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'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   		25  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggcttctgcaattgaatgcatcttgccctactcagtaacatcttgtatcggacattgtatgttgacaattggtcctttgctgtacagTAATCGTATTCCAGAAGCAGCACTGATGGCACGATCTTACCTTCCAAGCAAAGTTTCTGATATTGTCTCAATATGGAAAAAGGACCTCCAAAAG

Basic information

species Zea mays
transcript GRMZM2G443953_T03
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G443953_T01 (Zea mays), 3'ss of exon 21
lower sequence: AT3G15980.3 (Arabidopsis thaliana), 3'ss of exon 20
gtaggcttctgcaattgaatgcatcttgccctactcagtaacatcttgtatcggacattg--tatgttgacaattggtcctttgctgtacagTAATCGTATTCCAGAAGCAGCACTGATGGCACGATCTTACCTTCCAAGCAAAGTTTCTGATATTGTCTCAATATGGAAAAAGGACCTCCAAAAG
   |  ||     | ||  | ||  | ||| |  |  | || |||   |||  | | ||   ||| || |  |   |   ||  ||  ||||||| || || |||||||| || ||||||||||| ||||| ||||||||||||||||| || || ||  |  ||||||   | || |||   |||
---gtatttcattactg--ttcacttggccgt--ttggaaaaatcaaatatgtgtcttttgttatctttatgacaagaaattatcttgacagTAACCGGATACCAGAAGCTGCTCTGATGGCACGTTCTTATCTTCCAAGCAAAGTTTCGGAGATAGTAGCTCTATGGAGGGAAGATCTCAGCAAG

upper sequence: GRMZM2G443953_T01 (Zea mays), 3'ss of exon 21
lower sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 20
gtaggcttctgcaattgaatgcatcttgccctactcagtaacatct-tgtatcggacattgtatgt-tgacaattggtcctttgctgtacagTAATCGTATTCCAGAAGCAGCACTGATGGCACGATCTTACCTTCCAAGCAAAGTTTCTGATATTGTCTCAATATGGAAAAAGGACCTCCAAAAG
   |   |     | |     | |       |    | | | || | || | |     ||   ||| |||||||   |  ||| ||   |||||| || || |||||||| || |||||||||||||| || ||||| |||||||||||||| || ||  |  | ||||  || || |||   |||
---gtaattcattagtagtcacttgagagtttggaaaatcaaatttatgcacctttggttaactgtgtgacaat--attttttcct---cagTAACCGGATACCAGAAGCTGCTCTGATGGCACGATCATATCTTCCGAGCAAAGTTTCTGAGATAGTAGCTCTTTGGAGGAAAGATCTCAGCAAG

upper sequence: GRMZM2G443953_T01 (Zea mays), 3'ss of exon 21
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 20
-------------------------------------------------------------gtaggcttctgcaattgaatgcatcttgccctactcagtaacat----cttgtatcggacattgtatgttgacaattggtcctttg------ctgt-acagTAATCGTATTCCAGAAGCAGCACTGATGGCACGATCTTACCTTCCAAGCAAAGTTTCTGATATTGTCTCAATATGGAAAAAGGACCTCCAAAAG
                                                              |   ||| |   ||| ||   |   |    |  |   | | ||    |  | |   || ||||  | ||    ||| | |  |        ||||  ||||||||| || || ||||| ||  | |||||||||||||||||||||||||| ||| | || ||  || | || |||| ||| |||||| | |||
gtaatcattttccttaccatataaccatagaaaatcaactgctgatactaatttattacacatttacttatttcatttaacagacaatatggtggtagtttatatgacccaggaagttgagattgagt-ttactgattagactctgatatggtctgttgcagTAATCGGATACCTGAAGCTGCTTTAATGGCACGATCTTACCTTCCAAGCAAGGTTCCAGAGATAATCACGATTTGGAGAAATGACCTCAACAAG

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|91873400|gb|EB403357.1|EB403357
EST:     TTGTTTATGTTAGGCAAATTGGAAGAATGTCTTCAATTGTTGGTTGATAG                         TAATCGTATTCCAGAAGCAGCACTGATGGCACGATCTTACCTTCCAAGCAA
genomic: TTGTTTATGTTAGGCAAATTGGAAGAATGTCTTCAATTGTTGGTTGATAGgtaggcttct ... tgctgtacagTAATCGTATTCCAGAAGCAGCACTGATGGCACGATCTTACCTTCCAAGCAA
EST: gi|26557066|gb|CA829301.1|CA829301
EST:     TTGTTTATGTTAGGCAAATTGGAAGAATGTCTTCAATTGTTGGTTGATAG                         TAATCGTATTCCAGAAGCAGCGCTGATGGCACGATCTTACCTTCCAAGCAA
genomic: TTGTTTATGTTAGGCAAATTGGAAGAATGTCTTCAATTGTTGGTTGATAGgtaggcttct ... tgctgtacagTAATCGTATTCCAGAAGCAGCACTGATGGCACGATCTTACCTTCCAAGCAA
EST: gi|6227172|gb|AW155701.1|AW155701
EST:     TTGTTTATGTTAGGCAAATTGGAAGAATGTCTTCAATTGTTGGTTGATAG                         TAATCGTATTCCAGAAGCAGCACTGATGGCACGATCTTACCTTCCAAGCAA
genomic: TTGTTTATGTTAGGCAAATTGGAAGAATGTCTTCAATTGTTGGTTGATAGgtaggcttct ... tgctgtacagTAATCGTATTCCAGAAGCAGCACTGATGGCACGATCTTACCTTCCAAGCAA
EST: gi|78116813|gb|DV535200.1|DV535200
EST:     TTGTTTATGTTAGGCAAATTGGAAGAATGTCTTCAATTGTTGGTTGATAG                         TAATCGTATTCCAGAAGCAGCACTGATGGCACGATCTTACCTTCCAAGCAA
genomic: TTGTTTATGTTAGGCAAATTGGAAGAATGTCTTCAATTGTTGGTTGATAGgtaggcttct ... tgctgtacagTAATCGTATTCCAGAAGCAGCACTGATGGCACGATCTTACCTTCCAAGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagtaacatcttgtatcggacattgtatgttgacaattggtcctttgctgtacagTAATCGTATTCCAGAAGCAGCACTGATGGCACGATCTTACCTTCCAAGCAAAGTTTCTGATATTGTCTCAATATGGAAAAAGGACCTCCAAAAG
                                        tcctttgct  CT-rich tract
                     attgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggcttctgcaattgaatgcatcttgccctactcagtaacatcttgtatcggacattgtatgttgacaattggtcctttgctgtacagTAATCGTATTCCAGAAGCAGCACTGATGGCACGATCTTACCTTCCAAGCAAAGTTTCTGATATTGTCTCAATATGGAAAAAGGACCTCCAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG