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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtggtaatctaaattgctaaattgctgtttgatatactgtaggttattgctacacaagcatactgcatgctgatgtcggtattaactaatgtaattatttggttgcttgatttgtgcagCTTAAGGTAATTGGTGATGGTGGAGATCCAGATGGCCATGACGATGAAGATGATGGACATCACTAAGGATGCCTTGTGGTTCTGAAAATAAGAATCTGAT

Basic information

species Zea mays
transcript GRMZM2G134738_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G134738_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g42650.1 (Oryza sativa), 3'ss of exon 5
-----------------------gtggtaatctaaat----tgctaaattgctgtttg-atatactgtaggttattgctacacaagcatactgcatgc-tgatgtc--ggtattaactaatgtaattatttggttgcttgatttgtgcagCTTAAGGTAATTGGTGATGGTGGAGATCCAGATGGCCATGACGATGAAGATGATGGACATCACTAAGGA------TGCCTTGTGGTTCTGAAAATAAGAATCTGAT
                        |  || | ||| |    |  | | |  ||||||  ||  | ||||| | |  | | || |    |  ||  |   | ||||     | ||   ||||| |  | |   |||||| |  || ||||||||||||| |||||||||||||| ||||||||||| ||||| ||||| || ||    || |||||||||      ||||| |||||||||| ||||||||      
gtaattggaattcgttgtttgacatattactttaatttatgtatttagtaactgtttttattgaatgtagctcacagttcca-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|67025323|gb|CO454072.1|CO454072
EST:     TCCAGTCTGCT--CAATACTTTGTG                         CTTAAGGTAATTGGTGATGGTGGAGATCCAGATGGCCATGACGATGAAGA
genomic: TCCAGTCTGCTCGCAATAC-TT-T-gtggtaatct ... atttgtgcagCTTAAGGTAATTGGTGATGGTGGAGATCCAGATGGCCATGACGATGAAGA
EST: gi|67025323|gb|CO454072.1|CO454072
EST:     TCCAGTCTGCT--CAATACTTTGTG                         CTTAAGGTAATTGGTGATGGTGGAGATCCAGATGGCCATGACGATGAAGA
genomic: TCCAGTCTGCTCGCAATAC-TT-T-gtggtaatct ... atttgtgcagCTTAAGGTAATTGGTGATGGTGGAGATCCAGATGGCCATGACGATGAAGA
EST: gi|60340144|gb|DN207117.1|DN207117
EST:     GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGT                        
genomic: GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATAC-TT-Tgtggtaatct ... atttgtgca
EST: gi|60340144|gb|DN207117.1|DN207117
EST:     GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGT                        
genomic: GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATAC-TT-Tgtggtaatct ... atttgtgca
EST: gi|18173629|gb|BM349017.1|BM349017
EST:     GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGT                        
genomic: GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATAC-TT-Tgtggtaatct ... atttgtgca
EST: gi|18173629|gb|BM349017.1|BM349017
EST:     GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGT                        
genomic: GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATAC-TT-Tgtggtaatct ... atttgtgca
EST: gi|76288216|gb|DV027784.1|DV027784
EST:     GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGT                        
genomic: GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATAC-TT-Tgtggtaatct ... atttgtgca
EST: gi|76288216|gb|DV027784.1|DV027784
EST:     GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGT                        
genomic: GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATAC-TT-Tgtggtaatct ... atttgtgca
EST: gi|31354094|gb|CD438451.1|CD438451
EST:     GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGT                        
genomic: GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATAC-TT-Tgtggtaatct ... atttgtgca
EST: gi|31354094|gb|CD438451.1|CD438451
EST:     GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGT                        
genomic: GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATAC-TT-Tgtggtaatct ... atttgtgca
EST: gi|21759837|gb|BQ635378.1|BQ635378
EST:     GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGT                        
genomic: GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATAC-TT-Tgtggtaatct ... atttgtgca
EST: gi|21759837|gb|BQ635378.1|BQ635378
EST:     GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGT                        
genomic: GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATAC-TT-Tgtggtaatct ... atttgtgca
EST: gi|18450555|gb|BM428833.1|BM428833
EST:     GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTT                         G
genomic: GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTgtggtaatct ... atttgtgcag-
EST: gi|18450555|gb|BM428833.1|BM428833
EST:     GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTT                         G
genomic: GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTgtggtaatct ... atttgtgcag-
EST: gi|18450555|gb|BM428833.1|BM428833
EST:     GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTT                         G
genomic: GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTgtggtaatct ... atttgtgcag-
EST: gi|18450555|gb|BM428833.1|BM428833
EST:     GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTT                         G
genomic: GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTgtggtaatct ... atttgtgcag-
EST: gi|211038526|gb|FL455206.1|FL455206
EST:     GGTTGAAAAAASMCGASCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGT                        
genomic: GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATAC-TT-Tgtggtaatct ... atttgtgca
EST: gi|211038526|gb|FL455206.1|FL455206
EST:     GGTTGAAAAAASMCGASCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGT                        
genomic: GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATAC-TT-Tgtggtaatct ... atttgtgca
EST: gi|37383908|gb|CF628995.1|CF628995
EST:     GTGTCCAGTCTGCTCGCAATACTTT                         CTTAAGGTAATTGGTGATGGTGGAGATCCAGATGGCCATGACGATGAAGAT
genomic: GTGTCCAGTCTGCTCGCAATACTTTgtggtaatct ... atttgtgcagCTTAAGGTAATTGGTGATGGTGGAGATCCAGATGGCCATGACGATGAAGAT
EST: gi|28985245|gb|BQ538397.2|BQ538397
EST:     GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGT                        
genomic: GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATAC-TT-Tgtggtaatct ... atttgtgca
EST: gi|28985245|gb|BQ538397.2|BQ538397
EST:     GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGT                        
genomic: GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATAC-TT-Tgtggtaatct ... atttgtgca
EST: gi|18450528|gb|BM428806.1|BM428806
EST:     GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTT                         G
genomic: GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTgtggtaatct ... atttgtgcag-
EST: gi|18450528|gb|BM428806.1|BM428806
EST:     GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTT                         G
genomic: GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTgtggtaatct ... atttgtgcag-
EST: gi|32933852|gb|CF038664.1|CF038664
EST:     GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGT                        
genomic: GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATAC-TT-Tgtggtaatct ... atttgtgca
EST: gi|32933852|gb|CF038664.1|CF038664
EST:     GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGT                        
genomic: GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATAC-TT-Tgtggtaatct ... atttgtgca
EST: gi|60352341|gb|DN219314.1|DN219314
EST:     GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGT                        
genomic: GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATAC-TT-Tgtggtaatct ... atttgtgca
EST: gi|60352341|gb|DN219314.1|DN219314
EST:     GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGT                        
genomic: GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATAC-TT-Tgtggtaatct ... atttgtgca
EST: gi|60352817|gb|DN219790.1|DN219790
EST:     GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGT                        
genomic: GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATAC-TT-Tgtggtaatct ... atttgtgca
EST: gi|60352817|gb|DN219790.1|DN219790
EST:     GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGT                        
genomic: GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATAC-TT-Tgtggtaatct ... atttgtgca
EST: gi|37382992|gb|CF628470.1|CF628470
EST:     GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGT                        
genomic: GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATAC-TT-Tgtggtaatct ... atttgtgca
EST: gi|37382992|gb|CF628470.1|CF628470
EST:     GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGT                        
genomic: GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATAC-TT-Tgtggtaatct ... atttgtgca
EST: gi|24770192|gb|CA405321.1|CA405321
EST:     GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTT                         G
genomic: GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTgtggtaatct ... atttgtgcag-
EST: gi|24770192|gb|CA405321.1|CA405321
EST:     GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTT                         G
genomic: GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTgtggtaatct ... atttgtgcag-
EST: gi|24770192|gb|CA405321.1|CA405321
EST:     GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTT                         G
genomic: GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTgtggtaatct ... atttgtgcag-
EST: gi|24770192|gb|CA405321.1|CA405321
EST:     GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTT                         G
genomic: GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTgtggtaatct ... atttgtgcag-
EST: gi|60348157|gb|DN215130.1|DN215130
EST:     GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGT                        
genomic: GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATAC-TT-Tgtggtaatct ... atttgtgca
EST: gi|60348157|gb|DN215130.1|DN215130
EST:     GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGT                        
genomic: GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATAC-TT-Tgtggtaatct ... atttgtgca
EST: gi|15057046|gb|BI361018.1|BI361018
EST:     GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGT                        
genomic: GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATAC-TT-Tgtggtaatct ... atttgtgca
EST: gi|15057046|gb|BI361018.1|BI361018
EST:     GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGT                        
genomic: GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATAC-TT-Tgtggtaatct ... atttgtgca
EST: gi|60357675|gb|DN224648.1|DN224648
EST:     GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGT                        
genomic: GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATAC-TT-Tgtggtaatct ... atttgtgca
EST: gi|60357675|gb|DN224648.1|DN224648
EST:     GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGT                        
genomic: GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATAC-TT-Tgtggtaatct ... atttgtgca
EST: gi|18649503|gb|BM498322.1|BM498322
EST:     GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTT                         G
genomic: GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTgtggtaatct ... atttgtgcag-
EST: gi|18649503|gb|BM498322.1|BM498322
EST:     GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTT                         G
genomic: GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTgtggtaatct ... atttgtgcag-
EST: gi|18649503|gb|BM498322.1|BM498322
EST:     GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTT                         G
genomic: GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTgtggtaatct ... atttgtgcag-
EST: gi|18649503|gb|BM498322.1|BM498322
EST:     GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTT                         G
genomic: GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTgtggtaatct ... atttgtgcag-
EST: gi|76288217|gb|DV027785.1|DV027785
EST:     GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGT                        
genomic: GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATAC-TT-Tgtggtaatct ... atttgtgca
EST: gi|76288217|gb|DV027785.1|DV027785
EST:     GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGT                        
genomic: GGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATAC-TT-Tgtggtaatct ... atttgtgca

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 118

AGGACGAACATGATGTTGTATGGTTCTGGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTgtggtaatct ... atttgtgcagCTTAAGGTAATTGGTGATGGTGGAGATCCAGATGGCCATGACGATGAAGATGATGGACATCACTAAGGATGCCTTGTGGTTCTGAAAATAAGAATCTGAT


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 98

AGGACGAACATGATGTTGTATGGTTCTGGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTgtggtaatct ... atttgtgcagCTTAAGGTAATTGGTGATGGTGGAGATCCAGATGGCCATGACGATGAAGATGATGGACATCACTAAGGATGCCTTGTGGTTCTGAAAATAAGAATCTGAT


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 40

AGGACGAACATGATGTTGTATGGTTCTGGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTgtggtaatct ... atttgtgcagCTTAAGGTAATTGGTGATGGTGGAGATCCAGATGGCCATGACGATGAAGATGATGGACATCACTAAGGATGCCTTGTGGTTCTGAAAATAAGAATCTGAT


Block sizes: 48 (upstream exon), 40 (downstream exon)
Score: 94

AGGACGAACATGATGTTGTATGGTTCTGGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTgtggtaatct ... atttgtgcagCTTAAGGTAATTGGTGATGGTGGAGATCCAGATGGCCATGACGATGAAGATGATGGACATCACTAAGGATGCCTTGTGGTTCTGAAAATAAGAATCTGAT




 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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtggtaatctaaattgctaaattgctgtttgatatactgtaggttattgctacacaagcatactgcatgctgatgtcggtattaactaatgtaattatttggttgcttgatttgtgcagCTTAAGGTAATTGGTGATGGTGGAGATCCAGATGGCCATGACGATGAAGATGATGGACATCACTAAGGATGCCTTGTGGTTCTGAAAATAAGAATCTGAT

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