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

gtgagtattggaatttagaaccaagattttgcaagataggatcatgctttttaactcggagcatgcagtacagtaccgtagttgctttctacatttcagAAGTTGGTGAGCAGAAAAAGAAGAGGATCAAGTCTGATACAGATTCTGCACGATTTTCTGCTGCATCTATGAGGAATCAACTTGACCAAGCTGCAAGCCT

Basic information

species Zea mays
transcript GRMZM5G862959_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G862959_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os12g19350.1 (Oryza sativa), 3'ss of exon 3
gtgagtattggaatttagaaccaagattttgcaagataggatcatg-ctttttaactcggagcatgcagtacagtaccgtagttgctttctacattt-cagAAGTTGGTGAGCAGAAAAAGAAGAGGATCAAGTCTGATACAGATTCTGCACGATTTTCTGCTGCATCTATGAGGAATCAACTTGACCAAGCTGCAAGCCT
|| || | | |||         |||||||||| ||  ||| ||| | |   |||     ||||||| |  ||        || ||||| |||||||| ||||||||||||||||||||||||||||||| ||||||||||||||| || ||||||| ||  |||||||||||||||  ||||||||||||||| ||| |||
gtaagcactagaa---------aagattttgcgagtcaggttcaggacaaattattgttgagcatgaaaaac-----taaagatgcttgctacatttgcagAAGTTGGTGAGCAGAAAAAGAAGAGGATGAAGTCTGATACAGATACTACACGATTCTCCTCTGCATCTATGAGGAGCCAACTTGACCAAGCTACAAACCT
















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|4753396|gb|AI657306.1|AI657306
EST:     AGATGGTTTGTTGCAATCTGGAGCTTCAACTGCACAAAAGAAAAAGATAG                         AAGTTGGTGAGCAGAAAAAGAAGAGGATCAAGTCTGATACAGATTCTGCAC
genomic: AGATGGTTTGTTGCAATCTGGAGCTTCAACTGCACAAAAGAAAAAGATAGgtgagtattg ... tacatttcagAAGTTGGTGAGCAGAAAAAGAAGAGGATCAAGTCTGATACAGATTCTGCAC
EST: gi|148974314|gb|EE025087.2|EE025087
EST:     AGATGGTTTGTTGCAATCTGGAGCTTCAACTGCACAAAAGAAAAAGATAG                         AAGTTGGTGAGCAGAAAAAGAAGAGGATCAAGTCTGATACAGATTCTGCAC
genomic: AGATGGTTTGTTGCAATCTGGAGCTTCAACTGCACAAAAGAAAAAGATAGgtgagtattg ... tacatttcagAAGTTGGTGAGCAGAAAAAGAAGAGGATCAAGTCTGATACAGATTCTGCAC
EST: gi|29944945|gb|CB815389.1|CB815389
EST:     AGATGGTTTGTTGCAATCTGGAGCTTCAACTGCACAAAAGAAAAAGATAG                         ---TTGGTGAGCAGAAAAAGAAGAGGATCAAGTCTGATACAGATTCTGCAC
genomic: AGATGGTTTGTTGCAATCTGGAGCTTCAACTGCACAAAAGAAAAAGATAGgtgagtattg ... tacatttcagAAGTTGGTGAGCAGAAAAAGAAGAGGATCAAGTCTGATACAGATTCTGCAC
EST: gi|31358058|gb|CD442415.1|CD442415
EST:     AGATGGTTTGTTGCAATCTGGAGCTTCAACTGCACAAAAGAAAAAGATAG                         AAGTTGGTGAGCAGAAAAAGAAGAGGATCAAGTCTGATACAGATTCTGCAC
genomic: AGATGGTTTGTTGCAATCTGGAGCTTCAACTGCACAAAAGAAAAAGATAGgtgagtattg ... tacatttcagAAGTTGGTGAGCAGAAAAAGAAGAGGATCAAGTCTGATACAGATTCTGCAC
EST: gi|211484294|gb|FL254344.1|FL254344
EST:     AGATGGTTTGTTGCAATCTGGAGCTTCAACTGCACAAAAGAAAAAGATAG                         AAGTTGGTGAGCAGAWAAAGAAGAGGATCAAGTCTGATACAGATTCTGCAC
genomic: AGATGGTTTGTTGCAATCTGGAGCTTCAACTGCACAAAAGAAAAAGATAGgtgagtattg ... tacatttcagAAGTTGGTGAGCAGAAAAAGAAGAGGATCAAGTCTGATACAGATTCTGCAC
EST: gi|211487166|gb|FL254349.1|FL254349
EST:     AGATGGTTTGTTGCAATCTGGAGCTTCAACTGCACAAAAGAAAAAGATAG                         AAGTTGGTGAGCAGAAAAAGAAGAGGATCAAGTCTGATACAGATTCTGCAC
genomic: AGATGGTTTGTTGCAATCTGGAGCTTCAACTGCACAAAAGAAAAAGATAGgtgagtattg ... tacatttcagAAGTTGGTGAGCAGAAAAAGAAGAGGATCAAGTCTGATACAGATTCTGCAC
EST: gi|50326336|gb|CO521462.1|CO521462
EST:     AGATGGTTTGTTGCAATCTGGAGCTTCAACTGCACAAAAGAAAAAGATAG                         AAGTTGGTGAGCAGAAAAAGAAGAGGATCAAGTCTGATACAGATTCTGCAC
genomic: AGATGGTTTGTTGCAATCTGGAGCTTCAACTGCACAAAAGAAAAAGATAGgtgagtattg ... tacatttcagAAGTTGGTGAGCAGAAAAAGAAGAGGATCAAGTCTGATACAGATTCTGCAC
EST: gi|211384387|gb|FL373404.1|FL373404
EST:     AGATGGTTTGTTGCAATCTGGAGCTTCAACTGCACAAAAGAAAAAGATAG                         AAGTTGGTGAGCAGAAAAAGAAGAGGATCAAGTCTGATACAGATTCTGCAC
genomic: AGATGGTTTGTTGCAATCTGGAGCTTCAACTGCACAAAAGAAAAAGATAGgtgagtattg ... tacatttcagAAGTTGGTGAGCAGAAAAAGAAGAGGATCAAGTCTGATACAGATTCTGCAC
EST: gi|211484291|gb|FL254341.1|FL254341
EST:     AGATGGTTTGTTGCAATCTGGAGCTTCAACTGCWCWAAAGAAAWAGATAG                         AAGTTGGTGAGCAGAAAAAGAAGAGGATCAAGTCTGATACAGATTCTGCAC
genomic: AGATGGTTTGTTGCAATCTGGAGCTTCAACTGCACAAAAGAAAAAGATAGgtgagtattg ... tacatttcagAAGTTGGTGAGCAGAAAAAGAAGAGGATCAAGTCTGATACAGATTCTGCAC
EST: gi|32914541|gb|CF019353.1|CF019353
EST:     AGATGGTTTGTTGCAATCTGGAGCTTCAACTGCACAAAAGAAAAAGATAG                         AAGTTGGTGAGCAGAAAAAGAAGAGGATCAAGTCTGATACAGATTCTGCAC
genomic: AGATGGTTTGTTGCAATCTGGAGCTTCAACTGCACAAAAGAAAAAGATAGgtgagtattg ... tacatttcagAAGTTGGTGAGCAGAAAAAGAAGAGGATCAAGTCTGATACAGATTCTGCAC
EST: gi|28873324|gb|CB329328.1|CB329328
EST:     AGATGGTTTGTTGCAATCTGGAGCTTCAACTGCACAAAAGAAAAAGATAG                         AAGTTGGTGAGCAGAAAAAGAAGAGGATCAAGTCTGATACAGATTCTGCAC
genomic: AGATGGTTTGTTGCAATCTGGAGCTTCAACTGCACAAAAGAAAAAGATAGgtgagtattg ... tacatttcagAAGTTGGTGAGCAGAAAAAGAAGAGGATCAAGTCTGATACAGATTCTGCAC
EST: gi|211484296|gb|FL254346.1|FL254346
EST:     AGATGGTTTGTTGCAATCTGGAGCTTCAACTGCACAAAAGAAAAAGATAG                         ---TTGGTGAGCAGAAAAAGAAGAGGATCAAGTCTGATACAGATTCTGCAC
genomic: AGATGGTTTGTTGCAATCTGGAGCTTCAACTGCACAAAAGAAAAAGATAGgtgagtattg ... tacatttcagAAGTTGGTGAGCAGAAAAAGAAGAGGATCAAGTCTGATACAGATTCTGCAC
EST: gi|93012241|gb|EB637761.1|EB637761
EST:     AGATGGTTTGTTGCAATCTGGAGCTTCAACTGCACAAAAGAAAAAGATAG                         AAGTTGGTGAGCAGAAAAAGAAGAGGATCAAGTCTGATACAGATTCTGCAC
genomic: AGATGGTTTGTTGCAATCTGGAGCTTCAACTGCACAAAAGAAAAAGATAGgtgagtattg ... tacatttcagAAGTTGGTGAGCAGAAAAAGAAGAGGATCAAGTCTGATACAGATTCTGCAC

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: 159

TGCCTCAAATGCTTTGATTGGATTATTAGATGGTTTGTTGCAATCTGGAGCTTCAACTGCACAAAAGAAAAAGATAGgtgagtattg ... tacatttcagAAGTTGGTGAGCAGAAAAAGAAGAGGATCAAGTCTGATACAGATTCTGCACGATTTTCTGCTGCATCTATGAGGAATCAACTTGACCAAGCTGCAAGCCT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 100

TGCCTCAAATGCTTTGATTGGATTATTAGATGGTTTGTTGCAATCTGGAGCTTCAACTGCACAAAAGAAAAAGATAGgtgagtattg ... tacatttcagAAGTTGGTGAGCAGAAAAAGAAGAGGATCAAGTCTGATACAGATTCTGCACGATTTTCTGCTGCATCTATGAGGAATCAACTTGACCAAGCTGCAAGCCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 134

TGCCTCAAATGCTTTGATTGGATTATTAGATGGTTTGTTGCAATCTGGAGCTTCAACTGCACAAAAGAAAAAGATAGgtgagtattg ... tacatttcagAAGTTGGTGAGCAGAAAAAGAAGAGGATCAAGTCTGATACAGATTCTGCACGATTTTCTGCTGCATCTATGAGGAATCAACTTGACCAAGCTGCAAGCCT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 101

TGCCTCAAATGCTTTGATTGGATTATTAGATGGTTTGTTGCAATCTGGAGCTTCAACTGCACAAAAGAAAAAGATAGgtgagtattg ... tacatttcagAAGTTGGTGAGCAGAAAAAGAAGAGGATCAAGTCTGATACAGATTCTGCACGATTTTCTGCTGCATCTATGAGGAATCAACTTGACCAAGCTGCAAGCCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctttttaactcggagcatgcagtacagtaccgtagttgctttctacatttcagAAGTTGGTGAGCAGAAAAAGAAGAGGATCAAGTCTGATACAGATTCTGCACGATTTTCTGCTGCATCTATGAGGAATCAACTTGACCAAGCTGCAAGCCT
    ttttaac  putative branch site (score: 101)
                                     ttgctttct  putative PPT
     tttaact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtattggaatttagaaccaagattttgcaagataggatcatgctttttaactcggagcatgcagtacagtaccgtagttgctttctacatttcagAAGTTGGTGAGCAGAAAAAGAAGAGGATCAAGTCTGATACAGATTCTGCACGATTTTCTGCTGCATCTATGAGGAATCAACTTGACCAAGCTGCAAGCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC