Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacttatttttcactgaatttattatggcaattgtgaaacctgttctcatttggaatttcaccaattggtcttgacgtaacacactatcttggttgcagACAGATTTACCAGTTCGAGAAAAAATATTTCTTCTGTTAGATGCAACACAAACATCCCTTGGTGGAGCTAAAGAAAGGTTCCCTCAGTACTATGAGGCAT

Basic information

species Zea mays
transcript GRMZM2G123607_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G123607_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os08g01740.2 (Oryza sativa), 3'ss of exon 4
gtaacttatttttcactgaatttattatggcaattgtgaaacctgttctcatttggaatttcaccaattggtcttgacgtaacacactatcttggttgcagACAGATTTACCAGTTCGAGAAAAAATATTTCTTCTGTTAGATGCAACACAAACATCCCTTGGTGGAGCTAAAGAAAGGTTCCCTCAGTACTATGAGGCAT
|| | || || |    |   |||    ||| | |||                  ||||  |     |  | | ||||| ||||| |||||||   || |||||||| ||||||||||| ||||||||||||||| || | ||||| || ||||||||||||||||||| |||||  |  |||||||||||||||| |||||
gtgatttgttctcttttctttttccc-tggaagttgga----------------ggaaggttgttga--gatgttgacttaacatactatctgtatttcagACAGAATTACCAGTTCGTGAAAAAATATTTCTTTTGCTGGATGCGACCCAAACATCCCTTGGTGGAGTTAAAGGGAAATTCCCTCAGTACTATGGGGCAT

upper sequence: GRMZM2G123607_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA05G33150.1 (Glycine max), 3'ss of exon 5
gtaacttatttttcactgaatttattatggcaattgtgaaacctgttctcatttggaatttcaccaattgg-tcttgacgtaacacactatcttggt-tgcagACAGATTTACCAGTTCGAGAAAAAATATTTCTTCTGTTAGATGCAACACAAACATCCCTTGGTGGAGCTAAAGAAAGGTTCCCTCAGTACTATGAGGCAT
|| | || || | |||      |||| |  |  | |  ||     || ||||||    ||||   ||| |  |||     |       |  |||||  ||||| ||||||| || ||  | ||    |||||||| || |||||||| |||||||||||||||||||| |||   | || ||| || ||||| ||| | ||||
gtgagtttttctccacactgactattgtt-ctttagcaaagttatttttcattt----tttccttaatcgtctctctctctcttttttttccttggcatgcagTCAGATTTGCCTGTAAGGGAGCGGATATTTCTCCTATTAGATGCCACACAAACATCCCTTGGTGGTGCTTCTGGAAAGTTTCCACAGTATTATAATGCAT

upper sequence: GRMZM2G123607_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA06G16740.1 (Glycine max), 3'ss of exon 5
gtaacttatttttcactgaatttattatggcaattgtgaaacctgttctcatttggaatttcaccaattggtcttgacgtaacacactatcttggttgcagACAGATTTACCAGTTCGAGAAAAAATATTTCTTCTGTTAGATGCAACACAAACATCCCTTGGTGGAGCTAAAGAAAGGTTCCCTCAGTACTATGAGGCAT
|| | || || | |||  |   |  | |     | |      | ||| |  ||   ||  ||||   ||  |  |  ||        |   |||||||||| | ||||| || ||  | ||    |||||||| ||  ||||||| |||||||||||||||||||| ||    | || ||| || ||||| ||| | ||||
gtgagtt-ttctccacaaagacttctgttatt-tagcattgtcagtttttctt---aacctcacttttttattctctcg--------ttctttggttgcagTCTGATTTGCCTGTGAGGGAGCGGATATTTCTCCTACTAGATGCCACACAAACATCCCTTGGTGGTGCATCTGGAAAGTTTCCACAGTATTATAATGCAT

upper sequence: GRMZM2G123607_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv07s0031g03190.t01 (Vitis vinifera), 3'ss of exon 3
gtaacttatttttcactgaatttattatggcaattgtgaaacctgttctcatttggaatttcaccaattggtcttgacgtaacacactatcttggttgcagACAGATTTACCAGTTCGAGAAAAAATATTTCTTCTGTTAGATGCAACACAAACATCCCTTGGTGGAGCTAAAGAAAGGTTCCCTCAGTACTATGAGGCAT
                 |  ||| ||    |||       |  | |   ||||     |||    | |||    | |  |  |  |   | |   |  |||||||| || || || ||||| || ||||||||||| |||||||| ||||| ||||| ||||||||||||   | || ||||||||| |||||    ||||
-----------------gtgtttttttccccaagaacatgatttctggccattaactgtttt--tagttgaagctaaatttgcttatcttttctctcacagACAGACTTGCCCGTACGAGAGAAGATATTTCTTCTTTTAGATGCCACACAGACATCACTTGGTGGAGCTTCTGCAAAGTTCCCTCAATACTACAGTGCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcatttggaatttcaccaattggtcttgacgtaacacactatcttggttgcagACAGATTTACCAGTTCGAGAAAAAATATTTCTTCTGTTAGATGCAACACAAACATCCCTTGGTGGAGCTAAAGAAAGGTTCCCTCAGTACTATGAGGCAT
                              acgtaac  putative branch site (score: 3)
                                        ctatctt  putative PPT
          aatttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacttatttttcactgaatttattatggcaattgtgaaacctgttctcatttggaatttcaccaattggtcttgacgtaacacactatcttggttgcagACAGATTTACCAGTTCGAGAAAAAATATTTCTTCTGTTAGATGCAACACAAACATCCCTTGGTGGAGCTAAAGAAAGGTTCCCTCAGTACTATGAGGCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA