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'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTACAAAGgtacggaagttctctaccttttgtctttctttaatcaggtctcatttcttgctgttactggattggtattgaataatatttaacttgccacgccatttcttgctgttactgacaaactattgaagatcttaatgtgccattcttgcgctcag

Basic information

species Zea mays
transcript GRMZM2G540403_T02
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G540403_T02 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os03g15860.1 (Oryza sativa), 5'ss of exon 10
GCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTACAAAGgtacg--gaagttctctaccttttgt-ctttctttaatcaggtctcatttcttgctgttactggattggtattgaataatatttaacttgccacgccatttcttgctgttactgacaaactattgaagatctt---aatgtgccattct-tgcgctcag-------------------
|||||||||||||  ||||| || ||| | |||||||||||||| ||||||||||||||   |  |  || ||   |||   |||  ||| || |  |    |   ||  | ||    || || | |||    ||||     ||   |     |||  | || ||   |  | | ||||     |  |   | | ||  |     | ||||  |                   
GCAAGACTTCAGGTGAAGCAAATAATTGATGATGACAAGAGGCACCGCTACAAAGgtacatcgctggcctttattctttaaacttcattttattatttagagtgaattattatttaatgagtgatgttgctccatatcctgtttctgatagtctttacttctcttctggtaataatatttgctgttctctgactttgttaccaaatacgctatgcaaattttattgcttgcag
















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|149071943|gb|EE160330.2|EE160330
EST:     ACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTACAAAG                         GTACACTTGATGCGTTCACAAAGATGGTACGATATGAGGGTCTGTCAGGGA
genomic: ACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTACAAAGgtacggaagt ... ttgcgctcagGTACACTTGATGCGTTCACAAAGATGGTACGATATGAGGGTCTGTCAGGGA
EST: gi|211285343|gb|FL118292.1|FL118292
EST:     ACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTACAAAG                         GTACACTTGATGCGTTCACAAAGATGGTACGATATGAGGGTCTGTCAGGGA
genomic: ACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTACAAAGgtacggaagt ... ttgcgctcagGTACACTTGATGCGTTCACAAAGATGGTACGATATGAGGGTCTGTCAGGGA
EST: gi|4681209|gb|AI629879.1|AI629879
EST:     ACTTCAGGCAAAGCACATGATTATCGATGACAAGAGGCATCGCTACAAAG                         GTACACTTGATGCGTTCACAAAGATGGTACGATATGAGGGTCTGTCAGGGA
genomic: ACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTACAAAGgtacggaagt ... ttgcgctcagGTACACTTGATGCGTTCACAAAGATGGTACGATATGAGGGTCTGTCAGGGA
EST: gi|50330442|gb|CO525568.1|CO525568
EST:     ACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTACAAAG                         GTACACTTGATGCGTTCACAAAGATGGTACGATATGAGGGTCTGTCAGGGA
genomic: ACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTACAAAGgtacggaagt ... ttgcgctcagGTACACTTGATGCGTTCACAAAGATGGTACGATATGAGGGTCTGTCAGGGA
EST: gi|60343577|gb|DN210550.1|DN210550
EST:     ACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTACAAAG                         GTACACTTGATGCGTTCACAAAGATGGTACGATATGAGGGTCTGTCAGGGA
genomic: ACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTACAAAGgtacggaagt ... ttgcgctcagGTACACTTGATGCGTTCACAAAGATGGTACGATATGAGGGTCTGTCAGGGA
EST: gi|5714034|gb|AI944019.1|AI944019
EST:     ACTTCAGGCAAAGCCCATGATTACCGATGCCAAGAGGCATCGCTACAAAG                         GTACCCTTGATGCGTTCCCAAAGATGGTACGATATGAGGGTCTGTCAGGGA
genomic: ACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTACAAAGgtacggaagt ... ttgcgctcagGTACACTTGATGCGTTCACAAAGATGGTACGATATGAGGGTCTGTCAGGGA
EST: gi|86471991|gb|DY238361.1|DY238361
EST:     ACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTACAAAG                         GTACACTTGATGCGTTCACAAAGATGGTACGATATGAGGGTCTGTCAGGGA
genomic: ACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTACAAAGgtacggaagt ... ttgcgctcagGTACACTTGATGCGTTCACAAAGATGGTACGATATGAGGGTCTGTCAGGGA
EST: gi|91877626|gb|EB407583.1|EB407583
EST:     ACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTACAAAG                         GTACACTTGATGCGTTCACAAAGATGGTACGATATGAGGGTCTGTCAGGGA
genomic: ACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTACAAAGgtacggaagt ... ttgcgctcagGTACACTTGATGCGTTCACAAAGATGGTACGATATGAGGGTCTGTCAGGGA
EST: gi|60340184|gb|DN207157.1|DN207157
EST:     ACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTACAAAG                         GTACACTTGATGCGTTCACAAAGATGGTACGATATGAGGGTCTGTCAGGGA
genomic: ACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTACAAAGgtacggaagt ... ttgcgctcagGTACACTTGATGCGTTCACAAAGATGGTACGATATGAGGGTCTGTCAGGGA
EST: gi|88756339|gb|DY540480.1|DY540480
EST:     ACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTACAAAG                         GTACACTTGATGCGTTCACAAAGATGGTACGATATGAGGGTCTGTCAGGGA
genomic: ACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTACAAAGgtacggaagt ... ttgcgctcagGTACACTTGATGCGTTCACAAAGATGGTACGATATGAGGGTCTGTCAGGGA
EST: gi|78121536|gb|DV539920.1|DV539920
EST:     ACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTACAAAG                         GTACACTTGATGCGTTCACAAAGATGGTACGATATGAGGGTCTGTCAGGGA
genomic: ACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTACAAAGgtacggaagt ... ttgcgctcagGTACACTTGATGCGTTCACAAAGATGGTACGATATGAGGGTCTGTCAGGGA
EST: gi|211285345|gb|FL118294.1|FL118294
EST:     ACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTACAAAG                         GTACACTTGATGCGTTCACAAAGATGGTACGATATGAGGGTCTGTCAGGGA
genomic: ACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTACAAAGgtacggaagt ... ttgcgctcagGTACACTTGATGCGTTCACAAAGATGGTACGATATGAGGGTCTGTCAGGGA
EST: gi|29543455|gb|CB603851.1|CB603851
EST:     ACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTACAAAG                         GTACACTTGATGCGTTCACAAAGATGGTACGATATGAGGGTCTGTCAGGGA
genomic: ACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTACAAAGgtacggaagt ... ttgcgctcagGTACACTTGATGCGTTCACAAAGATGGTACGATATGAGGGTCTGTCAGGGA
EST: gi|71422917|gb|DR805896.1|DR805896
EST:     ACTTCAGGCAAAGCACATGATTAACGATGCCAAGAGGCATCGCTACAAAG                         GTACACTTGATGCGTTCACAAAGATGGTACGATATGAGGGTCTGTCAGGGA
genomic: ACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTACAAAGgtacggaagt ... ttgcgctcagGTACACTTGATGCGTTCACAAAGATGGTACGATATGAGGGTCTGTCAGGGA
EST: gi|32868675|gb|CF008357.1|CF008357
EST:     ACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTACAAAG                         GTACACTTGATGCGTTCACAAAGATGGTACGATATGAGGGTCTGTCAGGGA
genomic: ACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTACAAAGgtacggaagt ... ttgcgctcagGTACACTTGATGCGTTCACAAAGATGGTACGATATGAGGGTCTGTCAGGGA
EST: gi|71422924|gb|DR805897.1|DR805897
EST:     ACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTACAAAG                         GTACACTTGATGCGTTCACAAAGATGGTACGATATGAGGGTCTGTCAGGGA
genomic: ACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTACAAAGgtacggaagt ... ttgcgctcagGTACACTTGATGCGTTCACAAAGATGGTACGATATGAGGGTCTGTCAGGGA
EST: gi|211285341|gb|FL118290.1|FL118290
EST:     ACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTACAAAG                         GTACACTTGATGCGTTCACAAAGATGGTACGATATGAGGGTCTGTCAGGGA
genomic: ACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTACAAAGgtacggaagt ... ttgcgctcagGTACACTTGATGCGTTCACAAAGATGGTACGATATGAGGGTCTGTCAGGGA
EST: gi|211378309|gb|FL452851.1|FL452851
EST:     ACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTACAAAG                         GTACACTTGATGCGTTCACAAAGATGGTACGATATGAGGGTCTGTCAGGGA
genomic: ACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTACAAAGgtacggaagt ... ttgcgctcagGTACACTTGATGCGTTCACAAAGATGGTACGATATGAGGGTCTGTCAGGGA

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: 49 (upstream exon), 49 (downstream exon)
Score: 105

GCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTACAAAGgtacggaagt ... ttgcgctcagGTACACTTGATGCGTTCACAAAGATGGTACGATATGAGGGTCTGTCAGGGATGTACAAAGGAATGGGCACAAAAATTGTGCAAAGTGTTTTTGCTTCTGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 168

GCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTACAAAGgtacggaagt ... ttgcgctcagGTACACTTGATGCGTTCACAAAGATGGTACGATATGAGGGTCTGTCAGGGATGTACAAAGGAATGGGCACAAAAATTGTGCAAAGTGTTTTTGCTTCTGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 195

GCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTACAAAGgtacggaagt ... ttgcgctcagGTACACTTGATGCGTTCACAAAGATGGTACGATATGAGGGTCTGTCAGGGATGTACAAAGGAATGGGCACAAAAATTGTGCAAAGTGTTTTTGCTTCTGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 152

GCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTACAAAGgtacggaagt ... ttgcgctcagGTACACTTGATGCGTTCACAAAGATGGTACGATATGAGGGTCTGTCAGGGATGTACAAAGGAATGGGCACAAAAATTGTGCAAAGTGTTTTTGCTTCTGC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTACAAAGgtacggaagttctctaccttttgtctttctttaatcaggtctcatttcttgctgttactggattggtattgaataatatttaacttgccacgccatttcttgctgttactgacaaactattgaagatcttaatgtgccattcttgcgctcag

- - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - AAGAGG