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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacccgctatgaaacattcccttttagtgcaccttggcaacactaatgtattactcacatgcaactgttgacttttaaaaaactcccctactttctttgtgctatgtaagaatttaatgcaatagtggcttaagaagggataactgcatttacacacttaactgttcctctggtggctgcagTGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCATTTTCTCTTTGTTTAACACAGAAGCATTTCTCTCAAGTTGCATCAGCATA

Basic information

species Zea mays
transcript GRMZM2G047564_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047564_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os06g39344.3 (Oryza sativa), 3'ss of exon 6
gtacccgctatgaaacattcccttttagtgcaccttggcaacactaatgtattactcacatgcaactgttgacttttaaaaaactcccctactttctttgtgctatgtaagaatttaatgcaatagtggcttaagaagggataactgcatttacacacttaactgttcctctggtggctgcagTGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCATTTTCTCTTTGTTTAACACAGAAGCATTTCTCTCAAGTTGCATCAGCATA
                           || | |       |  |||| |  | |     |||    | |  | || |  | || | ||  ||  | ||| |    ||  |   ||| ||  | |    | |||  |  |  ||  ||||  |  |  |||      | |  || || |||||||||||||||||||||| || || || |||||| |  | ||||| |||||||||||||| |||||||| || || ||||| ||||||||||||||||||||
---------------------------gtactctgcttttaagctaaggcgtcaagagaatgttgttat--atttatgcacaagtgcca-acagtgtttctatattgagaccgttttataaatt--cagtttagtactgactagttgcacgtgtatcctt------ttcattgttgtctgcagTGGCAGAATGGGCCAACGAGGCCTTGGCAGGACTCAAAAAAGGGGCTCCATTTTCTCTATGTTTAACTCAAAAACATTTTTCTCAAGTTGCATCAGCATA

upper sequence: GRMZM2G047564_T02 (Zea mays), 3'ss of exon 7
lower sequence: Vv11s0016g04290.t01 (Vitis vinifera), 3'ss of exon 9
gtacccgctatgaaacattcccttttagtgcaccttggcaacactaatgtattactcacatg-caactgttgacttttaaaaaactcccctactttctttgtgctatgtaagaatttaatgcaatagtggcttaagaagggataactgcatttacacacttaactgttcctctggtggctg-cagTGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCATTTTCTCTTTGTTTAACACAGAAGCATTTCTCTCAAGTTGCATCAGCATA
                         ||    || ||    |||| | | | ||  |   |   || ||     | ||  | |   || ||||||   | |  |  ||||  | || || | |     | |||| ||      | | | |||  |     || | ||    | |         ||||| |||| ||||| || |||||  |   |||  |||  || || ||||| |||||||||||||||||||| |||||||||||   |||||| |  |||  
------------------------gtaagctacttt----acaccattctttttatggtagatcagctcggtgccttggacatcttctcctactcaatcta-gtaatgttggcatctagttc-----ttgcttcagc-----tcatttcatccatcattttgattgccattgtttccatgaacagTGTCAGAGTGGGCTAAGGAAGCCCTTTTAGGTCTTGGAAAGGGGGCTCCTTTTTCTCTTTGTTTAACACAAAAGCATTTCTCCAGAGTTGCTTTGGCACG
















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|37379970|gb|CF626760.1|CF626760
EST:     TGAATCTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAG                         TGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT
genomic: TGAATCTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAGgtacccgcta ... gtggctgcagTGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT
EST: gi|76012489|gb|DT939659.1|DT939659
EST:     CTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAG                         TGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT
genomic: CTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAGgtacccgcta ... gtggctgcagTGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT
EST: gi|91873503|gb|EB403460.1|EB403460
EST:     TGAATCTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAG                         TGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT
genomic: TGAATCTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAGgtacccgcta ... gtggctgcagTGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT
EST: gi|18166670|gb|BM336509.1|BM336509
EST:     GCTAAAGAAATGTAGCCGAAGTGGTGATGCTCCAG                         TGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT
genomic: GCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAGgtacccgcta ... gtggctgcagTGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT
EST: gi|88750160|gb|DY534301.1|DY534301
EST:     TGAATTTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAG                         TGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT
genomic: TGAATCTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAGgtacccgcta ... gtggctgcagTGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT
EST: gi|60345004|gb|DN211977.1|DN211977
EST:     TGAATCTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAG                         TGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT
genomic: TGAATCTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAGgtacccgcta ... gtggctgcagTGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT
EST: gi|149097994|gb|EE183939.2|EE183939
EST:     TGAATCTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAG                         TGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT
genomic: TGAATCTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAGgtacccgcta ... gtggctgcagTGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT
EST: gi|211171388|gb|FL176740.1|FL176740
EST:     TGAATCTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAG                         TGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT
genomic: TGAATCTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAGgtacccgcta ... gtggctgcagTGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT
EST: gi|76012490|gb|DT939660.1|DT939660
EST:     GTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAG                         TGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT
genomic: GTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAGgtacccgcta ... gtggctgcagTGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT
EST: gi|18165516|gb|BM335355.1|BM335355
EST:     TGAATCTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAG                         TGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT
genomic: TGAATCTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAGgtacccgcta ... gtggctgcagTGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT
EST: gi|60399515|gb|DN232327.1|DN232327
EST:     AATCTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAG                         TGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT
genomic: AATCTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAGgtacccgcta ... gtggctgcagTGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT
EST: gi|211528664|gb|FL445658.1|FL445658
EST:     TGAATCTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAG                         TGGCAGAATGGGCCATTGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT
genomic: TGAATCTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAGgtacccgcta ... gtggctgcagTGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT
EST: gi|88749306|gb|DY533447.1|DY533447
EST:     TGAATCTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAG                         TGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT
genomic: TGAATCTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAGgtacccgcta ... gtggctgcagTGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttaagaagggataactgcatttacacacttaactgttcctctggtggctgcagTGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCATTTTCTCTTTGTTTAACACAGAAGCATTTCTCTCAAGTTGCATCAGCATA
                            acttaac  putative branch site (score: 3)
                    atttaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacccgctatgaaacattcccttttagtgcaccttggcaacactaatgtattactcacatgcaactgttgacttttaaaaaactcccctactttctttgtgctatgtaagaatttaatgcaatagtggcttaagaagggataactgcatttacacacttaactgttcctctggtggctgcagTGGCAGAATGGGCCAATGAAGCTTTAGCAGGAATTGAGAAAGGCGCTCCATTTTCTCTTTGTTTAACACAGAAGCATTTCTCTCAAGTTGCATCAGCATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC