Skip to another splice site:
1  
 5'  3'   
2  
 5'  3'   
3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcaaggatgtttgttgtttacgatttggaattcaccttttgaagaaatgaacttaaggcccatagttgcttacgaatttgagaaaatactacattcgcagGTTCTGTAACGTCAAGACATCTCGAACACCCCCTCCACCGGATCCTGATGAGCCTTCCAATGTTGCTCAAGCTATTGCCTCATGGGGCCTTGAATATATA

Basic information

species Zea mays
transcript GRMZM2G071714_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G071714_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os04g38330.1 (Oryza sativa), 3'ss of exon 1
gcaaggatgtttgttgtttacgatttggaattcaccttttgaagaaatgaacttaaggccc-----atagttgcttacgaatttgagaaaatactacattcgcagGTTCTGTAACGTCAAGACATCTCGAACACCCCCTCCACCGGATCCTGATGAGCCTTCCAATGTTGCTCAAGCTATTGCCTCATGGGGCCTTGAATATATA
| | | | | || |||| | | ||||||| | || | ||| | | | | ||| | ||| || | | ||| ||||||| ||||| |||||||| || ||||| || || ||||| ||||||||||| ||||| ||||||||||||||||||||||| |||||||| || |||||
----gcactctaccttctcgtgaattggcactaaccttttagacaaggtattgcaagtcttctgttttgatcgtttagtgagttggcaagtcattg-atttgcagGTTTTGTAATGTCAAGACCTCGCGAACTCCTCCGCCACCAGATCCTGATGAACCTTCTAATGTTGCTCAAGCTATTGCCTCGTGGGGCCTGGAGTATATT
















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|91869951|gb|EB400624.1|EB400624
EST:     GCCACCGCCACAATTATGATCCTTGGGGACACCTGCACGCGCGGATGCAG                         GTTCTGTAACGTCAAGACATCTCGAACACCCCCTCCACCGGATCCTGATGA
genomic: GCCACCGCCACAATTATGATCCTTGGGGACACCTGCACGCGCGGATGCAGgtaagagatt ... acattcgcagGTTCTGTAACGTCAAGACATCTCGAACACCCCCTCCACCGGATCCTGATGA
EST: gi|50333848|gb|CO528974.1|CO528974
EST:     GCCACCGCCACAATTATGATCCTTGGGGACACCTGCACGCGCGGATGCAG                         GTTCTGTAACGTCAAGACATCTCGAACACCCCCTCCACCGGATCCTGATGA
genomic: GCCACCGCCACAATTATGATCCTTGGGGACACCTGCACGCGCGGATGCAGgtaagagatt ... acattcgcagGTTCTGTAACGTCAAGACATCTCGAACACCCCCTCCACCGGATCCTGATGA
EST: gi|91872938|gb|EB402895.1|EB402895
EST:     GCCACCGCCACAATTATGATCCTTGGGGACACCTGCACGCGCGGATGCAG                         GTTCTGTAACGTCAAGACATCTCGAACACCCCCTCCACCGGATCCTGATGA
genomic: GCCACCGCCACAATTATGATCCTTGGGGACACCTGCACGCGCGGATGCAGgtaagagatt ... acattcgcagGTTCTGTAACGTCAAGACATCTCGAACACCCCCTCCACCGGATCCTGATGA
EST: gi|149103480|gb|EE288873.2|EE288873
EST:     GCCACCGCCACAATTATGATCCTTGGGGACACCTGCACGCGCGGATGCAG                         GTTCTGTAACGTCAAGACATCTCGAACACCCCCTCCACCGGATCCTGATGA
genomic: GCCACCGCCACAATTATGATCCTTGGGGACACCTGCACGCGCGGATGCAGgtaagagatt ... acattcgcagGTTCTGTAACGTCAAGACATCTCGAACACCCCCTCCACCGGATCCTGATGA
EST: gi|149083380|gb|EE172687.2|EE172687
EST:     GCCACCGCCACAATTATGATCCTTGGGGACACCTGCACGCGCGGATGCAG                         GTTCTGTAACGTCAAGACATCTCGAACACCCCCTCCACCGGATCCTGATGA
genomic: GCCACCGCCACAATTATGATCCTTGGGGACACCTGCACGCGCGGATGCAGgtaagagatt ... acattcgcagGTTCTGTAACGTCAAGACATCTCGAACACCCCCTCCACCGGATCCTGATGA
EST: gi|74244797|gb|DT652711.1|DT652711
EST:     GCCACCGCCACAATTATGATCCTTGGGGACACCTGCACGCGCGGATGCAG                         GTTCTGTAACGTCAAGACATCTCGAACACCCCCTCCACCGGATCCTGATGA
genomic: GCCACCGCCACAATTATGATCCTTGGGGACACCTGCACGCGCGGATGCAGgtaagagatt ... acattcgcagGTTCTGTAACGTCAAGACATCTCGAACACCCCCTCCACCGGATCCTGATGA
EST: gi|149110556|gb|EE190481.2|EE190481
EST:     GCCACCGCCACAATTATGATCCTTGGGGACACCTGCACGCGCGGATGCAG                         GTTCTGTAACGTCAAGACATCTCGAACACCCCCTCCACCGGATCCTGATGA
genomic: GCCACCGCCACAATTATGATCCTTGGGGACACCTGCACGCGCGGATGCAGgtaagagatt ... acattcgcagGTTCTGTAACGTCAAGACATCTCGAACACCCCCTCCACCGGATCCTGATGA
EST: gi|91051622|gb|EB162040.1|EB162040
EST:     GCCACCGCCACAATTATGATCCTTGGGGACACCTGCACGCGCGGATGCAG                         GTTCTGTAACGTCAAGACATCTCGAACACCCCCTCCACCGGATCCTGATGA
genomic: GCCACCGCCACAATTATGATCCTTGGGGACACCTGCACGCGCGGATGCAGgtaagagatt ... acattcgcagGTTCTGTAACGTCAAGACATCTCGAACACCCCCTCCACCGGATCCTGATGA
EST: gi|74238618|gb|DT646532.1|DT646532
EST:     GCCACCGCCACAATTATGATCCTTGGGGACACCTGCACGCGCGGATGCAG                         GTTCTGTAACGTCAAGACATCTCGAACACCCCCTCCACCGGATCCTGATGA
genomic: GCCACCGCCACAATTATGATCCTTGGGGACACCTGCACGCGCGGATGCAGgtaagagatt ... acattcgcagGTTCTGTAACGTCAAGACATCTCGAACACCCCCTCCACCGGATCCTGATGA
EST: gi|93281869|gb|EB674133.1|EB674133
EST:     GCCACCGCCACAATTATGATCCTTGGGGACACCTGCACGCGCGGATGCAG                         GTTCTGTAACGTCAAGACATCTCGAACACCCCCTCCACCGGATCCTGATGA
genomic: GCCACCGCCACAATTATGATCCTTGGGGACACCTGCACGCGCGGATGCAGgtaagagatt ... acattcgcagGTTCTGTAACGTCAAGACATCTCGAACACCCCCTCCACCGGATCCTGATGA
EST: gi|78115617|gb|DV534005.1|DV534005
EST:     GCCACCGCCACAATTATGATCCTTGGGGACACCTGCACGCGCGGATGCAG                         GTTCTGTAACGTCAAGACATCTCGAACACCCCCTCCACCGGATCCTGATGA
genomic: GCCACCGCCACAATTATGATCCTTGGGGACACCTGCACGCGCGGATGCAGgtaagagatt ... acattcgcagGTTCTGTAACGTCAAGACATCTCGAACACCCCCTCCACCGGATCCTGATGA
EST: gi|86466056|gb|DY232429.1|DY232429
EST:     GCCACCGCCACAATTATGATCCTTGGGGACACCTGCACGCGCGGATGCAG                         GTTCTGTAACGTCAAGACATCTCGAACACCCCCTCCACCGGATCCTGATGA
genomic: GCCACCGCCACAATTATGATCCTTGGGGACACCTGCACGCGCGGATGCAGgtaagagatt ... acattcgcagGTTCTGTAACGTCAAGACATCTCGAACACCCCCTCCACCGGATCCTGATGA
EST: gi|148939280|gb|EC883774.2|EC883774
EST:     GCCACCGCCACAATTATGATCCTTGGGGACACCTGCACGCGCGGATGCAG                         GTTCTGTAACGTCAAGACATCTCGAACACCCCCTCCACCGGATCCTGATGA
genomic: GCCACCGCCACAATTATGATCCTTGGGGACACCTGCACGCGCGGATGCAGgtaagagatt ... acattcgcagGTTCTGTAACGTCAAGACATCTCGAACACCCCCTCCACCGGATCCTGATGA
EST: gi|71313820|gb|DR793501.1|DR793501
EST:     GCCACCGCCACAATTATGATCCTTGGGGACACCTGCACGCGCGGATGCAG                         GTTCTGTAACGTCAAGACATCTCGAACACCCCCTCCACCGGATCCTGATGA
genomic: GCCACCGCCACAATTATGATCCTTGGGGACACCTGCACGCGCGGATGCAGgtaagagatt ... acattcgcagGTTCTGTAACGTCAAGACATCTCGAACACCCCCTCCACCGGATCCTGATGA
EST: gi|149110880|gb|EE294378.2|EE294378
EST:     GCCACCGCCACAATTATGATCCTTGGGGACACCTGCACGCGCGGATGCAG                         GTTCTGTAACGTCAAGACATCTCGAACACCCCCTCCACCGGATCCTGATGA
genomic: GCCACCGCCACAATTATGATCCTTGGGGACACCTGCACGCGCGGATGCAGgtaagagatt ... acattcgcagGTTCTGTAACGTCAAGACATCTCGAACACCCCCTCCACCGGATCCTGATGA
EST: gi|91875685|gb|EB405642.1|EB405642
EST:     GCCACCGCCACAATTATGATCCTTGGGGACACCTGCACGCGCGGATGCAG                         GTTCTGTAACGTCAAGACATCTCGAACACCCCCTCCACCGGATCCTGATGA
genomic: GCCACCGCCACAATTATGATCCTTGGGGACACCTGCACGCGCGGATGCAGgtaagagatt ... acattcgcagGTTCTGTAACGTCAAGACATCTCGAACACCCCCTCCACCGGATCCTGATGA
EST: gi|71300477|gb|DR786296.1|DR786296
EST:     GCCACCGCCACAATTATGATCCTTGGGGACACCTGCACGCGCGGATGCAG                         GTTCTGTAACGTCAAGACATCTCGAACACCCCCTCCACCGGATCCTGATGA
genomic: GCCACCGCCACAATTATGATCCTTGGGGACACCTGCACGCGCGGATGCAGgtaagagatt ... acattcgcagGTTCTGTAACGTCAAGACATCTCGAACACCCCCTCCACCGGATCCTGATGA
EST: gi|71307737|gb|DR790087.1|DR790087
EST:     GCCACCGCCACAATTATGATCCTTGGGGACACCTGCACGCGCGGATGCAG                         GTTCTGTAACGTCAAGACATCTCGAACACCCCCTCCACCGGATCCTGATGA
genomic: GCCACCGCCACAATTATGATCCTTGGGGACACCTGCACGCGCGGATGCAGgtaagagatt ... acattcgcagGTTCTGTAACGTCAAGACATCTCGAACACCCCCTCCACCGGATCCTGATGA
EST: gi|74244354|gb|DT652268.1|DT652268
EST:     GCCACCGCCACAATTATGATCCTTGGGGACACCTGCACGCGCGGATGCAG                         GTTCTGTAACGTCAAGACATCTCGAACACCCCCTCCACCGGATCCTGATGA
genomic: GCCACCGCCACAATTATGATCCTTGGGGACACCTGCACGCGCGGATGCAGgtaagagatt ... acattcgcagGTTCTGTAACGTCAAGACATCTCGAACACCCCCTCCACCGGATCCTGATGA

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: 44 (upstream exon), 48 (downstream exon)
Score: 96

CCCGGTGCCCCAACCTCGGCGAGTGCTGGTCCGGCGGCGAGACTGGCACCGCCACCGCCACAATTATGATCCTTGGGGACACCTGCACGCGCGGATGCAGgtaagagatt ... acattcgcagGTTCTGTAACGTCAAGACATCTCGAACACCCCCTCCACCGGATCCTGATGAGCCTTCCAATGTTGCTCAAGCTATTGCCTCATGGGGCCTTGAATATATA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 62

CCCGGTGCCCCAACCTCGGCGAGTGCTGGTCCGGCGGCGAGACTGGCACCGCCACCGCCACAATTATGATCCTTGGGGACACCTGCACGCGCGGATGCAGgtaagagatt ... acattcgcagGTTCTGTAACGTCAAGACATCTCGAACACCCCCTCCACCGGATCCTGATGAGCCTTCCAATGTTGCTCAAGCTATTGCCTCATGGGGCCTTGAATATATA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 67

CCCGGTGCCCCAACCTCGGCGAGTGCTGGTCCGGCGGCGAGACTGGCACCGCCACCGCCACAATTATGATCCTTGGGGACACCTGCACGCGCGGATGCAGgtaagagatt ... acattcgcagGTTCTGTAACGTCAAGACATCTCGAACACCCCCTCCACCGGATCCTGATGAGCCTTCCAATGTTGCTCAAGCTATTGCCTCATGGGGCCTTGAATATATA


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 85

CCCGGTGCCCCAACCTCGGCGAGTGCTGGTCCGGCGGCGAGACTGGCACCGCCACCGCCACAATTATGATCCTTGGGGACACCTGCACGCGCGGATGCAGgtaagagatt ... acattcgcagGTTCTGTAACGTCAAGACATCTCGAACACCCCCTCCACCGGATCCTGATGAGCCTTCCAATGTTGCTCAAGCTATTGCCTCATGGGGCCTTGAATATATA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgaacttaaggcccatagttgcttacgaatttgagaaaatactacattcgcagGTTCTGTAACGTCAAGACATCTCGAACACCCCCTCCACCGGATCCTGATGAGCCTTCCAATGTTGCTCAAGCTATTGCCTCATGGGGCCTTGAATATATA
                     tgcttac  putative branch site (score: 85)
 aatttgagaaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaaggatgtttgttgtttacgatttggaattcaccttttgaagaaatgaacttaaggcccatagttgcttacgaatttgagaaaatactacattcgcagGTTCTGTAACGTCAAGACATCTCGAACACCCCCTCCACCGGATCCTGATGAGCCTTCCAATGTTGCTCAAGCTATTGCCTCATGGGGCCTTGAATATATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - -tgtttgt
- - - - - - - - - - - - - - - - - - - - gaagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcttac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaatac