATGTCTCCTCAGACTTAACTGAACTTGGAAAGACTCCTGTAGCTG
genomic: AGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACATGGTGAACAAAgtaagcagct ... ttcgatgcagCTATGGATGTCTCCTCAGACTTAACTGAACTTGGAAAGACTCCTGTAGCTG
EST: gi|211420492|gb|FL364949.1|FL364949
EST:     AGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACATGGTGAACAAA                         A
genomic: AGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACATGGTGAACAAAgtaagcagct ... ttcgatgcag-
EST: gi|211420492|gb|FL364949.1|FL364949
EST:     AGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACATGGTGAACAAA                         A
genomic: AGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACATGGTGAACAAAgtaagcagct ... ttcgatgcag-
EST: gi|211526578|gb|FL367182.1|FL367182
EST:     AGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACATGGTGAACAAA                         CTATGGATGTCTCCTCAGACTTAACTGAACTTGGAACAGACTCCTGT
genomic: AGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACATGGTGAACAAAgtaagcagct ... ttcgatgcagCTATGGATGTCTCCTCAGACTTAACTGAACTTGGAA-AGACTCCTGT
EST: gi|31355559|gb|CD439916.1|CD439916
EST:     AGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACATGGTGAACAAA                         CTATGGATGTCTCCTCAGACTTAACTGAACTTGGAAAGACTCCTGTAGCTG
genomic: AGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACATGGTGAACAAAgtaagcagct ... ttcgatgcagCTATGGATGTCTCCTCAGACTTAACTGAACTTGGAAAGACTCCTGTAGCTG
EST: gi|71764027|gb|DR961964.1|DR961964
EST:     AGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACATGGTGAACAAA                         CTATGGATGTCTCCTCAGACTTAACTGAACTTGGAAAGACTCCTGTAGCTG
genomic: AGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACATGGTGAACAAAgtaagcagct ... ttcgatgcagCTATGGATGTCTCCTCAGACTTAACTGAACTTGGAAAGACTCCTGTAGCTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGGCATACCAGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACATGGTGAACAAAgtaagcagcttcatattgcatacttattttgctatgcgttgactgttgacactggcaggaactcattgtatcttaactgttatgatttacctctttcaat

- - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - TGGAGG