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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctaattcttgtgttgggtttgggtagtaacttagtgtgatgagaaattttacagatatttgttttttatttgttcctactaacaacatttggtttttagATTGCAGCTATATCTGAACAGTCATCAGAATCTTCAAGCGCATCAGGAGCTGACTCCAGTGAGAACGCCAATGGAAGTCCTGAGTGGAGATCATTTGATA

Basic information

species Zea mays
transcript GRMZM5G817551_T04
intron # 11
splice site 3'
intron type U2

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|101388186|gb|EB816107.1|EB816107
EST:     TTCTTATATGTGACGATGGATCCATCAGATGGAATCGACTGGAAAGGCTG                         ATTGCAGCTATATCTGAACAGTCATCAGAATCTTCAAGCGCATCAGGAGCT
genomic: TTCTTATATGTGACGATGGATCCATCAGATGGAATCGACTGGAAAGGCTGgtacatgctt ... tggtttttagATTGCAGCTATATCTGAACAGTCATCAGAATCTTCAAGCGCATCAGGAGCT
EST: gi|71769295|gb|DR967232.1|DR967232
EST:     TTCTTATATGTGACGATGGATCCATCAGATGGAATCGACTGGAAAGGCTG                         ATTGCAGCTATATCTGAACAGTCATCAGAATCTTCAAGCGCATCAGGAGCT
genomic: TTCTTATATGTGACGATGGATCCATCAGATGGAATCGACTGGAAAGGCTGgtacatgctt ... tggtttttagATTGCAGCTATATCTGAACAGTCATCAGAATCTTCAAGCGCATCAGGAGCT
EST: gi|45847408|gb|CN071351.1|CN071351
EST:     TTCTTATATGTGACGATGGATCCATCAGATGGAATCGACTGGAAAGGC--                         --T---GCTATATCTGAACAGTCATCAGAATCTTCAAGCGCATCAGGAGCT
genomic: TTCTTATATGTGACGATGGATCCATCAGATGGAATCGACTGGAAAGGCTGgtacatgctt ... tggtttttagATTGCAGCTATATCTGAACAGTCATCAGAATCTTCAAGCGCATCAGGAGCT
EST: gi|32799168|gb|CD951404.1|CD951404
EST:     GATCCGTCAGATGGAATCGACTGGAAAGGCTG                         ATTGCAGCTATATCTGAACAGTCATCAGAATCTTCAAGCGCATCAGGAGCT
genomic: GATCCATCAGATGGAATCGACTGGAAAGGCTGgtacatgctt ... tggtttttagATTGCAGCTATATCTGAACAGTCATCAGAATCTTCAAGCGCATCAGGAGCT
EST: gi|32798884|gb|CD951120.1|CD951120
EST:     GATCCATCAGATGGAATCGACTGGAAAGGCTG                         ATTGCAGCTATATCTGAACAGTCATCAGAATCTTCAAGCGCATCAGGAGCT
genomic: GATCCATCAGATGGAATCGACTGGAAAGGCTGgtacatgctt ... tggtttttagATTGCAGCTATATCTGAACAGTCATCAGAATCTTCAAGCGCATCAGGAGCT
EST: gi|60350439|gb|DN217412.1|DN217412
EST:     TTCTTATATGTGACGATGGATCCATCAGATGGAATCGACTGGAAAGGCTG                         ATTGCAGCTATATCTGAACAGTCATCAGAATCTTCAAGCGCATCAGGAGCT
genomic: TTCTTATATGTGACGATGGATCCATCAGATGGAATCGACTGGAAAGGCTGgtacatgctt ... tggtttttagATTGCAGCTATATCTGAACAGTCATCAGAATCTTCAAGCGCATCAGGAGCT
EST: gi|71314000|gb|DR793612.1|DR793612
EST:     TTCTTATATGTGACGATGGATCCATCAGATGGAATCGACTGGAAAGGC--                         --T---GCTATATTTGAACAGTCATCAGAATCTTCAAGCGCATCAGGAGCT
genomic: TTCTTATATGTGACGATGGATCCATCAGATGGAATCGACTGGAAAGGCTGgtacatgctt ... tggtttttagATTGCAGCTATATCTGAACAGTCATCAGAATCTTCAAGCGCATCAGGAGCT
EST: gi|78093038|gb|DV521412.1|DV521412
EST:     TTCTTATATGTGACGATGGATCCATCAGATGGAATCGACTGGAAAGGCTG                         ATTGCAGCTATATCTGAACAGTCATCAGAATCTTCAAGCGCATCAGGAGCT
genomic: TTCTTATATGTGACGATGGATCCATCAGATGGAATCGACTGGAAAGGCTGgtacatgctt ... tggtttttagATTGCAGCTATATCTGAACAGTCATCAGAATCTTCAAGCGCATCAGGAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattttacagatatttgttttttatttgttcctactaacaacatttggtttttagATTGCAGCTATATCTGAACAGTCATCAGAATCTTCAAGCGCATCAGGAGCTGACTCCAGTGAGAACGCCAATGGAAGTCCTGAGTGGAGATCATTTGATA
                                tactaac  putative branch site (score: 0)
                                                ttttt  putative PPT
     tacagatatttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctaattcttgtgttgggtttgggtagtaacttagtgtgatgagaaattttacagatatttgttttttatttgttcctactaacaacatttggtttttagATTGCAGCTATATCTGAACAGTCATCAGAATCTTCAAGCGCATCAGGAGCTGACTCCAGTGAGAACGCCAATGGAAGTCCTGAGTGGAGATCATTTGATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA