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

...gtgttggtctgactagttacatttttgtgtaattaattgtgttggtctgactagttacatttttgtgtaattaattgtttttcacttttctgggttgaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTCATTGCTCAATGCTTTATA

Basic information

species Zea mays
transcript GRMZM2G059381_T03
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G059381_T03 (Zea mays), 3'ss of exon 5
lower sequence: AT5G27600.1 (Arabidopsis thaliana), 3'ss of exon 18
gtgttggtctgactagttacatttttgtgtaattaattgtgttggtctgactagttacatttttgtgtaattaattgtttttcacttttctgggttgaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTCATTGCTCAATGCTTTATA
      || | |  | | | |   || |    ||| || | |   | ||   |   | |  ||    |  ||  |     |||| | | |    |   ||||| |||||||| || ||||| || ||||||||||| ||||| ||||||||||| || ||||| ||| | || || |  ||| || | || || || || 
------gttttataaatcaaaacattctt--gttatttctttc--tttgcggaagaaaaagttgaaatgtttgttaaaacttcaatgtgc---atgacagGAAGAAGAACATATTTAAGTTGGCGCAAGGAGAATATATAGCACCAGAGAAGATCGAAAATGTTTATACCAAATGTAGATTCGTTTCGCAGTGTTTCATT

upper sequence: GRMZM2G059381_T03 (Zea mays), 3'ss of exon 5
lower sequence: Vv14s0128g00720.t01 (Vitis vinifera), 3'ss of exon 18
gtgttggtctgactagttacatttttgtgtaattaattgtgttgg-tctgactagttacatttttgtgtaattaattgtttttcacttttctgggttga-agGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTCATTGCTCAATGCTTTATA
   ||| |   |  ||  || || |   |      |   ||     | | | |  | | ||||| || |  |||       || |           ||| |||||||||||||| |||||| | || || || ||||| ||||| |||||||| ||||||||||| ||||| |||||||| ||  || | ||||| ||||| 
-aattgcttacaaaagaaactttgtgaagagcaggaacatgccaactttaagttatgaaattttagtctc-ttagcgaaaattgatggccaacttatgacagGAAAAAGAACATCTTCAAGCTGGCACAGGGTGAATATATAGCACCAGAGAAAATTGAGAATGTATATGCCAAGTGCAAATTTGTTTCCCAATGTTTTATC

upper sequence: GRMZM2G059381_T03 (Zea mays), 3'ss of exon 5
lower sequence: Vv05s0020g03080.t01 (Vitis vinifera), 3'ss of exon 18
--------------------------------------------------------------------------------------------gtgttggtctgactagttacatttttgtgtaattaattgtgttggtctgactagttacatttttgtgtaattaatt-gtttttcacttttctgggttgaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTCATTGCTCAATGCTTTATA
                                                                                             | ||||||     | ||   | ||  | ||||  | | |  |    |   |  |||| | |   | |  |   || || ||  |  ||  |   |   ||||| ||||||||||| ||||| || |||||||| ||||||||||||||||| ||||||||||| |||||||| ||||| ||  |||| || |||||| ||
gtaaagaccatatcatttttgttgacagttcttagacgaattaataatgactcctctctagttttggatgactcaattgactgtatgttcatatcttggtcctgtgattttgttattgatataatcgactataattacatacttcattacctgtgcatttcttagctttgtattaaaagttgttatatgacagGAAGAAGAACATTTTTAAGTTGGCACAAGGAGAGTACATAGCTCCAGAGAAAATTGAGAATGTATATGCTAAATGCAAATTTGTTGCCCAGTGCTTTGTA

upper sequence: GRMZM2G059381_T03 (Zea mays), 3'ss of exon 5
lower sequence: PP1S408_23V6.1 (Physcomitrella patens), 3'ss of exon 20
-gtgttggtctgactagttacatttttgtgtaattaattgtgttggtctgactagttacatttttgtgtaattaattgtttt-tcacttttc-tgggttgaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTCATTGCTCAATGCTTTATA
 ||  ||    ||  | ||    ||||   |  | |    ||||      | |||| |  || |  | |   |  |||||   ||| |  ||     ||| ||||| ||||| || || ||||| ||||||||||| ||||| || || |||||||| |||||||||||   |    |    |||||  | || || |  |||
tgtcgtgagtggatcaatttagcttttactttttcaggaatgttcac--aagtagt-atgttctgttcttcgtgtttgttgagtcattcatcacacattgcagGAAGAAGAATATCTTTAAGTTGGCTCAAGGAGAGTACATTGCCCCGGAGAAGATCGAGAATGTCTACCTTCGCAGTCGTTTCATAACACAGTGTTACATA

upper sequence: GRMZM2G059381_T03 (Zea mays), 3'ss of exon 5
lower sequence: PP1S33_126V6.1 (Physcomitrella patens), 3'ss of exon 21
------------------------------------------------------------------------------gtgttggtctgacta-gttacatttttgtgtaattaattgtgttggtctgactagttacatttttg----tgtaattaattgtttttcacttttctgg--gttgaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTCATTGCTCAATGCTTTATA
                                                                              ||       ||| || |||  | | || |    ||    |  |   ||  |||    | ||||  |    | | || | ||||   |   ||   |||   ||| || || ||||| || |||||||| ||||| ||||| ||||| || || |||||||||||||| |||||        |   ||||||||| || |||||||| 
gtactctggactagcgtcacccttagatgtatgctattgatatttttcatcattcaacgtctggtagtctagatcagtgtacccagttgagtatgttctactcttctaatgttcgaag-atcaatccaactttgaatatttcaggagctttcatgagttgtacgttctttccttggttattgcagAAAGAAGAATATCTTCAAGTTGGCTCAGGGAGAGTACATTGCGCCCGAGAAGATTGAGAACGTCTACCTGCGAAGTCGGTTCATTGCACAGTGCTTTATT

upper sequence: GRMZM2G059381_T03 (Zea mays), 3'ss of exon 5
lower sequence: PP1S12_178V6.2 (Physcomitrella patens), 3'ss of exon 20
--gtgttggtctgactagttacatttttgtgtaattaattgtgttggtctgactagttacatttttgtgtaattaattgtttttcacttttctgggttgaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTCATTGCTCAATGCTTTATA
  || ||  |||     |  || | |   |  ||  |||| | | |   || |   |   ||  |  |||  |   |||| |       |    |  || ||||| ||||||||||||||||||||||||||||||||||| || || || |||||||||||  | |||  |    |   ||| ||| | || || ||  ||
aagttttattcttctctgaaac-tgtaactagaaaaaattatctggaagtggcagttcttatgctcatgtt-tgttttgtatcctttaatcactgtctgcagGAAGAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATTGCACCGGAAAAGATTGAGAACATTTATCTTCGCAGTCGGTTTATTTCGCAGTGTTTCGTA

upper sequence: GRMZM2G059381_T03 (Zea mays), 3'ss of exon 5
lower sequence: EFJ37488 (Selaginella moellendorffii), 3'ss of exon 19
gtgttggtctgactagttacatttttgtgtaattaattgtgttggtctgactagttacat-ttttgtgtaatt-aattgtttttcacttttctgggttgaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTCATTGCTCAATGCTTTATA
                                                     || || |  ||||||| |||  ||| |  || || |   |   |   ||||||||||||||||| ||| | || || || ||||||||||| ||||||||||||||||||||||||   ||  |||||||| ||||||| || ||  | 
-----------------------------------------------------gtaacgtgctttgtgtcattcgattttgcttgacgtcattttttgccagGAAAAAGAACATTTTTAAGCTTGCACAGGGTGAATACATAGCGCCAGAGAAGATTGAGAATGTCTATCAAAAAAGCAAGTTCGTTGCTCAGTGTTTCGTC

upper sequence: GRMZM2G059381_T03 (Zea mays), 3'ss of exon 5
lower sequence: EFJ33980 (Selaginella moellendorffii), 3'ss of exon 19
gtgttggtctgactagttacatttttgtgtaattaattgtgttggtctgactagttacat-ttttgtgtaatt-aattgtttttcacttttctgggttgaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTCATTGCTCAATGCTTTATA
                                                     || || |  ||||||| |||  ||| |  || || |   |   |   ||||||||||||||||| ||| | || || || ||||||||||| ||||||||||||||||||||||||  |||  |||||||| ||||||| || ||  | 
-----------------------------------------------------gtaacgtgctttgtgtcattcgattttgcttgacgtcattttttgccagGAAAAAGAACATTTTTAAGCTTGCACAGGGTGAATACATAGCGCCAGAGAAGATTGAGAATGTCTATCATAAAAGCAAGTTCGTTGCTCAGTGTTTCGTC

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|33090935|gb|CF050929.1|CF050929
EST:     GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAG                         GAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAA
genomic: GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAGgtaaagctga ... tgggttgaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAA
EST: gi|87153602|gb|DY398391.1|DY398391
EST:     GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAG                         GAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAA
genomic: GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAGgtaaagctga ... tgggttgaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAA
EST: gi|19350747|gb|BM895279.1|BM895279
EST:     GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAG                         GAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAA
genomic: GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAGgtaaagctga ... tgggttgaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAA
EST: gi|60395514|gb|DN228384.1|DN228384
EST:     GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAG                         GAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAA
genomic: GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAGgtaaagctga ... tgggttgaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAA
EST: gi|58030032|gb|CX725459.1|CX725459
EST:     GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAG                         GAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAA
genomic: GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAGgtaaagctga ... tgggttgaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAA
EST: gi|93283329|gb|EB675593.1|EB675593
EST:     GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAG                         GAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAA
genomic: GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAGgtaaagctga ... tgggttgaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAA
EST: gi|32847207|gb|CD986888.1|CD986888
EST:     GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAG                         GAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAA
genomic: GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAGgtaaagctga ... tgggttgaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAA
EST: gi|211308069|gb|FL216534.1|FL216534
EST:     GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAG                         GAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAA
genomic: GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAGgtaaagctga ... tgggttgaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgactagttacatttttgtgtaattaattgtttttcacttttctgggttgaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTCATTGCTCAATGCTTTATA
                       aattaat  putative branch site (score: 3)
                             ttgtttttcacttttc  CT-rich tract
         ttacatttttgtgtaa  TA-rich tract