Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcaattcttgtattccatgcactgatactctgttaaatctcattttgactgcgattcctgtttgttgactactcacaagactttctgccttcagGTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGAACTTTTCAGGGTCTCTTGCTCATCATTCGGTGCCAAGGGTGGAGACAAC

Basic information

species Zea mays
transcript GRMZM2G420119_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G420119_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g38990.1 (Oryza sativa), 3'ss of exon 5
gtgcaattcttgtattccatgcactgatactctgttaaatctcattttgactgcgattcctgtttgttgactactcacaagactttctgccttcagGTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGAACTTTTCAGGGTCTCTTGCTCATCATTCGGTGCCAAGGGTGGAGACAAC
|| ||| |       ||  | ||  |||| |||||    | | |||| || ||| || ||||    || | |  ||||  |   | |||| ||||||||||||  |||||| | || ||| ||| ||||| ||||||||||||||| || |||||||||||    ||||| ||| ||||||| |||||||| ||||
gtacaaattaaactctcagt-caaagataatctgtgcgttataatttagattgcaatgcctg---attaattcttcacctg---tcctgcgttcagGTTCAGAATAAGCAGCCCCATAATGCGAACGATGCCTTCCGTATAAGAGGGACATTTCAGGGTCTAGCACTCATTATTAGGTGCCAGGGGTGGAGGCAAC
















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|148945466|gb|EC890700.2|EC890700
EST:     TTGGACAAACCCTCACTTATCCACTGGATGTTGTCCGGAGACAAATGCAG                         GTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGA
genomic: TTGGACAAACCCTCACTTATCCACTGGATGTTGTCCGGAGACAAATGCAGgtgcaattct ... ctgccttcagGTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGA
EST: gi|71761148|gb|DR959085.1|DR959085
EST:     TTGGACAAACCCTCACTTATCCACTGGATGTTGTCCGGAGACAAATGCAG                         GTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGA
genomic: TTGGACAAACCCTCACTTATCCACTGGATGTTGTCCGGAGACAAATGCAGgtgcaattct ... ctgccttcagGTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGA
EST: gi|32793155|gb|CD945391.1|CD945391
EST:     TTGGACAAACCCTCACTTATCCACTGGATGTTGTCCGGAGACAAATGCAG                         GTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGA
genomic: TTGGACAAACCCTCACTTATCCACTGGATGTTGTCCGGAGACAAATGCAGgtgcaattct ... ctgccttcagGTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGA
EST: gi|32825947|gb|CD965625.1|CD965625
EST:     TTGGACAAACCCTCACTTATCCACTGGATGTTGTCCGGAGACAAATGCAG                         GTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGA
genomic: TTGGACAAACCCTCACTTATCCACTGGATGTTGTCCGGAGACAAATGCAGgtgcaattct ... ctgccttcagGTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGA
EST: gi|60338979|gb|DN205952.1|DN205952
EST:     TTGGACAAACCCTCACTTATCCACTGGATGTTGTCCGGAGACAAATGCAG                         GTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGA
genomic: TTGGACAAACCCTCACTTATCCACTGGATGTTGTCCGGAGACAAATGCAGgtgcaattct ... ctgccttcagGTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGA
EST: gi|5739909|gb|AI947599.1|AI947599
EST:     TTGGCCAAACCCTCCCTTATCCCCTGGATGTTGTCCGGAGACAAATGCAG                         GTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGA
genomic: TTGGACAAACCCTCACTTATCCACTGGATGTTGTCCGGAGACAAATGCAGgtgcaattct ... ctgccttcagGTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGA
EST: gi|44900406|gb|CK826951.1|CK826951
EST:     TTGGACAAACCCTCACTTATCCACTGGATGTTGTCCGGAGACAAATGCAG                         GTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGA
genomic: TTGGACAAACCCTCACTTATCCACTGGATGTTGTCCGGAGACAAATGCAGgtgcaattct ... ctgccttcagGTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGA
EST: gi|32837555|gb|CD977233.1|CD977233
EST:     TTGGACAAACCCTCACTTATCCACTGGATGTTGTCCGGAGACAAATGCAG                         GTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGA
genomic: TTGGACAAACCCTCACTTATCCACTGGATGTTGTCCGGAGACAAATGCAGgtgcaattct ... ctgccttcagGTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGA
EST: gi|78118637|gb|DV537021.1|DV537021
EST:     TTGGACAAACCCTCACTTATCCACTGGATGTTGTCCGGAGACAAATGCAG                         GTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGA
genomic: TTGGACAAACCCTCACTTATCCACTGGATGTTGTCCGGAGACAAATGCAGgtgcaattct ... ctgccttcagGTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGA
EST: gi|74244724|gb|DT652638.1|DT652638
EST:     TTGGACAAACCCTCACTTATCCACTGGATGTTGTCCGGAGACAAATGCAG                         GTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGA
genomic: TTGGACAAACCCTCACTTATCCACTGGATGTTGTCCGGAGACAAATGCAGgtgcaattct ... ctgccttcagGTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGA
EST: gi|149079552|gb|EE168537.2|EE168537
EST:     TTGGACAAACCCTCACTTATCCACTGGATGTTGTCCGGAGACAAATGCAG                         GTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGA
genomic: TTGGACAAACCCTCACTTATCCACTGGATGTTGTCCGGAGACAAATGCAGgtgcaattct ... ctgccttcagGTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGA
EST: gi|149013497|gb|EE042998.2|EE042998
EST:     TTGGACAAACCCTCACTTATCCACTGGATGTTGTCCGGAGACAAATGCAG                         GTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGA
genomic: TTGGACAAACCCTCACTTATCCACTGGATGTTGTCCGGAGACAAATGCAGgtgcaattct ... ctgccttcagGTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGA
EST: gi|74234934|gb|DT642848.1|DT642848
EST:     TTGGACAAACCCTCACTTATCCACTGGATGTTGTCCGGAGACAAATGCAG                         GTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGA
genomic: TTGGACAAACCCTCACTTATCCACTGGATGTTGTCCGGAGACAAATGCAGgtgcaattct ... ctgccttcagGTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGA
EST: gi|71441966|gb|DR823016.1|DR823016
EST:     TTGGACAAACCCTCACTTATCCACTGGATGTTGTCCGGAGACAAATGCAG                         GTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGA
genomic: TTGGACAAACCCTCACTTATCCACTGGATGTTGTCCGGAGACAAATGCAGgtgcaattct ... ctgccttcagGTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGA
EST: gi|71324252|gb|DR798826.1|DR798826
EST:     TTGGACAAACCCTCACTTATCCACTGGATGTTGTCCGGAGACAAATGCAG                         GTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGA
genomic: TTGGACAAACCCTCACTTATCCACTGGATGTTGTCCGGAGACAAATGCAGgtgcaattct ... ctgccttcagGTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGA
EST: gi|37422064|gb|CF648737.1|CF648737
EST:     TTGGACAAACCCTCACTTATCCACTGGATGTTGTCCGGAGACAAATGCAG                         GTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGA
genomic: TTGGACAAACCCTCACTTATCCACTGGATGTTGTCCGGAGACAAATGCAGgtgcaattct ... ctgccttcagGTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGA
EST: gi|110941380|gb|EE161537.1|EE161537
EST:     TTGGACAAACCCTCACTTATCCACTGGATGTTGTCCGGAGACAAATGCAG                         GTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGA
genomic: TTGGACAAACCCTCACTTATCCACTGGATGTTGTCCGGAGACAAATGCAGgtgcaattct ... ctgccttcagGTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGA
EST: gi|37421795|gb|CF648599.1|CF648599
EST:     TTGGACAAACCCTCACTTATCCACTGGATGTTGTCCGGAGACAAATGCAG                         GTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGA
genomic: TTGGACAAACCCTCACTTATCCACTGGATGTTGTCCGGAGACAAATGCAGgtgcaattct ... ctgccttcagGTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGA
EST: gi|166527801|gb|EG059440.1|EG059440
EST:     GTTGTCCGGAGACAAATGCAG                         GTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAGGAGGA
genomic: GTTGTCCGGAGACAAATGCAGgtgcaattct ... ctgccttcagGTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGA
EST: gi|148937578|gb|EC881763.2|EC881763
EST:     TTGGACAAACCCTCACTTATCCACTGGATGTTGTCCGGAGACAAATGCAG                         GTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGA
genomic: TTGGACAAACCCTCACTTATCCACTGGATGTTGTCCGGAGACAAATGCAGgtgcaattct ... ctgccttcagGTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGA
EST: gi|149060805|gb|EE157256.2|EE157256
EST:     TTGGACAAACCCTCACTTATCCACTGGATGTTGTCCGGAGACAAATGCAG                         GTTCAGAGCAAGCAGTTTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGA
genomic: TTGGACAAACCCTCACTTATCCACTGGATGTTGTCCGGAGACAAATGCAGgtgcaattct ... ctgccttcagGTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGA
EST: gi|32826072|gb|CD965750.1|CD965750
EST:     TTGGACAAACCCTCACTTATCCACTGGATGTTGTCCGGAGACAAATGCAG                         GTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGA
genomic: TTGGACAAACCCTCACTTATCCACTGGATGTTGTCCGGAGACAAATGCAGgtgcaattct ... ctgccttcagGTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGA
EST: gi|76924684|gb|DV170083.1|DV170083
EST:     TTGGACAAACCCTCACTTATCCACTGGATGTTGTCCGGAGACAAATGCAG                         GTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGA
genomic: TTGGACAAACCCTCACTTATCCACTGGATGTTGTCCGGAGACAAATGCAGgtgcaattct ... ctgccttcagGTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGA
EST: gi|148930077|gb|EE286023.2|EE286023
EST:     TTGGACAAACCCTCACTTATCCACTGGATGTTGTCCGGAGACAAATGCAG                         GTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGA
genomic: TTGGACAAACCCTCACTTATCCACTGGATGTTGTCCGGAGACAAATGCAGgtgcaattct ... ctgccttcagGTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGA
EST: gi|88756309|gb|DY540450.1|DY540450
EST:     TTGGACAAACCCTCACTTATCCACTGGATGTTGTCCGGAGACAAATGCAG                         GTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGA
genomic: TTGGACAAACCCTCACTTATCCACTGGATGTTGTCCGGAGACAAATGCAGgtgcaattct ... ctgccttcagGTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGA
EST: gi|149027733|gb|EE154578.2|EE154578
EST:     TTGGACAAACCCTCACTTATCCACTGGATGTTGTCCGGAGACAAATGCAG                         GTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGA
genomic: TTGGACAAACCCTCACTTATCCACTGGATGTTGTCCGGAGACAAATGCAGgtgcaattct ... ctgccttcagGTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGA
EST: gi|161593236|gb|EY964028.1|EY964028
EST:     CGGAGACAAATGCAG                         GTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGA
genomic: CGGAGACAAATGCAGgtgcaattct ... ctgccttcagGTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGA
EST: gi|149042104|gb|EE047082.2|EE047082
EST:     TTGGACAAACCCTCACTTATCCACTGGATGTTGTCCGGAGACAAATGCAG                         GTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGA
genomic: TTGGACAAACCCTCACTTATCCACTGGATGTTGTCCGGAGACAAATGCAGgtgcaattct ... ctgccttcagGTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGA
EST: gi|89249817|gb|DY621603.1|DY621603
EST:     TTGGACAAACCCTCACTTTTCCACTGGATGTTGTCCGGAGACAAATGCAG                         GTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGA
genomic: TTGGACAAACCCTCACTTATCCACTGGATGTTGTCCGGAGACAAATGCAGgtgcaattct ... ctgccttcagGTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGA
EST: gi|67016215|gb|CO444964.1|CO444964
EST:     TTGGACAAACCCTCACTTATCCACTGGATGTTGTCCGGAGACAAATGCAG                         GTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGA
genomic: TTGGACAAACCCTCACTTATCCACTGGATGTTGTCCGGAGACAAATGCAGgtgcaattct ... ctgccttcagGTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGA

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: 47 (upstream exon), 49 (downstream exon)
Score: 106

CAAGGATTCTGTTATACTGAAGCTCTCTTGTGGAGCTTTAGCTGGTCTATTTGGACAAACCCTCACTTATCCACTGGATGTTGTCCGGAGACAAATGCAGgtgcaattct ... ctgccttcagGTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGAACTTTTCAGGGTCTCTTGCTCATCATTCGGTGCCAAGGGTGGAGACAAC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 100

CAAGGATTCTGTTATACTGAAGCTCTCTTGTGGAGCTTTAGCTGGTCTATTTGGACAAACCCTCACTTATCCACTGGATGTTGTCCGGAGACAAATGCAGgtgcaattct ... ctgccttcagGTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGAACTTTTCAGGGTCTCTTGCTCATCATTCGGTGCCAAGGGTGGAGACAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 185

CAAGGATTCTGTTATACTGAAGCTCTCTTGTGGAGCTTTAGCTGGTCTATTTGGACAAACCCTCACTTATCCACTGGATGTTGTCCGGAGACAAATGCAGgtgcaattct ... ctgccttcagGTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGAACTTTTCAGGGTCTCTTGCTCATCATTCGGTGCCAAGGGTGGAGACAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 55

CAAGGATTCTGTTATACTGAAGCTCTCTTGTGGAGCTTTAGCTGGTCTATTTGGACAAACCCTCACTTATCCACTGGATGTTGTCCGGAGACAAATGCAGgtgcaattct ... ctgccttcagGTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGAACTTTTCAGGGTCTCTTGCTCATCATTCGGTGCCAAGGGTGGAGACAAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcattttgactgcgattcctgtttgttgactactcacaagactttctgccttcagGTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGAACTTTTCAGGGTCTCTTGCTCATCATTCGGTGCCAAGGGTGGAGACAAC
                              tactcac  putative branch site (score: 55)
                                         ctttctgccttc  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcaattcttgtattccatgcactgatactctgttaaatctcattttgactgcgattcctgtttgttgactactcacaagactttctgccttcagGTTCAGAGCAAGCAGTCTCAAAATTCGAGCGATGGCTTCCGTATAAGAGGAACTTTTCAGGGTCTCTTGCTCATCATTCGGTGCCAAGGGTGGAGACAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA