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'   		10  
 5'  3'   		11  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAATGGTGGCACGTGGAGACCTTGGTGCTGAACTTCCGATTGAGGATGTTCCTTTGCTACAGgtgagatcacattacatgtacagttttaggtgcaccaagtcatttcttactgtatctagtaaaggatgatgtgtaaaaacgcaaccaagcatcagcatagtataaattgtgactgttttacttctcttttttcag

Basic information

species Zea mays
transcript GRMZM2G144730_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G144730_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os10g42100.1 (Oryza sativa), 5'ss of exon 7
GCAATGGTGGCACGTGGAGACCTTGGTGCTGAACTTCCGATTGAGGATGTTCCTTTGCTACAGgtgagatcacattacatgtacagtttta--ggtgcaccaag-------------------tcatttcttac----------tgtatctagta--aaggatgatgtgtaaaaacgcaaccaagcatcagcatagtataaattgtgactgttttacttctcttttttcag
|| ||||||||| | || || ||||||||||||||||| |||||||| ||||||||||| ||||| || | | |||   |  | | |||||   |||||  ||                    ||| |   |||          | | | || ||  | |  | |  || || ||   ||  |||||  | ||   | |||||      |||||||||||||         
GCGATGGTGGCAAGAGGGGATCTTGGTGCTGAACTTCCAATTGAGGAAGTTCCTTTGCTGCAGgttagtttaaatt-tgtagataattttactagtgcaagaaaacatgtgtttgttcccccctcactctctacatcccttttatttgtttattagcacgcctaaaatgcaacaaatgaataaagcactaacaacatttaaatcacatgtgttttacttctccag------

upper sequence: GRMZM2G144730_T01 (Zea mays), 5'ss of exon 7
lower sequence: AT1G32440.1 (Arabidopsis thaliana), 5'ss of exon 7
GCAATGGTGGCACGTGGAGACCTTGGTGCTGAACTTCCGATTGAGGATGTTCCTTTGCTACAGgtgagatcacattacatgtacagttttaggtgcaccaagtcatttcttactg-tatcta-gtaaaggatgatgtgtaaaaacgcaaccaagcatcagcatagtataaattgtgactgttttacttctcttttttcag
|||||||| || |||||||| ||||| ||||||||||| ||||| || || || ||| ||||||| |   ||      |      ||||  |   ||  |  | |     |  || ||| || | |   | |  |||||   ||    |                                                   
GCAATGGTTGCTCGTGGAGATCTTGGAGCTGAACTTCCCATTGAAGAGGTCCCGTTGTTACAGgtaaatcca------agacttggtttctgaaacattactttagactctgttggtatttatgcatttgctattgtgtcttaattttag--------------------------------------------------

upper sequence: GRMZM2G144730_T01 (Zea mays), 5'ss of exon 7
lower sequence: Vv02s0012g01170.t01 (Vitis vinifera), 5'ss of exon 7
GCAATGGTGGCACGTGGAGACCTTGGTGCTGAACTTCCGATTGAGGATGTTCCTTTGCTACAGgtgagatcacattacatgtacagttttaggtgcaccaagtcatttct-tactgtatctagtaaaggatgatgtgtaaaaacgcaaccaagcatcagcatagtataaattgtgactgttttacttctcttttttcag
|||||||| |||||||| || ||||| ||||||||||| |||||||| || |||||  | ||||| |  | |   ||    ||       |  | | ||    || | || || | |||     | |   | ||    ||||     |   || ||     ||| |                                 
GCAATGGTTGCACGTGGGGATCTTGGAGCTGAACTTCCAATTGAGGAAGTCCCTTTATTGCAGgtaacttgatgctaataatatgtagacaaattcccctttacactcctatattttat---acatattgttatcctcaaaagtttgaattaggatgtaattagaa---------------------------------

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|32930333|gb|CF035145.1|CF035145
EST:     GTGGAGACCTTGGTGCTGAACTTCCGATTGAGGATGTTCCTTTGCTACAG                         GCAGAGATTGTTCAAACATGTCGAAACATGGAGAAACCAGTTATTGTCGCC
genomic: GTGGAGACCTTGGTGCTGAACTTCCGATTGAGGATGTTCCTTTGCTACAGgtgagatcac ... cttttttcagGCAGAGATTGTTCAAACATGTCGAAACATGGAGAAACCAGTTATTGTCGCC
EST: gi|71764041|gb|DR961978.1|DR961978
EST:     GTGGAGACCTTGGTGCTGAACTTCCGATTGAGGATGTTCCTTTGCTACAG                         GCAGAGATTGTTCAAACATGTCGAAACATGGAGAAACCAGTTATTGTCGCC
genomic: GTGGAGACCTTGGTGCTGAACTTCCGATTGAGGATGTTCCTTTGCTACAGgtgagatcac ... cttttttcagGCAGAGATTGTTCAAACATGTCGAAACATGGAGAAACCAGTTATTGTCGCC
EST: gi|7238117|gb|AW573339.1|AW573339
EST:     GTGGAGACCTTGGTGCTGAACTTCCGATTGAGGATGTTCCTTTGCTACAG                         GCAGAGATTGTTCAAACATGTCGAAACATGGAGAAACCAGTTATTGTCGCC
genomic: GTGGAGACCTTGGTGCTGAACTTCCGATTGAGGATGTTCCTTTGCTACAGgtgagatcac ... cttttttcagGCAGAGATTGTTCAAACATGTCGAAACATGGAGAAACCAGTTATTGTCGCC
EST: gi|26456209|gb|CA827792.1|CA827792
EST:     GTGGAGACCTTGGTGCTGAACTTCCGATTGAGGATGTTCCTTTGCTACAG                         GCAGAGATTGTTCAAACATGTCGAAACATGGAGAAACCA
genomic: GTGGAGACCTTGGTGCTGAACTTCCGATTGAGGATGTTCCTTTGCTACAGgtgagatcac ... cttttttcagGCAGAGATTGTTCAAACATGTCGAAACATGGAGAAACCA
EST: gi|32935309|gb|CF040121.1|CF040121
EST:     GTGGAGACCTTGGTGCTGAACTTCCGATTGAGGATGTTCCTTTGCTACAG                         GCAGAGATTGTTCAAACATGTCGAAACATGGAGAAACCAGTTATTGTCGCC
genomic: GTGGAGACCTTGGTGCTGAACTTCCGATTGAGGATGTTCCTTTGCTACAGgtgagatcac ... cttttttcagGCAGAGATTGTTCAAACATGTCGAAACATGGAGAAACCAGTTATTGTCGCC
EST: gi|78075400|gb|DV503834.1|DV503834
EST:     GTGGAGACCTTGGTGCTGAACTTCCGATTGAGGATGTTCCTTTGCTACAG                         GCAGAGATTGTTCAAACATGTCGAAACATGGAGAAACCAGTTATTGTCGCC
genomic: GTGGAGACCTTGGTGCTGAACTTCCGATTGAGGATGTTCCTTTGCTACAGgtgagatcac ... cttttttcagGCAGAGATTGTTCAAACATGTCGAAACATGGAGAAACCAGTTATTGTCGCC
EST: gi|20301238|gb|BQ164181.1|BQ164181
EST:     GTGGAGACCTTGGTGCTGAACTTCCGATTGAGGATGTTCCTTTGCTACAG                         GCAGAGATTGCTCAAACATGTCGAAACATGGAGAAAC
genomic: GTGGAGACCTTGGTGCTGAACTTCCGATTGAGGATGTTCCTTTGCTACAGgtgagatcac ... cttttttcagGCAGAGATTGTTCAAACATGTCGAAACATGGAGAAAC

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: 224

GCAATGGTGGCACGTGGAGACCTTGGTGCTGAACTTCCGATTGAGGATGTTCCTTTGCTACAGgtgagatcac ... cttttttcagGCAGAGATTGTTCAAACATGTCGAAACATGGAGAAACCAGTTATTGTCGCCACAAATATGTTGGAAAGCATGATTGACCATCCTACTCCAACTAGGGCAG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 218

GCAATGGTGGCACGTGGAGACCTTGGTGCTGAACTTCCGATTGAGGATGTTCCTTTGCTACAGgtgagatcac ... cttttttcagGCAGAGATTGTTCAAACATGTCGAAACATGGAGAAACCAGTTATTGTCGCCACAAATATGTTGGAAAGCATGATTGACCATCCTACTCCAACTAGGGCAG


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 148

GCAATGGTGGCACGTGGAGACCTTGGTGCTGAACTTCCGATTGAGGATGTTCCTTTGCTACAGgtgagatcac ... cttttttcagGCAGAGATTGTTCAAACATGTCGAAACATGGAGAAACCAGTTATTGTCGCCACAAATATGTTGGAAAGCATGATTGACCATCCTACTCCAACTAGGGCAG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 372

GCAATGGTGGCACGTGGAGACCTTGGTGCTGAACTTCCGATTGAGGATGTTCCTTTGCTACAGgtgagatcac ... cttttttcagGCAGAGATTGTTCAAACATGTCGAAACATGGAGAAACCAGTTATTGTCGCCACAAATATGTTGGAAAGCATGATTGACCATCCTACTCCAACTAGGGCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAATGGTGGCACGTGGAGACCTTGGTGCTGAACTTCCGATTGAGGATGTTCCTTTGCTACAGgtgagatcacattacatgtacagttttaggtgcaccaagtcatttcttactgtatctagtaaaggatgatgtgtaaaaacgcaaccaagcatcagcatagtataaattgtgactgttttacttctcttttttcag

- - - - - -  GTGGAG
- - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - -  AGGATG