Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgatatccatagaggtttttctttgttttcttcattgtctttgctttgatgagactgttcttggataatttcatggaatgcactcttgttgtttcggtagGTGCAAGGATAGGCAACAAGTGTTCAAAAACACGTCTGTGGATCAATTGACTTGTATTTCAGCCTTTCAGTTGAGGATTAAAGTGGAGGTTTAAGAAGCT

Basic information

species Zea mays
transcript GRMZM2G162175_T04
intron # 1
splice site 3'
intron type U2

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|32825440|gb|CD965162.1|CD965162
EST:     AGGACGAGAGCGTGCAAGAAGAGAAGGCCCGTGTCAGCCGGCGGCTATAG                         GTGCAAGGATAGGCAACAAGTGTTCAAAAACACGTCTGTGGATCAATTGAC
genomic: AGGACGAGAGCGTGCAAGAAGAGAAGGCCCGTGTCAGGCGGCGGCTATAGgtattggcct ... gtttcggtagGTGCAAGGATAGGCAACAAGTGTTCAAAAACACGTCTGTGGATCAATTGAC
EST: gi|76925183|gb|DV170318.1|DV170318
EST:     AGGACGAGAGCGTGCAAGAAGAGAAGGCCCGTGTCAGGCGGCGGCTATAG                         GTGCAAGGATAGGCAACAAGTGTTCAAAAACACGTCTGTGGATCAATTGAC
genomic: AGGACGAGAGCGTGCAAGAAGAGAAGGCCCGTGTCAGGCGGCGGCTATAGgtattggcct ... gtttcggtagGTGCAAGGATAGGCAACAAGTGTTCAAAAACACGTCTGTGGATCAATTGAC
EST: gi|149084680|gb|EE174165.2|EE174165
EST:     AGGACGAGAGCGTGCAAGAAGAGAAGGCCCGTGTCAGGCGGCGGCTATAG                         GTGCAAGGATAGGCAACAAGTGTTCAAAAACACGTCTGTGGATCAATTGAC
genomic: AGGACGAGAGCGTGCAAGAAGAGAAGGCCCGTGTCAGGCGGCGGCTATAGgtattggcct ... gtttcggtagGTGCAAGGATAGGCAACAAGTGTTCAAAAACACGTCTGTGGATCAATTGAC
EST: gi|211239856|gb|FL007408.1|FL007408
EST:     AGGACGAGAGCGTGCAAGAAGAGAAGGCCCGTGTCAGGCGGCGGCTATAG                         GTGCAAGGATAGGCAACAAGTGTTCAAAAACACGTCTGTG
genomic: AGGACGAGAGCGTGCAAGAAGAGAAGGCCCGTGTCAGGCGGCGGCTATAGgtattggcct ... gtttcggtagGTGCAAGGATAGGCAACAAGTGTTCAAAAACACGTCTGTG
EST: gi|149096944|gb|EE182743.2|EE182743
EST:     AGGACGAGAGCGTGCAAGAAGAGAAGGCCCGTGTCAGGCGGCGGCTATAG                         GTGCAAGGATAGGCAACAAGTGTTCAAAAACACGTCTGTGGATCAATTGAC
genomic: AGGACGAGAGCGTGCAAGAAGAGAAGGCCCGTGTCAGGCGGCGGCTATAGgtattggcct ... gtttcggtagGTGCAAGGATAGGCAACAAGTGTTCAAAAACACGTCTGTGGATCAATTGAC
EST: gi|50329441|gb|CO524567.1|CO524567
EST:     AGGACGAGAGCGTGCAAGAAGAGAAGGCCCGTGTCAGGCGGCGGCTATAG                         GTGCAAGGATAGGCAACAAGTGTTCAAAAACACGTCTGTGGATCAATTGAC
genomic: AGGACGAGAGCGTGCAAGAAGAGAAGGCCCGTGTCAGGCGGCGGCTATAGgtattggcct ... gtttcggtagGTGCAAGGATAGGCAACAAGTGTTCAAAAACACGTCTGTGGATCAATTGAC
EST: gi|149078131|gb|EE166880.2|EE166880
EST:     AGGACGAGAGCGTGCAAGAAGAGAAGGCCCGTGTCAGGCGGCGGCTATAG                         GTGCAAGGATAGGCAACAAGTGTTCAAAAACACGTCTGTGGATCAATTGAC
genomic: AGGACGAGAGCGTGCAAGAAGAGAAGGCCCGTGTCAGGCGGCGGCTATAGgtattggcct ... gtttcggtagGTGCAAGGATAGGCAACAAGTGTTCAAAAACACGTCTGTGGATCAATTGAC
EST: gi|74240567|gb|DT648481.1|DT648481
EST:     AGGACGAGAGCGTGCAAGAAGAGAAGGCCCGTGTCAGGCGGCGGCTATAG                         GTGCAAGGATAGGCAACAAGTGTTCAAAAACACGTCTGTGGATCAATTGAC
genomic: AGGACGAGAGCGTGCAAGAAGAGAAGGCCCGTGTCAGGCGGCGGCTATAGgtattggcct ... gtttcggtagGTGCAAGGATAGGCAACAAGTGTTCAAAAACACGTCTGTGGATCAATTGAC
EST: gi|101382866|gb|EB813487.1|EB813487
EST:     AGGACGAGAGCGTGCAAGAAGAGAAGGCCCGTGTCAGGCGGCGGCTATAG                         GTGCAAGGATAGGCAACAAGTGTTCAAAAACACGTCTGTGGATCAATTGAC
genomic: AGGACGAGAGCGTGCAAGAAGAGAAGGCCCGTGTCAGGCGGCGGCTATAGgtattggcct ... gtttcggtagGTGCAAGGATAGGCAACAAGTGTTCAAAAACACGTCTGTGGATCAATTGAC
EST: gi|76012159|gb|DT939329.1|DT939329
EST:     AGGACGAGAGCGTGCAAGAAGAGAAGGCCCGTGTCAGGCGGCGGCTATAG                         GTGCAAGGATAGGCAACAAGTGTTCAAAAACACGTCTGTGGATCAATTGAC
genomic: AGGACGAGAGCGTGCAAGAAGAGAAGGCCCGTGTCAGGCGGCGGCTATAGgtattggcct ... gtttcggtagGTGCAAGGATAGGCAACAAGTGTTCAAAAACACGTCTGTGGATCAATTGAC
EST: gi|149013590|gb|EE043059.2|EE043059
EST:     AGGACGAGAGCGTGCAAGAAGAGAAGGCCCGTGTCAGGCGGCGGCTATAG                         GTGCAAGGATAGGCAACAAGTGTTCAAAAACACGTCTGTGGATCAATTGAC
genomic: AGGACGAGAGCGTGCAAGAAGAGAAGGCCCGTGTCAGGCGGCGGCTATAGgtattggcct ... gtttcggtagGTGCAAGGATAGGCAACAAGTGTTCAAAAACACGTCTGTGGATCAATTGAC
EST: gi|148969813|gb|EE020704.2|EE020704
EST:     AGGACGAGAGCGTGCAAGAAGAGAAGGCCCGTGTCAGGCGGCGGCTATAG                         GTGCAAGGATAGGCAACAAGTGTTCAAAAACACGTCTGTGGATCAATTGAC
genomic: AGGACGAGAGCGTGCAAGAAGAGAAGGCCCGTGTCAGGCGGCGGCTATAGgtattggcct ... gtttcggtagGTGCAAGGATAGGCAACAAGTGTTCAAAAACACGTCTGTGGATCAATTGAC
EST: gi|78119801|gb|DV538185.1|DV538185
EST:     AGGACGAGAGCGTGCAAGAAGAGAAGGCCCGTGTCAGGCGGCGGCTATAG                         GTGCAAGGATAGGCAACAAGTGTTCAAAAACACGTCTGTGGATCAATTGAC
genomic: AGGACGAGAGCGTGCAAGAAGAGAAGGCCCGTGTCAGGCGGCGGCTATAGgtattggcct ... gtttcggtagGTGCAAGGATAGGCAACAAGTGTTCAAAAACACGTCTGTGGATCAATTGAC
EST: gi|149110902|gb|EE294399.2|EE294399
EST:     AGGACGAGAGCGTGCAAGAAGAGAAGGCCCGTGTCAGGCGGCGGCTATAG                         GTGCAAGGATAGGCAACAAGTGTTCAAAAACACGTCTGTGGATCAATTGAC
genomic: AGGACGAGAGCGTGCAAGAAGAGAAGGCCCGTGTCAGGCGGCGGCTATAGgtattggcct ... gtttcggtagGTGCAAGGATAGGCAACAAGTGTTCAAAAACACGTCTGTGGATCAATTGAC
EST: gi|149109833|gb|EE293628.2|EE293628
EST:     AGGACGAGAGCGTGCAAGAAGAGAAGGCCCGTGTCAGGCGGCGGCTATAG                         GTGCAAGGATAGGCAACAAGTGTTCAAAAACACGTCTGTGGATCAATTGAC
genomic: AGGACGAGAGCGTGCAAGAAGAGAAGGCCCGTGTCAGGCGGCGGCTATAGgtattggcct ... gtttcggtagGTGCAAGGATAGGCAACAAGTGTTCAAAAACACGTCTGTGGATCAATTGAC
EST: gi|31359391|gb|CD443748.1|CD443748
EST:     AGGACGAGAGCGTGCAAGAAGAGAAGGCCCGTGTCAGGCGGCGGCTATAG                         GTGCAAGGATAAGCAACAAGTCTTCAAAAACACGTCTGTGGATCAATTGAC
genomic: AGGACGAGAGCGTGCAAGAAGAGAAGGCCCGTGTCAGGCGGCGGCTATAGgtattggcct ... gtttcggtagGTGCAAGGATAGGCAACAAGTGTTCAAAAACACGTCTGTGGATCAATTGAC
EST: gi|74243679|gb|DT651593.1|DT651593
EST:     AGGACGAGAGCGTGCAAGAAGAGAAGGCCCGTGTCAGGCGGCGGCTATAG                         GTGCAAGGATAGGCAACAAGTGTTCAAAAACACGTCTGTGGATCAATTGAC
genomic: AGGACGAGAGCGTGCAAGAAGAGAAGGCCCGTGTCAGGCGGCGGCTATAGgtattggcct ... gtttcggtagGTGCAAGGATAGGCAACAAGTGTTCAAAAACACGTCTGTGGATCAATTGAC
EST: gi|29130093|gb|CB380797.1|CB380797
EST:     AGGACGAGAGCGTGCAAGAAGAGAAGGNCCGTGTCAGGCGGCGGCTATAG                         GTGCAAGGATAGGCAACAAGGGTTCAAAAACACGTCTGTGGATCAATTGAC
genomic: AGGACGAGAGCGTGCAAGAAGAGAAGGCCCGTGTCAGGCGGCGGCTATAGgtattggcct ... gtttcggtagGTGCAAGGATAGGCAACAAGTGTTCAAAAACACGTCTGTGGATCAATTGAC
EST: gi|148938224|gb|EC882513.2|EC882513
EST:     AGGACGAGAGCGTGCAAGAAGAGAAGGCCCGTGTCAGGCGGCGGCTATAG                         GTGCAAGGATAGGCAACAAGTGTTCAAAAACACGTCTGTGGATCAATTGAC
genomic: AGGACGAGAGCGTGCAAGAAGAGAAGGCCCGTGTCAGGCGGCGGCTATAGgtattggcct ... gtttcggtagGTGCAAGGATAGGCAACAAGTGTTCAAAAACACGTCTGTGGATCAATTGAC
EST: gi|71445078|gb|DR826128.1|DR826128
EST:     AGGACGAGAGCGTGCAAGAAGAGAAGGCCCGTGTCAGGCGGCGGCTATAG                         GTGCAAGGATAGGCAACAAGTGTTCAAAAACACGTCTGTGGATCAATTGAC
genomic: AGGACGAGAGCGTGCAAGAAGAGAAGGCCCGTGTCAGGCGGCGGCTATAGgtattggcct ... gtttcggtagGTGCAAGGATAGGCAACAAGTGTTCAAAAACACGTCTGTGGATCAATTGAC

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: 46 (upstream exon), 45 (downstream exon)
Score: 78

ACCCTATCTAGGAGACGGAGCGGCGGGCCAGCGGCTACGCGGGCAAAGAGAGGACGAGAGCGTGCAAGAAGAGAAGGCCCGTGTCAGGCGGCGGCTATAGgtattggcct ... gtttcggtagGTGCAAGGATAGGCAACAAGTGTTCAAAAACACGTCTGTGGATCAATTGACTTGTATTTCAGCCTTTCAGTTGAGGATTAAAGTGGAGGTTTAAGAAGCT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 70

ACCCTATCTAGGAGACGGAGCGGCGGGCCAGCGGCTACGCGGGCAAAGAGAGGACGAGAGCGTGCAAGAAGAGAAGGCCCGTGTCAGGCGGCGGCTATAGgtattggcct ... gtttcggtagGTGCAAGGATAGGCAACAAGTGTTCAAAAACACGTCTGTGGATCAATTGACTTGTATTTCAGCCTTTCAGTTGAGGATTAAAGTGGAGGTTTAAGAAGCT


Block sizes: 46 (upstream exon), 45 (downstream exon)
Score: 50

ACCCTATCTAGGAGACGGAGCGGCGGGCCAGCGGCTACGCGGGCAAAGAGAGGACGAGAGCGTGCAAGAAGAGAAGGCCCGTGTCAGGCGGCGGCTATAGgtattggcct ... gtttcggtagGTGCAAGGATAGGCAACAAGTGTTCAAAAACACGTCTGTGGATCAATTGACTTGTATTTCAGCCTTTCAGTTGAGGATTAAAGTGGAGGTTTAAGAAGCT


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 51

ACCCTATCTAGGAGACGGAGCGGCGGGCCAGCGGCTACGCGGGCAAAGAGAGGACGAGAGCGTGCAAGAAGAGAAGGCCCGTGTCAGGCGGCGGCTATAGgtattggcct ... gtttcggtagGTGCAAGGATAGGCAACAAGTGTTCAAAAACACGTCTGTGGATCAATTGACTTGTATTTCAGCCTTTCAGTTGAGGATTAAAGTGGAGGTTTAAGAAGCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgatgagactgttcttggataatttcatggaatgcactcttgttgtttcggtagGTGCAAGGATAGGCAACAAGTGTTCAAAAACACGTCTGTGGATCAATTGACTTGTATTTCAGCCTTTCAGTTGAGGATTAAAGTGGAGGTTTAAGAAGCT
 ctttgat  putative branch site (score: 51)
                                           ttgtttc  putative PPT
                   ataatttcat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgatatccatagaggtttttctttgttttcttcattgtctttgctttgatgagactgttcttggataatttcatggaatgcactcttgttgtttcggtagGTGCAAGGATAGGCAACAAGTGTTCAAAAACACGTCTGTGGATCAATTGACTTGTATTTCAGCCTTTCAGTTGAGGATTAAAGTGGAGGTTTAAGAAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC