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

AGTTGTCAACATTGCGGTATCCACTCGTTATGAGATCAACAGGGCCTTTGCTAATCTCCGCCGAATTGCTCTTGGCCGGGACATTAAGAAGTTCCTAATGgtatgcccactgtgtcatttgcctatgatgtacaatggtttgtacagcaatcaagctacacttgcctcatttttttctctattggaaaatttag

Basic information

species Zea mays
transcript GRMZM2G359018_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G359018_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g12650.1 (Oryza sativa), 5'ss of exon 3
AGTTGTCAACATTGCGGTATCCACTCGTTATGAGATCAACAGGGCCTTTGCTAATCTCCGCCGAATTGCTCTTGGCCGGGACATTAAGAAGTTCCTAATGgtatgcccactgtgtcatttgcctatgatgtacaatggtttgtacagcaatcaagctacacttgcctcatttttttctctattggaaaatttag
 ||||||||||||||  |||| || |||||||||||||||||||||||||| ||||| || |  |||||||||||||||||||| ||||||||||| || ||||| |     ||   ||||  | ||    |  || |||   | ||||| |    ||    ||    ||      || |  | |         
GGTTGTCAACATTGCTCTATCTACACGTTATGAGATCAACAGGGCCTTTGCCAATCTTCGTCAGATTGCTCTTGGCCGGGACATCAAGAAGTTCCTTATTgtatgtctgtgatgct-tttgtgtttgtataattattgttcccatagcaaactgaatatttatgatctataccacacttt--tag---------
















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|88757769|gb|DY541910.1|DY541910
EST:     CTAATCTCCGCCGAATTGCTCTTGGCCGGGACATTAAGAAGTTCCTAATG                         GTTATTGCTGGGCTTTGGTTGCTTTCTGTCCTTGGAAGTTGCTGCAACTTA
genomic: CTAATCTCCGCCGAATTGCTCTTGGCCGGGACATTAAGAAGTTCCTAATGgtatgcccac ... gaaaatttagGTTATTGCTGGGCTTTGGTTGCTTTCTGTCCTTGGAAGTTGCTGCAACTTA
EST: gi|161587439|gb|EY961051.1|EY961051
EST:     CGGGACATTAAGAAGTTCCTAATG                         GTTATTGCTGGGCTTTGGTTGCTTTCTGTCCTTGGAAGTTGCTGCAACTTA
genomic: CGGGACATTAAGAAGTTCCTAATGgtatgcccac ... gaaaatttagGTTATTGCTGGGCTTTGGTTGCTTTCTGTCCTTGGAAGTTGCTGCAACTTA
EST: gi|29543942|gb|CB604322.1|CB604322
EST:     CTAATCTCCGCCGAATTGCTCTTGGCCGGGACATTAAGAAGTTCCTAATG                         GTTATTGCTGGGCTTTGGTTGCTTTCTGTCCTTGGAAGTTGCTGCAACTTA
genomic: CTAATCTCCGCCGAATTGCTCTTGGCCGGGACATTAAGAAGTTCCTAATGgtatgcccac ... gaaaatttagGTTATTGCTGGGCTTTGGTTGCTTTCTGTCCTTGGAAGTTGCTGCAACTTA
EST: gi|20508136|gb|BQ279910.1|BQ279910
EST:     CTAATCTCCGCCAAATTGCTCTTGGCCGGGACATTAAGAAGTTCCTAATG                         GTTATTGCTGGGCTTTGGTTGCTTTCTGTCCTTGGAAGTTGCTGCAACTTA
genomic: CTAATCTCCGCCGAATTGCTCTTGGCCGGGACATTAAGAAGTTCCTAATGgtatgcccac ... gaaaatttagGTTATTGCTGGGCTTTGGTTGCTTTCTGTCCTTGGAAGTTGCTGCAACTTA
EST: gi|32934217|gb|CF039029.1|CF039029
EST:     CTAATCTCCGCCGAATTGCACTTGGCCGGGACATTAAGAAGTTCCTAATG                         GTTATTGCTGGGCTTTGGTTGCTTTCTGTCCTTGGAAGTTGCTGCAACTTA
genomic: CTAATCTCCGCCGAATTGCTCTTGGCCGGGACATTAAGAAGTTCCTAATGgtatgcccac ... gaaaatttagGTTATTGCTGGGCTTTGGTTGCTTTCTGTCCTTGGAAGTTGCTGCAACTTA
EST: gi|213191862|gb|FM185649.1|FM185649
EST:     AGAAGTTCCTAATG                         GTTATTGCTGGGCTTTGGTTGCTTTCTGTCCTTGGAAGTTGCTGCAACTTA
genomic: AGAAGTTCCTAATGgtatgcccac ... gaaaatttagGTTATTGCTGGGCTTTGGTTGCTTTCTGTCCTTGGAAGTTGCTGCAACTTA
EST: gi|60395596|gb|DN228466.1|DN228466
EST:     CTAATCTCCGCCGAATTGCTCTTGGCCGGGACATTAAGAAGTTCCTAATG                         GTTATTGCTGGGCTTTGGTTGCTTTCTGTCCTTGGAAGTTGCTGCAACTTA
genomic: CTAATCTCCGCCGAATTGCTCTTGGCCGGGACATTAAGAAGTTCCTAATGgtatgcccac ... gaaaatttagGTTATTGCTGGGCTTTGGTTGCTTTCTGTCCTTGGAAGTTGCTGCAACTTA
EST: gi|31355597|gb|CD439954.1|CD439954
EST:     CTAATCTCCGCCAAATTGCTCTTGGCCGGGACATTAAGAAGTTCCTAATG                         GTTATTGCTGGGCTTTGGTTGCTTTCTGTCCTTGGAAGTTGCTGCAACTTA
genomic: CTAATCTCCGCCGAATTGCTCTTGGCCGGGACATTAAGAAGTTCCTAATGgtatgcccac ... gaaaatttagGTTATTGCTGGGCTTTGGTTGCTTTCTGTCCTTGGAAGTTGCTGCAACTTA
EST: gi|211035914|gb|FK990121.1|FK990121
EST:     CTAATCTCCGCCAAATTGCTCTTGGCCGGGACATTAAGAAGTTCCTAATG                         GTTATTGCTGGGCTTTGGTTGCTTTCTGTCCTTGGAAGTTGCTGCAACTTA
genomic: CTAATCTCCGCCGAATTGCTCTTGGCCGGGACATTAAGAAGTTCCTAATGgtatgcccac ... gaaaatttagGTTATTGCTGGGCTTTGGTTGCTTTCTGTCCTTGGAAGTTGCTGCAACTTA
EST: gi|22546350|gb|BU098661.1|BU098661
EST:     CTAATCTCCGCCAAATTGCTCTTGGCCGGGACATTAAGAAGTTCCTAATG                         GTTATTGCTGGGCTTTGGTTGCTTTCTGTCCTTGGAAGTTGCTGCAACTTA
genomic: CTAATCTCCGCCGAATTGCTCTTGGCCGGGACATTAAGAAGTTCCTAATGgtatgcccac ... gaaaatttagGTTATTGCTGGGCTTTGGTTGCTTTCTGTCCTTGGAAGTTGCTGCAACTTA
EST: gi|20508141|gb|BQ279911.1|BQ279911
EST:     TAATCTCCGCCAAATCTGCTCTTGGCCGGGACATTAAGAAGTTCCTAATG                         GTTATTGCTGGGCTTTGGTTGCTTTCTGTCCTTGGAAGCTGCTGCAACTTA
genomic: TAATCTCCGCCGAAT-TGCTCTTGGCCGGGACATTAAGAAGTTCCTAATGgtatgcccac ... gaaaatttagGTTATTGCTGGGCTTTGGTTGCTTTCTGTCCTTGGAAGTTGCTGCAACTTA
EST: gi|29543376|gb|CB603772.1|CB603772
EST:     CTAATCTCCGCCGAATTGCTCTTGGCCGGGACATTAAGAAGTTCCTAATG                         GTTATTGCTGGGCTTTGGTTGCTTTCTGTCCTTGGAAGTTGCTGCAACTTA
genomic: CTAATCTCCGCCGAATTGCTCTTGGCCGGGACATTAAGAAGTTCCTAATGgtatgcccac ... gaaaatttagGTTATTGCTGGGCTTTGGTTGCTTTCTGTCCTTGGAAGTTGCTGCAACTTA
EST: gi|15589953|gb|BI674569.1|BI674569
EST:     CTAATCTCCGCCAAATTGCTCTTGGCCGGGACATTAAGAAGTTCCTAATG                         GTTATTGCTGGGCTTTGGTTGCTTTCTGTCCTTGGAAGTTGCTGCAACTTA
genomic: CTAATCTCCGCCGAATTGCTCTTGGCCGGGACATTAAGAAGTTCCTAATGgtatgcccac ... gaaaatttagGTTATTGCTGGGCTTTGGTTGCTTTCTGTCCTTGGAAGTTGCTGCAACTTA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 358

AGTTGTCAACATTGCGGTATCCACTCGTTATGAGATCAACAGGGCCTTTGCTAATCTCCGCCGAATTGCTCTTGGCCGGGACATTAAGAAGTTCCTAATGgtatgcccac ... gaaaatttagGTTATTGCTGGGCTTTGGTTGCTTTCTGTCCTTGGAAGTTGCTGCAACTTATTGACCTTAGTCTACATTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 144

AGTTGTCAACATTGCGGTATCCACTCGTTATGAGATCAACAGGGCCTTTGCTAATCTCCGCCGAATTGCTCTTGGCCGGGACATTAAGAAGTTCCTAATGgtatgcccac ... gaaaatttagGTTATTGCTGGGCTTTGGTTGCTTTCTGTCCTTGGAAGTTGCTGCAACTTATTGACCTTAGTCTACATTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 82

AGTTGTCAACATTGCGGTATCCACTCGTTATGAGATCAACAGGGCCTTTGCTAATCTCCGCCGAATTGCTCTTGGCCGGGACATTAAGAAGTTCCTAATGgtatgcccac ... gaaaatttagGTTATTGCTGGGCTTTGGTTGCTTTCTGTCCTTGGAAGTTGCTGCAACTTATTGACCTTAGTCTACATTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 123

AGTTGTCAACATTGCGGTATCCACTCGTTATGAGATCAACAGGGCCTTTGCTAATCTCCGCCGAATTGCTCTTGGCCGGGACATTAAGAAGTTCCTAATGgtatgcccac ... gaaaatttagGTTATTGCTGGGCTTTGGTTGCTTTCTGTCCTTGGAAGTTGCTGCAACTTATTGACCTTAGTCTACATTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTTGTCAACATTGCGGTATCCACTCGTTATGAGATCAACAGGGCCTTTGCTAATCTCCGCCGAATTGCTCTTGGCCGGGACATTAAGAAGTTCCTAATGgtatgcccactgtgtcatttgcctatgatgtacaatggtttgtacagcaatcaagctacacttgcctcatttttttctctattggaaaatttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT