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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGAAGAATAGGATAAATAAAGATGGAGAGCTTGTTATATCTTCTACAAAAACTAGAACACAGAAgtaattattgttctattatccttctagtctttttttattgcaactgatttgatttaccatcttag

Basic information

species Zea mays
transcript GRMZM2G170532_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G170532_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os03g14510.2 (Oryza sativa), 5'ss of exon 4
GAGAAGAATAGGATAAATAAAGATGGAGAGCTTGTTATATCTTCTACAAAAACTAGAACACAGAAgtaattattgttctattatccttctagtctt-tttttattgcaactgatttgatttaccatcttag
|| |||||  |||||||||||||||| |||||||| |||||||||||||||||||| ||||| |||||| | ||  ||  || |  |  | ||||| |||  |  ||||||||    ||||| | | ||||
GAAAAGAACCGGATAAATAAAGATGGGGAGCTTGTGATATCTTCTACAAAAACTAGGACACAAAAgtaaatgttactcagttcttttgattgtcttgtttggacagcaactgacacaatttatccttttag

upper sequence: GRMZM2G170532_T02 (Zea mays), 5'ss of exon 4
lower sequence: AT1G62850.3 (Arabidopsis thaliana), 5'ss of exon 4
GAGAAGAATAGGATAAATAAAGATGGAGAGCTTGTTATATCTTCTACAAAAACTAGAACACAGAAgtaattattgttctattatccttctagtctttttttattgcaactgatttgatttaccatcttag---------------
||||||||| |||| || || ||||| || ||||| ||||||||||| ||||| ||||| ||||||| | ||       ||  ||||     || | ||  |||   | | | ||   |    ||   ||               
GAGAAGAATCGGATCAACAAGGATGGTGAACTTGTGATATCTTCTACCAAAACCAGAACGCAGAAgtcagta--acctaatagtcctctctttcatattccattctcaataacttctctatttatgacagtatgttcccttgcag

upper sequence: GRMZM2G170532_T02 (Zea mays), 5'ss of exon 4
lower sequence: Vv02s0241g00090.t01 (Vitis vinifera), 5'ss of exon 5
GAGAAGAATAGGATAAATAAAGATGGAGAGCTTGTTATATCTTCTACAAAAACTAGAACACAGAAgt-aattattgttctattatccttctagt----------------ctttttttattgcaactgatttgatt-taccatcttag-----
|| |||||| |||| || |||||||| ||| |||| || ||||| |||||||||||||||||||||| ||||  ||  |  || ||||| | ||                || ||   |  |||| || ||| ||| | ||||  |       
GAAAAGAATCGGATTAACAAAGATGGGGAGATTGTGATTTCTTCAACAAAAACTAGAACACAGAAgttaatttctgcccacttctcctttttgttatacattttggttctctgttcccaaagcaattggtttcattctgccattcttcttcag

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|18164644|gb|BM334483.1|BM334483
EST:     AATAAAGATGGAGAGCTTGTTATATCTTCTACAAAAACTAGAACACAGAA                         GGGCAATATT-AAGATGCATTGCAGAAAA-ACAG
genomic: AATAAAGATGGAGAGCTTGTTATATCTTCTACAAAAACTAGAACACAGAAgtaattattg ... accatcttagGGGCAATATTGAAGATGCATTGCAGAAAATACAG
EST: gi|18168069|gb|BM337909.1|BM337909
EST:     ATAAAGATGGAGAGCTGTGTTATATCTTCTACAAAAACTAGAACACAGAA                         GGGCAATATTGAAGATGCATTGCAGAAAATACAG
genomic: ATAAAGATGGAGAGCT-TGTTATATCTTCTACAAAAACTAGAACACAGAAgtaattattg ... accatcttagGGGCAATATTGAAGATGCATTGCAGAAAATACAG
EST: gi|18166092|gb|BM335931.1|BM335931
EST:     ATAAAGATGGAGAGCTTGTTATAGTCTTCTACAAAAACTAGAACACAGAA                         GGGCAATATTGAAGATGCATTGCAGAAAATACAG
genomic: ATAAAGATGGAGAGCTTGTTATA-TCTTCTACAAAAACTAGAACACAGAAgtaattattg ... accatcttagGGGCAATATTGAAGATGCATTGCAGAAAATACAG
EST: gi|18173601|gb|BM348989.1|BM348989
EST:     ATAAAGATGGAGAGCTTGATTATATCTTCTACAAAAACTAGAACACAGAA                         GGGCAATATTGAAGATGCATTGCAGAAAATACAG
genomic: ATAAAGATGGAGAGCTTG-TTATATCTTCTACAAAAACTAGAACACAGAAgtaattattg ... accatcttagGGGCAATATTGAAGATGCATTGCAGAAAATACAG
EST: gi|18175793|gb|BM350979.1|BM350979
EST:     ATAAAGATGGAGAGCTTGGTTATATCTTCTACAAAAACTAGAACACAGAA                         GGGCAATATTGAAGATGCATTGCAGAAAATACAG
genomic: ATAAAGATGGAGAGCTTG-TTATATCTTCTACAAAAACTAGAACACAGAAgtaattattg ... accatcttagGGGCAATATTGAAGATGCATTGCAGAAAATACAG
EST: gi|18175280|gb|BM350651.1|BM350651
EST:     ATAAAGATGGAGAGCTTGGTTATATCTTCTACAAAAACTAGAACACAGAA                         GGGCAATATTGAAGATGCATTGCAGAAAATACAG
genomic: ATAAAGATGGAGAGCTTG-TTATATCTTCTACAAAAACTAGAACACAGAAgtaattattg ... accatcttagGGGCAATATTGAAGATGCATTGCAGAAAATACAG
EST: gi|17931962|gb|BM268922.1|BM268922
EST:     ATAAAGATGGAGAGCTTGTTATATTCTTCTACAAAAACTAGAACACAGAA                         GGGCAATATTGAAGATGCATTGCAGAAAATACAG
genomic: ATAAAGATGGAGAGCTTGTTATAT-CTTCTACAAAAACTAGAACACAGAAgtaattattg ... accatcttagGGGCAATATTGAAGATGCATTGCAGAAAATACAG
EST: gi|17931672|gb|BM268632.1|BM268632
EST:     ATAAAGATGGAGAGCTTGTTATAATCTTCTACAAAAACTAGAACACAGAA                         GGGCAATATTGAAGATGCATTGCAGAAAATACAG
genomic: ATAAAGATGGAGAGCTTGTTATA-TCTTCTACAAAAACTAGAACACAGAAgtaattattg ... accatcttagGGGCAATATTGAAGATGCATTGCAGAAAATACAG

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: 48 (upstream exon), 34 (downstream exon)
Score: 45

GAGAAGAATAGGATAAATAAAGATGGAGAGCTTGTTATATCTTCTACAAAAACTAGAACACAGAAgtaattattg ... accatcttagGGGCAATATTGAAGATGCATTGCAGAAAATACAG


Block sizes: 49 (upstream exon), 34 (downstream exon)
Score: 56

GAGAAGAATAGGATAAATAAAGATGGAGAGCTTGTTATATCTTCTACAAAAACTAGAACACAGAAgtaattattg ... accatcttagGGGCAATATTGAAGATGCATTGCAGAAAATACAG


Block sizes: 49 (upstream exon), 34 (downstream exon)
Score: 32

GAGAAGAATAGGATAAATAAAGATGGAGAGCTTGTTATATCTTCTACAAAAACTAGAACACAGAAgtaattattg ... accatcttagGGGCAATATTGAAGATGCATTGCAGAAAATACAG


Block sizes: 49 (upstream exon), 34 (downstream exon)
Score: 68

GAGAAGAATAGGATAAATAAAGATGGAGAGCTTGTTATATCTTCTACAAAAACTAGAACACAGAAgtaattattg ... accatcttagGGGCAATATTGAAGATGCATTGCAGAAAATACAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGAAGAATAGGATAAATAAAGATGGAGAGCTTGTTATATCTTCTACAAAAACTAGAACACAGAAgtaattattgttctattatccttctagtctttttttattgcaactgatttgatttaccatcttag

- - - - - - - - -  AAGATG
- - - - - - - - - -  GATGGA
- - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - -  GAGCTT