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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggtatttttcttttgtttctcttttccgtatagtggttcgttttcaatttgtttaattgtctttcccatcttattacagATTCTTCATGAGAACATATATCAAACCTTCCTTGATCAGCTTGTTGAGGTATACAAACAAGTCCGAATTGGGGATCCGTTGGAGAAAGGCACCTTACTGG

Basic information

species Zea mays
transcript GRMZM2G130440_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G130440_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os09g26880.4 (Oryza sativa), 3'ss of exon 8
gtatggtatttttcttttgtttctcttttccgtatagtggttcgttttcaatttgtttaattgtctttcccatcttattacagATTCTTCATGAGAACATATATCAAACCTTCCTTGATCAGCTTGTTGAGGTATACAAACAAGTCCGAATTGGGGATCCGTTGGAGAAAGGCACCTTACTGG
||| | ||  ||| | || | |  |          | ||| | || |   | | || ||| ||  |||    | |||  |||| ||||||| || | |||||| | ||| || |||||||| ||||||||||| || ||||||||||||||||||||||| |||||||| || || |||||||
gtaagataggtttttcttatctgcccc--------aatggctggtgtatgagtagtctaaatgcttttgttttgttaacacagCTTCTTCACGAAAGCATATACCGAACATTTCTTGATCAACTTGTTGAGGTTTATAAACAAGTCCGAATTGGGGATCCTTTGGAGAATGGTACGTTACTGG
















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|14204228|gb|BG837905.1|BG837905
EST:     TCGCTGCTGTTGGTACAGCAGGACAACGCTGCACTACATGTCGTAGGCTG                         ATTCTTCATGAGAACATATATCAAACCTTCCTTGATCAGCTTGTTGAGGTA
genomic: TCGCTGCTGTTGGTACAGCAGGACAACGCTGCACTACATGTCGTAGGCTGgtatggtatt ... cttattacagATTCTTCATGAGAACATATATCAAACCTTCCTTGATCAGCTTGTTGAGGTA
EST: gi|32922323|gb|CF027135.1|CF027135
EST:     ACAGCAGGACAACGCTGCACTACATGTCGTAGGCTG                         ATTCTTCATGAGAACATATATCAAACCTTCCTTGATCAGC-TGNCTGAGGT
genomic: ACAGCAGGACAACGCTGCACTACATGTCGTAGGCTGgtatggtatt ... cttattacagATTCTTCATGAGAACATATATCAAACCTTCCTTGATCAGCTTG-TTGAGGT
EST: gi|32922524|gb|CF027336.1|CF027336
EST:     TACAGCAGGACAACGCTGCACTACATGTCGTAGGCTG                         ATTCTTCATGAGAACATATATCAAACCTTCCTTGATCAGCTTGTTGAGGTA
genomic: TACAGCAGGACAACGCTGCACTACATGTCGTAGGCTGgtatggtatt ... cttattacagATTCTTCATGAGAACATATATCAAACCTTCCTTGATCAGCTTGTTGAGGTA
EST: gi|32923501|gb|CF028313.1|CF028313
EST:     CTACATGTCGTAGGCTG                         ATTCTTCATGAGAACATATATCAAACCTTCCTTGATCAGCTTGTTGAGGTA
genomic: CTACATGTCGTAGGCTGgtatggtatt ... cttattacagATTCTTCATGAGAACATATATCAAACCTTCCTTGATCAGCTTGTTGAGGTA
EST: gi|60397385|gb|DN230201.1|DN230201
EST:     TCGCTGCTGTTGGTACAGCAGGACAACGCTGCACTACATGTCGTAGGCTG                         ATTCTTCATGAGAACATATATCAAACCTTCCTTGATCAGCTTGTTGAGGTA
genomic: TCGCTGCTGTTGGTACAGCAGGACAACGCTGCACTACATGTCGTAGGCTGgtatggtatt ... cttattacagATTCTTCATGAGAACATATATCAAACCTTCCTTGATCAGCTTGTTGAGGTA
EST: gi|18659627|gb|BM500437.1|BM500437
EST:     TCGCTGCTGTTGGTACAGCAGGACAACGCTGCACTACATGTCGTAAGCTG                         AATCCTCATGAGAACATATATCAAA
genomic: TCGCTGCTGTTGGTACAGCAGGACAACGCTGCACTACATGTCGTAGGCTGgtatggtatt ... cttattacagATTCTTCATGAGAACATATATCAAA
EST: gi|32923528|gb|CF028340.1|CF028340
EST:     TACAGCAGGACAACGCTGCACTACATGTCGTAGGCTG                         ATTCTTCATGAGAACATATATCAAACCTTCCTTGATCAGTTTGTTGAGGTA
genomic: TACAGCAGGACAACGCTGCACTACATGTCGTAGGCTGgtatggtatt ... cttattacagATTCTTCATGAGAACATATATCAAACCTTCCTTGATCAGCTTGTTGAGGTA
EST: gi|32833586|gb|CD973264.1|CD973264
EST:     GGTACAGCAGGACAACGCTGCACTACATGTCGTAGGCTG                         ATTCTTCATGAGAACATATATCAAACCTTCCTTGATCAGCTTGTTGAGGTA
genomic: GGTACAGCAGGACAACGCTGCACTACATGTCGTAGGCTGgtatggtatt ... cttattacagATTCTTCATGAGAACATATATCAAACCTTCCTTGATCAGCTTGTTGAGGTA
EST: gi|32844476|gb|CD984157.1|CD984157
EST:     ACAGCAGGACAACGCTGCACTACATGTCGTAGGCTG                         ATTCTTCATGAGGACATATATCAAACCTTCCTTGATCAGCTTGGTGAGGTA
genomic: ACAGCAGGACAACGCTGCACTACATGTCGTAGGCTGgtatggtatt ... cttattacagATTCTTCATGAGAACATATATCAAACCTTCCTTGATCAGCTTGTTGAGGTA
EST: gi|33099261|gb|CF059221.1|CF059221
EST:     ACAGCAGGACAACGCTGCACTACATGTCGTAGGCTG                         ATTCTTCATGAGAACATATATCAAACCTTCCTTGATCAGCTTGTTGAGGTA
genomic: ACAGCAGGACAACGCTGCACTACATGTCGTAGGCTGgtatggtatt ... cttattacagATTCTTCATGAGAACATATATCAAACCTTCCTTGATCAGCTTGTTGAGGTA
EST: gi|5895823|gb|AW037069.1|AW037069
EST:     TCGCTGCTGTTGGTACAGCAGGACGGCGCTGCACTACATGTCGTAGGCTG                         ATTCTTCATGAGAACATATATCAAACCTTCCTTGATCAGCTTGTTGAGGTA
genomic: TCGCTGCTGTTGGTACAGCAGGACAACGCTGCACTACATGTCGTAGGCTGgtatggtatt ... cttattacagATTCTTCATGAGAACATATATCAAACCTTCCTTGATCAGCTTGTTGAGGTA
EST: gi|32845522|gb|CD985203.1|CD985203
EST:     ACAGCAGGACAACGCTGCACTACATGTCGTAGGCTG                         ATTCTTCATGAGGACATATATCAAACCTTCCTTGATCAGCTTGTTGAGGTA
genomic: ACAGCAGGACAACGCTGCACTACATGTCGTAGGCTGgtatggtatt ... cttattacagATTCTTCATGAGAACATATATCAAACCTTCCTTGATCAGCTTGTTGAGGTA
EST: gi|32828428|gb|CD968106.1|CD968106
EST:     ATGTCGTAGGCTG                         ATTCTTCATGAG-ACATATATCAAACCTTCCTTGATCAGCTTGTTGAGGTA
genomic: ATGTCGTAGGCTGgtatggtatt ... cttattacagATTCTTCATGAGAACATATATCAAACCTTCCTTGATCAGCTTGTTGAGGTA
EST: gi|32923608|gb|CF028420.1|CF028420
EST:     TACAGCAGGACAACGCTGCACTACATGTCGTAGGCTG                         ATTCTTCATGAGAACATATATCAAACCTTCCTTGATCAGCTTGTTGAGGTA
genomic: TACAGCAGGACAACGCTGCACTACATGTCGTAGGCTGgtatggtatt ... cttattacagATTCTTCATGAGAACATATATCAAACCTTCCTTGATCAGCTTGTTGAGGTA
EST: gi|32922556|gb|CF027368.1|CF027368
EST:     ACAGCAGGACAACGCTGCACTACATGTCGTAGGCTG                         ATTCTTCATGAGAACATATATCAAACCTTCCTTGATCAGCTTGTTGAGGTA
genomic: ACAGCAGGACAACGCTGCACTACATGTCGTAGGCTGgtatggtatt ... cttattacagATTCTTCATGAGAACATATATCAAACCTTCCTTGATCAGCTTGTTGAGGTA
EST: gi|67034827|gb|CO463360.1|CO463360
EST:     TCGCTGCTGTTGGTACAGCAGGACAACGCTGCACTACATGTCGTAGGCTG                         ATTCTTCATGAGAACATATATCAAACCTTCCTTGATCAGCTTGTTGAGGTA
genomic: TCGCTGCTGTTGGTACAGCAGGACAACGCTGCACTACATGTCGTAGGCTGgtatggtatt ... cttattacagATTCTTCATGAGAACATATATCAAACCTTCCTTGATCAGCTTGTTGAGGTA
EST: gi|67026004|gb|CO454753.1|CO454753
EST:     TCGCTGCTGTTGGTACAGCAGGACAACGCTGCACTACATGTCGTAGGCTG                         ATTCTTCATGAGAACATATATCAAACCTTCCTTGATCAGCTTGTTGAGGTA
genomic: TCGCTGCTGTTGGTACAGCAGGACAACGCTGCACTACATGTCGTAGGCTGgtatggtatt ... cttattacagATTCTTCATGAGAACATATATCAAACCTTCCTTGATCAGCTTGTTGAGGTA
EST: gi|211364319|gb|FL429344.1|FL429344
EST:     TCGCTGCTGTTGGTACAGCAGGACAACGCTGCACTACATGTCGTAGGCTG                         ATTCTTCATGAGAACATATATCAAACCTTCCTTGATCAGCTTGTTGAGGTA
genomic: TCGCTGCTGTTGGTACAGCAGGACAACGCTGCACTACATGTCGTAGGCTGgtatggtatt ... cttattacagATTCTTCATGAGAACATATATCAAACCTTCCTTGATCAGCTTGTTGAGGTA
EST: gi|8102664|gb|AW927311.1|AW927311
EST:     TCGCTGCTGTTGGTACAGCAGGACAACGCTGCACTACATGTCGTAGGCTG                         ATTCTTCATGAGAACATATATCAAACCTTCCTTGATCAGCTTGTTGAGGTA
genomic: TCGCTGCTGTTGGTACAGCAGGACAACGCTGCACTACATGTCGTAGGCTGgtatggtatt ... cttattacagATTCTTCATGAGAACATATATCAAACCTTCCTTGATCAGCTTGTTGAGGTA
EST: gi|213168098|gb|FM193492.1|FM193492
EST:     TCGCTGCTGTTGGTACAGCAGGACAACGCTGCACTACATGTCGTAGGCTG                         ATTCTTCATGAGAACATATATCAAACCTTCCTTGATCAGCTTGTTGAGGTA
genomic: TCGCTGCTGTTGGTACAGCAGGACAACGCTGCACTACATGTCGTAGGCTGgtatggtatt ... cttattacagATTCTTCATGAGAACATATATCAAACCTTCCTTGATCAGCTTGTTGAGGTA
EST: gi|32835746|gb|CD975424.1|CD975424
EST:     ACAGCAGGACAACGCTGCACTACATGTCGTAGGCTG                         ATTCTTCATGAGAACATATATCAAACCTTCCTTGATCAGCTTGTTGAGGTA
genomic: ACAGCAGGACAACGCTGCACTACATGTCGTAGGCTGgtatggtatt ... cttattacagATTCTTCATGAGAACATATATCAAACCTTCCTTGATCAGCTTGTTGAGGTA
EST: gi|32922276|gb|CF027088.1|CF027088
EST:     ACAGCAGGACAACGCTGCACTACATGTCGTAGGCTG                         ATTCTTCATGAGAACATATATCAAACCTTCCTTGATCAGCTTGTTGAGGTA
genomic: ACAGCAGGACAACGCTGCACTACATGTCGTAGGCTGgtatggtatt ... cttattacagATTCTTCATGAGAACATATATCAAACCTTCCTTGATCAGCTTGTTGAGGTA
EST: gi|32923568|gb|CF028380.1|CF028380
EST:     CACTACATGTCGTAGGCTG                         ATTCTTCATGAGAACATATATCAAACCTTCCTTGATCAGCTTGTTGAGGTA
genomic: CACTACATGTCGTAGGCTGgtatggtatt ... cttattacagATTCTTCATGAGAACATATATCAAACCTTCCTTGATCAGCTTGTTGAGGTA
EST: gi|32923279|gb|CF028091.1|CF028091
EST:     TACAGCAGGACAACGCTGCACTACATGTCGTAGGCTG                         ATTCTTCATGAGAACATATATCAAACCTTCCTTGATCAGCTTGTTGAGGTA
genomic: TACAGCAGGACAACGCTGCACTACATGTCGTAGGCTGgtatggtatt ... cttattacagATTCTTCATGAGAACATATATCAAACCTTCCTTGATCAGCTTGTTGAGGTA
EST: gi|33099158|gb|CF059118.1|CF059118
EST:     TACAGCAGTACATCGCTGCACTACATGTCGTAGGCTG                         ATTCTTCATGAGAACATATATCAAACCTTCCTTGATCAGCTTGTTGAGGTA
genomic: TACAGCAGGACAACGCTGCACTACATGTCGTAGGCTGgtatggtatt ... cttattacagATTCTTCATGAGAACATATATCAAACCTTCCTTGATCAGCTTGTTGAGGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccgtatagtggttcgttttcaatttgtttaattgtctttcccatcttattacagATTCTTCATGAGAACATATATCAAACCTTCCTTGATCAGCTTGTTGAGGTATACAAACAAGTCCGAATTGGGGATCCGTTGGAGAAAGGCACCTTACTGG
                          gtttaat  putative branch site (score: 4)
                                ttgtctttcccatctt  CT-rich tract
                ttttcaatttgtttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggtatttttcttttgtttctcttttccgtatagtggttcgttttcaatttgtttaattgtctttcccatcttattacagATTCTTCATGAGAACATATATCAAACCTTCCTTGATCAGCTTGTTGAGGTATACAAACAAGTCCGAATTGGGGATCCGTTGGAGAAAGGCACCTTACTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA