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'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtattgaactcgtacgtttctccttacatgttctctggagatttggcattttagaggactgatttataggaggaataaaatatctttctcatgattttagGAACAAAAGCTCCGATCTGAAATTGCTGAGGTGGAAAAGAAGTATCAGGAATTGTTGGGAGAGCTCAGATCATTGGATGTGAAGAAAGAGAAACAATGAA

Basic information

species Zea mays
transcript GRMZM2G030596_T02
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G030596_T02 (Zea mays), 3'ss of exon 18
lower sequence: LOC_Os01g36840.1 (Oryza sativa), 3'ss of exon 18
------gtattgaactc-gtacgtt--tctccttacatgttctctggagatttggcattttagaggactgatttataggaggaataaaatatctttctcatgat-tttagGAACAAAAGCTCCGATCTGAAATTGCTGAGGTGGAAAAGAAGTATCAGGAATTGTTGGGAGAGCTCAGATCATTGGATGTGAAGAAAGAGAAACAATGAA
       | ||| |||| ||  | |   | | |||||| ||   |     ||   | ||||       | | | || |  |     ||||  |   |||||| | ||||||||||||||||||||||| ||||||||  ||    |||||| ||| ||||||| ||   ||||||||| || ||||||||||||| ||||||| |   ||
tttattattttggactctgtttgatgccccctttacatatttcttcagtgtt---ctttttg------taactcattgttgttgagaaatggccc-ctcatgttctttagGAACAAAAGCTCCGATCTCAAATTGCTTTGGAAAGAAAGAAATATGAGGAATTATTACAAGAGCTCAGGTCGTTGGATGTGAAGACAGAGAAATAGCAAA
















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|78114930|gb|DV533318.1|DV533318
EST:     ATGCTTACAATACGAGGGATCAGAGAAACAACTTGTCCTGAAG                         GAACAAAAGCTCCGATCTGAAATTGCTGAGGTGGAAAAGAAGTATCAGGAA
genomic: ATGCTTACAATACGAGGGATCAGAGAAACAACTTGTCCTGAAGgtatacctct ... atgattttagGAACAAAAGCTCCGATCTGAAATTGCTGAGGTGGAAAAGAAGTATCAGGAA
EST: gi|31349834|gb|CD434191.1|CD434191
EST:     ATGCTTACAATACGAGGGATCAGAGAAACAACTTGTCCTGAAG                         GAACAAAAGCTCCGATCTGAAATTGCTGAGGTGGAAAAGAAGTATCAGGAA
genomic: ATGCTTACAATACGAGGGATCAGAGAAACAACTTGTCCTGAAGgtatacctct ... atgattttagGAACAAAAGCTCCGATCTGAAATTGCTGAGGTGGAAAAGAAGTATCAGGAA
EST: gi|60357772|gb|DN224745.1|DN224745
EST:     ATGCTTACAATACGAGGGATCAGAGAAACAACTTGTCCTGAAG                         GAACAAAAGCTCCGATCTGAAATTGCTGAGGTGGAAAAGAAGTATCAGGAA
genomic: ATGCTTACAATACGAGGGATCAGAGAAACAACTTGTCCTGAAGgtatacctct ... atgattttagGAACAAAAGCTCCGATCTGAAATTGCTGAGGTGGAAAAGAAGTATCAGGAA
EST: gi|78121767|gb|DV540151.1|DV540151
EST:     CAGAGAAACAACTTGTCCTGAAG                         GAACAAAAGCTCCGATCTGAAATTGCTGAGGTGGAAAAGAAGTATCAGGAA
genomic: CAGAGAAACAACTTGTCCTGAAGgtatacctct ... atgattttagGAACAAAAGCTCCGATCTGAAATTGCTGAGGTGGAAAAGAAGTATCAGGAA
EST: gi|6742642|gb|AW313457.1|AW313457
EST:     ATGCTTACAATACGAGGGATCAGAGAAACAACTTGTCCTGAAG                         GAACAAAAGCTCCGATCTGAAATTGCTGTGGAGGAAAAGAAGTATCAGGAA
genomic: ATGCTTACAATACGAGGGATCAGAGAAACAACTTGTCCTGAAGgtatacctct ... atgattttagGAACAAAAGCTCCGATCTGAAATTGCTGAGGTGGAAAAGAAGTATCAGGAA
EST: gi|78075869|gb|DV504303.1|DV504303
EST:     ATGCTTACAATACGAGGGATCAGAGAAACAACTTGTCCTGAAG                         GAACAAAAGCTCCGATCTGAAATTGCTGAGGTGGAAAAGAAGTATCAGGAA
genomic: ATGCTTACAATACGAGGGATCAGAGAAACAACTTGTCCTGAAGgtatacctct ... atgattttagGAACAAAAGCTCCGATCTGAAATTGCTGAGGTGGAAAAGAAGTATCAGGAA
EST: gi|211385800|gb|FL436087.1|FL436087
EST:     ATGCTTHCAATACGAGGGATCAGAGAAACAACTTGTCCTGAAG                         GAACAAAAGCTCCGATCTGAAATTGCTGAGGTGGAAAAGAAGTATCAGGAA
genomic: ATGCTTACAATACGAGGGATCAGAGAAACAACTTGTCCTGAAGgtatacctct ... atgattttagGAACAAAAGCTCCGATCTGAAATTGCTGAGGTGGAAAAGAAGTATCAGGAA

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: 43 (upstream exon), 49 (downstream exon)
Score: 181

ATGCTTACAATACGAGGGATCAGAGAAACAACTTGTCCTGAAGgtatacctct ... atgattttagGAACAAAAGCTCCGATCTGAAATTGCTGAGGTGGAAAAGAAGTATCAGGAATTGTTGGGAGAGCTCAGATCATTGGATGTGAAGAAAGAGAAACAATGAA


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 71

ATGCTTACAATACGAGGGATCAGAGAAACAACTTGTCCTGAAGgtatacctct ... atgattttagGAACAAAAGCTCCGATCTGAAATTGCTGAGGTGGAAAAGAAGTATCAGGAATTGTTGGGAGAGCTCAGATCATTGGATGTGAAGAAAGAGAAACAATGAA


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 118

ATGCTTACAATACGAGGGATCAGAGAAACAACTTGTCCTGAAGgtatacctct ... atgattttagGAACAAAAGCTCCGATCTGAAATTGCTGAGGTGGAAAAGAAGTATCAGGAATTGTTGGGAGAGCTCAGATCATTGGATGTGAAGAAAGAGAAACAATGAA


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 99

ATGCTTACAATACGAGGGATCAGAGAAACAACTTGTCCTGAAGgtatacctct ... atgattttagGAACAAAAGCTCCGATCTGAAATTGCTGAGGTGGAAAAGAAGTATCAGGAATTGTTGGGAGAGCTCAGATCATTGGATGTGAAGAAAGAGAAACAATGAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcattttagaggactgatttataggaggaataaaatatctttctcatgattttagGAACAAAAGCTCCGATCTGAAATTGCTGAGGTGGAAAAGAAGTATCAGGAATTGTTGGGAGAGCTCAGATCATTGGATGTGAAGAAAGAGAAACAATGAA
           gactgat  putative branch site (score: 99)
                                     tctttctcat  putative PPT
                            aataaaatatctttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattgaactcgtacgtttctccttacatgttctctggagatttggcattttagaggactgatttataggaggaataaaatatctttctcatgattttagGAACAAAAGCTCCGATCTGAAATTGCTGAGGTGGAAAAGAAGTATCAGGAATTGTTGGGAGAGCTCAGATCATTGGATGTGAAGAAAGAGAAACAATGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - catgttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -actgatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aataaaa