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

gtacgtgcggtctcggtttcctccgcagcatgaatggatggattatattatgcgtgaatacgatacgtacgattacatcatgctacgtacgtacagGAAGCGATGGCCTTCCACGGTTTCGGGGACTCTGGTGGCGCAATACCTGCTCATTGCTCTTGGAGG

Basic information

species Zea mays
transcript GRMZM2G135044_T02
intron # 1
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|71298977|gb|DR785482.1|DR785482
EST:     GGAGCCGCCTACGCCGCCTTCTGCTTTCCCTTCGCCGTCGCCCTCGAGAG                         GAAGCGATGGCCTTCCACGGTTTCGGGGACTCTGGTGGCGCAATACCTGCT
genomic: GGAGCCGCCTACGCCGCCTTCTGCTTTCCCTTCGCCGTCGCCCTCGAGAGgtacgtgcgg ... gtacgtacagGAAGCGATGGCCTTCCACGGTTTCGGGGACTCTGGTGGCGCAATACCTGCT
EST: gi|211033315|gb|FL100502.1|FL100502
EST:     GGAGCCGCCTACGCCGCCTTCTGCTTTCCCTTCGCCGTCGCCCTCGAGAG                         GAAGCGATGGCCTTCCACGGTTTCGGGGACTCTGGTGGCGCAATACCTGCT
genomic: GGAGCCGCCTACGCCGCCTTCTGCTTTCCCTTCGCCGTCGCCCTCGAGAGgtacgtgcgg ... gtacgtacagGAAGCGATGGCCTTCCACGGTTTCGGGGACTCTGGTGGCGCAATACCTGCT
EST: gi|93282539|gb|EB674803.1|EB674803
EST:     GGAGCCGCCTACGCCGCCTTCTGCTTTCCCTTCGCCGTCGCCCTCGAGAG                         GAAGCGATGGCCTTCCACGGTTTCGGGGACTCTGGTGGCGCAATACCTGCT
genomic: GGAGCCGCCTACGCCGCCTTCTGCTTTCCCTTCGCCGTCGCCCTCGAGAGgtacgtgcgg ... gtacgtacagGAAGCGATGGCCTTCCACGGTTTCGGGGACTCTGGTGGCGCAATACCTGCT
EST: gi|88755773|gb|DY539914.1|DY539914
EST:     GGAGCCGCCTACGCCGCCTTCTGCTTTCCCTTCGCCGTCGCCCTCGAGAG                         GAAGCGATGGCCTTCCACGGTTTCGGGGACTCTGGTGGCGCAATACCTGCT
genomic: GGAGCCGCCTACGCCGCCTTCTGCTTTCCCTTCGCCGTCGCCCTCGAGAGgtacgtgcgg ... gtacgtacagGAAGCGATGGCCTTCCACGGTTTCGGGGACTCTGGTGGCGCAATACCTGCT
EST: gi|94472819|gb|EB701777.1|EB701777
EST:     GGAGCCGCCTACGCCGCCTTCTGCTTTCCCTTCGCCGTCGCCCTCGAGAG                         GAAGCGATGGCCTTCCACGGTTTCGGGGACTCTGGTGGCGCAATACCTGCT
genomic: GGAGCCGCCTACGCCGCCTTCTGCTTTCCCTTCGCCGTCGCCCTCGAGAGgtacgtgcgg ... gtacgtacagGAAGCGATGGCCTTCCACGGTTTCGGGGACTCTGGTGGCGCAATACCTGCT
EST: gi|50337658|gb|CO532784.1|CO532784
EST:     GGAGCCGCCTACGCCGCCTTCTGCTTTCCCTTCGCCGTCGCCCTCGAGAG                         GAAGCGATGGCCTTCCACGGTTTCGGGGACTCTGGTGGCGCAATACCTGCT
genomic: GGAGCCGCCTACGCCGCCTTCTGCTTTCCCTTCGCCGTCGCCCTCGAGAGgtacgtgcgg ... gtacgtacagGAAGCGATGGCCTTCCACGGTTTCGGGGACTCTGGTGGCGCAATACCTGCT
EST: gi|71426206|gb|DR807256.1|DR807256
EST:     GGAGCCGCCTACGCCGCCTTCTGCTTTCCCTTCGCCGTCGCCCTCGAGAG                         GAAGCGATGGCCTTCCACGGTTTCGGGGACTCTGGTGGCGCAATACCTGCT
genomic: GGAGCCGCCTACGCCGCCTTCTGCTTTCCCTTCGCCGTCGCCCTCGAGAGgtacgtgcgg ... gtacgtacagGAAGCGATGGCCTTCCACGGTTTCGGGGACTCTGGTGGCGCAATACCTGCT
EST: gi|211033314|gb|FL100501.1|FL100501
EST:     GGAGCCGCCTACGCCGCCTTCTGCTTTCCCTTCGCCGTCGCCCTCGAGAG                         GAAGCGATGGCCTTCCACGGTTTCGGGGACTCTGGTGGCGCAATACCTGCT
genomic: GGAGCCGCCTACGCCGCCTTCTGCTTTCCCTTCGCCGTCGCCCTCGAGAGgtacgtgcgg ... gtacgtacagGAAGCGATGGCCTTCCACGGTTTCGGGGACTCTGGTGGCGCAATACCTGCT
EST: gi|18169261|gb|BM339101.1|BM339101
EST:     GGAGCCGCCTACGCCGCCTTCTGCTTTCCCTTCGCCGTCGCCCTCGAGAG                         GAAGCGATGGCCTTCCACGGTTTCGGGGACTCTGGTGGCGCAATACCTGCT
genomic: GGAGCCGCCTACGCCGCCTTCTGCTTTCCCTTCGCCGTCGCCCTCGAGAGgtacgtgcgg ... gtacgtacagGAAGCGATGGCCTTCCACGGTTTCGGGGACTCTGGTGGCGCAATACCTGCT
EST: gi|78088288|gb|DV516681.1|DV516681
EST:     GGAGCCGCCTACGCCGCCTTCTGCTTTCCCTTCGCCGTCGCCCTCGAGAG                         GAAGCGATGGCCTTCCACGGTTTCGGGGACTCTGGTGGCGCAATACCTGCT
genomic: GGAGCCGCCTACGCCGCCTTCTGCTTTCCCTTCGCCGTCGCCCTCGAGAGgtacgtgcgg ... gtacgtacagGAAGCGATGGCCTTCCACGGTTTCGGGGACTCTGGTGGCGCAATACCTGCT
EST: gi|78121589|gb|DV539973.1|DV539973
EST:     GGAGCCGCCTACGCCGCCTTCTGCTTTCCCTTCGCCGTCGCCCTCGAGAG                         GAAGCGATGGCCTTCCACGGTTTCGGGGACTCTGGTGGCGCAATACCTGCT
genomic: GGAGCCGCCTACGCCGCCTTCTGCTTTCCCTTCGCCGTCGCCCTCGAGAGgtacgtgcgg ... gtacgtacagGAAGCGATGGCCTTCCACGGTTTCGGGGACTCTGGTGGCGCAATACCTGCT
EST: gi|93282784|gb|EB675048.1|EB675048
EST:     GGAGCCGCCTACGCCGCCTTCTGCTTTCCCTTCGCCGTCGCCCTCGAGAG                         GAAGCGATGGCCTTCCACGGTTTCGGGGACTCTGGTGGCGCAATACCTGCT
genomic: GGAGCCGCCTACGCCGCCTTCTGCTTTCCCTTCGCCGTCGCCCTCGAGAGgtacgtgcgg ... gtacgtacagGAAGCGATGGCCTTCCACGGTTTCGGGGACTCTGGTGGCGCAATACCTGCT
EST: gi|211033313|gb|FL100500.1|FL100500
EST:     GGAGCCGCCTACGCCGCCTTCTGCTTTCCCTTCGCCGTCGCCCTCGARAG                         GAAGCGATGGC-TTCCACGGTTTCGGGGAC
genomic: GGAGCCGCCTACGCCGCCTTCTGCTTTCCCTTCGCCGTCGCCCTCGAGAGgtacgtgcgg ... gtacgtacagGAAGCGATGGCCTTCCACGGTTTCGGGGAC

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), 47 (downstream exon)
Score: 14

ACCACCTGCTCGCCCTCGGCGCCGACCCGCTGGCCGTCGTCGTCGTCGCCGGAGCCGCCTACGCCGCCTTCTGCTTTCCCTTCGCCGTCGCCCTCGAGAGgtacgtgcgg ... gtacgtacagGAAGCGATGGCCTTCCACGGTTTCGGGGACTCTGGTGGCGCAATACCTGCTCATTGCTCTTGGAGG


Block sizes: 42 (upstream exon), 49 (downstream exon)
Score: 40

ACCACCTGCTCGCCCTCGGCGCCGACCCGCTGGCCGTCGTCGTCGTCGCCGGAGCCGCCTACGCCGCCTTCTGCTTTCCCTTCGCCGTCGCCCTCGAGAGgtacgtgcgg ... gtacgtacagGAAGCGATGGCCTTCCACGGTTTCGGGGACTCTGGTGGCGCAATACCTGCTCATTGCTCTTGGAGG


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 8

ACCACCTGCTCGCCCTCGGCGCCGACCCGCTGGCCGTCGTCGTCGTCGCCGGAGCCGCCTACGCCGCCTTCTGCTTTCCCTTCGCCGTCGCCCTCGAGAGgtacgtgcgg ... gtacgtacagGAAGCGATGGCCTTCCACGGTTTCGGGGACTCTGGTGGCGCAATACCTGCTCATTGCTCTTGGAGG


Block sizes: 44 (upstream exon), 40 (downstream exon)
Score: 9

ACCACCTGCTCGCCCTCGGCGCCGACCCGCTGGCCGTCGTCGTCGTCGCCGGAGCCGCCTACGCCGCCTTCTGCTTTCCCTTCGCCGTCGCCCTCGAGAGgtacgtgcgg ... gtacgtacagGAAGCGATGGCCTTCCACGGTTTCGGGGACTCTGGTGGCGCAATACCTGCTCATTGCTCTTGGAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attatattatgcgtgaatacgatacgtacgattacatcatgctacgtacgtacagGAAGCGATGGCCTTCCACGGTTTCGGGGACTCTGGTGGCGCAATACCTGCTCATTGCTCTTGGAGG
                              attacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtgcggtctcggtttcctccgcagcatgaatggatggattatattatgcgtgaatacgatacgtacgattacatcatgctacgtacgtacagGAAGCGATGGCCTTCCACGGTTTCGGGGACTCTGGTGGCGCAATACCTGCTCATTGCTCTTGGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG