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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTGCGCTGATGCATGCTTGTCGGCATGGGCACTGGGAGGTGGTGCAGATGCTTCTTCTATTTAGATGCAATgtaagacggcacgtaagatagtacctttttctgctacattttttagttaggacaaggtaagtgctaactgttgtttgttttttggctgattcag

Basic information

species Zea mays
transcript AC194389.3_FGT001
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC194389.3_FGT001 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os10g37730.3 (Oryza sativa), 5'ss of exon 3
ACTGCGCTGATGCATGCTTGTCGGCATGGGCACTGGGAGGTGGTGCAGATGCTTCTTCTATTTAGATGCAATgtaagacggcacgtaagatagtacctttt-tctgctacattttttagttaggacaaggtaagtgctaactgttgtttgttttttggctgattcag---
|||||| ||||||| || || |||||||| |||||||||||||| ||||||||||| || || |||||||||||| |       |||   | | |  | || |  | | ||| ||||   |   ||| || | ||||| ||   | | ||| ||| ||  | ||  |   
ACTGCGTTGATGCACGCATGCCGGCATGGCCACTGGGAGGTGGTTCAGATGCTTCTGCTCTTCAGATGCAATgtatggtatt--gtagcgtggcatttcttgttagttccatatttt--ctgacacatggaaggtgctgacctctctgtgtgtttgggtggcttgtgaag
















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|50326933|gb|CO522059.1|CO522059
EST:     GGCATGGGCACTGGGAGGTGGTGCAGATGCTTCTTCTATTTAGATGCAAT                         GTTACTAGGGCAGATTACTTGAGTGGTCGAACAGCACTGCATTTTGCTGCA
genomic: GGCATGGGCACTGGGAGGTGGTGCAGATGCTTCTTCTATTTAGATGCAATgtaagacggc ... gctgattcagGTTACTAGGGCAGATTACTTGAGTGGTCGAACAGCACTGCATTTTGCTGCA
EST: gi|149014811|gb|EE044512.2|EE044512
EST:     GGCATGGGCACTGGGAGGTGGTGCAGATGCTTCTTCTATTTAGATGCAAT                         GTTACTAGGGCAGATTACTTGAGTGGTCGAACAGCACTGCATTTTGCTGCA
genomic: GGCATGGGCACTGGGAGGTGGTGCAGATGCTTCTTCTATTTAGATGCAATgtaagacggc ... gctgattcagGTTACTAGGGCAGATTACTTGAGTGGTCGAACAGCACTGCATTTTGCTGCA
EST: gi|148961455|gb|EE012203.2|EE012203
EST:     GGCATGGGCACTGGGAGGTGGTGCAGATGCTTCTTCTATTTAGATGCAAT                         GTTACTAGGGCAGATTACTTGAGTGGTCGAACAGCACTGCATTTTGCTGCA
genomic: GGCATGGGCACTGGGAGGTGGTGCAGATGCTTCTTCTATTTAGATGCAATgtaagacggc ... gctgattcagGTTACTAGGGCAGATTACTTGAGTGGTCGAACAGCACTGCATTTTGCTGCA
EST: gi|211432410|gb|FL439403.1|FL439403
EST:     GGCATGGGCACTGGGAGGTGGTGCAGATGCTTCTTCTATTTAGATGCAAT                         GTTACTAGGGCAGATTACTTGAGTGGTCGAACAGCACTGCATTTTGCTGCA
genomic: GGCATGGGCACTGGGAGGTGGTGCAGATGCTTCTTCTATTTAGATGCAATgtaagacggc ... gctgattcagGTTACTAGGGCAGATTACTTGAGTGGTCGAACAGCACTGCATTTTGCTGCA
EST: gi|211065139|gb|FL368215.1|FL368215
EST:     GGCATGGGCACTGGGAGGTGGTGCAGATGCTTCTTCTATTTAGATGCAAT                         GTTACTAGGGCAGATTACTTGAGTGGTCGAACAGCACTGCATTTTGCTGCA
genomic: GGCATGGGCACTGGGAGGTGGTGCAGATGCTTCTTCTATTTAGATGCAATgtaagacggc ... gctgattcagGTTACTAGGGCAGATTACTTGAGTGGTCGAACAGCACTGCATTTTGCTGCA
EST: gi|148942318|gb|EC887337.2|EC887337
EST:     GGCATGGGCACTGGGAGGTGGTGCAGATGCTTCTTCTATTTAGATGCAAT                         GTTACTAGGGCAGATTACTTGAGTGGTCGAACAGCACTGCATTTTGCTGCA
genomic: GGCATGGGCACTGGGAGGTGGTGCAGATGCTTCTTCTATTTAGATGCAATgtaagacggc ... gctgattcagGTTACTAGGGCAGATTACTTGAGTGGTCGAACAGCACTGCATTTTGCTGCA
EST: gi|211243066|gb|FL400453.1|FL400453
EST:     GGCATGGGCACTGGGAGGTGGTGCAGATGCTTCTTCTATTTAGATGCAAT                         GTTACTAGGGCAGATTACTTGAGTGGTCGAACAGCACTGCATTTTGCTGCA
genomic: GGCATGGGCACTGGGAGGTGGTGCAGATGCTTCTTCTATTTAGATGCAATgtaagacggc ... gctgattcagGTTACTAGGGCAGATTACTTGAGTGGTCGAACAGCACTGCATTTTGCTGCA
EST: gi|74238026|gb|DT645940.1|DT645940
EST:     GGCATGGGCACTGGGAGGTGGTGCAGATGCTTCTTCTATTTAGATGCAAT                         GTTACTAGGGCAGATTACTTGAGTGGTCGAACAGCACTGCATTTTGCTGCA
genomic: GGCATGGGCACTGGGAGGTGGTGCAGATGCTTCTTCTATTTAGATGCAATgtaagacggc ... gctgattcagGTTACTAGGGCAGATTACTTGAGTGGTCGAACAGCACTGCATTTTGCTGCA

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), 45 (downstream exon)
Score: 50

ACTGCGCTGATGCATGCTTGTCGGCATGGGCACTGGGAGGTGGTGCAGATGCTTCTTCTATTTAGATGCAATgtaagacggc ... gctgattcagGTTACTAGGGCAGATTACTTGAGTGGTCGAACAGCACTGCATTTTGCTGCACATGATGGATTTGTTCGGTGTATTAGGCTTTTAGTTGCAGACTTTGTCC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 44

ACTGCGCTGATGCATGCTTGTCGGCATGGGCACTGGGAGGTGGTGCAGATGCTTCTTCTATTTAGATGCAATgtaagacggc ... gctgattcagGTTACTAGGGCAGATTACTTGAGTGGTCGAACAGCACTGCATTTTGCTGCACATGATGGATTTGTTCGGTGTATTAGGCTTTTAGTTGCAGACTTTGTCC


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 57

ACTGCGCTGATGCATGCTTGTCGGCATGGGCACTGGGAGGTGGTGCAGATGCTTCTTCTATTTAGATGCAATgtaagacggc ... gctgattcagGTTACTAGGGCAGATTACTTGAGTGGTCGAACAGCACTGCATTTTGCTGCACATGATGGATTTGTTCGGTGTATTAGGCTTTTAGTTGCAGACTTTGTCC


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 32

ACTGCGCTGATGCATGCTTGTCGGCATGGGCACTGGGAGGTGGTGCAGATGCTTCTTCTATTTAGATGCAATgtaagacggc ... gctgattcagGTTACTAGGGCAGATTACTTGAGTGGTCGAACAGCACTGCATTTTGCTGCACATGATGGATTTGTTCGGTGTATTAGGCTTTTAGTTGCAGACTTTGTCC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTGCGCTGATGCATGCTTGTCGGCATGGGCACTGGGAGGTGGTGCAGATGCTTCTTCTATTTAGATGCAATgtaagacggcacgtaagatagtacctttttctgctacattttttagttaggacaaggtaagtgctaactgttgtttgttttttggctgattcag

- - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - -  CAGATG