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

ACATCAAGAATTAATTATAAGATCATTGTTGGCTGCAAGGGATGCTTGCCTTGAGATAAGGCTTCACATGCGAGAGATGGGCATAGCAGCTGGTGTTCCAgtaaggtcccctatacataactgcaagtactgtagtatagcatgctcgaaggaagtatattcagtatgacgtttggcataatcacagcagtatgggtgactaagttacgaaattgtaggtataatataacagggtcaatattcttattcaatcttgtttgacatctttgccctaattttgtag

Basic information

species Zea mays
transcript GRMZM2G030839_T02
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G030839_T02 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os03g14830.1 (Oryza sativa), 5'ss of exon 9
ACATCAAGAATTAATTATAAGATCATTGTTGGCTGCAAGGGATGCTTGCCTTGAGATAAGGCTTCACATGCGAGAGATGGGCATAGCAGCTGGTGTTCCAgtaagg------tcccctatacataactgcaagtactgtagtatagcatgctcgaaggaagtatattcagtatgacgtttggcataatcacagcagtatgggtgactaagttacgaaattgtaggtataatataacagggtcaatattcttattcaatcttgtttgacatctttgccctaattttgtag
|||||||||| ||||| | ||||||||  |||| ||||| ||||||| |||||| ||||||||||| ||||||||||||||||||||||||||||||||||||||       |||  |  |   || |     |  || || ||| |||| ||||        | |||   |||  |  ||||||| | ||| |   |    |   | || ||  || ||||||       ||||  ||| || |||  | ||  |  | ||| |     | ||| ||| |||||| ||
ACATCAAGAACTAATTGTTAGATCATTACTGGCCGCAAGAGATGCTTTCCTTGAAATAAGGCTTCATATGCGAGAGATGGGCATAGCAGCTGGTGTTCCAgtaagacttagttccttttaatgaaattatggatgttgaag-ataacatgatcgat-------tcttctacatggtggctggcatagttacatctagacaaattgtttagctattaatttgtag-------ataatggggacattatagtaatatacacctgtct-----cgttgtcctcattttgcag
















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|211419603|gb|FL445135.1|FL445135
EST:     TTGAGATAAGGCTTCACATGCGAGAGATGGGCATAGCAGCTGGTGNTCCA                         ATTGAGCCAGATTCACAAACACGGCTACTAGATGCCACTATGAATATGGAG
genomic: TTGAGATAAGGCTTCACATGCGAGAGATGGGCATAGCAGCTGGTGTTCCAgtaaggtccc ... aattttgtagATTGAGCCAGATTCACAAACACGGCTACTAGATGCCACTATGAATATGGAG
EST: gi|149015115|gb|EE044876.2|EE044876
EST:     TTGAGATAAGGCTTCACATGCGAGAGATGGGCATAGCAGCTGGTGTTCCA                         ATTGAGCCAGATTCACAAACACGGCTACTAGATGCCACTATGAATATGGAG
genomic: TTGAGATAAGGCTTCACATGCGAGAGATGGGCATAGCAGCTGGTGTTCCAgtaaggtccc ... aattttgtagATTGAGCCAGATTCACAAACACGGCTACTAGATGCCACTATGAATATGGAG
EST: gi|211002004|gb|FL458771.1|FL458771
EST:     TTGAGATAAGGCTTCACATGCGAGAGATGGGCATAGCAGCTGGTGTTCCA                         ATTGAGCCAGATTCACAAACACGGCTACTAGATGCCACTATGAATATGGAG
genomic: TTGAGATAAGGCTTCACATGCGAGAGATGGGCATAGCAGCTGGTGTTCCAgtaaggtccc ... aattttgtagATTGAGCCAGATTCACAAACACGGCTACTAGATGCCACTATGAATATGGAG
EST: gi|60346805|gb|DN213778.1|DN213778
EST:     TTGAGATAAGGCTTCACATGCGAGAGATGGGCATAGCAGCTGGTGTTCCA                         ATTGAGCCAGATTCACAAACACGGCTACTAGATGCCACTATGAATATGGAG
genomic: TTGAGATAAGGCTTCACATGCGAGAGATGGGCATAGCAGCTGGTGTTCCAgtaaggtccc ... aattttgtagATTGAGCCAGATTCACAAACACGGCTACTAGATGCCACTATGAATATGGAG
EST: gi|31664397|gb|CD573122.1|CD573122
EST:     TTGAGATAAGGCTTCACATGCGAGAGATGGGCATAGCAGCTGGTGTTCCA                         ATTGAGCCAGATTCACAAACNCGGCTACTAGATGCCACTATGAATATGGAG
genomic: TTGAGATAAGGCTTCACATGCGAGAGATGGGCATAGCAGCTGGTGTTCCAgtaaggtccc ... aattttgtagATTGAGCCAGATTCACAAACACGGCTACTAGATGCCACTATGAATATGGAG
EST: gi|60344724|gb|DN211697.1|DN211697
EST:     TTGAGATAAGGCTTCACATGCGAGAGATGGGCATAGCAGCTGGTGTTCCA                         ATTGAGCCAGATTCACAAACACGGCTACTAGATGCCACTATGAATATGGAG
genomic: TTGAGATAAGGCTTCACATGCGAGAGATGGGCATAGCAGCTGGTGTTCCAgtaaggtccc ... aattttgtagATTGAGCCAGATTCACAAACACGGCTACTAGATGCCACTATGAATATGGAG
EST: gi|30307085|gb|CD001758.1|CD001758
EST:     TTGAGATAAGGCTTCACATGCGAGAGATGGGCATAGCAGCTGGTGTTCCA                         ATTGAGCCAGATTCACAAACACGGCTACTAGATGCCACTATGAATATGGAG
genomic: TTGAGATAAGGCTTCACATGCGAGAGATGGGCATAGCAGCTGGTGTTCCAgtaaggtccc ... aattttgtagATTGAGCCAGATTCACAAACACGGCTACTAGATGCCACTATGAATATGGAG
EST: gi|149108945|gb|EE189920.2|EE189920
EST:     GTGAGATAAGGCTTCACATGCGAGAGATGGGCATAGCAGCTGGTGTTCCA                         ATTGAGCCAGATTCACAAACACGGCTACTAGATGCCACTATGAATATGGAG
genomic: TTGAGATAAGGCTTCACATGCGAGAGATGGGCATAGCAGCTGGTGTTCCAgtaaggtccc ... aattttgtagATTGAGCCAGATTCACAAACACGGCTACTAGATGCCACTATGAATATGGAG
EST: gi|31664517|gb|CD573450.1|CD573450
EST:     TTGAGATAAGGCTTCACATGCGAGAGATGGGCATAGCAGCTGGTGTTCCA                         ATTGAGCCAGATTCACAAACACGGCTACTAGATGCCACTATGAATATGGAG
genomic: TTGAGATAAGGCTTCACATGCGAGAGATGGGCATAGCAGCTGGTGTTCCAgtaaggtccc ... aattttgtagATTGAGCCAGATTCACAAACACGGCTACTAGATGCCACTATGAATATGGAG
EST: gi|30306453|gb|CD001126.1|CD001126
EST:     TTGAGATAAGGCTTCACATGCGAGAGATGGGCATAGCAGCTGGTGTTCCA                         ATTGAGCCAGATTCACAAACACGGCTACTAGATGCCACTATGAATATGGAG
genomic: TTGAGATAAGGCTTCACATGCGAGAGATGGGCATAGCAGCTGGTGTTCCAgtaaggtccc ... aattttgtagATTGAGCCAGATTCACAAACACGGCTACTAGATGCCACTATGAATATGGAG

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: 68

ACATCAAGAATTAATTATAAGATCATTGTTGGCTGCAAGGGATGCTTGCCTTGAGATAAGGCTTCACATGCGAGAGATGGGCATAGCAGCTGGTGTTCCAgtaaggtccc ... aattttgtagATTGAGCCAGATTCACAAACACGGCTACTAGATGCCACTATGAATATGGAGGGTGTTTTACTGGCTGGAGTTCCGGGAGCTGGTGGCTTCGATGCAGTGT


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 22

ACATCAAGAATTAATTATAAGATCATTGTTGGCTGCAAGGGATGCTTGCCTTGAGATAAGGCTTCACATGCGAGAGATGGGCATAGCAGCTGGTGTTCCAgtaaggtccc ... aattttgtagATTGAGCCAGATTCACAAACACGGCTACTAGATGCCACTATGAATATGGAGGGTGTTTTACTGGCTGGAGTTCCGGGAGCTGGTGGCTTCGATGCAGTGT


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 53

ACATCAAGAATTAATTATAAGATCATTGTTGGCTGCAAGGGATGCTTGCCTTGAGATAAGGCTTCACATGCGAGAGATGGGCATAGCAGCTGGTGTTCCAgtaaggtccc ... aattttgtagATTGAGCCAGATTCACAAACACGGCTACTAGATGCCACTATGAATATGGAGGGTGTTTTACTGGCTGGAGTTCCGGGAGCTGGTGGCTTCGATGCAGTGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 69

ACATCAAGAATTAATTATAAGATCATTGTTGGCTGCAAGGGATGCTTGCCTTGAGATAAGGCTTCACATGCGAGAGATGGGCATAGCAGCTGGTGTTCCAgtaaggtccc ... aattttgtagATTGAGCCAGATTCACAAACACGGCTACTAGATGCCACTATGAATATGGAGGGTGTTTTACTGGCTGGAGTTCCGGGAGCTGGTGGCTTCGATGCAGTGT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACATCAAGAATTAATTATAAGATCATTGTTGGCTGCAAGGGATGCTTGCCTTGAGATAAGGCTTCACATGCGAGAGATGGGCATAGCAGCTGGTGTTCCAgtaaggtcccctatacataactgcaagtactgtagtatagcatgctcgaaggaagtatattcagtatgacgtttggcataatcacagcagtatgggtgactaagttacgaaattgtaggtataatataacagggtcaatattcttattcaatcttgtttgacatctttgccctaattttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG