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

gtactaacttgctctctttacaggtgtcttagtttgtttatcaatggtggcccattatacactgtctgtaaacattgactgaaccttgtttctgaaccagAGAGGAGTCTCCCCCATCGAAGAAGTTATCAAAACAGGTGTAGTTCCAAGATTTGTGCAGTCTCTCACCAGAGAGGATTTCCCCCAGCTGCAG

Basic information

species Zea mays
transcript GRMZM2G088231_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G088231_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g14950.1 (Oryza sativa), 3'ss of exon 2
gtactaacttgctctctttacaggtgtcttagtttgtttatcaatggtggcccattatacactgtctgtaaacattgactgaaccttgtttctgaaccagAGAGGAGTCTCCCCCATCGAAGAAGTTATCAAAACAGGTGTAGTTCCAAGATTTGTGCAGTCTCTCACCAGAGAGGATTTCCCCCAGCTGCAG
|||| ||| |  |   | |   ||  | |||  ||||  |  |||  | |   |  | |   |   |   ||      |   |      || | ||  ||||||||| | | || || ||||| |||||  || |||| || ||||| ||||| ||||||| ||| ||||||||||||||||||||||| |||
gtacaaacctcttaaatgttttgggctgttaccttgtgaa--aataatagttgaacaaaagttaattactaattacaccc--attacaatttttaattagAGAGGAGCC-CTCCAATTGAAGAGGTTATTCAATCAGGCGTTGTTCCTAGATTCGTGCAGTTTCTTACCAGAGAGGATTTCCCCCAGCTACAG
















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|71440662|gb|DR821712.1|DR821712
EST:     TAACCTTCAGCTTGAGGCCACCACACAGTTCCGCAAATTGCTCTCTATAG                         AGAGGAGTC-CCCCCATCGAAGAAGTTATCAAAACAGGTGTAGTTCCAAGA
genomic: TAACCTTCAGCTTGAGGCCACCACACAGTTCCGCAAATTGCTCTCTATAGgtactaactt ... tctgaaccagAGAGGAGTCTCCCCCATCGAAGAAGTTATCAAAACAGGTGTAGTTCCAAGA
EST: gi|211383277|gb|FK983407.1|FK983407
EST:     TAACCTTCAGCTTGAGGCCACCACACAGTTCCGCAAATTGCTCTCTATAG                         AGAGGAGTC-CCCCCATCGAAGAAGTTATCAAAACAGGTGTAGTTCCAAGA
genomic: TAACCTTCAGCTTGAGGCCACCACACAGTTCCGCAAATTGCTCTCTATAGgtactaactt ... tctgaaccagAGAGGAGTCTCCCCCATCGAAGAAGTTATCAAAACAGGTGTAGTTCCAAGA
EST: gi|211385914|gb|FK983423.1|FK983423
EST:     TAACCTTCAGCTTGAGGCCACCACACAGTTCCGCAAATTGCTCTCTATAG                         AGAGGAGTC-CCCCCATCGAAGAAGTTATCAAAACAGGTGTAGTTCCAAGA
genomic: TAACCTTCAGCTTGAGGCCACCACACAGTTCCGCAAATTGCTCTCTATAGgtactaactt ... tctgaaccagAGAGGAGTCTCCCCCATCGAAGAAGTTATCAAAACAGGTGTAGTTCCAAGA
EST: gi|28987202|gb|CB351514.1|CB351514
EST:     TAACCTTCAGCTTGAGGCCACCACACAGTTCCGCAAATTGCTCTCTATAG                         AGAGGAGTC-CCCCCATCGAAGAAGTTATCAAAACAGGTGTAGTTCCAAGA
genomic: TAACCTTCAGCTTGAGGCCACCACACAGTTCCGCAAATTGCTCTCTATAGgtactaactt ... tctgaaccagAGAGGAGTCTCCCCCATCGAAGAAGTTATCAAAACAGGTGTAGTTCCAAGA
EST: gi|149111962|gb|EE191122.2|EE191122
EST:     TAACCTTCAGCTTGAGGCCACCACACAGTTCCGCAAATTGCTCTCTATAG                         AGAGGAGTC-CCCCCATCGAAGAAGTTATCAAAACAGGTGTAGTTCCAAGA
genomic: TAACCTTCAGCTTGAGGCCACCACACAGTTCCGCAAATTGCTCTCTATAGgtactaactt ... tctgaaccagAGAGGAGTCTCCCCCATCGAAGAAGTTATCAAAACAGGTGTAGTTCCAAGA
EST: gi|87151836|gb|DY396625.1|DY396625
EST:     TAACCTTCAGCTTGAGGCCACCACACAGTTCCGCAAATTGCTCTCTATAG                         AGAGGAGTC-CCCCCATCGAAGAAGTTATCAAAACAGGTGTAGTTCCAAGA
genomic: TAACCTTCAGCTTGAGGCCACCACACAGTTCCGCAAATTGCTCTCTATAGgtactaactt ... tctgaaccagAGAGGAGTCTCCCCCATCGAAGAAGTTATCAAAACAGGTGTAGTTCCAAGA
EST: gi|30087090|gb|CB885298.1|CB885298
EST:     TAACCTTCAGCTTGAGGCCACCACACAGTTCCGCAAATTGCTCTCTATAG                         AGAGGAGTC-CCCCCATCGAAGAAGTTATCAAAACAGGTGTAGTTCCAAGA
genomic: TAACCTTCAGCTTGAGGCCACCACACAGTTCCGCAAATTGCTCTCTATAGgtactaactt ... tctgaaccagAGAGGAGTCTCCCCCATCGAAGAAGTTATCAAAACAGGTGTAGTTCCAAGA
EST: gi|76021460|gb|DT948630.1|DT948630
EST:     TAACCTTCAGCTTGAGGCCACCACACAGTTCCGCAAATTGCTCTCTATAG                         AGAGGAGTC-CCCCCATCGAAGAAGTTATCAAAACAGGTGTAGTTCCAAGA
genomic: TAACCTTCAGCTTGAGGCCACCACACAGTTCCGCAAATTGCTCTCTATAGgtactaactt ... tctgaaccagAGAGGAGTCTCCCCCATCGAAGAAGTTATCAAAACAGGTGTAGTTCCAAGA
EST: gi|31664557|gb|CD573490.1|CD573490
EST:     TAACCTTCAGCTTGAGGCCACCACACAGTTCCGCAAATTGCTCTCTATAG                         AGAGGAGTC-CCCCCATCGAAGAAGTTATCAAAACAGGTGTAGTTCCAAGA
genomic: TAACCTTCAGCTTGAGGCCACCACACAGTTCCGCAAATTGCTCTCTATAGgtactaactt ... tctgaaccagAGAGGAGTCTCCCCCATCGAAGAAGTTATCAAAACAGGTGTAGTTCCAAGA
EST: gi|78179900|gb|DV550273.1|DV550273
EST:     TAACCTTCAGCTTGAGGCCACCACACAGTTCCGCAAATTGCTCTCTATAG                         AGAGGAGTC-CCCCCATCGAAGAAGTTATCAAAACAGGTGTAGTTCCAAGA
genomic: TAACCTTCAGCTTGAGGCCACCACACAGTTCCGCAAATTGCTCTCTATAGgtactaactt ... tctgaaccagAGAGGAGTCTCCCCCATCGAAGAAGTTATCAAAACAGGTGTAGTTCCAAGA
EST: gi|211385909|gb|FK983418.1|FK983418
EST:     TAACCTTCAGCTTGAGGCCACCACACAGTTCCGCAAATTGCTCTCTATAG                         AGAGGAGTC-CCCCCATCGAAGAAGTTATCAAAACAGGTGTAGTTCCAAGA
genomic: TAACCTTCAGCTTGAGGCCACCACACAGTTCCGCAAATTGCTCTCTATAGgtactaactt ... tctgaaccagAGAGGAGTCTCCCCCATCGAAGAAGTTATCAAAACAGGTGTAGTTCCAAGA
EST: gi|18963328|gb|BM660373.1|BM660373
EST:     TAACCTTCAGCTTGAGGCCACCACACAGTTCCGCAAATTGCTCTCTATAG                         AGAGGAGTC-CCCCCATCGAAGAAGTTATCAAAACAGGTGTAGTTCCAAGA
genomic: TAACCTTCAGCTTGAGGCCACCACACAGTTCCGCAAATTGCTCTCTATAGgtactaactt ... tctgaaccagAGAGGAGTCTCCCCCATCGAAGAAGTTATCAAAACAGGTGTAGTTCCAAGA
EST: gi|22490161|gb|BU050084.1|BU050084
EST:     TAACCTTCAGCTTGAGGCCACCACACAGTTCCGCAAATTGCTCTCTATAG                         AGAGGAGTC-CCCCCATCGAAGAAGTTATCAAAACAGGTGTAGTTCCAAGA
genomic: TAACCTTCAGCTTGAGGCCACCACACAGTTCCGCAAATTGCTCTCTATAGgtactaactt ... tctgaaccagAGAGGAGTCTCCCCCATCGAAGAAGTTATCAAAACAGGTGTAGTTCCAAGA
EST: gi|211391186|gb|FK983447.1|FK983447
EST:     TAACCTTCAGCTTGAGGCCACCACACAGTTCCGCAAATTGCTCTCTATAG                         AGAGGAGTC-CCCCCATCGAAGAAGTTATCAAAACAGGTGTAGTTCC
genomic: TAACCTTCAGCTTGAGGCCACCACACAGTTCCGCAAATTGCTCTCTATAGgtactaactt ... tctgaaccagAGAGGAGTCTCCCCCATCGAAGAAGTTATCAAAACAGGTGTAGTTCC
EST: gi|211383281|gb|FK983411.1|FK983411
EST:     TAACCTTCAGCTTGAGGCCACCACACAGTTCCGCAAATTGCTCTCTATAG                         AGAGGAGTC-CCCCCATCGAAGAA-TTATCAAAACAGGTGTAGTTCCAAGA
genomic: TAACCTTCAGCTTGAGGCCACCACACAGTTCCGCAAATTGCTCTCTATAGgtactaactt ... tctgaaccagAGAGGAGTCTCCCCCATCGAAGAAGTTATCAAAACAGGTGTAGTTCCAAGA
EST: gi|18963326|gb|BM660372.1|BM660372
EST:     TAGCCTTCAGCTTGAGGCCACCACACAGTTCCGCAAATTGCTCTCTATAG                         AGAGGAGTC-CCCCCATCGAAGAAGTTATCAAAACAGGTGTAGTTCCAAGA
genomic: TAACCTTCAGCTTGAGGCCACCACACAGTTCCGCAAATTGCTCTCTATAGgtactaactt ... tctgaaccagAGAGGAGTCTCCCCCATCGAAGAAGTTATCAAAACAGGTGTAGTTCCAAGA
EST: gi|6952404|gb|AW424472.1|AW424472
EST:     TAACCTTCAGCTTGAGGCCACCACACAGTTCCGCAAATTGCTCTCTATAG                         AGAGGAGTC-CCCCCATCGAAGAAGTTATCAAAACAGGTGTAGTTCCAAGA
genomic: TAACCTTCAGCTTGAGGCCACCACACAGTTCCGCAAATTGCTCTCTATAGgtactaactt ... tctgaaccagAGAGGAGTCTCCCCCATCGAAGAAGTTATCAAAACAGGTGTAGTTCCAAGA
EST: gi|211385917|gb|FK983426.1|FK983426
EST:     TAACCTTCAGCTTGAGGCCACCACACAGTTCCGCAAATTGCTCTCTATAG                         AGAGGAGTC-CCCCCATCGAAGAA-TTATCAAAACAGGTGTAGTTCCAAGA
genomic: TAACCTTCAGCTTGAGGCCACCACACAGTTCCGCAAATTGCTCTCTATAGgtactaactt ... tctgaaccagAGAGGAGTCTCCCCCATCGAAGAAGTTATCAAAACAGGTGTAGTTCCAAGA
EST: gi|211385910|gb|FK983419.1|FK983419
EST:     TAACCTTCAGCTTGAGGCCACCACACAGTTCCGCAAATTGCTCTCTATAG                         AGAGGAGTC-CCCCCATCGAAGAAGTTATCAAAACAGGTGTAGTTCCAAGA
genomic: TAACCTTCAGCTTGAGGCCACCACACAGTTCCGCAAATTGCTCTCTATAGgtactaactt ... tctgaaccagAGAGGAGTCTCCCCCATCGAAGAAGTTATCAAAACAGGTGTAGTTCCAAGA
EST: gi|211383287|gb|FK983417.1|FK983417
EST:     TAACCTTCAGCTTGAGGCCACCACACAGTTCCGCAAATTGCTCTCTATAG                         AGAGGAGTC-CCCCCATCGAAGAAGTTATCAAAACAGGTGTAGTTCCAAGA
genomic: TAACCTTCAGCTTGAGGCCACCACACAGTTCCGCAAATTGCTCTCTATAGgtactaactt ... tctgaaccagAGAGGAGTCTCCCCCATCGAAGAAGTTATCAAAACAGGTGTAGTTCCAAGA
EST: gi|148946964|gb|EC892254.2|EC892254
EST:     TAACCTTCAGCTTGAGGCCACCACACAGTTCCGCANATTGCTCTCTATAG                         AGAGGAGTC-CCCCCATCGAAGAAGTTATCAAAACAGGTGTAGTTCCAAGA
genomic: TAACCTTCAGCTTGAGGCCACCACACAGTTCCGCAAATTGCTCTCTATAGgtactaactt ... tctgaaccagAGAGGAGTCTCCCCCATCGAAGAAGTTATCAAAACAGGTGTAGTTCCAAGA
EST: gi|12045741|gb|BF727880.1|BF727880
EST:     TAACCTTCAGCTTGAGGCCACCACACAGTTCCGCAAATTGCTCTCTATAG                         AGAGGAGTC-CCCCCATCGAAGAAGTTATCAAAACAGGTGTAGTTCCAAGA
genomic: TAACCTTCAGCTTGAGGCCACCACACAGTTCCGCAAATTGCTCTCTATAGgtactaactt ... tctgaaccagAGAGGAGTCTCCCCCATCGAAGAAGTTATCAAAACAGGTGTAGTTCCAAGA

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: 413

CTTGAAAGCCTCCCAGCTATGGTTAGTGGGGTTTATTCGGATGATAATAACCTTCAGCTTGAGGCCACCACACAGTTCCGCAAATTGCTCTCTATAGgtactaactt ... tctgaaccagAGAGGAGTCTCCCCCATCGAAGAAGTTATCAAAACAGGTGTAGTTCCAAGATTTGTGCAGTCTCTCACCAGAGAGGATTTCCCCCAGCTGCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 248

CTTGAAAGCCTCCCAGCTATGGTTAGTGGGGTTTATTCGGATGATAATAACCTTCAGCTTGAGGCCACCACACAGTTCCGCAAATTGCTCTCTATAGgtactaactt ... tctgaaccagAGAGGAGTCTCCCCCATCGAAGAAGTTATCAAAACAGGTGTAGTTCCAAGATTTGTGCAGTCTCTCACCAGAGAGGATTTCCCCCAGCTGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 244

CTTGAAAGCCTCCCAGCTATGGTTAGTGGGGTTTATTCGGATGATAATAACCTTCAGCTTGAGGCCACCACACAGTTCCGCAAATTGCTCTCTATAGgtactaactt ... tctgaaccagAGAGGAGTCTCCCCCATCGAAGAAGTTATCAAAACAGGTGTAGTTCCAAGATTTGTGCAGTCTCTCACCAGAGAGGATTTCCCCCAGCTGCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 316

CTTGAAAGCCTCCCAGCTATGGTTAGTGGGGTTTATTCGGATGATAATAACCTTCAGCTTGAGGCCACCACACAGTTCCGCAAATTGCTCTCTATAGgtactaactt ... tctgaaccagAGAGGAGTCTCCCCCATCGAAGAAGTTATCAAAACAGGTGTAGTTCCAAGATTTGTGCAGTCTCTCACCAGAGAGGATTTCCCCCAGCTGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtggcccattatacactgtctgtaaacattgactgaaccttgtttctgaaccagAGAGGAGTCTCCCCCATCGAAGAAGTTATCAAAACAGGTGTAGTTCCAAGATTTGTGCAGTCTCTCACCAGAGAGGATTTCCCCCAGCTGCAG
                           cattgac  putative branch site (score: 316)
                                      ccttgtttct  putative PPT
        attataca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactaacttgctctctttacaggtgtcttagtttgtttatcaatggtggcccattatacactgtctgtaaacattgactgaaccttgtttctgaaccagAGAGGAGTCTCCCCCATCGAAGAAGTTATCAAAACAGGTGTAGTTCCAAGATTTGTGCAGTCTCTCACCAGAGAGGATTTCCCCCAGCTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG