Skip to another splice site:
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 5'  3'   		2  
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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatctaaattgctaaattgctgtttgatatactgtaggttattgctacacaagcatactgcatgctgatgtcggtattaactaatgtaattatttggttgcttgatttgtgcagCTTAAGGTAATTGGTGATGGTGGAGATCCAGATGGCCATGACGATGAAGATGATGGACATCACTAAGGATGCCTTGTGGTTCTGAAAATAAGAATCTGAT

Basic information

species Zea mays
transcript GRMZM2G134738_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G134738_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g42650.1 (Oryza sativa), 3'ss of exon 5
-------------------------------gtaatctaaattgctaaattgctgtttg-atatactgtaggttattgctacacaagcatactgcatgc-tgatgtc--ggtattaactaatgtaattatttggttgcttgatttgtgcagCTTAAGGTAATTGGTGATGGTGGAGATCCAGATGGCCATGACGATGAAGATGATGGACATCACTAAGGA------TGCCTTGTGGTTCTGAAAATAAGAATCTGAT
                                |||| ||  |   | | |  ||||||  ||  | ||||| | |  | | || |    |  ||  |   | ||||     | ||   ||||| |  | |   |||||| |  || ||||||||||||| |||||||||||||| ||||||||||| ||||| ||||| || ||    || |||||||||      ||||| |||||||||| ||||||||      
gtaattggaattcgttgtttgacatattactttaatttatgt-atttagtaactgtttttattgaatgtagctcacagttcca-agctgttttgattctgtaatgttctattgttctttaatggatcttt---gttgctcgccttttgcagCTTAAGGTCATTGGTGATGGTGGTGATCCAGATGGACATGATGATGACGACGAGCATCACCACTAAGGACGCCCATGCCTCGTGGTTCTGATAATAAGAA------
















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|60357675|gb|DN224648.1|DN224648
EST:     TGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGTG                         CTTAAGGTAATTGGTGATGGTGGAGATCCAGATGGCCATGACGATGAAGAT
genomic: TGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGTGgtaatctaaa ... atttgtgcagCTTAAGGTAATTGGTGATGGTGGAGATCCAGATGGCCATGACGATGAAGAT
EST: gi|32933852|gb|CF038664.1|CF038664
EST:     TGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGTG                         CTTAAGGTAATTGGTGATGGTGGAGATCCAGATGGCCATGACGATGAGGAT
genomic: TGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGTGgtaatctaaa ... atttgtgcagCTTAAGGTAATTGGTGATGGTGGAGATCCAGATGGCCATGACGATGAAGAT
EST: gi|211038526|gb|FL455206.1|FL455206
EST:     TGAAAAAASMCGASCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGTG                         CTTAAGGTAATTGGTGATGGTGGAGATCCAGATGGCCATGACGATGAAGAT
genomic: TGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGTGgtaatctaaa ... atttgtgcagCTTAAGGTAATTGGTGATGGTGGAGATCCAGATGGCCATGACGATGAAGAT
EST: gi|76288217|gb|DV027785.1|DV027785
EST:     TGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGTG                         CTTAAGGTAATTGGTGATGGTGGAGATCCAGATGGCCATGACGATGAAGAT
genomic: TGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGTGgtaatctaaa ... atttgtgcagCTTAAGGTAATTGGTGATGGTGGAGATCCAGATGGCCATGACGATGAAGAT
EST: gi|28985245|gb|BQ538397.2|BQ538397
EST:     TGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGTG                         CTTAAGGTAATTGGTGATGGTGGAGATCCAGATGGCCATGACGATGAAGAT
genomic: TGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGTGgtaatctaaa ... atttgtgcagCTTAAGGTAATTGGTGATGGTGGAGATCCAGATGGCCATGACGATGAAGAT
EST: gi|18173629|gb|BM349017.1|BM349017
EST:     TGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGTG                         CTTAAGGTAATTGGTGATGGTGGAGATCCAGATGGCCATGACGATGAAGAT
genomic: TGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGTGgtaatctaaa ... atttgtgcagCTTAAGGTAATTGGTGATGGTGGAGATCCAGATGGCCATGACGATGAAGAT
EST: gi|67025323|gb|CO454072.1|CO454072
EST:     TGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCT--CAATACTTTGTG                         CTTAAGGTAATTGGTGATGGTGGAGATCCAGATGGCCATGACGATGAAGAT
genomic: TGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGTGgtaatctaaa ... atttgtgcagCTTAAGGTAATTGGTGATGGTGGAGATCCAGATGGCCATGACGATGAAGAT
EST: gi|18450528|gb|BM428806.1|BM428806
EST:     TGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGCG                         CTTAAGGTAATTGGTGATGGTGGAGATCCAGATGGCCATGACGATGAAGAT
genomic: TGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGTGgtaatctaaa ... atttgtgcagCTTAAGGTAATTGGTGATGGTGGAGATCCAGATGGCCATGACGATGAAGAT
EST: gi|60352817|gb|DN219790.1|DN219790
EST:     TGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGTG                         CTTAAGGTAATTGGTGATGGTGGAGATCCAGATGGCCATGACGATGAAGAT
genomic: TGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGTGgtaatctaaa ... atttgtgcagCTTAAGGTAATTGGTGATGGTGGAGATCCAGATGGCCATGACGATGAAGAT
EST: gi|37382992|gb|CF628470.1|CF628470
EST:     TGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGTG                         CTTAAGGTAATTGGTGATGGTGGAGATCCAGATGGCCATGACGATGAAGAT
genomic: TGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGTGgtaatctaaa ... atttgtgcagCTTAAGGTAATTGGTGATGGTGGAGATCCAGATGGCCATGACGATGAAGAT
EST: gi|18649503|gb|BM498322.1|BM498322
EST:     TGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGTG                         CTTAAGGTAATTGGTGATGGTGGAGATCCAGATGGCCATGACGATGAAGAT
genomic: TGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGTGgtaatctaaa ... atttgtgcagCTTAAGGTAATTGGTGATGGTGGAGATCCAGATGGCCATGACGATGAAGAT
EST: gi|15057046|gb|BI361018.1|BI361018
EST:     TGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGTG                         CTTAAGGTAATTGGTGATGGTGGAGATCCAGATGGCCATGACGATGAAGAT
genomic: TGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGTGgtaatctaaa ... atttgtgcagCTTAAGGTAATTGGTGATGGTGGAGATCCAGATGGCCATGACGATGAAGAT
EST: gi|18450555|gb|BM428833.1|BM428833
EST:     TGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGTG                         CTTAAGGTAATTG
genomic: TGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGTGgtaatctaaa ... atttgtgcagCTTAAGGTAATTG
EST: gi|60352341|gb|DN219314.1|DN219314
EST:     TGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGTG                         CTTAAGGTAATTGGTGATGGTGGAGATCCAGATGGCCATGACGATGAAGAT
genomic: TGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGTGgtaatctaaa ... atttgtgcagCTTAAGGTAATTGGTGATGGTGGAGATCCAGATGGCCATGACGATGAAGAT
EST: gi|60340144|gb|DN207117.1|DN207117
EST:     TGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGTG                         CTTAAGGTAATTGGTGATGGTGGAGATCCAGATGGCCATGACGATGAAGAT
genomic: TGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGTGgtaatctaaa ... atttgtgcagCTTAAGGTAATTGGTGATGGTGGAGATCCAGATGGCCATGACGATGAAGAT
EST: gi|24770192|gb|CA405321.1|CA405321
EST:     TGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGTG                         CTTAAGGTAATTGGTGATGGTGGAGATCCAGATGGCCATGACGATGAAGAT
genomic: TGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGTGgtaatctaaa ... atttgtgcagCTTAAGGTAATTGGTGATGGTGGAGATCCAGATGGCCATGACGATGAAGAT
EST: gi|76288216|gb|DV027784.1|DV027784
EST:     TGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGTG                         CTTAAGGTAATTGGTGATGGTGGAGATCCAGATGGCCATGACGATGAAGAT
genomic: TGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGTGgtaatctaaa ... atttgtgcagCTTAAGGTAATTGGTGATGGTGGAGATCCAGATGGCCATGACGATGAAGAT
EST: gi|60348157|gb|DN215130.1|DN215130
EST:     TGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGTG                         CTTAAGGTAATTGGTGATGGTGGAGATCCAGATGGCCATGACGATGAAGAT
genomic: TGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGTGgtaatctaaa ... atttgtgcagCTTAAGGTAATTGGTGATGGTGGAGATCCAGATGGCCATGACGATGAAGAT
EST: gi|31354094|gb|CD438451.1|CD438451
EST:     TGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGTG                         CTTAAGGTAATTGGTGATGGTGGAGATCCAGATGGCCATGACGATGAAGAT
genomic: TGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGTGgtaatctaaa ... atttgtgcagCTTAAGGTAATTGGTGATGGTGGAGATCCAGATGGCCATGACGATGAAGAT
EST: gi|21759837|gb|BQ635378.1|BQ635378
EST:     TGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGTG                         CTTAAGGTAATTGGTGATGGTGGAGATCCAGATGGCCATGACGATGAAGAT
genomic: TGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGTGgtaatctaaa ... atttgtgcagCTTAAGGTAATTGGTGATGGTGGAGATCCAGATGGCCATGACGATGAAGAT
EST: gi|37383908|gb|CF628995.1|CF628995
EST:     GTGTCCAGTCTGCTCGCAATAC-TT-T-                         CTTAAGGTAATTGGTGATGGTGGAGATCCAGATGGCCATGACGATGAAGAT
genomic: GTGTCCAGTCTGCTCGCAATACTTTGTGgtaatctaaa ... atttgtgcagCTTAAGGTAATTGGTGATGGTGGAGATCCAGATGGCCATGACGATGAAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatgctgatgtcggtattaactaatgtaattatttggttgcttgatttgtgcagCTTAAGGTAATTGGTGATGGTGGAGATCCAGATGGCCATGACGATGAAGATGATGGACATCACTAAGGATGCCTTGTGGTTCTGAAAATAAGAATCTGAT
               tattaactaatgtaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatctaaattgctaaattgctgtttgatatactgtaggttattgctacacaagcatactgcatgctgatgtcggtattaactaatgtaattatttggttgcttgatttgtgcagCTTAAGGTAATTGGTGATGGTGGAGATCCAGATGGCCATGACGATGAAGATGATGGACATCACTAAGGATGCCTTGTGGTTCTGAAAATAAGAATCTGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG