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

gtacttggtggttctgcagactgcactatattagttgtaaagaaatgtactacctagtgttttctatttccatgtattggatggatttgctttgctgacagGTTCTTGGTACCCCAACGCGCGAGGAAATCCGATGTATGAATCCAAACTACACCGAGTTTAGATTTCCTCAGATCAAAGCTCACCCATGGCACAAG

Basic information

species Zea mays
transcript GRMZM2G121790_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G121790_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os02g14130.1 (Oryza sativa), 3'ss of exon 8
gtacttggtggttctgcagactgcactatattagttgtaaagaaatgtactacctagtgtttt-ctatttccatgtattggatggatttgctttgctgacagGTTCTTGGTACCCCAACGCGCGAGGAAATCCGATGTATGAATCCAAACTACACCGAGTTTAGATTTCCTCAGATCAAAGCTCACCCATGGCACAAG
||| |  ||    |      || || || ||  | | ||||||||   | | | || |||||| |||||| |||  | || ||| |||| ||||| ||  ||||||||||||| ||||| || ||||||||||| || |||||||| |||||||| || || |||||||||||||| |||||||||||||||||||||
gtagtatgttaggcactgctctacagtacatgcggtctaaagaaa---atttcttaatgtttttctattttcataaactgaatgaattttctttgttggtagGTTCTTGGTACTCCAACACGTGAGGAAATCCGCTGCATGAATCCCAACTACACAGAATTCAGATTTCCTCAGATTAAAGCTCACCCATGGCACAAG

upper sequence: GRMZM2G121790_T01 (Zea mays), 3'ss of exon 8
lower sequence: PP1S60_100V6.1 (Physcomitrella patens), 3'ss of exon 8
----------------gtacttggtggttctgcagactgcactatattagttgtaaagaaatgtactacctagtgttttctatttccatgtattggatggatttgc-------tttgctgacagGTTCTTGGTACCCCAACGCGCGAGGAAATCCGATGTATGAATCCAAACTACACCGAGTTTAGATTTCCTCAGATCAAAGCTCACCCATGGCACAAG
                | ||   || ||  || ||  ||   ||  ||  |||             |  |  | || || |  | |  || | || |||   |||        |||  || |||||  | || || || || || ||||| |||   || |||||||| |||||||| ||||| |  ||||| || ||||| ||||||||||||||||| 
gtagggcacaggcgatgcacggtgttgtgttgaagggtggcgtac-ttgcttgctggttgtgactgttgcgggagtgttatgatgctgtggagtgtatgttattgaggaaaagttttgtggcagGTGTTGGGGACACCGACTCGTGAGGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCGCAAATCAAGGCTCACCCATGGCACAAA

upper sequence: GRMZM2G121790_T01 (Zea mays), 3'ss of exon 8
lower sequence: EFJ07216 (Selaginella moellendorffii), 3'ss of exon 9
gtacttggtggttctgcagactgcactatattagttgtaaagaaatgtactacctagtgttttctatttccatgtattggatggatttgctttgctgacagGTTCTTGGTACCCCAACGCGCGAGGAAATCCGATGTATGAATCCAAACTACACCGAGTTTAGATTTCCTCAGATCAAAGCTCACCCATGGCACAAG
                      | ||   ||   || |       | |  |   |  | ||| | | |  |   |  |  |  || |||||||     |||||  | ||||| || || ||||||||||||  ||| ||||||||||||||||| |||||||  || |||||||| ||||| || || |||||||||
----------------------gtac-gcatgcattcttgctcttttttttctgttttttttgcgagtcgctcttgctcaa--gacttgctttt---gcagGTCTTAGGTACTCCTACTCGCGAGGAAATCAAATGCATGAATCCAAACTACACGGAGTTTAAGTTCCCTCAGATTAAAGCGCATCCCTGGCACAAG

upper sequence: GRMZM2G121790_T01 (Zea mays), 3'ss of exon 8
lower sequence: EFJ07923 (Selaginella moellendorffii), 3'ss of exon 9
gtacttggtggttctgcagactgcactatattagttgtaaagaaatgtact-acctagtgttttctatttccatgtattggatggatttgctttgctg--acagGTTCTTGGTACCCCAACGCGCGAGGAAATCCGATGTATGAATCCAAACTACACCGAGTTTAGATTTCCTCAGATCAAAGCTCACCCATGGCACAAG
                                    |||   |    | ||  |    | |||||| ||| |  ||      ||     |  |||||    |||||  | ||||| || || || |||||||||  ||| ||||||||||||||||| |||||||  || |||||||| ||||| || || |||||||||
------------------------------------gtacgcatgcattcttgctctcttttttctttttgcgagtcgctcttgctcaagacttgcttttgcagGTCTTAGGTACTCCTACTCGGGAGGAAATCAAATGCATGAATCCAAACTACACGGAGTTTAAGTTCCCTCAGATTAAAGCGCATCCCTGGCACAAG

upper sequence: GRMZM2G121790_T01 (Zea mays), 3'ss of exon 8
lower sequence: EFJ04915 (Selaginella moellendorffii), 3'ss of exon 8
gtacttggtggttctgcagactgcactatattagttgtaaagaaatgtactacctagtgttttctatttccatgtattggatggatttgctttgctgacagGTTCTTGGTACCCCAACGCGCGAGGAAATCCGATGTATGAATCCAAACTACACCGAGTTTAGATTTCCTCAGATCAAAGCTCACCCATGGCACAAG
                                 ||||    |   | |  | |||  || |  ||     |   ||   | |||| |||       | ||||||||||| ||||| || |||||||| |||   ||||||||||| |||||||| || || |  || ||||| ||||| || ||||| |||||||||
---------------------------------gttggctcgttgt-ttttgccttatggtggctgggcgctcataa-agttggacttg-------ggcagGTTCTTGGAACCCCTACTCGCGAGGAGATCAAGTGTATGAATCCCAACTACACGGAATTCAAGTTCCCTCAAATCAAGGCCCACCCTTGGCACAAG

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|19770441|gb|BQ035162.1|BQ035162
EST:     CTCTCTTCCCTGGTGAAAGTGCTGTGGATCAGCTTGTTGAGATAATAAAG                         GTTCTTGGTACCCCAACGCGCGAGGAAATCCGATGTATGAATCCAAACTAC
genomic: CTCTCTTCCCTGGTGAAAGTGCTGTGGATCAGCTTGTTGAGATAATAAAGgtacttggtg ... ttgctgacagGTTCTTGGTACCCCAACGCGCGAGGAAATCCGATGTATGAATCCAAACTAC
EST: gi|211251114|gb|FL353291.1|FL353291
EST:     CTCTCTTCCCTGGTGAAAGTGCTGTGGATCAGCTTGTTGAGATAATAAAG                         GTTCTTGGTACCCCAACGCGCGAGGAAATCCGATGTATGAATCCAAACTAC
genomic: CTCTCTTCCCTGGTGAAAGTGCTGTGGATCAGCTTGTTGAGATAATAAAGgtacttggtg ... ttgctgacagGTTCTTGGTACCCCAACGCGCGAGGAAATCCGATGTATGAATCCAAACTAC
EST: gi|71441697|gb|DR822747.1|DR822747
EST:     CTCTCTTCCCTGGTGAAAGTGCTGTGGATCAGCTTGTTGAGATAATAAAG                         GTTCCTGGTACCCCAACGCGCGAGGAAATC
genomic: CTCTCTTCCCTGGTGAAAGTGCTGTGGATCAGCTTGTTGAGATAATAAAGgtacttggtg ... ttgctgacagGTTCTTGGTACCCCAACGCGCGAGGAAATC
EST: gi|32855414|gb|CD995095.1|CD995095
EST:     CTCTCTTCCCTGGTGAAAGTGCTGTGGATCAGCTTGTTGAGATAATAAAG                         GTTCTTGGTACTCCAACGCGCGAGGAAATCCGATGTATGAATCCAAACTAC
genomic: CTCTCTTCCCTGGTGAAAGTGCTGTGGATCAGCTTGTTGAGATAATAAAGgtacttggtg ... ttgctgacagGTTCTTGGTACCCCAACGCGCGAGGAAATCCGATGTATGAATCCAAACTAC
EST: gi|211298028|gb|FL233897.1|FL233897
EST:     CTCTCTTCCCTGGTGAAAGTGCTGTGGATCAGCTTGTTGAGATAATAAAG                         GTTCTTGGTACCCCAACGCGCGAGGAAATCCGATGTATGAATCCAAACTAC
genomic: CTCTCTTCCCTGGTGAAAGTGCTGTGGATCAGCTTGTTGAGATAATAAAGgtacttggtg ... ttgctgacagGTTCTTGGTACCCCAACGCGCGAGGAAATCCGATGTATGAATCCAAACTAC
EST: gi|71430637|gb|DR811687.1|DR811687
EST:     AGTGCTGTGGATCAGCTTGTTGAGATAATAAAG                         GTTCTTGGTACCCCAACGCGCGAGGAAATCCGATGTATGAATCCAAACTAC
genomic: AGTGCTGTGGATCAGCTTGTTGAGATAATAAAGgtacttggtg ... ttgctgacagGTTCTTGGTACCCCAACGCGCGAGGAAATCCGATGTATGAATCCAAACTAC
EST: gi|110961978|gb|EE182030.1|EE182030
EST:     CTCTCTTCCCTGGTGAAAGTGCTGTGAATCAGCTTGTTGAGATAATAAAG                         GTTCTTGGTACCCCAACGCGCGAGGAAATCCGATGTATGAATCCAAACTAC
genomic: CTCTCTTCCCTGGTGAAAGTGCTGTGGATCAGCTTGTTGAGATAATAAAGgtacttggtg ... ttgctgacagGTTCTTGGTACCCCAACGCGCGAGGAAATCCGATGTATGAATCCAAACTAC
EST: gi|211326797|gb|FL341548.1|FL341548
EST:     CTCTCTTCCCTGGTGAAAGTGCTGTGGATCAGCTTGTTGAGATAATAAAG                         GTTCTTGGTACCCCAACGCGCGAGGAAATCCGATGTATGAATCCAAACTAC
genomic: CTCTCTTCCCTGGTGAAAGTGCTGTGGATCAGCTTGTTGAGATAATAAAGgtacttggtg ... ttgctgacagGTTCTTGGTACCCCAACGCGCGAGGAAATCCGATGTATGAATCCAAACTAC
EST: gi|211298026|gb|FL233895.1|FL233895
EST:     CTCTCTTCCCTGGTGAAAGTGCTGTGGATCAGCTTGTTGAGATAATAAAG                         GTTCTTGGTACCCCAACGCGCGAGGAAATCCGATGTATG
genomic: CTCTCTTCCCTGGTGAAAGTGCTGTGGATCAGCTTGTTGAGATAATAAAGgtacttggtg ... ttgctgacagGTTCTTGGTACCCCAACGCGCGAGGAAATCCGATGTATG
EST: gi|87153591|gb|DY398380.1|DY398380
EST:     GGTGAAAGTGCTGTGGATCAGCTTGTTGAGATAATAAAG                         GTTCTTGGTACCCCAACGCGCGAGGAAATCCGATGTATGAATCCAAACTAC
genomic: GGTGAAAGTGCTGTGGATCAGCTTGTTGAGATAATAAAGgtacttggtg ... ttgctgacagGTTCTTGGTACCCCAACGCGCGAGGAAATCCGATGTATGAATCCAAACTAC
EST: gi|31352553|gb|CD436910.1|CD436910
EST:     TGAAAGTGCTGTGGATCAGCTTGTTGAGATAATAAAG                         GTTCTTGGTACCCCAACGCGCGAGGAAATCCGATGTATGAATCCAAACTAC
genomic: TGAAAGTGCTGTGGATCAGCTTGTTGAGATAATAAAGgtacttggtg ... ttgctgacagGTTCTTGGTACCCCAACGCGCGAGGAAATCCGATGTATGAATCCAAACTAC
EST: gi|20300401|gb|BQ163344.1|BQ163344
EST:     CTCTCTTCCCTGGTGAAAGTGCTGTGGATCAGCTTGTTGAGATAATAAAG                         GTTCTTGGTACCCCAACGCGCGAGGAAATCCGATGTATGAATCCAAACTAC
genomic: CTCTCTTCCCTGGTGAAAGTGCTGTGGATCAGCTTGTTGAGATAATAAAGgtacttggtg ... ttgctgacagGTTCTTGGTACCCCAACGCGCGAGGAAATCCGATGTATGAATCCAAACTAC

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: 49 (upstream exon), 49 (downstream exon)
Score: 201

CCTCTCTTCCCTGGTGAAAGTGCTGTGGATCAGCTTGTTGAGATAATAAAGgtacttggtg ... ttgctgacagGTTCTTGGTACCCCAACGCGCGAGGAAATCCGATGTATGAATCCAAACTACACCGAGTTTAGATTTCCTCAGATCAAAGCTCACCCATGGCACAAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 170

CCTCTCTTCCCTGGTGAAAGTGCTGTGGATCAGCTTGTTGAGATAATAAAGgtacttggtg ... ttgctgacagGTTCTTGGTACCCCAACGCGCGAGGAAATCCGATGTATGAATCCAAACTACACCGAGTTTAGATTTCCTCAGATCAAAGCTCACCCATGGCACAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 165

CCTCTCTTCCCTGGTGAAAGTGCTGTGGATCAGCTTGTTGAGATAATAAAGgtacttggtg ... ttgctgacagGTTCTTGGTACCCCAACGCGCGAGGAAATCCGATGTATGAATCCAAACTACACCGAGTTTAGATTTCCTCAGATCAAAGCTCACCCATGGCACAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 148

CCTCTCTTCCCTGGTGAAAGTGCTGTGGATCAGCTTGTTGAGATAATAAAGgtacttggtg ... ttgctgacagGTTCTTGGTACCCCAACGCGCGAGGAAATCCGATGTATGAATCCAAACTACACCGAGTTTAGATTTCCTCAGATCAAAGCTCACCCATGGCACAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtactacctagtgttttctatttccatgtattggatggatttgctttgctgacagGTTCTTGGTACCCCAACGCGCGAGGAAATCCGATGTATGAATCCAAACTACACCGAGTTTAGATTTCCTCAGATCAAAGCTCACCCATGGCACAAG
                                       tttgcttt  CT-rich tract
             ttttctattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacttggtggttctgcagactgcactatattagttgtaaagaaatgtactacctagtgttttctatttccatgtattggatggatttgctttgctgacagGTTCTTGGTACCCCAACGCGCGAGGAAATCCGATGTATGAATCCAAACTACACCGAGTTTAGATTTCCTCAGATCAAAGCTCACCCATGGCACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA