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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttcacgctagacactatttgaggtagagggaaaagaatgactctgctttgactctgtttcaaactatggctatctgttgggcgttgtcagGGTGAAAAGGATGACAAGATAATAGCAGTCTGTGCTGATGATCCTGAATATCGTCACTACAACGACATCAGTGAGCTGTCTCCTCATCGCCTGCAAGAGA

Basic information

species Zea mays
transcript GRMZM2G061928_T04
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G061928_T04 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os04g59040.3 (Oryza sativa), 3'ss of exon 6
--gtatttcacgctagacactatttgaggtagagggaaaagaatgactctgctttgactct----gtttcaaactatggctatc-----tgttgggcgttgt---cagGGTGAAAAGGATGACAAGATAATAGCAGTCTGTGCTGATGATCCTGAATATCGTCACTACAACGACATCAGTGAGCTGTCTCCTCATCGCCTGCAAGAGA
   |||||    ||     || ||||  | | ||||||||  |       |  || |||||    ||||     | |   ||       | ||||   ||||   |||||||| ||||||||||||||||||||||| |||||||||||||||||||| ||||| ||||| ||||||||||||||||||||||| ||||| |||||||
gtatattttctactg--ttctgtttgtagcaaagggaaaaagacctgcacgggttcactctttttgttttgttttttttttactgacgatattggattttgtgatcagGGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATACCGTCATTACAATGACATCAGTGAGCTGTCTCCTCACCGCCTCCAAGAGA

upper sequence: GRMZM2G061928_T04 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os04g59040.2 (Oryza sativa), 3'ss of exon 5
gtatttcacgctagacactatttgaggtagagggaaaagaatgactctgctttgactc----tgtttcaaactatggctatc-----tgttgggcgttg---tcagGGTGAAAAGGATGACAAGATAATAGCAGTCTGTGCTGATGATCCTGAATATCGTCACTACAACGACATCAGTGAGCTGTCTCCTCATCGCCTGCAAGAGA
    ||    ||     || ||||  | | ||||||||  |       |  || ||||    |||||     | |   ||       | ||||   |||   ||||||||| ||||||||||||||||||||||| |||||||||||||||||||| ||||| ||||| ||||||||||||||||||||||| ||||| |||||||
----tttctactg--ttctgtttgtagcaaagggaaaaagacctgcacgggttcactctttttgttttgttttttttttactgacgatattggattttgtgatcagGGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATACCGTCATTACAATGACATCAGTGAGCTGTCTCCTCACCGCCTCCAAGAGA

upper sequence: GRMZM2G061928_T04 (Zea mays), 3'ss of exon 6
lower sequence: AT1G01050.1 (Arabidopsis thaliana), 3'ss of exon 6
--------------------gtatttcacgctagacactatttgaggtagagggaaaagaatgactctgctttgactctgtttcaaactatggctatctgttgggcgttgt-----cagGGTGAAAAGGATGACAAGATAATAGCAGTCTGTGCTGATGATCCTGAATATCGTCACTACAACGACATCAGTGAGCTGTCTCCTCATCGCCTGCAAGAGA
                     |           |    | |||    |      ||     |   || | ||  |   | ||  |  | |    | | | || |||| |||      |||||||||| ||||||||||| || ||||| |||| ||||||||||||||||   |||||||  |||||||  || ||  ||||||| || ||    || |
gtaaaacctaaacttgatcaatgaaaagactctgttttttttttctcttactctaatcctttaggtcagtttaaatggtcttgtactccaatcttgtatttttggcgctgtaattttagGGTGAAAAAGATGACAAGATCATTGCAGTGTGTGTTGATGATCCTGAATATAAGCACTACACTGACATCAAAGAACTTCCTCCTCACCGTCTCTCTGAAA

upper sequence: GRMZM2G061928_T04 (Zea mays), 3'ss of exon 6
lower sequence: AT4G01480.1 (Arabidopsis thaliana), 3'ss of exon 6
---gtatttcacgctagacactatttgaggtagagggaaaagaatgactctgctttgactctgtttcaaactatggctatctgttgggcgttgtcagGGTGAAAAGGATGACAAGATAATAGCAGTCTGTGCTGATGATCCTGAATATCGTCACTACAACGACATCAGTGAGCTGTCTCCTCATCGCCTGCAAGAGA
     ||   | |||  |   | ||   | |     |      | |  | ||     | | |   | |  || |||   | || | |   |    |||||||||| ||||||||||| || ||||| |||| |||||||||||| |||   |||  ||   |||||| ||| ||  |||||||||| ||    || |
gtaacatcctaagcttta-gtttttcatgtttccttgtgcttcaagtttgtgtaaccattgtagctaattctttggggttttggttgaaataa--agGGTGAAAAAGATGACAAGATCATTGCAGTTTGTGTTGATGATCCTGAGTATAAGCACATCACTAACATCAATGAACTTCCTCCTCATCGTCTTTCTGAAA

upper sequence: GRMZM2G061928_T04 (Zea mays), 3'ss of exon 6
lower sequence: PP1S46_53V6.1 (Physcomitrella patens), 3'ss of exon 7
------------------------------gtatttcacgctagacactatttgaggtagagggaaaaga---atgactctgctttgactctgtttcaaactatggcta--tctgttgggcgttgtcagGGTGAAAAGGATGACAAGATAATAGCAGTCTGTGCTGATGATCCTGAATATCGTCACTACAACGACATCAGTGAGCTGTCTCCTCATCGCCTGCAAGAGA
                              | |   ||  ||||    ||||     |      | |       |  ||   | |  ||| | | | || |||  | ||  | |||  ||   ||| |||| || |||||||||||||| || || ||||||||||| ||||| || ||| | |||| ||| ||||||| |||| |  |||| ||||| ||    || |
gtgagggactattatgccgtactctttgacggaaaccaaactagcttgtattgatcatgttctcatattgttcgtacctaatcatccactatatgtaaatctaatgttaaatttgtaaggacctgt-agGGAGAGAAGGATGACAAGATCATCGCTGTCTGTGCTGACGATCCGGAGTATAGACACTTCAAAGACATCAATGAGTTTCCTCCACATCGACTTGCCGAAA

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|31909409|gb|CD650904.1|CD650904
EST:     GTTCGTTCCTGCGAGCAAGAGCAATCGGCCTTATGCCCATGATTGACCAG                         GGTGAAAAGGATGACAAGATAATAGCAGTCTGTGCTGATGATCCTGAATAT
genomic: GTTCGTTCCTGCGAGCAAGAGCAATCGGCCTTATGCCCATGATTGACCAGgtatttcacg ... gcgttgtcagGGTGAAAAGGATGACAAGATAATAGCAGTCTGTGCTGATGATCCTGAATAT
EST: gi|211146692|gb|FK994974.1|FK994974
EST:     GTTCGTTCCTGCGAGCAAGAGCAATCGGCCTTATGCCCATGATTGACCAG                         GGTGAAAAGGATGACAAGATAATAGCAGTCTGTGCTGATGATCCTGAATAT
genomic: GTTCGTTCCTGCGAGCAAGAGCAATCGGCCTTATGCCCATGATTGACCAGgtatttcacg ... gcgttgtcagGGTGAAAAGGATGACAAGATAATAGCAGTCTGTGCTGATGATCCTGAATAT
EST: gi|211145267|gb|FK994967.1|FK994967
EST:     GTTCGTTCCTGCGAGCAAGAGCAATCGGCCTTATGCCCATGATTGACCAG                         GGTGAAAAGGATGACAAGATAATAGCAGTCTGTGCTGATGATCCTGAATAT
genomic: GTTCGTTCCTGCGAGCAAGAGCAATCGGCCTTATGCCCATGATTGACCAGgtatttcacg ... gcgttgtcagGGTGAAAAGGATGACAAGATAATAGCAGTCTGTGCTGATGATCCTGAATAT
EST: gi|211091461|gb|FK999164.1|FK999164
EST:     GTTCGTTCCTGCGAGCAAGAGCAATCGGCCTTATGCCCATGATTGACCAG                         GGTGAAAAGGATGACAAGATAATAGCAGTCTGTGCTGATGATCCTGAATAT
genomic: GTTCGTTCCTGCGAGCAAGAGCAATCGGCCTTATGCCCATGATTGACCAGgtatttcacg ... gcgttgtcagGGTGAAAAGGATGACAAGATAATAGCAGTCTGTGCTGATGATCCTGAATAT
EST: gi|211145265|gb|FK994965.1|FK994965
EST:     GTTCGTTCCTGCGAGCAAGAGCAATCGGCCTTATGCCCATGATTGACCAG                         GGTGAAAAGGATGACAAGATAATAGCAGTCTGTGCTGATGATCCTGAATAT
genomic: GTTCGTTCCTGCGAGCAAGAGCAATCGGCCTTATGCCCATGATTGACCAGgtatttcacg ... gcgttgtcagGGTGAAAAGGATGACAAGATAATAGCAGTCTGTGCTGATGATCCTGAATAT
EST: gi|211148126|gb|FK994994.1|FK994994
EST:     GTTCGTTCCTGCGAGCAAGAGCAATCGGNCTTATGCCCATGATTGACCAG                         GGTGAAAAGGATGACAAGATAATAGCAGTCTGTGCTGATGATCCTGA
genomic: GTTCGTTCCTGCGAGCAAGAGCAATCGGCCTTATGCCCATGATTGACCAGgtatttcacg ... gcgttgtcagGGTGAAAAGGATGACAAGATAATAGCAGTCTGTGCTGATGATCCTGA
EST: gi|28930839|gb|CB334200.1|CB334200
EST:     GTTCGTTCCTGCGAGCAAGAGCAATCGGCCTTATGCCCATGATTGACCAG                         GGTGAAAAGGATGACAAGATAATAGCAGTCTGTGCTGATGATCCTGAATAT
genomic: GTTCGTTCCTGCGAGCAAGAGCAATCGGCCTTATGCCCATGATTGACCAGgtatttcacg ... gcgttgtcagGGTGAAAAGGATGACAAGATAATAGCAGTCTGTGCTGATGATCCTGAATAT
EST: gi|211098874|gb|FK999203.1|FK999203
EST:     GTTCGTTCCTGCGAGCAAGAGCAATCGGCCTTATGCCCATGATTGACCAG                         GGTGAAAAGGATGACAAGATAATAGCAGTCTGTGCTGATGATCCTGAATAT
genomic: GTTCGTTCCTGCGAGCAAGAGCAATCGGCCTTATGCCCATGATTGACCAGgtatttcacg ... gcgttgtcagGGTGAAAAGGATGACAAGATAATAGCAGTCTGTGCTGATGATCCTGAATAT
EST: gi|211091460|gb|FK999163.1|FK999163
EST:     GTTCGTTCCTGCGAGCAAGAGCAATCGGCCTTATGCCCATGATTGACCAG                         GGTGAAAAGGATGACAAGATAATAGCAGTCTGTGCTGATGATCCTGAATAT
genomic: GTTCGTTCCTGCGAGCAAGAGCAATCGGCCTTATGCCCATGATTGACCAGgtatttcacg ... gcgttgtcagGGTGAAAAGGATGACAAGATAATAGCAGTCTGTGCTGATGATCCTGAATAT
EST: gi|74237956|gb|DT645870.1|DT645870
EST:     GTTCGTTCCTGCGAGCAAGAGCAATCGGCCTTATGCCCATGATTGACCAG                         GGTGAAAAGGATGACAAGATAATAGCAGTCTGTGCTGATGATCCTGAATAT
genomic: GTTCGTTCCTGCGAGCAAGAGCAATCGGCCTTATGCCCATGATTGACCAGgtatttcacg ... gcgttgtcagGGTGAAAAGGATGACAAGATAATAGCAGTCTGTGCTGATGATCCTGAATAT
EST: gi|211149576|gb|FK995007.1|FK995007
EST:     GTTCGTTCCTGCGAGCAAGAGCAATCGGCCTTATGCC-ATGATTGACCAG                         GGTGAAA-GGATGACAAGATAATAGCAGTCT
genomic: GTTCGTTCCTGCGAGCAAGAGCAATCGGCCTTATGCCCATGATTGACCAGgtatttcacg ... gcgttgtcagGGTGAAAAGGATGACAAGATAATAGCAGTCT
EST: gi|211093927|gb|FK999180.1|FK999180
EST:     GTTCGTTCCTGCGAGCAAGAGCAATCGGCCTTATGCCCATGATTGACCAG                         GGTGAAAAGGATGACAAGATAATA-CNANTCTGTGCTGATGATCCTGAATA
genomic: GTTCGTTCCTGCGAGCAAGAGCAATCGGCCTTATGCCCATGATTGACCAGgtatttcacg ... gcgttgtcagGGTGAAAAGGATGACAAGATAATAGC-AGTCTGTGCTGATGATCCTGAATA
EST: gi|211270190|gb|FL112873.1|FL112873
EST:     GTTCGTTCCTGCGAGCAAGAGCAATCGGCCTTATGCCCATGATTGACCAG                         GGTGAAAAGGATGACAAGATAATAGCAGTCTGTGCTGATGATCCTGAATAT
genomic: GTTCGTTCCTGCGAGCAAGAGCAATCGGCCTTATGCCCATGATTGACCAGgtatttcacg ... gcgttgtcagGGTGAAAAGGATGACAAGATAATAGCAGTCTGTGCTGATGATCCTGAATAT
EST: gi|211143830|gb|FK994952.1|FK994952
EST:     GTTCGTTCCTGCGAGCAAGAGCAATCGGCCTTATGCC-ATGATTGACCAG                         GGTGAAAAGGATGACAAGAT
genomic: GTTCGTTCCTGCGAGCAAGAGCAATCGGCCTTATGCCCATGATTGACCAGgtatttcacg ... gcgttgtcagGGTGAAAAGGATGACAAGAT
EST: gi|211148121|gb|FK994989.1|FK994989
EST:     GTTCGTTCCTGCGAGCAAGAGCAATCGGCCTTATGCCCATGATTGACCAG                         GGTGAAAAGGATGACAAGATAATAGCAGTCTGTGCTGATGATCCTGAATAT
genomic: GTTCGTTCCTGCGAGCAAGAGCAATCGGCCTTATGCCCATGATTGACCAGgtatttcacg ... gcgttgtcagGGTGAAAAGGATGACAAGATAATAGCAGTCTGTGCTGATGATCCTGAATAT
EST: gi|211270194|gb|FL112877.1|FL112877
EST:     GTTCGTTCCTGCGAGCAAGAGCAATCGGCCTTATGCCCATGATTGACCAG                         GGTGAAAAGGATGACAAGATAATAGCAGTCTGTGCTGATGATCCTGAATAT
genomic: GTTCGTTCCTGCGAGCAAGAGCAATCGGCCTTATGCCCATGATTGACCAGgtatttcacg ... gcgttgtcagGGTGAAAAGGATGACAAGATAATAGCAGTCTGTGCTGATGATCCTGAATAT
EST: gi|211093928|gb|FK999181.1|FK999181
EST:     TGCGAGCAAGAGCAATCGGCCTTANGCCCATGATTGACCAG                         GGTGAAAAGGATGACAAGATAATAGCAGTCTGTGCTGATGATCCTGAATAT
genomic: TGCGAGCAAGAGCAATCGGCCTTATGCCCATGATTGACCAGgtatttcacg ... gcgttgtcagGGTGAAAAGGATGACAAGATAATAGCAGTCTGTGCTGATGATCCTGAATAT
EST: gi|32838675|gb|CD978353.1|CD978353
EST:     GTTCGTTCCTGCGAGCAAGAGCAATCGGCCTTATGCCCATGATTGACCAG                         GGTGAAAAGGATGACAAGATAATAGCAGTCTGTGCTGATGATCCTGAATAT
genomic: GTTCGTTCCTGCGAGCAAGAGCAATCGGCCTTATGCCCATGATTGACCAGgtatttcacg ... gcgttgtcagGGTGAAAAGGATGACAAGATAATAGCAGTCTGTGCTGATGATCCTGAATAT
EST: gi|5325092|gb|AI783283.1|AI783283
EST:     GTTCGTTCCTGCGAGCAAGAGCAATTGGCCTTATGCCCATGATTGACCAG                         GGTGAAAAGGATGACAAGATAATAGCAGTCTGTGCTGATGATCCTGAATAT
genomic: GTTCGTTCCTGCGAGCAAGAGCAATCGGCCTTATGCCCATGATTGACCAGgtatttcacg ... gcgttgtcagGGTGAAAAGGATGACAAGATAATAGCAGTCTGTGCTGATGATCCTGAATAT
EST: gi|211143829|gb|FK994951.1|FK994951
EST:     GTTCGTTCCTGCGAGCAAGAGCAATCAGCCTTATGCCCATGATTGACCAG                         GGTGAAAAGGATGACAAGATAATAGCAGTCTGTGCTG
genomic: GTTCGTTCCTGCGAGCAAGAGCAATCGGCCTTATGCCCATGATTGACCAGgtatttcacg ... gcgttgtcagGGTGAAAAGGATGACAAGATAATAGCAGTCTGTGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgactctgctttgactctgtttcaaactatggctatctgttgggcgttgtcagGGTGAAAAGGATGACAAGATAATAGCAGTCTGTGCTGATGATCCTGAATATCGTCACTACAACGACATCAGTGAGCTGTCTCCTCATCGCCTGCAAGAGA
          ctttgac  putative branch site (score: 4)
                     tttcaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttcacgctagacactatttgaggtagagggaaaagaatgactctgctttgactctgtttcaaactatggctatctgttgggcgttgtcagGGTGAAAAGGATGACAAGATAATAGCAGTCTGTGCTGATGATCCTGAATATCGTCACTACAACGACATCAGTGAGCTGTCTCCTCATCGCCTGCAAGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA