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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgccacccctgttctgtcgttactggccactgttacatgtttccgaagcgggggaatcctggtgttatcgactggcttagctgatgttttgtgctctgccgatgcagTGCAAGCTTCCATCGCAGCAAACACATGGGTGGTCAGTGGATCTCCACAGACGAAAA

Basic information

species Zea mays
transcript GRMZM2G023242_T05
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G023242_T05 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g63400.1 (Oryza sativa), 3'ss of exon 3
gtatgccacccctgttctgtcgttactggccactgttacatgtttccgaagcgggggaatcctggtgttatcgactggcttagctgatgttttgtgctctgccgatgcagTGCAAGCTTCCATCGCAGCAAACACATGGGTGGTCAGTGGATCTCCACAGACGAAAA
||||    |  |  | ||||      || | || ||  ||||     |||  |       | |  || | |    |  |||| |  |||||   |   |  ||  ||||||||||||||||||||| ||||||||||||||||||||||| || |||||||| || |
gtataa-gcatccctcctgtt----ttgcctaccgtaccatg-----gaaatgccaactgcttcttggtgttagattacttatcc-atgttcgat--ccgacctgtgcagTGCAAGCTTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGACCAAGA

upper sequence: GRMZM2G023242_T05 (Zea mays), 3'ss of exon 3
lower sequence: PP1S359_31V6.2 (Physcomitrella patens), 3'ss of exon 2
gtatgccacccctgttctgtcgttactggccactgtt-acatgtttccgaagcgggggaatcctggtgttatcgactggcttagctgatgttttgtgctctgccgatgcagTGCAAGCTTCCATCGCAGCAAACACATGGGTGGTCAGTGGATCTCCACAGACGAAAA
           | ||| | |    |||  | | |||| | ||| |   | || |    | |  |  | ||  |   |   |||  |   || ||   ||     | ||||||||||||||||||||| || ||||||||||| || |||||| |  ||||||| || |
-------tttgcagtttttttaggactcac-attgttgatatgatattggagtgcttaattgtt--tctttccatttttattaattatcgtctt-cacttatttggtgcagTGCAAGCTTCCATCGCTGCCAACACATGGGTTGTAAGTGGACCATCACAGACCAAGA
















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|71428113|gb|DR809163.1|DR809163
EST:     GGTGAACATATTCAAGGACGATCTCGTCATCCAGTTCTTGAACCCCAAAG                         TGCAAGCTTCCATCGCAGCAAACACATGGGTGGTCAGTGGATCTCCACAGA
genomic: GGTGAACATATTCAAGGACGATCTCGTCATCCAGTTCTTGAACCCCAAAGgtatgccacc ... gccgatgcagTGCAAGCTTCCATCGCAGCAAACACATGGGTGGTCAGTGGATCTCCACAGA
EST: gi|211137082|gb|FK986272.1|FK986272
EST:     GGTGAACATATTCAAGGACGATCTCGTCATCCAGTTCTTGAACCCCAAAG                         TGCAAGCTTCCATCGCAGCAAACACATGGGTGGTCAGTGGATCTCCACAGA
genomic: GGTGAACATATTCAAGGACGATCTCGTCATCCAGTTCTTGAACCCCAAAGgtatgccacc ... gccgatgcagTGCAAGCTTCCATCGCAGCAAACACATGGGTGGTCAGTGGATCTCCACAGA
EST: gi|211137087|gb|FK986277.1|FK986277
EST:     GGTGAACATATTCAAGGACGATCTCGTCATCCAGTTCTTGAACCCCAAAG                         TGCAAGCTTCCATCGCGGCAAACACATGGGTGGTCAGTGGATCTCCACAGA
genomic: GGTGAACATATTCAAGGACGATCTCGTCATCCAGTTCTTGAACCCCAAAGgtatgccacc ... gccgatgcagTGCAAGCTTCCATCGCAGCAAACACATGGGTGGTCAGTGGATCTCCACAGA
EST: gi|211134255|gb|FK986235.1|FK986235
EST:     GGTGAACATATTCAAGGACGATCTCGTCATCCAGTTCTTGAACCCCAAAG                         TGCAAGCTTCCATCGCAGCAAACACATGGGTGGTCAGTGGATCTCCACAGA
genomic: GGTGAACATATTCAAGGACGATCTCGTCATCCAGTTCTTGAACCCCAAAGgtatgccacc ... gccgatgcagTGCAAGCTTCCATCGCAGCAAACACATGGGTGGTCAGTGGATCTCCACAGA
EST: gi|211138026|gb|FK986294.1|FK986294
EST:     GGTGAACATATTCAAGGACGATCTCGTCATCCAGTTCTTGAACCCCAAAG                         TGCAAGCTTCCATCGCGGCAAACACATGGGTGGTCAGTGGATCTCCACAGA
genomic: GGTGAACATATTCAAGGACGATCTCGTCATCCAGTTCTTGAACCCCAAAGgtatgccacc ... gccgatgcagTGCAAGCTTCCATCGCAGCAAACACATGGGTGGTCAGTGGATCTCCACAGA
EST: gi|211134254|gb|FK986234.1|FK986234
EST:     GGTGAACATATTCAAGGACGATCTCGTCATCCAGTTCTTGAACCCCAAAG                         TGCAAGCTTCCATCGCAGCAAACACATGGGTGGTCAGTGGATCTCCACAGA
genomic: GGTGAACATATTCAAGGACGATCTCGTCATCCAGTTCTTGAACCCCAAAGgtatgccacc ... gccgatgcagTGCAAGCTTCCATCGCAGCAAACACATGGGTGGTCAGTGGATCTCCACAGA
EST: gi|211136141|gb|FK986266.1|FK986266
EST:     GGTGAACATATTCAAGGACGATCTCGTCATCSAGTTCTTGAACCCCAAAG                         TGCAAGCTTCCATCGCGGCAAACACATGGGTGGTCAGTBGATCTCCACAGA
genomic: GGTGAACATATTCAAGGACGATCTCGTCATCCAGTTCTTGAACCCCAAAGgtatgccacc ... gccgatgcagTGCAAGCTTCCATCGCAGCAAACACATGGGTGGTCAGTGGATCTCCACAGA
EST: gi|211136144|gb|FK986269.1|FK986269
EST:     GGTGAACATATTCAAGGACGATCTCGTCATCCAGTTCTTGAACCCCAAAG                         TGCAAGCTTCCATCGCGGCAAACACATGGGTGGTCAGTGGATCTCCACAGA
genomic: GGTGAACATATTCAAGGACGATCTCGTCATCCAGTTCTTGAACCCCAAAGgtatgccacc ... gccgatgcagTGCAAGCTTCCATCGCAGCAAACACATGGGTGGTCAGTGGATCTCCACAGA
EST: gi|211137095|gb|FK986285.1|FK986285
EST:     GGTGAACATATTCAAGGACGATCTCGTCATCCAGTTCTTGAACCCCAAAG                         TGCAAGCTTCCATCGCAGCAAACACATGGGTGGTCAGTGGATCTCCACAGA
genomic: GGTGAACATATTCAAGGACGATCTCGTCATCCAGTTCTTGAACCCCAAAGgtatgccacc ... gccgatgcagTGCAAGCTTCCATCGCAGCAAACACATGGGTGGTCAGTGGATCTCCACAGA
EST: gi|211136143|gb|FK986268.1|FK986268
EST:     GGTGAACATATTCAAGGACGATCTCGTCATCCAGTTCTTGAACCCCAAAG                         TGCAAGCTTCCATCGCGGCAAACACATGGGTGGTCAGTGGATCTCCACAGA
genomic: GGTGAACATATTCAAGGACGATCTCGTCATCCAGTTCTTGAACCCCAAAGgtatgccacc ... gccgatgcagTGCAAGCTTCCATCGCAGCAAACACATGGGTGGTCAGTGGATCTCCACAGA
EST: gi|211134249|gb|FK986229.1|FK986229
EST:     GGTGAACATATTCAAGGACGATCTCGTCATCCAGTTCTTGAACCCCAAAG                         TGCAAGCTTCCATCGCAGCAAACACATGGGTGGTCAGTGGATCTCCACAGA
genomic: GGTGAACATATTCAAGGACGATCTCGTCATCCAGTTCTTGAACCCCAAAGgtatgccacc ... gccgatgcagTGCAAGCTTCCATCGCAGCAAACACATGGGTGGTCAGTGGATCTCCACAGA
EST: gi|211135194|gb|FK986245.1|FK986245
EST:     GGTGAACATATTCAAGGACGATCTCGTCATCCAGTTCTTGAACCCCAAAG                         TGCAAGCTTCCATCGCAGCAAACACATGGGTGGTCAGTGGATCTCCACAGA
genomic: GGTGAACATATTCAAGGACGATCTCGTCATCCAGTTCTTGAACCCCAAAGgtatgccacc ... gccgatgcagTGCAAGCTTCCATCGCAGCAAACACATGGGTGGTCAGTGGATCTCCACAGA
EST: gi|211135198|gb|FK986249.1|FK986249
EST:     GGTGAACATATTCAAGGACKATCTCGTCATCCAGTTCTTGAACCCCAAAG                         TGCAAGCTTCCATCGCAGCAAACACWTGGGTGGTCAGTGGATCTCCACAGA
genomic: GGTGAACATATTCAAGGACGATCTCGTCATCCAGTTCTTGAACCCCAAAGgtatgccacc ... gccgatgcagTGCAAGCTTCCATCGCAGCAAACACATGGGTGGTCAGTGGATCTCCACAGA
EST: gi|211135197|gb|FK986248.1|FK986248
EST:     GGTGAACATATTCAAGGACGATCTCGTCATCCAGTTCTTGAACCCCAAAG                         TKCAAGCTTCCATCGCAGCAAACACATTGGTGGTCANTGGATCTCCACAGA
genomic: GGTGAACATATTCAAGGACGATCTCGTCATCCAGTTCTTGAACCCCAAAGgtatgccacc ... gccgatgcagTGCAAGCTTCCATCGCAGCAAACACATGGGTGGTCAGTGGATCTCCACAGA
EST: gi|211136139|gb|FK986264.1|FK986264
EST:     GGTGAACATATTCAAGGACGATCTCGTCATCCAGTTCTTGAACCCCAAAG                         TGCAAGCTTCCATCGCAGCAAACACATGGGTGGTCAGTGGATCTCCACAGA
genomic: GGTGAACATATTCAAGGACGATCTCGTCATCCAGTTCTTGAACCCCAAAGgtatgccacc ... gccgatgcagTGCAAGCTTCCATCGCAGCAAACACATGGGTGGTCAGTGGATCTCCACAGA
EST: gi|211136146|gb|FK986271.1|FK986271
EST:     GGTGAACATATTCAAGGACGATCTCGTCATCCAGTTCTTGAACCCCAAAG                         TGCAAGCTTCCATCGCAGCAAACACATGGGTGGTCAGTGGATCTCCACAGA
genomic: GGTGAACATATTCAAGGACGATCTCGTCATCCAGTTCTTGAACCCCAAAGgtatgccacc ... gccgatgcagTGCAAGCTTCCATCGCAGCAAACACATGGGTGGTCAGTGGATCTCCACAGA
EST: gi|211136136|gb|FK986261.1|FK986261
EST:     GGTGAACATATTCAAGGACGATCTCGTCATCCAGTTCTTGAACCCCAAAG                         TGCAAGCTTCCATCGCGGCAAACACATGGGTGGTCAGTGGATCTCCACAGA
genomic: GGTGAACATATTCAAGGACGATCTCGTCATCCAGTTCTTGAACCCCAAAGgtatgccacc ... gccgatgcagTGCAAGCTTCCATCGCAGCAAACACATGGGTGGTCAGTGGATCTCCACAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggaatcctggtgttatcgactggcttagctgatgttttgtgctctgccgatgcagTGCAAGCTTCCATCGCAGCAAACACATGGGTGGTCAGTGGATCTCCACAGACGAAAA
                          agctgat  putative branch site (score: 4)
                                         ctctgcc  putative PPT
                               atgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgccacccctgttctgtcgttactggccactgttacatgtttccgaagcgggggaatcctggtgttatcgactggcttagctgatgttttgtgctctgccgatgcagTGCAAGCTTCCATCGCAGCAAACACATGGGTGGTCAGTGGATCTCCACAGACGAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA