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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGACCATGAAACAACCATATACCCAAAGCGAGGTAAAGTGTTTGATGCTTCAGCTGCTAGAAGGTGTAAAATATCTACATGACAATTGGGTGCTTCATAGgtaattattgtttgctttcttttttcggttcacgtgttgtcttgaatctgttattgtgttgttgatacatggccagcttttttacag

Basic information

species Zea mays
transcript GRMZM2G179097_T04
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G179097_T03 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os04g41100.6 (Oryza sativa), 5'ss of exon 2
AGACCATGAAACAACCATATACCCAAAGCGAGGTAAAGTGTTTGATGCTTCAGCTGCTAGAAGGTGTAAAATATCTACATGACAATTGGGTGCTTCATAGgtaattattg--tttgctttcttttttcggttcacgtgttgtcttgaatctgttattgtgt-tgttgatacatggccagcttttttacag---
|| | ||||| || ||||||| |||||| ||||| || ||  ||||||| |||||| | || ||||| || ||||| ||||| |||||||| |||||||||||| | |||  ||  |  ||| |||| | ||  |  ||   ||  || || |  |  ||  |||  |   ||   ||  ||   || |    
AGGCAATGAAGCAGCCATATAGCCAAAGTGAGGTCAAATGCCTGATGCTCCAGCTGTTGGAGGGTGTGAAGTATCTTCATGATAATTGGGTACTTCATAGgtaactgttgatttgacgctctatttttgtttgccaagtatcctcaaacctatcctgatgcctgtatactgatatgcattttccatataccag
















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|32863690|gb|CF003372.1|CF003372
EST:     AGCTGCTAGAAGGTGTAAAATATCTACATGACCATTTGGGTGCTTCATAG                         GGATCTGAAGACCTCAAATCTTTTGTTGAATAACCGTGGTGAGTTAAAAAT
genomic: AGCTGCTAGAAGGTGTAAAATATCTACATGA-CAATTGGGTGCTTCATAGgtaattattg ... ttttttacagGGATCTGAAGACCTCAAATCTTTTGTTGAATAACCGTGGTGAGTTAAAAAT
EST: gi|211527636|gb|FL412986.1|FL412986
EST:     CAGCTGCTAGAAGGTGTAAAATATCTACATGACAATTGGGTGCTTCATAG                         GGATCTGAAGACCTCAAATCTTTTGTTGAATAACCGTGGTGAGTTAAAAAT
genomic: CAGCTGCTAGAAGGTGTAAAATATCTACATGACAATTGGGTGCTTCATAGgtaattattg ... ttttttacagGGATCTGAAGACCTCAAATCTTTTGTTGAATAACCGTGGTGAGTTAAAAAT
EST: gi|211214733|gb|FL396537.1|FL396537
EST:     CAGCTGCTAGAAGGTGTAAAATATCTACATGACAATTGGGTGCTTCATAG                         GGATCTGAAGACCTCAAATCTTTTGTTGAATAACCGTGGTGAGTTAAAAAT
genomic: CAGCTGCTAGAAGGTGTAAAATATCTACATGACAATTGGGTGCTTCATAGgtaattattg ... ttttttacagGGATCTGAAGACCTCAAATCTTTTGTTGAATAACCGTGGTGAGTTAAAAAT
EST: gi|211527625|gb|FL412975.1|FL412975
EST:     CAGCTGCTAGAAGGTGTAAAATATCTACATGACAATTGGGTGCTTCATAG                         GGATCTGAAGACCTCAAATCTTTTGTTGAATAACCGTGGTGAGTTAAAAAT
genomic: CAGCTGCTAGAAGGTGTAAAATATCTACATGACAATTGGGTGCTTCATAGgtaattattg ... ttttttacagGGATCTGAAGACCTCAAATCTTTTGTTGAATAACCGTGGTGAGTTAAAAAT
EST: gi|211055687|gb|FL451729.1|FL451729
EST:     CAGCTGCTAGAAGGTGTAAAATATCTACATGACAATTGGGTGCTTCATAG                         GGATCTGAAGACCTCAAATCTTTT-TTGAATAACCGTGGTGAGTTAAAAAT
genomic: CAGCTGCTAGAAGGTGTAAAATATCTACATGACAATTGGGTGCTTCATAGgtaattattg ... ttttttacagGGATCTGAAGACCTCAAATCTTTTGTTGAATAACCGTGGTGAGTTAAAAAT
EST: gi|6095722|gb|AW120389.1|AW120389
EST:     CAGCTGCTAGAAGGTGTAAAATATCTACATGACAATTGGGTGCTTCATAG                         GGATCTGAAGACCTCAAATCTTTTGTTGAATAACCG-GGTGAGTTAAAAAT
genomic: CAGCTGCTAGAAGGTGTAAAATATCTACATGACAATTGGGTGCTTCATAGgtaattattg ... ttttttacagGGATCTGAAGACCTCAAATCTTTTGTTGAATAACCGTGGTGAGTTAAAAAT
EST: gi|211219367|gb|FL386088.1|FL386088
EST:     CAGCTGCTAGAAGGTGTAAAATATCTACATGACAATTGGGTGCTTCATAG                         GGATCTGAAGACCTCAAATCTTTTGTTGAATAACCGTGGTGAGTTAAAAAT
genomic: CAGCTGCTAGAAGGTGTAAAATATCTACATGACAATTGGGTGCTTCATAGgtaattattg ... ttttttacagGGATCTGAAGACCTCAAATCTTTTGTTGAATAACCGTGGTGAGTTAAAAAT
EST: gi|6056442|gb|AW090952.1|AW090952
EST:     CAGCTGCTAGAAGGTGTAAAATATCTACATGACAATTGGGTGCTTCATAG                         GGATCTGAAGACCTCAAATCTTTTGTTGAATAACCGTGGTGAGTTAAAAAT
genomic: CAGCTGCTAGAAGGTGTAAAATATCTACATGACAATTGGGTGCTTCATAGgtaattattg ... ttttttacagGGATCTGAAGACCTCAAATCTTTTGTTGAATAACCGTGGTGAGTTAAAAAT
EST: gi|6020498|gb|AW065426.1|AW065426
EST:     AGCTGCTAGAAGGTGT-AGGGAGTGTACATGACAATTGGGTGCTTCATAG                         GGATCTGAAGACCTCAAATCTTTTGTTGAATAACCGTGGTGAGTTAAAAAT
genomic: AGCTGCTAGAAGGTGTAAAATA-TCTACATGACAATTGGGTGCTTCATAGgtaattattg ... ttttttacagGGATCTGAAGACCTCAAATCTTTTGTTGAATAACCGTGGTGAGTTAAAAAT
EST: gi|22543030|gb|BU093468.1|BU093468
EST:     CAGCTGCTAGAAGGTGTAAAATATCTGCATGACAATTGGGTGCTTCATAG                         GGATCTGAAGACCTCAAATCTTTTGTTGAATAACCGTGGGGAGTTAAAAAT
genomic: CAGCTGCTAGAAGGTGTAAAATATCTACATGACAATTGGGTGCTTCATAGgtaattattg ... ttttttacagGGATCTGAAGACCTCAAATCTTTTGTTGAATAACCGTGGTGAGTTAAAAAT

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: 48 (upstream exon), 49 (downstream exon)
Score: 71

AGACCATGAAACAACCATATACCCAAAGCGAGGTAAAGTGTTTGATGCTTCAGCTGCTAGAAGGTGTAAAATATCTACATGACAATTGGGTGCTTCATAGgtaattattg ... ttttttacagGGATCTGAAGACCTCAAATCTTTTGTTGAATAACCGTGGTGAGTTAAAAATATGTGATTTTGGACTGTCTCGTCAATATGGAAGCCCATTAAAACCTTAT


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 43

AGACCATGAAACAACCATATACCCAAAGCGAGGTAAAGTGTTTGATGCTTCAGCTGCTAGAAGGTGTAAAATATCTACATGACAATTGGGTGCTTCATAGgtaattattg ... ttttttacagGGATCTGAAGACCTCAAATCTTTTGTTGAATAACCGTGGTGAGTTAAAAATATGTGATTTTGGACTGTCTCGTCAATATGGAAGCCCATTAAAACCTTAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 78

AGACCATGAAACAACCATATACCCAAAGCGAGGTAAAGTGTTTGATGCTTCAGCTGCTAGAAGGTGTAAAATATCTACATGACAATTGGGTGCTTCATAGgtaattattg ... ttttttacagGGATCTGAAGACCTCAAATCTTTTGTTGAATAACCGTGGTGAGTTAAAAATATGTGATTTTGGACTGTCTCGTCAATATGGAAGCCCATTAAAACCTTAT


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 34

AGACCATGAAACAACCATATACCCAAAGCGAGGTAAAGTGTTTGATGCTTCAGCTGCTAGAAGGTGTAAAATATCTACATGACAATTGGGTGCTTCATAGgtaattattg ... ttttttacagGGATCTGAAGACCTCAAATCTTTTGTTGAATAACCGTGGTGAGTTAAAAATATGTGATTTTGGACTGTCTCGTCAATATGGAAGCCCATTAAAACCTTAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGACCATGAAACAACCATATACCCAAAGCGAGGTAAAGTGTTTGATGCTTCAGCTGCTAGAAGGTGTAAAATATCTACATGACAATTGGGTGCTTCATAGgtaattattgtttgctttcttttttcggttcacgtgttgtcttgaatctgttattgtgttgttgatacatggccagcttttttacag

- - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT