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

...gagttgcagacaggcaatagtttcatgaaatttgtttgtcaattgaatatcttccattgctactcgctttatgcaaaaaagagtaatattcttcttgcagGTAGCTTGGGTTACTAAATCTGGGAAATCTGACCTGGAAGCACCGATTGCAATCCGCCCCACAAGTGAGACTGTCATGTATCCATACTTCTCCAAATGGA

Basic information

species Zea mays
transcript GRMZM2G094123_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G094123_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os12g25710.3 (Oryza sativa), 3'ss of exon 4
---gagttgcagacaggcaatagtttcatgaaatttgtttgtcaattgaatatcttccattgctactcgctttatgcaaaaaagagtaat---attcttcttgcagGTAGCTTGGGTTACTAAATCTGGGAAATCTGACCTGGAAGCACCGATTGCAATCCGCCCCACAAGTGAGACTGTCATGTATCCATACTTCTCCAAATGGA
   |  |||         ||  ||| |||  |  ||     | | ||  |     |   |||  ||| | |  | | || | ||  |  |   |||| ||||||||||||| ||||| |||||||| || |||||||| |||||||| || || |||||||| || ||||||||||||||||||||||||||||||||||||||||
tctgttttgtttgttataaactgttgcatacacatt-----ttacttttaggctatttgttggaacttgataca-gtaacatagtcttttgtaattcatcttgcagGTAGCATGGGTCACTAAATCAGGAAAATCTGATCTGGAAGCTCCTATCGCAATCCGTCCTACAAGTGAGACTGTCATGTATCCATACTTCTCCAAATGGA

upper sequence: GRMZM2G094123_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv07s0005g02620.t01 (Vitis vinifera), 3'ss of exon 5
gagttgcagacaggcaatagt-ttcatgaaatttgtttgtcaattgaatatcttccattgctactcgctttatgcaaaaaagagtaatatt---cttcttgcagGTAGCTTGGGTTACTAAATCTGGGAAATCTGACCTGGAAGCACCGATTGCAATCCGCCCCACAAGTGAGACTGTCATGTATCCATACTTCTCCAAATGGA
 | |     | |    || ||  ||||   |      ||| |  ||||| | ||  |||  | ||  ||      | |     ||||| ||    || |   |||| |||||||| || ||||||||  |||| ||  ||||||  || ||||| || || || ||||||||||||||||||||||| || |  || || ||||
-attgtttaagaactcatggtgctcatttgacaaaaatgtta--tgaat-tattttattaatcctatctcacctaatattttggtaatgttgactttttcctagGTCGCTTGGGTAACAAAATCTGGACAATCAGATTTGGAAGTGCCTATTGCTATTCGTCCAACAAGTGAGACTGTCATGTATCCCTATTATTCTAAGTGGA
















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|71332073|gb|DR802941.1|DR802941
EST:     AGAATGTTCTACAGAAGGAAAAGGACCACATTGAGGGCTTTGCACCTGAG                         GTAGCTTGGGTTACTAAATCTGGGAAATCTGACCTGGAAGCACCGATTGCA
genomic: AGAATGTTCTACAGAAGGAAAAGGACCACATTGAGGGCTTTGCACCTGAGgtgtgccttt ... cttcttgcagGTAGCTTGGGTTACTAAATCTGGGAAATCTGACCTGGAAGCACCGATTGCA
EST: gi|15312974|gb|BI478491.1|BI478491
EST:     AGAATGTTCTACAGAAGGAAAAGGACCACATTGAGGGCTTTGCACCTGAG                         GTAGCTTGGGTTACTAAATCTGGGAAATCTGACCTGGAAGCACCGATTGCA
genomic: AGAATGTTCTACAGAAGGAAAAGGACCACATTGAGGGCTTTGCACCTGAGgtgtgccttt ... cttcttgcagGTAGCTTGGGTTACTAAATCTGGGAAATCTGACCTGGAAGCACCGATTGCA
EST: gi|6865183|gb|AW360533.1|AW360533
EST:     AGAATGTTCTACAGAAGGAAAAGGACCACATTGAGGGCTTTGCACCTGAG                         GTAGCTTGGGTTACTAAATCTGGGAAATCTGACCTGGAAGCACCGATTGCA
genomic: AGAATGTTCTACAGAAGGAAAAGGACCACATTGAGGGCTTTGCACCTGAGgtgtgccttt ... cttcttgcagGTAGCTTGGGTTACTAAATCTGGGAAATCTGACCTGGAAGCACCGATTGCA
EST: gi|211280528|gb|FL042846.1|FL042846
EST:     AGAATGTTCTACAGAAGGAAAAGGACCACATTGAGGGCTTTGCACCTGAG                         GTAGCTTGGGTTACTAAATCTGGGAAATCTGACCTGGAAGCACCGATTGCA
genomic: AGAATGTTCTACAGAAGGAAAAGGACCACATTGAGGGCTTTGCACCTGAGgtgtgccttt ... cttcttgcagGTAGCTTGGGTTACTAAATCTGGGAAATCTGACCTGGAAGCACCGATTGCA
EST: gi|67027739|gb|CO456488.1|CO456488
EST:     AGAATGTTCTACAGAAGGAAAAGGACCACATTGAGGGCTTTGCACCTGAG                         GTAGCTTGGGTTACTAAATCTGGGAAATCTGACCTGGAAGCACCGATTGCA
genomic: AGAATGTTCTACAGAAGGAAAAGGACCACATTGAGGGCTTTGCACCTGAGgtgtgccttt ... cttcttgcagGTAGCTTGGGTTACTAAATCTGGGAAATCTGACCTGGAAGCACCGATTGCA
EST: gi|211280526|gb|FL042844.1|FL042844
EST:     AGAATGTTCTACAGAAGGAAAAGGACCACATTGAGGGCTTTGCACCTGAN                         GTAGCTTGGGTTACTAAATCTGGGAAATCTGACCTGGAAGCACCGATTGCA
genomic: AGAATGTTCTACAGAAGGAAAAGGACCACATTGAGGGCTTTGCACCTGAGgtgtgccttt ... cttcttgcagGTAGCTTGGGTTACTAAATCTGGGAAATCTGACCTGGAAGCACCGATTGCA
EST: gi|211280529|gb|FL042847.1|FL042847
EST:     AGAATGTTCTACAGAAGGAAAAGGACCACATTGAGGGCTTTGCACCTGAG                         GTAGCTTGGGTTACTAAATCTGGGAAATCTGACCTGGAAGCACCGATTGCA
genomic: AGAATGTTCTACAGAAGGAAAAGGACCACATTGAGGGCTTTGCACCTGAGgtgtgccttt ... cttcttgcagGTAGCTTGGGTTACTAAATCTGGGAAATCTGACCTGGAAGCACCGATTGCA
EST: gi|32929788|gb|CF034600.1|CF034600
EST:     AGAATGTTCTACAGAAGGAAAAGGACCACATTGAGGGCTTTGCACCTGAG                         GTAGCTTGGGTTACTAAGTCAGGGAAATCTGACCTGGAAGCACCTATTGCA
genomic: AGAATGTTCTACAGAAGGAAAAGGACCACATTGAGGGCTTTGCACCTGAGgtgtgccttt ... cttcttgcagGTAGCTTGGGTTACTAAATCTGGGAAATCTGACCTGGAAGCACCGATTGCA
EST: gi|148961334|gb|EE012063.2|EE012063
EST:     GAATGTTCTACAGAAGGAAAAGGACCACATTGAGGGCTTTGCCCCCTGAG                         GTAGCTTGGGTTACTAAATCTGGGAAATCTGACCTGGAAGCACCGATTGC
genomic: GAATGTTCTACAGAAGGAAAAGGACCACATTGAGGGCTTTGCACC-TGAGgtgtgccttt ... cttcttgcagGTAGCTTGGGTTACTAAATCTGGGAAATCTGACCTGGAAGCACCGATTGC
EST: gi|211280527|gb|FL042845.1|FL042845
EST:     AGAATGTTCTACAGAAGGAAAAGGACCACATTGAGGGCTTTGCACCTGAG                         GTAGCTTGAGTTACTAAATCTGGGATATCTGACCTGGAAGCACCGATTGCA
genomic: AGAATGTTCTACAGAAGGAAAAGGACCACATTGAGGGCTTTGCACCTGAGgtgtgccttt ... cttcttgcagGTAGCTTGGGTTACTAAATCTGGGAAATCTGACCTGGAAGCACCGATTGCA

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: 782

AATTAAAAAGCTGAAGCTCAAACCATATTATTTCCCTTTGTTTGTTACTGAGAATGTTCTACAGAAGGAAAAGGACCACATTGAGGGCTTTGCACCTGAGgtgtgccttt ... cttcttgcagGTAGCTTGGGTTACTAAATCTGGGAAATCTGACCTGGAAGCACCGATTGCAATCCGCCCCACAAGTGAGACTGTCATGTATCCATACTTCTCCAAATGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 599

AATTAAAAAGCTGAAGCTCAAACCATATTATTTCCCTTTGTTTGTTACTGAGAATGTTCTACAGAAGGAAAAGGACCACATTGAGGGCTTTGCACCTGAGgtgtgccttt ... cttcttgcagGTAGCTTGGGTTACTAAATCTGGGAAATCTGACCTGGAAGCACCGATTGCAATCCGCCCCACAAGTGAGACTGTCATGTATCCATACTTCTCCAAATGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 566

AATTAAAAAGCTGAAGCTCAAACCATATTATTTCCCTTTGTTTGTTACTGAGAATGTTCTACAGAAGGAAAAGGACCACATTGAGGGCTTTGCACCTGAGgtgtgccttt ... cttcttgcagGTAGCTTGGGTTACTAAATCTGGGAAATCTGACCTGGAAGCACCGATTGCAATCCGCCCCACAAGTGAGACTGTCATGTATCCATACTTCTCCAAATGGA


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 471

AATTAAAAAGCTGAAGCTCAAACCATATTATTTCCCTTTGTTTGTTACTGAGAATGTTCTACAGAAGGAAAAGGACCACATTGAGGGCTTTGCACCTGAGgtgtgccttt ... cttcttgcagGTAGCTTGGGTTACTAAATCTGGGAAATCTGACCTGGAAGCACCGATTGCAATCCGCCCCACAAGTGAGACTGTCATGTATCCATACTTCTCCAAATGGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatatcttccattgctactcgctttatgcaaaaaagagtaatattcttcttgcagGTAGCTTGGGTTACTAAATCTGGGAAATCTGACCTGGAAGCACCGATTGCAATCCGCCCCACAAGTGAGACTGTCATGTATCCATACTTCTCCAAATGGA
                                         tattcttctt  CT-rich tract
                             aaaaaagagtaatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gagttgcagacaggcaatagtttcatgaaatttgtttgtcaattgaatatcttccattgctactcgctttatgcaaaaaagagtaatattcttcttgcagGTAGCTTGGGTTACTAAATCTGGGAAATCTGACCTGGAAGCACCGATTGCAATCCGCCCCACAAGTGAGACTGTCATGTATCCATACTTCTCCAAATGGA

- gttgcag
- - - - - caggcaa
- - - - - - - - - - - -catgaaa
- - - - - - - - - - - - - - - - tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctactc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caaaaaa