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

...ggttaagttagcagcagtctacttgcaactgtacaagcacttaaatatctatttgatcgagcctaggttttgacacaaattgttctaatcatttgtgcagGTGCATGGATTTGTGCAAGATAATAGAACAGGGCAAAAAGTAGCTATGTTAATTGGAAAATGGGATGAAGCTATGTATTATGTGCTTGGGGATCCAAGTG

Basic information

species Zea mays
transcript GRMZM2G156608_T04
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G156608_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os12g18770.1 (Oryza sativa), 3'ss of exon 6
--ggttaagttagcagcagtctactt-gcaactgtacaagcacttaaatatctatttgatcgagcctaggttttgacac-aaattgttctaatcatttgtgcagGTGCATGGATTTGTGCAAGATAATAGAACAGGGCAAAAAGTAGCTATGTTAATTGGAAAATGGGATGAAGCTATGTATTATGTGCTTGGGGATCCAAGTG
     | | |    || |||||  || |    | || || ||  | ||| |  |    |  |  || ||  |   |||  |||| |||  |||   | ||||||||||||||||||||||||||||||||||||||||| ||||| ||||||||||| ||||||||||||||||||||||||||||| ||||||||||||||||
gcatatcaatatctagtagtctgttttgtggttttataaacatattaat-tggac---actgttcccagcctcccacattaaatagtttgaattgctcgtgcagGTGCATGGATTTGTGCAAGATAATAGAACAGGGCAGAAAGTTGCTATGTTAATCGGAAAATGGGATGAAGCTATGTATTATGTTCTTGGGGATCCAAGTG

upper sequence: GRMZM2G156608_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA18G01590.1 (Glycine max), 3'ss of exon 6
ggttaagttagcagcagtctacttgcaactgtacaagcacttaaatatctatttgatcgagcctaggtttt--gacacaaattg---ttctaatcatttgtg-cagGTGCATGGATTTGTGCAAGATAATAGAACAGGGCAAAAAGTAGCTATGTTAATTGGAAAATGGGATGAAGCTATGTATTATGTGCTTGGGGATCCAAGTG
    || || |||    || |  || |   ||    | | |    ||||   ||        ||  |||||  || ||  |  |   || ||||||| | |  ||||| ||||| ||||| ||||| || ||||| ||  | || ||||| ||||||||||| || ||||||||||| ||||| ||||| || ||||||||||   
-agaaatttggcaat--tccaaatg-agtagttt--ggattcgtctatccgcttttcttgttctgagttttatgagactgaaagaacttttaatcatatataacagGTCCATGGGTTTGTTCAAGACAACAGAACTGGAGAGAAGGTAGCGATGTTAATTGGGAAGTGGGATGAAGCAATGTACTATGTACTCGGGGATCCAACCA

upper sequence: GRMZM2G156608_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA11G37650.1 (Glycine max), 3'ss of exon 6
ggttaagttagcagca--gtctacttgcaactgtacaagcacttaaatatctatttgatcgagcctaggttttgacacaaattg-ttctaatcatttgtg-cagGTGCATGGATTTGTGCAAGATAATAGAACAGGGCAAAAAGTAGCTATGTTAATTGGAAAATGGGATGAAGCTATGTATTATGTGCTTGGGGATCCAAGTG
    || | |  | |   |||||   | |  |    |    ||  | | || |||   |     |     |  |||  |||    || ||||| | | |  ||||| ||||| ||||| ||||| || ||||| ||  | || ||||| ||||||||||| || ||||||||||| ||||| ||||| |||||||||||||   
----aaataaagaactccgtctagcaggattttcttacctgctgcactttcaattcagttagcacatttataagactgaaagaacttttaatcttatataacagGTCCATGGGTTTGTTCAAGACAACAGAACTGGAGAGAAGGTAGCGATGTTAATTGGGAAGTGGGATGAAGCAATGTACTATGTACTTGGGGATCCAACCA

upper sequence: GRMZM2G156608_T03 (Zea mays), 3'ss of exon 1
lower sequence: AT1G13170.1 (Arabidopsis thaliana), 3'ss of exon 6
ggttaagttagcagcagtctacttgcaactgtacaagcacttaaatatctatttgatcgagcctaggttttgacacaaattgttctaatcatttgtgcagGTGCATGGATTTGTGCAAGATAATAGAACAGGGCAAAAAGTAGCTATGTTAATTGGAAAATGGGATGAAGCTATGTATTATGTGCTTGGGGATCCAAGTG
                              ||| ||  | ||  || ||| | |    |  | || |    | |    |   |   | |   |  ||||||| ||||| ||||||||||| || ||||| ||| | |||||||||||  | || || |||||||||||||| ||||| |||||  | || ||||| |   
---------------------------gtagtagaatgatttttatttctgtctttctgctcgtatgaacaggcctttaa-atggaatttggtaatgcagGTTCATGGGTTTGTGCAAGACAACAGAACCGGGGAGAAAGTAGCTATACTGATAGGCAAATGGGATGAAGCAATGTACTATGTATTGGGAGATCCGACAA

upper sequence: GRMZM2G156608_T03 (Zea mays), 3'ss of exon 1
lower sequence: Vv01s0137g00290.t01 (Vitis vinifera), 3'ss of exon 6
ggttaagttagcagcagtct-acttgcaactgtacaagcacttaaatatctatttgatcgagcctaggttttgacacaaattgttctaat-catttgtgcagGTGCATGGATTTGTGCAAGATAATAGAACAGGGCAAAAAGTAGCTATGTTAATTGGAAAATGGGATGAAGCTATGTATTATGTGCTTGGGGATCCAAGTG
    | | |   | || ||| | | |   || |   |  | ||||    ||   | |   | |  |   | |   |       || |  |  ||   ||||||| ||||||||||||||||||||| |||| ||  | || |||||||||||  | || ||||||||||| || |||||||||||| | || |||||||   
-caaacggtgctatcactctgaatcgatgctttttgaata-ttaatggcctgggtaagaaaactgaatatatataaatttacattttggtatataattgcagGTTCATGGATTTGTGCAAGATAATCGAACTGGAGAGAAGGTAGCTATGTTGGTGGGGAAATGGGATGAGGCAATGTATTATGTGTTGGGAGATCCAACAA

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|32933280|gb|CF038092.1|CF038092
EST:     GCAAGCTTAAATTTAAAGAACAGTCAATTATTGATCGCAATCCACACCAG                         GTGCATGGATTTGTGCAAGATAATAGAACAGGGCAAAAAGTAGCTATGTTA
genomic: GCAAGCTTAAATTTAAAGAACAGTCAATTATTGATCGCAATCCACACCAGgtaactcagt ... atttgtgcagGTGCATGGATTTGTGCAAGATAATAGAACAGGGCAAAAAGTAGCTATGTTA
EST: gi|60400940|gb|DN233747.1|DN233747
EST:     GCAAGCTTAAATTTAAAGAACAGTCAATTATTGATCGCAATCCACACCAG                         GTGCATGGATTTGTGCAAGATAATAGAACAGGGCAAAAAGTAGCTATGTTA
genomic: GCAAGCTTAAATTTAAAGAACAGTCAATTATTGATCGCAATCCACACCAGgtaactcagt ... atttgtgcagGTGCATGGATTTGTGCAAGATAATAGAACAGGGCAAAAAGTAGCTATGTTA
EST: gi|108953726|gb|EC364860.1|EC364860
EST:     GCAAGCTTAAATTTAAAGAACAGTCAATTATTGATCGCAATCCACACCAG                         GTGCATGGATTTGTGCAAGATAATAGAACAGGGCAAAAAGTAGCTATGTTA
genomic: GCAAGCTTAAATTTAAAGAACAGTCAATTATTGATCGCAATCCACACCAGgtaactcagt ... atttgtgcagGTGCATGGATTTGTGCAAGATAATAGAACAGGGCAAAAAGTAGCTATGTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatctatttgatcgagcctaggttttgacacaaattgttctaatcatttgtgcagGTGCATGGATTTGTGCAAGATAATAGAACAGGGCAAAAAGTAGCTATGTTAATTGGAAAATGGGATGAAGCTATGTATTATGTGCTTGGGGATCCAAGTG
                                     ttctaat  putative branch site (score: 2)
                                        taatcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggttaagttagcagcagtctacttgcaactgtacaagcacttaaatatctatttgatcgagcctaggttttgacacaaattgttctaatcatttgtgcagGTGCATGGATTTGTGCAAGATAATAGAACAGGGCAAAAAGTAGCTATGTTAATTGGAAAATGGGATGAAGCTATGTATTATGTGCTTGGGGATCCAAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - gcagcag
- - - - - - - - - -tacttgc
- - - - - - - - - - - - - - - - -caagcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acacaaa