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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCTTGTCCTTTCCAACAAGTTGGTTATCTATGACTTGGAAAATCGAGTCATTGGGTGGACTGACTACAACTgtaagtgttagcacgttccaatctgctcatgccctatatatatttccacaactatttggtcatccgcctgtaaaatttcag

Basic information

species Zea mays
transcript AC190609.3_FGT004
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC190609.3_FGT004 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os04g26834.1 (Oryza sativa), 5'ss of exon 10
ATCTTGTCCTTTCCAACAAGTTGGTTATCTATGACTTGGAAAATCGAGTCATTGGGTGGACTGACTACAACTgtaagtgttagcacgttccaatctgctcat-----gccctatatatatttccacaactatttggtcatccg--cctg-taaaatttcag------------
|||| |||||||| || ||||| ||| |||||||| ||||||||| ||||||||| |||||||| ||||||||||||| ||| ||| ||| ||| || | | | | | ||| | | | | ||| ||| | | || ||| | |
ATCTGGTCCTTTCAAATAAGTTAGTTGTCTATGACCTGGAAAATCAAGTCATTGGCTGGACTGAGTACAACTgtaagt-ttaacacattcaaatttgattgttatgagttcattccatagtactttacatgtttagtctattgttcttgctaatgtcttgacaatccgaaaat

upper sequence: AC190609.3_FGT004 (Zea mays), 5'ss of exon 9
lower sequence: AT1G05840.1 (Arabidopsis thaliana), 5'ss of exon 9
ATCTTGTCCTTTCCAACAAGTTGGTTATCTATGACTTGGAAAATCGAGTCATTGGGTGGACTGACTACAACTgtaagtgtta-gcacgttc---caatctgctcatgccctat----------atatatttc-----cacaactatttggtcatccgcctgtaaaatttcag--
|| | || ||||| |||||| | ||| |||| || | ||||||| |||||||||||||||| |||||||||||||| || | | | ||| | ||||| | || | | ||||| | |||||||| || | | | ||
ATTTGGTGCTTTCAAACAAGCTTGTTCTCTACGATCTCGAAAATCAGCTCATTGGGTGGACTGAATACAACTgtaagtgctatattcatacactcaaacgattcatgtctcattgtgagtgggaaagatttcgaatttaaaactattttatctttgttttatctgtctttgcag
















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|32870684|gb|CF010366.1|CF010366
EST:     GGTTATCTATGACTTGGAAAATCGAGTCATTGGGTGGACTGACTACAACT                         GTTCGTCGAGCATTAAAATTAAGGACGACAAAACGGGCGCAACATCTACTG
genomic: GGTTATCTATGACTTGGAAAATCGAGTCATTGGGTGGACTGACTACAACTgtaagtgtta ... aaaatttcagGTTCGTCGAGCATTAAAATTAAGGACGACAAAACGGGCGCAACATCTACTG
EST: gi|78116811|gb|DV535198.1|DV535198
EST:     GGTTATCTATGACTGGGAAAATCGAGTCATTGGGTGGACTGACTACAACT                         GTTCGTCGAGCATTAAAATTAAGGAGGACAAAACGGGCGCAACATCTACTG
genomic: GGTTATCTATGACTTGGAAAATCGAGTCATTGGGTGGACTGACTACAACTgtaagtgtta ... aaaatttcagGTTCGTCGAGCATTAAAATTAAGGACGACAAAACGGGCGCAACATCTACTG
EST: gi|37379778|gb|CF626648.1|CF626648
EST:     GGTTATCTATGACTTGGAAAATCGAGTCATTGGGTGGACTGACTACAACT                         GTTCGTCGAGCATTAAAATTAAGGACGACAAAT-GGGCGCAACATCTACTG
genomic: GGTTATCTATGACTTGGAAAATCGAGTCATTGGGTGGACTGACTACAACTgtaagtgtta ... aaaatttcagGTTCGTCGAGCATTAAAATTAAGGACGACAAAACGGGCGCAACATCTACTG
EST: gi|211431081|gb|FL481796.1|FL481796
EST:     GGTTATCTATGACTTGGAAAATCGAGTCATTGGGTGGACTGACTACAACT                         GTTCGTCGAGCATTAAAATTAAGGACGACAAAACGGGCGCAACATCTACTG
genomic: GGTTATCTATGACTTGGAAAATCGAGTCATTGGGTGGACTGACTACAACTgtaagtgtta ... aaaatttcagGTTCGTCGAGCATTAAAATTAAGGACGACAAAACGGGCGCAACATCTACTG
EST: gi|86469808|gb|DY236178.1|DY236178
EST:     GGTTATCTATGACTTGGAAAATCGAGTCATTGGGTGGACTGACTACAACT                         GTTCGTCGAGCATTAAAATTAAGGACGACAAAACGGGCGCAACATCTACTG
genomic: GGTTATCTATGACTTGGAAAATCGAGTCATTGGGTGGACTGACTACAACTgtaagtgtta ... aaaatttcagGTTCGTCGAGCATTAAAATTAAGGACGACAAAACGGGCGCAACATCTACTG

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: 45 (upstream exon), 49 (downstream exon)
Score: 22

ATCTTGTCCTTTCCAACAAGTTGGTTATCTATGACTTGGAAAATCGAGTCATTGGGTGGACTGACTACAACTgtaagtgtta ... aaaatttcagGTTCGTCGAGCATTAAAATTAAGGACGACAAAACGGGCGCAACATCTACTGTTAATTCACATGACTTGTCCTCAGGATGGAAGTTCCACTGGCACATGTC


Block sizes: 33 (upstream exon), 38 (downstream exon)
Score: 5

ATCTTGTCCTTTCCAACAAGTTGGTTATCTATGACTTGGAAAATCGAGTCATTGGGTGGACTGACTACAACTgtaagtgtta ... aaaatttcagGTTCGTCGAGCATTAAAATTAAGGACGACAAAACGGGCGCAACATCTACTGTTAATTCACATGACTTGTCCTCAGGATGGAAGTTCCACTGGCACATGTC


Block sizes: 46 (upstream exon), 45 (downstream exon)
Score: 4

ATCTTGTCCTTTCCAACAAGTTGGTTATCTATGACTTGGAAAATCGAGTCATTGGGTGGACTGACTACAACTgtaagtgtta ... aaaatttcagGTTCGTCGAGCATTAAAATTAAGGACGACAAAACGGGCGCAACATCTACTGTTAATTCACATGACTTGTCCTCAGGATGGAAGTTCCACTGGCACATGTC


Block sizes: 40 (upstream exon), 49 (downstream exon)
Score: 17

ATCTTGTCCTTTCCAACAAGTTGGTTATCTATGACTTGGAAAATCGAGTCATTGGGTGGACTGACTACAACTgtaagtgtta ... aaaatttcagGTTCGTCGAGCATTAAAATTAAGGACGACAAAACGGGCGCAACATCTACTGTTAATTCACATGACTTGTCCTCAGGATGGAAGTTCCACTGGCACATGTC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCTTGTCCTTTCCAACAAGTTGGTTATCTATGACTTGGAAAATCGAGTCATTGGGTGGACTGACTACAACTgtaagtgttagcacgttccaatctgctcatgccctatatatatttccacaactatttggtcatccgcctgtaaaatttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA