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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattctctttgctgcacactattaaaaggatgctaccatgtatatgttaattgttatgaaatagtcatgagattttcaatcttttcctattgcgtagGATTGTTGCCTCCTGGCACACAGTTTGATTTATTTAGAGGAACTGCTGCAATGAAGCAGGATGAAGAAGAAACATACCCTACTTCCTTATCTCATCAAAT

Basic information

species Zea mays
transcript GRMZM2G037683_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G037683_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g21940.1 (Oryza sativa), 3'ss of exon 4
gtattctctttgctgcacactattaa--aaggatgcta--ccatgtatatgtta-----attgttatgaaatagtcatgagattttcaatcttttcctattgcgtagGATTGTTGCCTCCTGGCACACAGTTTGATTTATTTAGAGGAACTGCTGCAATGAAGCAGGATGAAGAAGAAACATACCCTACTTCCTTATCTCATCAAAT
||| | || | | |||||  ||||||   | ||| |||  | ||    || | |     | |  |||||| |  || |||| |  |    |   |  | |  |  ||||||||| || ||||||||||||||||||||||||||||||||||||||||||||||| |||||||| |||||||| |||||| | ||||| ||||||| 
gtactttcctggttgcacgttattaacttatgatactatactataatgatctcagcacgactagtatgaactcatcttgaggtccttcccccacttttgtcac--agGATTGTTACCACCTGGCACACAGTTTGATTTATTTAGAGGAACTGCTGCAATGAAGCAAGATGAAGAGGAAACATATCCTACTACTTTATCACATCAAAC
















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|60351616|gb|DN218589.1|DN218589
EST:     TCGTCTTATGGCACTGATTGGTCAGGCTTTGAAGTGGCAACAGCACCAAG                         GATTGTTGCCTCCTGGCACACAGTTTGATTTATTTAGAGGAACTGCTGCAA
genomic: TCGTCTTATGGCACTGATTGGTCAGGCTTTGAAGTGGCAACAGCACCAAGgtattctctt ... tattgcgtagGATTGTTGCCTCCTGGCACACAGTTTGATTTATTTAGAGGAACTGCTGCAA
EST: gi|76010783|gb|DT937953.1|DT937953
EST:     TCGTCTTATGGCACTGATTGGTCAGGCTTTGAAGTGGCAACAGCACCAAG                         GATTGTTGCCTCCTGGCACACAGTTTGATTTATTTAGAGGAACTGCTGCAA
genomic: TCGTCTTATGGCACTGATTGGTCAGGCTTTGAAGTGGCAACAGCACCAAGgtattctctt ... tattgcgtagGATTGTTGCCTCCTGGCACACAGTTTGATTTATTTAGAGGAACTGCTGCAA
EST: gi|67019283|gb|CO448032.1|CO448032
EST:     GTCTTATGGCACTGATTGGTCAGGCTTTGAAGTGGCAACAGCACCAAG                         GATTGTTGCCTCCTGGCACACAGTTTGATTTATTTAGAGGAACTGCTGCAA
genomic: GTCTTATGGCACTGATTGGTCAGGCTTTGAAGTGGCAACAGCACCAAGgtattctctt ... tattgcgtagGATTGTTGCCTCCTGGCACACAGTTTGATTTATTTAGAGGAACTGCTGCAA
EST: gi|23357683|gb|BU645332.1|BU645332
EST:     GGCAACAGCACCAAG                         GATTGTTGCCTCCTGGCACACAGTTTGATTTATTTAGAGGAACTGCTGCAA
genomic: GGCAACAGCACCAAGgtattctctt ... tattgcgtagGATTGTTGCCTCCTGGCACACAGTTTGATTTATTTAGAGGAACTGCTGCAA
EST: gi|22521028|gb|BU079839.1|BU079839
EST:     GGTCAGGCTTTGAAG-GGCAACAGCACCAAG                         GATTGTTGCCTCCTGGCACACAGTTTGATTTATTTAGAGGAACTGCTGCAA
genomic: GGTCAGGCTTTGAAGTGGCAACAGCACCAAGgtattctctt ... tattgcgtagGATTGTTGCCTCCTGGCACACAGTTTGATTTATTTAGAGGAACTGCTGCAA
EST: gi|26457208|gb|CA828791.1|CA828791
EST:     GGTCAGGCTTTGAAG-GGCAACAGCTACCAAG                         GATTGTTGCCTCCTGGCACACAGTTTGATTTATTTAGAGGAACTGCTGCA
genomic: GGTCAGGCTTTGAAGTGGCAACAGC-ACCAAGgtattctctt ... tattgcgtagGATTGTTGCCTCCTGGCACACAGTTTGATTTATTTAGAGGAACTGCTGCA
EST: gi|91873183|gb|EB403140.1|EB403140
EST:     TCGTCTTATGGCACTGATTGGTCAGGCTTTGAAGTGGCAACAGCACCAAG                         GATTGTTGCCTCCTGGCACACAGTTTGATTTATTTAGAGGAACTGCTGCAA
genomic: TCGTCTTATGGCACTGATTGGTCAGGCTTTGAAGTGGCAACAGCACCAAGgtattctctt ... tattgcgtagGATTGTTGCCTCCTGGCACACAGTTTGATTTATTTAGAGGAACTGCTGCAA

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), 48 (downstream exon)
Score: 303

CTGTTGCTTCAGAAGTCTCAGTAGTACCGCCATCTCGTCTTATGGCACTGATTGGTCAGGCTTTGAAGTGGCAACAGCACCAAGgtattctctt ... tattgcgtagGATTGTTGCCTCCTGGCACACAGTTTGATTTATTTAGAGGAACTGCTGCAATGAAGCAGGATGAAGAAGAAACATACCCTACTTCCTTATCTCATCAAAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 148

CTGTTGCTTCAGAAGTCTCAGTAGTACCGCCATCTCGTCTTATGGCACTGATTGGTCAGGCTTTGAAGTGGCAACAGCACCAAGgtattctctt ... tattgcgtagGATTGTTGCCTCCTGGCACACAGTTTGATTTATTTAGAGGAACTGCTGCAATGAAGCAGGATGAAGAAGAAACATACCCTACTTCCTTATCTCATCAAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 121

CTGTTGCTTCAGAAGTCTCAGTAGTACCGCCATCTCGTCTTATGGCACTGATTGGTCAGGCTTTGAAGTGGCAACAGCACCAAGgtattctctt ... tattgcgtagGATTGTTGCCTCCTGGCACACAGTTTGATTTATTTAGAGGAACTGCTGCAATGAAGCAGGATGAAGAAGAAACATACCCTACTTCCTTATCTCATCAAAT


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 84

CTGTTGCTTCAGAAGTCTCAGTAGTACCGCCATCTCGTCTTATGGCACTGATTGGTCAGGCTTTGAAGTGGCAACAGCACCAAGgtattctctt ... tattgcgtagGATTGTTGCCTCCTGGCACACAGTTTGATTTATTTAGAGGAACTGCTGCAATGAAGCAGGATGAAGAAGAAACATACCCTACTTCCTTATCTCATCAAAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgttaattgttatgaaatagtcatgagattttcaatcttttcctattgcgtagGATTGTTGCCTCCTGGCACACAGTTTGATTTATTTAGAGGAACTGCTGCAATGAAGCAGGATGAAGAAGAAACATACCCTACTTCCTTATCTCATCAAAT
  tgttaat  putative branch site (score: 84)
                              ttttcaatcttttcct  putative PPT
     taattgttatgaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattctctttgctgcacactattaaaaggatgctaccatgtatatgttaattgttatgaaatagtcatgagattttcaatcttttcctattgcgtagGATTGTTGCCTCCTGGCACACAGTTTGATTTATTTAGAGGAACTGCTGCAATGAAGCAGGATGAAGAAGAAACATACCCTACTTCCTTATCTCATCAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA