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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGCAACGGCTAGCACTCTACCAGGGCGTCATCCCTATTCACATGCAGTTCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTGgtaagaccatgtgctgtgaagttccattactgaccttttgcagtcagttcatcagataaacacatctctgttttacttgaatattttgcccttttgttattatattttactgattattcgtggattggaatgttgaacag

Basic information

species Zea mays
transcript GRMZM2G033526_T02
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G033526_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os10g42100.1 (Oryza sativa), 5'ss of exon 11
GAAGCAACGGCTAGCACTCTACCAGGGCGTCATCCCTATTCACATGCAGTTCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTGgtaagaccatgtgctgtgaagttccattactgaccttttgcagtcagttcatcagataaacacatctctgttttacttgaatattttgcccttttgttattatattttactgattattcgtggattggaatgttgaacag
||||||||| || |||||||||||||| ||  | || ||| ||||| |||| ||||| || ||||| ||||||||||| ||||||||||| ||||||||||||||   |||| ||      |  |  | | |||          ||||| ||   ||  |||        |  |  || | |  |||  |    |  |  | | |||  || || |  ||||| || |||||||  ||||
GAAGCAACGTCTGGCACTCTACCAGGGTGTGGTTCCCATTTACATGAAGTTTTCTGATGATGCAGAGGAAACTTTCTCTAGAGCAATTAGTAGCTTGCTGgtaagcatatgtact------tcacgctgccgaca---------cagttgatattattgaca--------tcatttttcagtccttttacaaagtactcctgtgtttctcttatgaaccgtggttttgaatgtttgacag
















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|211275556|gb|FL192922.1|FL192922
EST:     TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTG                         AAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
genomic: TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTGgtaagaccat ... tgttgaacagAAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
EST: gi|6526771|gb|AW216050.1|AW216050
EST:     TGTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTG                         AAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
genomic: TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTGgtaagaccat ... tgttgaacagAAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
EST: gi|21759868|gb|BQ635409.1|BQ635409
EST:     TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTG                         AAAGCCCAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
genomic: TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTGgtaagaccat ... tgttgaacagAAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
EST: gi|60395622|gb|DN228492.1|DN228492
EST:     TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTG                         AAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
genomic: TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTGgtaagaccat ... tgttgaacagAAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
EST: gi|60356976|gb|DN223949.1|DN223949
EST:     TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTG                         AAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
genomic: TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTGgtaagaccat ... tgttgaacagAAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
EST: gi|45567965|gb|CK985835.1|CK985835
EST:     TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTG                         AAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
genomic: TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTGgtaagaccat ... tgttgaacagAAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
EST: gi|13177888|gb|BG349071.1|BG349071
EST:     TCTCTGGCGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTG                         AAAGCCCAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
genomic: TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTGgtaagaccat ... tgttgaacagAAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
EST: gi|20802326|gb|BQ293376.1|BQ293376
EST:     TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTG                         AAAGCCCAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
genomic: TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTGgtaagaccat ... tgttgaacagAAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
EST: gi|31357830|gb|CD442187.1|CD442187
EST:     TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTG                         AAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
genomic: TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTGgtaagaccat ... tgttgaacagAAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
EST: gi|60355665|gb|DN222638.1|DN222638
EST:     TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTG                         AAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
genomic: TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTGgtaagaccat ... tgttgaacagAAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
EST: gi|76287860|gb|DV027428.1|DV027428
EST:     TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTG                         AAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
genomic: TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTGgtaagaccat ... tgttgaacagAAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
EST: gi|60355637|gb|DN222610.1|DN222610
EST:     TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTG                         AAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
genomic: TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTGgtaagaccat ... tgttgaacagAAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
EST: gi|71595869|gb|DR906620.1|DR906620
EST:     TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTG                         AAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
genomic: TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTGgtaagaccat ... tgttgaacagAAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
EST: gi|116822697|gb|EC866119.1|EC866119
EST:     TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTG                         AAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
genomic: TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTGgtaagaccat ... tgttgaacagAAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
EST: gi|60351363|gb|DN218336.1|DN218336
EST:     TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTG                         AAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
genomic: TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTGgtaagaccat ... tgttgaacagAAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
EST: gi|15199098|gb|BI423655.1|BI423655
EST:     AACTTTCTCCAGAGCAATTAGCAGCTTGCTG                         AAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
genomic: AACTTTCTCCAGAGCAATTAGCAGCTTGCTGgtaagaccat ... tgttgaacagAAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
EST: gi|37418065|gb|CF646693.1|CF646693
EST:     TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTG                         AAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
genomic: TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTGgtaagaccat ... tgttgaacagAAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
EST: gi|33467026|gb|CF244075.1|CF244075
EST:     TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTG                         AAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
genomic: TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTGgtaagaccat ... tgttgaacagAAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
EST: gi|213182699|gb|FM195337.1|FM195337
EST:     TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTG                         AAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
genomic: TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTGgtaagaccat ... tgttgaacagAAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
EST: gi|149102472|gb|EE287835.2|EE287835
EST:     TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTG                         AAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
genomic: TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTGgtaagaccat ... tgttgaacagAAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
EST: gi|78025170|gb|DV493557.1|DV493557
EST:     TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTG                         AAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
genomic: TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTGgtaagaccat ... tgttgaacagAAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
EST: gi|24765370|gb|CA400529.1|CA400529
EST:     TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTG                         AAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
genomic: TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTGgtaagaccat ... tgttgaacagAAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
EST: gi|60394678|gb|DN227548.1|DN227548
EST:     TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTG                         AAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
genomic: TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTGgtaagaccat ... tgttgaacagAAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
EST: gi|12969057|gb|BG266002.1|BG266002
EST:     TTTCTGACGACGCAGAAGAANCTTTCTCCAGAGCAATTAGCAGCTTGCTG                         AAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
genomic: TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTGgtaagaccat ... tgttgaacagAAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
EST: gi|5739696|gb|AI947272.1|AI947272
EST:     TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTG                         AAGGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
genomic: TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTGgtaagaccat ... tgttgaacagAAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
EST: gi|60397119|gb|DN229938.1|DN229938
EST:     TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTG                         AAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
genomic: TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTGgtaagaccat ... tgttgaacagAAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
EST: gi|4967114|gb|AI692056.1|AI692056
EST:     TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTG                         AAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
genomic: TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTGgtaagaccat ... tgttgaacagAAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
EST: gi|60400092|gb|DN232899.1|DN232899
EST:     TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTG                         AAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
genomic: TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTGgtaagaccat ... tgttgaacagAAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
EST: gi|60338482|gb|DN205455.1|DN205455
EST:     TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTG                         AAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
genomic: TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTGgtaagaccat ... tgttgaacagAAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
EST: gi|60354896|gb|DN221869.1|DN221869
EST:     TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTG                         AAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
genomic: TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTGgtaagaccat ... tgttgaacagAAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA
EST: gi|148929002|gb|EC874192.2|EC874192
EST:     TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTG                         AAAGCACAATATGTGAAGAAGGGGGAGTACGTCACTCTTGTTCAGAGCGGA
genomic: TCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTGgtaagaccat ... tgttgaacagAAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGA

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: 440

GAAGCAACGGCTAGCACTCTACCAGGGCGTCATCCCTATTCACATGCAGTTCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTGgtaagaccat ... tgttgaacagAAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGAGTGACTTCAATCTGGAGAGAGGAATCCACTCACCACATCCAAGTGAGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 287

GAAGCAACGGCTAGCACTCTACCAGGGCGTCATCCCTATTCACATGCAGTTCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTGgtaagaccat ... tgttgaacagAAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGAGTGACTTCAATCTGGAGAGAGGAATCCACTCACCACATCCAAGTGAGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 286

GAAGCAACGGCTAGCACTCTACCAGGGCGTCATCCCTATTCACATGCAGTTCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTGgtaagaccat ... tgttgaacagAAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGAGTGACTTCAATCTGGAGAGAGGAATCCACTCACCACATCCAAGTGAGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 735

GAAGCAACGGCTAGCACTCTACCAGGGCGTCATCCCTATTCACATGCAGTTCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTGgtaagaccat ... tgttgaacagAAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGAGTGACTTCAATCTGGAGAGAGGAATCCACTCACCACATCCAAGTGAGGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGCAACGGCTAGCACTCTACCAGGGCGTCATCCCTATTCACATGCAGTTCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGCAGCTTGCTGgtaagaccatgtgctgtgaagttccattactgaccttttgcagtcagttcatcagataaacacatctctgttttacttgaatattttgcccttttgttattatattttactgattattcgtggattggaatgttgaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT