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

gtcagagttctttttctcccatttcaaccttcgagatttaccacctgctagcattatcatttcatccatcttcatcaaaaaccagGGAAGCCCTTGGGCCGTGGGCGTGGCCGTGGTCGTGGGCGCGGTCGGGGTCGGGGACGTTGAGCATGCTAGCTGCTTTTGGAAATTGCATTGCGTGCATC

Basic information

species Zea mays
transcript GRMZM2G416061_T03
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G416061_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g37430.1 (Oryza sativa), 3'ss of exon 3
gtcagagttctttttctcccatttcaaccttcgagatttaccacctgctagcattatcatttcatcca-tcttcatcaaaaaccagGGAAGCCCTTGGGCCGTGGGCGTGGCCGTGGTCGTGGGCGCGGTCGGGGTCGGGGACGTTGAGCATGCTAGCTGCTTTTGGAAATTGCATTGCGTGCATC
||  ||    | |||   |  | | |    | ||  ||    | |||||    |  |  | | ||| |  ||| |||   || |||||||||| ||||| |||||||| ||||||||||||||||||||||| ||  ||||||| ||||| |     | | |        | | |     ||||||
gtttgataattgttttgtctctctaag---ttgattttactgagctgctgaactgtttgtctgatcaaaccttaatccggaaacagGGAAGCCTTTGGGGCGTGGGCGCGGCCGTGGTCGTGGGCGCGGTCGTGGCAGGGGACGCTGAGCTTCACTCCAGTTCCCTATCTTGGAAACTTTTGCATC
















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|211058973|gb|FL460147.1|FL460147
EST:     TTTGCTGGTTGAGGAAACACCAAGGGTCAAGCCTAAGAAGCCTACTTCTG                         GGAAGCCCTTGGGCCGTGGGCGTGGCCGTGGTCGTGGGCGCGGTCGGGGTC
genomic: TTTGCTGGTTGAGGAAACACCAAGGGTCAAGCCTAAGAAGCCTACTTCTGgtcagagttc ... caaaaaccagGGAAGCCCTTGGGCCGTGGGCGTGGCCGTGGTCGTGGGCGCGGTCGGGGTC
EST: gi|60353877|gb|DN220850.1|DN220850
EST:     TTTGCTGGTTGAGGAAACACCAAGGGTCAAGCCTAAGAAGCCTACTTCTG                         GGAAGCCCTTGGGCCGTGGGCGTGGCCGTGGTCGTGGGCGCGGTCGGGGTC
genomic: TTTGCTGGTTGAGGAAACACCAAGGGTCAAGCCTAAGAAGCCTACTTCTGgtcagagttc ... caaaaaccagGGAAGCCCTTGGGCCGTGGGCGTGGCCGTGGTCGTGGGCGCGGTCGGGGTC
EST: gi|32828991|gb|CD968669.1|CD968669
EST:     TTTGCTGGTTGAGGAAACACCAAGGGTCAAGCCTAAGAAGCCTACTTCTG                         GGAAGCCCTTGGGCCGTGGGCGTGGCCGTGGTCGTGCGCGCGGTCGGGGTC
genomic: TTTGCTGGTTGAGGAAACACCAAGGGTCAAGCCTAAGAAGCCTACTTCTGgtcagagttc ... caaaaaccagGGAAGCCCTTGGGCCGTGGGCGTGGCCGTGGTCGTGGGCGCGGTCGGGGTC
EST: gi|211405279|gb|FL027503.1|FL027503
EST:     TTTGCTGGTTGAGGAAACACCAAGGGTCAAGCCTAAGAAGCCTACTTCTG                         GGAAGCCCTTGGGACGTGGGCGTGGCCGTGGTCGTGGGCGCG
genomic: TTTGCTGGTTGAGGAAACACCAAGGGTCAAGCCTAAGAAGCCTACTTCTGgtcagagttc ... caaaaaccagGGAAGCCCTTGGGCCGTGGGCGTGGCCGTGGTCGTGGGCGCG
EST: gi|211405278|gb|FL027502.1|FL027502
EST:     TTTGCTGGTTGAGGAAACACCAAGGGTCAAGCCTAAGAAGCCTACTTCTG                         GGAAGCCCTTGGGCCGTGGGCGTGGCCGTGGTCGTGGGCGCGGTCGGGGTC
genomic: TTTGCTGGTTGAGGAAACACCAAGGGTCAAGCCTAAGAAGCCTACTTCTGgtcagagttc ... caaaaaccagGGAAGCCCTTGGGCCGTGGGCGTGGCCGTGGTCGTGGGCGCGGTCGGGGTC
EST: gi|67011942|gb|CO440691.1|CO440691
EST:     TTTGCTGGTTGAGGAAACACCAAGGGTCAAGCCTAAGAAGCCTACTTCTG                         GGAAGCCCTTGGGACGTGGGCGTGGCCGTGGTCGTGGGCGCGGTCGGGGTC
genomic: TTTGCTGGTTGAGGAAACACCAAGGGTCAAGCCTAAGAAGCCTACTTCTGgtcagagttc ... caaaaaccagGGAAGCCCTTGGGCCGTGGGCGTGGCCGTGGTCGTGGGCGCGGTCGGGGTC
EST: gi|26557688|gb|CA829923.1|CA829923
EST:     TTTGCTGGTTGAGGAAACACCAAGGGTCAAGCCTAAGAAGCCTACTTCTG                         GGAAGCCCTTGGGCCGTGGGCGTGGCCGTGGTCGTGGGCGCGGTCGGGGTC
genomic: TTTGCTGGTTGAGGAAACACCAAGGGTCAAGCCTAAGAAGCCTACTTCTGgtcagagttc ... caaaaaccagGGAAGCCCTTGGGCCGTGGGCGTGGCCGTGGTCGTGGGCGCGGTCGGGGTC
EST: gi|211405280|gb|FL027504.1|FL027504
EST:     TTTGCTGGTTGAGGAAACACCAAGGGTCAAGCCTAARAAGCCTACTTCTG                         GGAAGCCCTTGGGCCGTGGGCGTG
genomic: TTTGCTGGTTGAGGAAACACCAAGGGTCAAGCCTAAGAAGCCTACTTCTGgtcagagttc ... caaaaaccagGGAAGCCCTTGGGCCGTGGGCGTG
EST: gi|32847843|gb|CD987524.1|CD987524
EST:     TTTGCTGGTTGAGGAAACACCAAGGGTCAAGCCTAAGAAGCCTACTTCTG                         GGAAGCCCTTGGGCCGTGGGCGTGGCCGTGGTCGTGGGCGCGGTCGGGGTC
genomic: TTTGCTGGTTGAGGAAACACCAAGGGTCAAGCCTAAGAAGCCTACTTCTGgtcagagttc ... caaaaaccagGGAAGCCCTTGGGCCGTGGGCGTGGCCGTGGTCGTGGGCGCGGTCGGGGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgagatttaccacctgctagcattatcatttcatccatcttcatcaaaaaccagGGAAGCCCTTGGGCCGTGGGCGTGGCCGTGGTCGTGGGCGCGGTCGGGGTCGGGGACGTTGAGCATGCTAGCTGCTTTTGGAAATTGCATTGCGTGCATC
                                      tcttcatc  CT-rich tract
                      attatcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagagttctttttctcccatttcaaccttcgagatttaccacctgctagcattatcatttcatccatcttcatcaaaaaccagGGAAGCCCTTGGGCCGTGGGCGTGGCCGTGGTCGTGGGCGCGGTCGGGGTCGGGGACGTTGAGCATGCTAGCTGCTTTTGGAAATTGCATTGCGTGCATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT