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

GAAAGTTATGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTGTACAAAGAGCTTAAACTGGAGgtttgtcctgaccgttccatgttcttatgattctgtttgtaagcatcacggttcgttgttattatctgaaaacaattaaggaggtgttttatttttaggg...

Basic information

species Zea mays
transcript GRMZM2G147721_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147721_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os01g50760.1 (Oryza sativa), 5'ss of exon 10
GAAAGTTATGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTGTACAAAGAGCTTAAACTGGAGgtttgtcctgaccgttccatgttcttatgattctgtttgtaagcatcacggttcgttgttattatctgaaaacaat-taaggaggtgttttatttttaggg----
|||| |||||| ||| | ||||| |  ||||||||||| ||||||||  |||| ||||| ||||| ||||||||||||| | |||||||  |||  ||||| || ||| | | | ||||||    |   || |  || || | |||   || | ||||||   |             
GAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAGgtttgtcttaaccgttctctgtatttatg-ttatgtgtatcatcatcac----ctgagtaaacatatgcagacatcatacgcaggtgtgaaaaagaataattacc
















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|148986684|gb|EE030466.2|EE030466
EST:     CAGCGTGTGTTGCAAAGGTGAAGGACTTGTACAAAGAGCTTAAACTGGAG                         GAGGTTTTCCAGGCGTACGAGAGGGAGAGTTACAACAAGCTGATTGCCGAC
genomic: CAGCGTGTGTTGCAAAGGTGAAGGACTTGTACAAAGAGCTTAAACTGGAGgtttgtcctg ... atgaatccagGAGGTTTTCCAGGCGTACGAGAGGGAGAGTTACAACAAGCTGATTGCCGAC
EST: gi|60355786|gb|DN222759.1|DN222759
EST:     CAGCGTGTGTTGCAAAGGTGAAGGACTTGTACAAAGAGCTTAAACTGGAG                         GAGGTTTTCCAGGCGTACGAGAGGGAGAGTTACAACAAGCTGATTGCCGAC
genomic: CAGCGTGTGTTGCAAAGGTGAAGGACTTGTACAAAGAGCTTAAACTGGAGgtttgtcctg ... atgaatccagGAGGTTTTCCAGGCGTACGAGAGGGAGAGTTACAACAAGCTGATTGCCGAC
EST: gi|148995918|gb|EE035161.2|EE035161
EST:     CAGCGTGTGTTGCAAAGGTGAAGGACTTGTACAAAGAGCTTAAACTGGAG                         GAGGTTTTCCAGGCGTACGAGAGGGAGAGTTACAACAAGCTGATTGCCGAC
genomic: CAGCGTGTGTTGCAAAGGTGAAGGACTTGTACAAAGAGCTTAAACTGGAGgtttgtcctg ... atgaatccagGAGGTTTTCCAGGCGTACGAGAGGGAGAGTTACAACAAGCTGATTGCCGAC
EST: gi|148972760|gb|EE023733.2|EE023733
EST:     CAGCGTGTGTTGCAAAGGTGAAGGACTTGTACAAAGAGCTTAAACTGGAG                         GAGGTTTTCCAGGCGTACGAGAGGGAGAGTTACAACAAGCTGATTGCCGAC
genomic: CAGCGTGTGTTGCAAAGGTGAAGGACTTGTACAAAGAGCTTAAACTGGAGgtttgtcctg ... atgaatccagGAGGTTTTCCAGGCGTACGAGAGGGAGAGTTACAACAAGCTGATTGCCGAC
EST: gi|211433629|gb|FL480968.1|FL480968
EST:     CAGCGTGTGTTGCAAAGGTGAAGGACTTGTACAAAGAGCTTAAACTGGAG                         GAGGTTTTCCAGGCGTACGAGAGGGAGAGTTACAACAAGCTGATTGCCGAC
genomic: CAGCGTGTGTTGCAAAGGTGAAGGACTTGTACAAAGAGCTTAAACTGGAGgtttgtcctg ... atgaatccagGAGGTTTTCCAGGCGTACGAGAGGGAGAGTTACAACAAGCTGATTGCCGAC
EST: gi|166662589|gb|EG268717.1|EG268717
EST:     CAAAGAGCTTAAACTGGAG                         GAGGTTTTCCAGGCGTACGAGAGGGAGAGTTACAACAAGCTGATTGCCGAC
genomic: CAAAGAGCTTAAACTGGAGgtttgtcctg ... atgaatccagGAGGTTTTCCAGGCGTACGAGAGGGAGAGTTACAACAAGCTGATTGCCGAC
EST: gi|211420061|gb|FL460750.1|FL460750
EST:     CAGCGTGTGTTGCAAAGGTGAAGGACTTGTACAAAGAGCTTAAACTGGAG                         GAGGTTTTCCAGGCGTACGAGAGGGAGAGTTACAACAAGCTGATTGCCGAC
genomic: CAGCGTGTGTTGCAAAGGTGAAGGACTTGTACAAAGAGCTTAAACTGGAGgtttgtcctg ... atgaatccagGAGGTTTTCCAGGCGTACGAGAGGGAGAGTTACAACAAGCTGATTGCCGAC
EST: gi|148943252|gb|EC888313.2|EC888313
EST:     CAGCGTGTGTTGCAAAGGTGAAGGACTTGTACAAAGAGCTTAAACTGGAG                         GGGGTTTTCCAGGCGTACGAGAGGGAGAGTTACAACAAGCTGATTGCCGAC
genomic: CAGCGTGTGTTGCAAAGGTGAAGGACTTGTACAAAGAGCTTAAACTGGAGgtttgtcctg ... atgaatccagGAGGTTTTCCAGGCGTACGAGAGGGAGAGTTACAACAAGCTGATTGCCGAC
EST: gi|110950036|gb|EE170193.1|EE170193
EST:     CGGGTGGTTGCCAAAGGGGGAAGGACTTGTACAAAGAGCTTAAACTGGAG                         GAGGTTTTCCAGGCGTACGAGAGGGAGAGTTACAACAAGCTGATTGCCGAC
genomic: CGTGT-GTTG-CAAA-GGTGAAGGACTTGTACAAAGAGCTTAAACTGGAGgtttgtcctg ... atgaatccagGAGGTTTTCCAGGCGTACGAGAGGGAGAGTTACAACAAGCTGATTGCCGAC
EST: gi|111189546|gb|EE287682.1|EE287682
EST:     CAGCGTGTGTTGCAAAGGTGAAGGACTTGTACAAAGAGCTTAAACTGGAG                         GAGGTTTTCCAGGCGTACGAGAGGGAGAGTTACAACAAGCTGATTGCCGAC
genomic: CAGCGTGTGTTGCAAAGGTGAAGGACTTGTACAAAGAGCTTAAACTGGAGgtttgtcctg ... atgaatccagGAGGTTTTCCAGGCGTACGAGAGGGAGAGTTACAACAAGCTGATTGCCGAC

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: 79

GAAAGTTATGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTGTACAAAGAGCTTAAACTGGAGgtttgtcctg ... atgaatccagGAGGTTTTCCAGGCGTACGAGAGGGAGAGTTACAACAAGCTGATTGCCGACATCGAGGCCCAGCCCAGCAAGGCAGTCCAGAGTGTTTTGAAGTCCTTCC


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

GAAAGTTATGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTGTACAAAGAGCTTAAACTGGAGgtttgtcctg ... atgaatccagGAGGTTTTCCAGGCGTACGAGAGGGAGAGTTACAACAAGCTGATTGCCGACATCGAGGCCCAGCCCAGCAAGGCAGTCCAGAGTGTTTTGAAGTCCTTCC


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 113

GAAAGTTATGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTGTACAAAGAGCTTAAACTGGAGgtttgtcctg ... atgaatccagGAGGTTTTCCAGGCGTACGAGAGGGAGAGTTACAACAAGCTGATTGCCGACATCGAGGCCCAGCCCAGCAAGGCAGTCCAGAGTGTTTTGAAGTCCTTCC


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 93

GAAAGTTATGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTGTACAAAGAGCTTAAACTGGAGgtttgtcctg ... atgaatccagGAGGTTTTCCAGGCGTACGAGAGGGAGAGTTACAACAAGCTGATTGCCGACATCGAGGCCCAGCCCAGCAAGGCAGTCCAGAGTGTTTTGAAGTCCTTCC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAAGTTATGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTGTACAAAGAGCTTAAACTGGAGgtttgtcctgaccgttccatgttcttatgattctgtttgtaagcatcacggttcgttgttattatctgaaaacaattaaggaggtgttttatttttaggg

- - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaacaa