Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtaccttttgtcatatgtttcttgttctgtggaaaaattggaattgaaccaacatgggattcttttgtgataacagGCGGAGGGAAAGTACTGATGTTGAGGACATGTTTCTTGCCCATATCTCCGGAATGGACACCCTGGCACGTGGCCTCCGTAACGTTGCCAAGCTGATTGGG

Basic information

species Zea mays
transcript GRMZM2G081682_T02
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G081682_T01 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os07g47290.1 (Oryza sativa), 3'ss of exon 17
-------------------gtcagtaccttttgt-catatgtttcttgttctgtggaaaaattggaattgaaccaacatgggattcttttgtgataacagGCGGAGGGAAAGTACTGATGTTGAGGACATGTTTCTTGCCCATATCTCCGGAATGGACACCCTGGCACGTGGCCTCCGTAACGTTGCCAAGCTGATTGGG
                   ||   |   ||||||   | |||   ||| ||| ||    || || | || ||   || ||| ||||| || ||  |||||| ||||||| |||||||||||||||||||||||||| || ||||| || |||||||||||||| || || ||||| || || |||| ||||||||| | |
gttggttcccgctgacattgttttttttttttgtgtgtgtgtaaattggtctctgattcaactgaatttcaattgacttggaattctattatgtcaacagGAGGAGGGAGAGTACTGATGTTGAGGACATGTTTCTGGCTCATATATCGGGAATGGACACCCTAGCCCGCGGCCTTCGGAATGTTGTCAAGCTGATCGAG
















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|21389890|gb|BQ527939.1|BQ527939
EST:     GGTGGACTTGCACCTGGTGGTTTCAACTTTGATGCCAAATT                         GCGGAGGGAAAGTACTGATGTTGAGGACATGTTTCTTGCCCATATCTCCGG
genomic: GGTGGACTTGCACCTGGTGGTTTCAACTTTGATGCCAAATTgtcagtacct ... gtgataacagGCGGAGGGAAAGTACTGATGTTGAGGACATGTTTCTTGCCCATATCTCCGG
EST: gi|21331635|gb|BQ487016.1|BQ487016
EST:     GGTGGACTTGCACCTGGTGGTTTCAACCTTGATGCCAAATT                         GCGGAGGGAAAGTACTGATGTTGAGGACATGTTTCTTGCCCATATCTCCGG
genomic: GGTGGACTTGCACCTGGTGGTTTCAACTTTGATGCCAAATTgtcagtacct ... gtgataacagGCGGAGGGAAAGTACTGATGTTGAGGACATGTTTCTTGCCCATATCTCCGG
EST: gi|32909378|gb|CF014190.1|CF014190
EST:     GGTGGACTTGCACCTGGTGGTTTCAACTTTGATGCCAAATT                         GCGGAGGGAAAGTACTGATGTTGAGGACATGTTTCTTGCCCATATCTCCGG
genomic: GGTGGACTTGCACCTGGTGGTTTCAACTTTGATGCCAAATTgtcagtacct ... gtgataacagGCGGAGGGAAAGTACTGATGTTGAGGACATGTTTCTTGCCCATATCTCCGG
EST: gi|22715088|gb|BU197571.1|BU197571
EST:     GGTGGACTTGCCCCTGGTGGTTTCAACTTTGATGCCAAATT                         GCGGAGGGAAAGTACTGATGTTGAGGACATGTTTCTTGCCCATATCTCCGG
genomic: GGTGGACTTGCACCTGGTGGTTTCAACTTTGATGCCAAATTgtcagtacct ... gtgataacagGCGGAGGGAAAGTACTGATGTTGAGGACATGTTTCTTGCCCATATCTCCGG
EST: gi|60397236|gb|DN230052.1|DN230052
EST:     GTTTAACAGGGTGGACTTGCACCTGGTGGTTTCAACTTTGATGCCAAATT                         GCGGAGGGAAAGTACTGATGTTGAGGACATGTTTCTTGCCCATATCTCCGG
genomic: GTTTAACAGGGTGGACTTGCACCTGGTGGTTTCAACTTTGATGCCAAATTgtcagtacct ... gtgataacagGCGGAGGGAAAGTACTGATGTTGAGGACATGTTTCTTGCCCATATCTCCGG
EST: gi|6095640|gb|AW120307.1|AW120307
EST:     GGTGGCCTTGCACCTGGTGGTTTCANACTTTAATGCCAAATT                         GCGGAGGGAAAGTACTGATGTTGAGGACATGTTTCTTGCCCATATCTCCGG
genomic: GGTGGACTTGCACCTGGTGGTTTCA-ACTTTGATGCCAAATTgtcagtacct ... gtgataacagGCGGAGGGAAAGTACTGATGTTGAGGACATGTTTCTTGCCCATATCTCCGG
EST: gi|9794851|gb|BE553159.1|BE553159
EST:     GGTGGACTTGCACCTGGTGGTTTCAACTTTGATGCCAAATT                         GCGGAGGGAAAGTACTGATGTTGAGGACATGTTTCTTGCCCATATCTCCGG
genomic: GGTGGACTTGCACCTGGTGGTTTCAACTTTGATGCCAAATTgtcagtacct ... gtgataacagGCGGAGGGAAAGTACTGATGTTGAGGACATGTTTCTTGCCCATATCTCCGG

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), 49 (downstream exon)
Score: 198

AGTTTGCCTATGTACTTCCTGGTTGCACTCATATAAGCTGCTGCATTTTTGTTTAACAGGGTGGACTTGCACCTGGTGGTTTCAACTTTGATGCCAAATTgtcagtacct ... gtgataacagGCGGAGGGAAAGTACTGATGTTGAGGACATGTTTCTTGCCCATATCTCCGGAATGGACACCCTGGCACGTGGCCTCCGTAACGTTGCCAAGCTGATTGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 190

AGTTTGCCTATGTACTTCCTGGTTGCACTCATATAAGCTGCTGCATTTTTGTTTAACAGGGTGGACTTGCACCTGGTGGTTTCAACTTTGATGCCAAATTgtcagtacct ... gtgataacagGCGGAGGGAAAGTACTGATGTTGAGGACATGTTTCTTGCCCATATCTCCGGAATGGACACCCTGGCACGTGGCCTCCGTAACGTTGCCAAGCTGATTGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 171

AGTTTGCCTATGTACTTCCTGGTTGCACTCATATAAGCTGCTGCATTTTTGTTTAACAGGGTGGACTTGCACCTGGTGGTTTCAACTTTGATGCCAAATTgtcagtacct ... gtgataacagGCGGAGGGAAAGTACTGATGTTGAGGACATGTTTCTTGCCCATATCTCCGGAATGGACACCCTGGCACGTGGCCTCCGTAACGTTGCCAAGCTGATTGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 189

AGTTTGCCTATGTACTTCCTGGTTGCACTCATATAAGCTGCTGCATTTTTGTTTAACAGGGTGGACTTGCACCTGGTGGTTTCAACTTTGATGCCAAATTgtcagtacct ... gtgataacagGCGGAGGGAAAGTACTGATGTTGAGGACATGTTTCTTGCCCATATCTCCGGAATGGACACCCTGGCACGTGGCCTCCGTAACGTTGCCAAGCTGATTGGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttctgtggaaaaattggaattgaaccaacatgggattcttttgtgataacagGCGGAGGGAAAGTACTGATGTTGAGGACATGTTTCTTGCCCATATCTCCGGAATGGACACCCTGGCACGTGGCCTCCGTAACGTTGCCAAGCTGATTGGG
                                      ttcttttgt  CT-rich tract
           aaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtaccttttgtcatatgtttcttgttctgtggaaaaattggaattgaaccaacatgggattcttttgtgataacagGCGGAGGGAAAGTACTGATGTTGAGGACATGTTTCTTGCCCATATCTCCGGAATGGACACCCTGGCACGTGGCCTCCGTAACGTTGCCAAGCTGATTGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT