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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgaacttaagcaattactgatagaacaatctgagagaagatgtaatttgacttactttttcaatgctgaatttaacagAAATTGAGTATATTGCCAAGGTCAGGAGGTGCATTAGGCTTTACATACACCCCTCCCACCACAGAGGATAGATATTTACTCTTTGTTGATGAACTACGTG

Basic information

species Zea mays
transcript GRMZM2G163193_T03
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G163193_T03 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os02g43350.1 (Oryza sativa), 3'ss of exon 10
gtttgaacttaagcaattactgatagaacaatctgagagaagatgtaatttgacttactttttcaatgctgaattt------aacagAAATTGAGTATATTGCCAAGGTCAGGAGGTGCATTAGGCTTTACATACACCCCTCCCACCACAGAGGATAGATATTTACTCTTTGTTGATGAACTACGTG
||||||||  |||||| ||  ||||||||| | | ||| ||  |     |||   |    ||| | || ||   ||      | ||||||||||||||||||||||||||||| |||||||| ||||||||||||||||||||||| ||||| ||||||||||| ||||||||||||||||| ||||
gtttgaacgcaagcaactatcgatagaacagtttaagaaaatgttcgtcttgggcttacattttagtgttgttcttttttccaccagAAATTGAGTATATTGCCAAGGTCAGGTGGTGCATTGGGCTTTACATACACCCCTCCCACAACAGAAGATAGATATTTGCTCTTTGTTGATGAACTGCGTG

upper sequence: GRMZM2G163193_T03 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA18G07280.1 (Glycine max), 3'ss of exon 10
-------gtttgaacttaagcaattactg-atagaacaatctgagagaagatgtaattt------gacttactttttcaat--gctgaattt---aacagAAATTGAGTATATTGCCAAGGTCAGGAGGTGCATTAGGCTTTACATACACCCCTCCCACCACAGAGGATAGATATTTACTCTTTGTTGATGAACTACGTG
         ||| |  |  | |||  ||   | | |||   | ||     |  || |||      || | | |   | |||  | ||  |||   | |||||| | ||||||||||||||||||||||| || || |||||||| || |  ||||| || || ||||||||||| || || ||||| |||||  | | ||
gtatataagttgtatcttggaaatctctatgttgcacatcattagtccttaaatactttaaggatgattcaatgccttaatatgttgtgtttgtcatcagAAACTAAGTATATTGCCAAGGTCAGGAGGGGCTTTGGGCTTTACTTATATTCCTCCAACAACTGAGGATAGATACTTGCTATTTGTCGATGAGTTGCATG

upper sequence: GRMZM2G163193_T03 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA0028S00210.1 (Glycine max), 3'ss of exon 10
-------gtttgaacttaagcaattactg-atagaacaatctgagagaagatgtaattt------gacttactttttcaatgc--tgaattt---aacagAAATTGAGTATATTGCCAAGGTCAGGAGGTGCATTAGGCTTTACATACACCCCTCCCACCACAGAGGATAGATATTTACTCTTTGTTGATGAACTACGTG
         ||| |  |  | |||  ||   | | ||| | | ||     |  || |||      || | | |   | |||    ||  |||   | |||||| | ||||||||||||||||||||||| || || |||||||| || |  ||||| || || ||||||||||| || || ||||| |||||  | | ||
gtatataagttgtatcttggaaatctctatgttgcacattattagtccttaaatactttaaggatgattcagtgccttaatatcttgtgtttgtcatcagAAACTAAGTATATTGCCAAGGTCAGGAGGGGCTTTGGGCTTTACTTATATTCCTCCAACAACTGAGGATAGATACTTGCTATTTGTCGATGAGTTGCATG

upper sequence: GRMZM2G163193_T03 (Zea mays), 3'ss of exon 9
lower sequence: AT5G58870.1 (Arabidopsis thaliana), 3'ss of exon 10
gtttgaacttaagcaattactgatag---aacaatctgagagaagatgtaatttgacttactttttcaatgctgaatttaacagAAATTGAGTATATTGCCAAGGTCAGGAGGTGCATTAGGCTTTACATACACCCCTCCCACCACAGAGGATAGATATTTACTCTTTGTTGATGAACTACGTG
  |  | |      ||   |   | |    | | ||       | ||||  |    ||    |  |  ||  || ||||   ||||||| || ||||| ||||| |||||||| ||||| |||||||||||||  || || ||    || || |||||||| |||||| |||||||||||| ||
-gtaaagcagtgagaaccgcatgttgcttgatactcattttttacatgtgttaatgctctgctaatacatattgtatttt-tagAAATTAAGCATATTACCAAGATCAGGAGGGGCATTGGGCTTTACATACATTCCCCCAACGCATGAAGACAGATATTTGCTCTTTATTGATGAACTACATG

upper sequence: GRMZM2G163193_T03 (Zea mays), 3'ss of exon 9
lower sequence: AT3G47060.1 (Arabidopsis thaliana), 3'ss of exon 10
------------------gtttgaacttaagcaattactgatagaacaatctgagagaag-atgtaatttgacttactttttcaatgctgaatttaacagAAATTGAGTATATTGCCAAGGTCAGGAGGTGCATTAGGCTTTACATACACCCCTCCCACCACAGAGGATAGATATTTACTCTTTGTTGATGAACTACGTG
                  || |  | ||| ||  | | || |       | |   |   | |  | |||  | ||    |     |  ||   ||  |||||||| || |||||||||||  ||||||| ||||| || ||||||||||  ||||| || |  || || ||||||||||||||  ||||||| || | ||
gtaaaatgcaaaaactttgtctacatttacgc--tcattgtttatgttgtttagtacgtgcaaatgattcaagttttgctcatctttgtggtgttgtcagAAATTAAGCATATTGCCAAGAACAGGAGGGGCATTGGGATTTACATACATTCCTCCTACTAGTGAAGACAGATATTTACTCTTCATTGATGAGCTGCTTG

upper sequence: GRMZM2G163193_T03 (Zea mays), 3'ss of exon 9
lower sequence: Vv06s0004g06120.t01 (Vitis vinifera), 3'ss of exon 10
--------------------gtttgaacttaagcaattactgatagaacaatctgagagaagatgtaatttgacttactttttcaatgctgaatttaacagAAATTGAGTATATTGCCAAGGTCAGGAGGTGCATTAGGCTTTACATACACCCCTCCCACCACAGAGGATAGATATTTACTCTTTGTTGATGAACTACGTG
                       || |   | ||  |  |   |  ||   || | |  |   |  |   |    | || | |  ||  ||  || | ||||| ||||| ||||||||||| |||||||| ||||| || |||||||| || ||||||||||  ||||| |||||||| || ||  |||||||  ||||||
tactaggatgtgagtccatcacatgcatacatgctttgtcattttaaatcgtccgcgtaacattagatggtccaatgctatctgtattttgtgttca-cagAAGTTGAGCATATTGCCAAGATCAGGAGGGGCATTGGGTTTTACATATACTCCTCCCACCAATGAGGACAGATATTTGCTGTTCATTGATGAGTTACGTG

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|67033989|gb|CO462738.1|CO462738
EST:     TCGTGGGAACTGCTGTAGCGAACCTTCTTCCTGGACAGCCACGTGTTGAG                         AAATTGAGTATATTGCCAAGGTCAGGAGGTGCATTAGGCTTTACATACACC
genomic: TCGTGGGAACTGCTGTAGCGAACCTTCTTCCTGGACAGCCACGTGTTGAGgtttgaactt ... aatttaacagAAATTGAGTATATTGCCAAGGTCAGGAGGTGCATTAGGCTTTACATACACC
EST: gi|32823635|gb|CD963357.1|CD963357
EST:     TCGTGGGAACTGCTGTAGCGAACCTTCTTCCTGGACAGCCACGTGTTGAG                         AAATTGAGTATATTGCCAAGGTCAGGAGGTGCATTAGGCTTTACATACACC
genomic: TCGTGGGAACTGCTGTAGCGAACCTTCTTCCTGGACAGCCACGTGTTGAGgtttgaactt ... aatttaacagAAATTGAGTATATTGCCAAGGTCAGGAGGTGCATTAGGCTTTACATACACC
EST: gi|71329683|gb|DR801566.1|DR801566
EST:     TCGTGGGAACTGCTGTAGCGAACCTTCTTCCTGGACAGCCACGTGTTGAG                         AAATTGAGTATATTGCCAAGGTCAGGAGGTGCATTAGGCTTTACATACACC
genomic: TCGTGGGAACTGCTGTAGCGAACCTTCTTCCTGGACAGCCACGTGTTGAGgtttgaactt ... aatttaacagAAATTGAGTATATTGCCAAGGTCAGGAGGTGCATTAGGCTTTACATACACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacaatctgagagaagatgtaatttgacttactttttcaatgctgaatttaacagAAATTGAGTATATTGCCAAGGTCAGGAGGTGCATTAGGCTTTACATACACCCCTCCCACCACAGAGGATAGATATTTACTCTTTGTTGATGAACTACGTG
                         gacttac  putative branch site (score: 2)
                atgtaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgaacttaagcaattactgatagaacaatctgagagaagatgtaatttgacttactttttcaatgctgaatttaacagAAATTGAGTATATTGCCAAGGTCAGGAGGTGCATTAGGCTTTACATACACCCCTCCCACCACAGAGGATAGATATTTACTCTTTGTTGATGAACTACGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT