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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACTTTTGAGGGAACAAACCAATTAATATATCCAGAGACTTGGTTCTTTATGCTTGTTGTGGCTACTTGTGTGTTGACTCAGATGAATTATCTGAACAAGgtttgttcaacttgttacacattgctttcattcagtaaccttagttctatgacataactatgtacattctagctgcaaaaatggtatgttgatagagaag...

Basic information

species Zea mays
transcript GRMZM2G120175_T04
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G120175_T03 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os05g43790.2 (Oryza sativa), 5'ss of exon 6
TACTTTTGAGGGAACAAACCAATTAATATATCCAGAGACTTGGTTCTTTATGCTTGTTGTGGCTACTTGTGTGTTGACTCAGATGAATTATCTGAACAAGgtttgttca-----acttgttacacattgctttcattcagtaaccttagttctatgacataactatgtacattctagctgcaaaaatggtatgttgatagagaag
 || |||||||| ||||| || ||  ||||||||||||||||||||||| ||||| | ||||| ||||||||| | || |||||||||||  |||||||||| ||||        |   |    || || |  |||    |     || || ||||   |   |      | || ||||    |   | |   || ||| |    
GACGTTTGAGGGGACAAATCAGTTGGTATATCCAGAGACTTGGTTCTTTGTGCTTATAGTGGCCACTTGTGTGCTAACACAGATGAATTACTTGAACAAGgtctgtttgttaatgcccttagggcactgataccataggtttgtgatatttatatgttctttgtcaaagtactccagctagtcagg-gattgattaataaa----

upper sequence: GRMZM2G120175_T03 (Zea mays), 5'ss of exon 6
lower sequence: Vv06s0009g03650.t01 (Vitis vinifera), 5'ss of exon 6
TACTTTTGAGGGAACAAACCAATTAATATATCCAGAGACTTGGTTCTTTATGCTTGTTGTGGCTACTTGTGTGTTGACTCAGATGAATTATCTGAACAAGgtttgtt-caacttgttacacattgctt-tcattcagtaaccttagttctatgacataactatgtacattctagctgcaaaaatggtatgttgatagagaag
 || ||||||||||  ||||| ||||| | ||| ||||||||||| || ||| | || ||||||| ||||||  | || |||||||||||||| ||||||||| ||    |  || |||   |   || | |     |    |||||  |     |    | | | | |  | |  |  | ||   |   ||| | |     
GACCTTTGAGGGAAAGAACCAGTTAATCTTTCCGGAGACTTGGTTTTTCATGGTGGTGGTGGCTATTTGTGTCATCACACAGATGAATTATCTCAACAAGgttggtaatgaagtgctactgctaatttattagatgattcaattagtcatgcacaagctttgttttcctctttgtggttataacttttgcttgttgggct--
















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|101381796|gb|EB812955.1|EB812955
EST:     CAGATGAATTATCTGAACAAG                         GCACTTGACACGTTCAACACGGCAATTGTATCTCCAATATATTATGTAATG
genomic: CAGATGAATTATCTGAACAAGgtttgttcaa ... tttgctgtagGCACTTGACACGTTCAACACGGCAATTGTATCTCCAATATATTATGTAATG
EST: gi|60354097|gb|DN221070.1|DN221070
EST:     TGCTTGTTGTGGCTACTTGTGTGTTGACTCAGATGAATTATCTGAACAAG                         GCACTTGACACGTTCAACACGGCAATTGTATCTCCAATATATTATGTAATG
genomic: TGCTTGTTGTGGCTACTTGTGTGTTGACTCAGATGAATTATCTGAACAAGgtttgttcaa ... tttgctgtagGCACTTGACACGTTCAACACGGCAATTGTATCTCCAATATATTATGTAATG
EST: gi|78120401|gb|DV538785.1|DV538785
EST:     TGCTTGTTGTGGCTACTTGTGTGTTGACTCAGATGAATTATCTGAACAAG                         GCACTTGACACGTTCAACACGGCAATTGTATCTCCAATATATTATGTAATG
genomic: TGCTTGTTGTGGCTACTTGTGTGTTGACTCAGATGAATTATCTGAACAAGgtttgttcaa ... tttgctgtagGCACTTGACACGTTCAACACGGCAATTGTATCTCCAATATATTATGTAATG
EST: gi|148943740|gb|EC888810.2|EC888810
EST:     TGCTTGTTGTGGCTACTTGTGTGTTGACTCAGATGAATTATCTGAACAAG                         GCACTTGACACGTTCAACACGGCAATTGTATCTCCAATATATTATGTAATG
genomic: TGCTTGTTGTGGCTACTTGTGTGTTGACTCAGATGAATTATCTGAACAAGgtttgttcaa ... tttgctgtagGCACTTGACACGTTCAACACGGCAATTGTATCTCCAATATATTATGTAATG
EST: gi|149085220|gb|EE174728.2|EE174728
EST:     TGCTTGTTGTGGCTACTTGTGTGTTGACTCAGATGAATTATCTGAACAAG                         GCACTTGACACGTTCAACACGGCAATTGTATCTCCAATATATTATGTAATG
genomic: TGCTTGTTGTGGCTACTTGTGTGTTGACTCAGATGAATTATCTGAACAAGgtttgttcaa ... tttgctgtagGCACTTGACACGTTCAACACGGCAATTGTATCTCCAATATATTATGTAATG
EST: gi|76287457|gb|DV027025.1|DV027025
EST:     TGCTTGTTGTGGCTACTTGTGTGTTGACTCAGATGAATTATCTGAACAAG                         GCACTTGACACGTTCAACACGGCAATTGTATCTCCAATATATTATGTAATG
genomic: TGCTTGTTGTGGCTACTTGTGTGTTGACTCAGATGAATTATCTGAACAAGgtttgttcaa ... tttgctgtagGCACTTGACACGTTCAACACGGCAATTGTATCTCCAATATATTATGTAATG
EST: gi|76281094|gb|DV020662.1|DV020662
EST:     TGCTTGTTGTGGCTACTTGTGTGTTGACTCAGATGAATTATCTGAACAAG                         GCACTTGACACGTTTCA-CACGGNCA-TTGTATCTCCAATATATTA
genomic: TGCTTGTTGTGGCTACTTGTGTGTTGACTCAGATGAATTATCTGAACAAGgtttgttcaa ... tttgctgtagGCACTTGACACGTT-CAACACGG-CAATTGTATCTCCAATATATTA

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: 40 (upstream exon), 48 (downstream exon)
Score: 34

TACTTTTGAGGGAACAAACCAATTAATATATCCAGAGACTTGGTTCTTTATGCTTGTTGTGGCTACTTGTGTGTTGACTCAGATGAATTATCTGAACAAGgtttgttcaa ... tttgctgtagGCACTTGACACGTTCAACACGGCAATTGTATCTCCAATATATTATGTAATGTTCACAACTCTTACAATACTTGCCAGCGTCATAATGTTCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 89

TACTTTTGAGGGAACAAACCAATTAATATATCCAGAGACTTGGTTCTTTATGCTTGTTGTGGCTACTTGTGTGTTGACTCAGATGAATTATCTGAACAAGgtttgttcaa ... tttgctgtagGCACTTGACACGTTCAACACGGCAATTGTATCTCCAATATATTATGTAATGTTCACAACTCTTACAATACTTGCCAGCGTCATAATGTTCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 127

TACTTTTGAGGGAACAAACCAATTAATATATCCAGAGACTTGGTTCTTTATGCTTGTTGTGGCTACTTGTGTGTTGACTCAGATGAATTATCTGAACAAGgtttgttcaa ... tttgctgtagGCACTTGACACGTTCAACACGGCAATTGTATCTCCAATATATTATGTAATGTTCACAACTCTTACAATACTTGCCAGCGTCATAATGTTCAAG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 58

TACTTTTGAGGGAACAAACCAATTAATATATCCAGAGACTTGGTTCTTTATGCTTGTTGTGGCTACTTGTGTGTTGACTCAGATGAATTATCTGAACAAGgtttgttcaa ... tttgctgtagGCACTTGACACGTTCAACACGGCAATTGTATCTCCAATATATTATGTAATGTTCACAACTCTTACAATACTTGCCAGCGTCATAATGTTCAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TACTTTTGAGGGAACAAACCAATTAATATATCCAGAGACTTGGTTCTTTATGCTTGTTGTGGCTACTTGTGTGTTGACTCAGATGAATTATCTGAACAAGgtttgttcaacttgttacacattgctttcattcagtaaccttagttctatgacataactatgtacattctagctgcaaaaatggtatgttgatagagaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcaaaaat