Skip to another splice site:
1  
 5'  3'   
2  
 5'  3'   
3  
 5'  3'   
4  
 5'  3'   
5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actttgtttcatatggcaaacaataaatgtgttatttagctagcttctacatgtgtttgtgagatagcaagcaacatgtaactccctacatttacgacagAGCCTTGCAGACAGTTGCTTTCCTATTAATCAAGGTCTTGCTGCCAGCCGTCTTCATGGTAAGTGGAATGTGAGTGAATGTAATGATCATTCACTCATAT

Basic information

species Zea mays
transcript GRMZM2G095323_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G095323_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os12g13130.4 (Oryza sativa), 3'ss of exon 6
-actttgtttcatatggc-aaacaataaatgtgttatttagctagcttctacatgtgt-ttgtgagatagcaagcaacatgtaactccctacatttacgacagAGCCTTGCAGACAGTTGCTTTCCTATTAATCAAGGTCTTGCTGCCAGCCGTCTTCATGGTAAGTGGAATGTGAGTGAATGTAATGATCATTCACTCATAT
|| ||| ||| ||||| |||||||| ||||| ||| | ||| | | | | | || || | | ||| | | | | | ||||||||||||| ||||||||||||||||||||||| | ||||||||||||||||||
taccttggttcttatggttaaacaatagatgtgatatacattgagcattttctggcctactgatggaaattatctaactcagttttgcttctgct---aatagAGCCTTGCAGATAGTTGCTTTCCTATTAATCAAGGGCAATCTGCCAGCCGTCTTCATG------------------------------------------
















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|71428073|gb|DR809123.1|DR809123
EST:     NNNGTAAATGCAATGCAGCTGCAGCTACAAGGAATCGTCATCTTTGTGAG                         AGCCTTGCAGACAGTTGCTTTCCTATTAATCAAGGTCTTGCTGCCAGCCGT
genomic: AAAGTAAATGCAATGCAGCTGCAGCTACAAGGAATCGTCATCTTTGTGAGgttcttatca ... tttacgacagAGCCTTGCAGACAGTTGCTTTCCTATTAATCAAGGTCTTGCTGCCAGCCGT
EST: gi|71330742|gb|DR802158.1|DR802158
EST:     NNNGTAAATGCAATGCAGCTGCAGCTACAAGGAATCGTCATCTTTGTGAG                         AGCCTTGCAGACAGTTGCTTTCCTATTAATNCA-GGTCTTGCTGCCAGCCG
genomic: AAAGTAAATGCAATGCAGCTGCAGCTACAAGGAATCGTCATCTTTGTGAGgttcttatca ... tttacgacagAGCCTTGCAGACAGTTGCTTTCCTATTAAT-CAAGGTCTTGCTGCCAGCCG
EST: gi|148956175|gb|EC901959.2|EC901959
EST:     NNNGTAAATGCAATGCAGCTGCAGCTACCAGGAATCGTCATCTTTGTGAG                         AGCCTTGCAGACAGTTGCTTTCCTATTAATCAAGGTCTTGCTGCCAGCC
genomic: AAAGTAAATGCAATGCAGCTGCAGCTACAAGGAATCGTCATCTTTGTGAGgttcttatca ... tttacgacagAGCCTTGCAGACAGTTGCTTTCCTATTAATCAAGGTCTTGCTGCCAGCC
EST: gi|76293362|gb|DV032930.1|DV032930
EST:     NNNGTAAATGCAATGCAGCTGCAGCTACAAGGAATCGTCATCTTTGTGAG                         AGCCTTGCAGACAGTTGCTTTCCTATTAATCAAGGTCTTGCTGCCAGCCGT
genomic: AAAGTAAATGCAATGCAGCTGCAGCTACAAGGAATCGTCATCTTTGTGAGgttcttatca ... tttacgacagAGCCTTGCAGACAGTTGCTTTCCTATTAATCAAGGTCTTGCTGCCAGCCGT
EST: gi|78116974|gb|DV535361.1|DV535361
EST:     NNNGTAAATGCAATGCAGCTGCAGCTACAAGGAATCGTCATCTTTGTGAG                         AGCCTTGCAGACAGTTGCTTTCCTATTAATCAAGGTCTTGCTGCCAGCCGT
genomic: AAAGTAAATGCAATGCAGCTGCAGCTACAAGGAATCGTCATCTTTGTGAGgttcttatca ... tttacgacagAGCCTTGCAGACAGTTGCTTTCCTATTAATCAAGGTCTTGCTGCCAGCCGT
EST: gi|71770155|gb|DR968092.1|DR968092
EST:     NNNGTAAATGCAATGCAGCTGCAGCTACAAGGAATCGTCATCTTTGTGAG                         AGCCTTGCAGACAGTTGCTTTCCTATTAA
genomic: AAAGTAAATGCAATGCAGCTGCAGCTACAAGGAATCGTCATCTTTGTGAGgttcttatca ... tttacgacagAGCCTTGCAGACAGTTGCTTTCCTATTAA
EST: gi|71428072|gb|DR809122.1|DR809122
EST:     NNNGTAAATGCAATGCAGCTGCAGCTACAAGGAATCGTCATCTTTGTGAG                         AGCCTTGCAGACAGTTGCTTTCCTATTAATCAAGGTCTTGCTGCCAGCCGT
genomic: AAAGTAAATGCAATGCAGCTGCAGCTACAAGGAATCGTCATCTTTGTGAGgttcttatca ... tttacgacagAGCCTTGCAGACAGTTGCTTTCCTATTAATCAAGGTCTTGCTGCCAGCCGT
EST: gi|71439253|gb|DR820303.1|DR820303
EST:     NNNGTAAATGCAATGCAGCTGCAGCTACAAGGAATCGTCATCTTTGTGAG                         AGCCTTGCAGACAGTTGCTTTCCTATTAATCAAGGTCTTGCTGCCAGCCGT
genomic: AAAGTAAATGCAATGCAGCTGCAGCTACAAGGAATCGTCATCTTTGTGAGgttcttatca ... tttacgacagAGCCTTGCAGACAGTTGCTTTCCTATTAATCAAGGTCTTGCTGCCAGCCGT
EST: gi|71310796|gb|DR791700.1|DR791700
EST:     NNNGTAAATGCAATGCAGCTGCAGCTACAAGGAATCGTCATCTTTGTGAG                         AGCCTTGCAGACAGTTGCTTTCCTATTAATCAAGGTCTTGCTGCCAGCCGT
genomic: AAAGTAAATGCAATGCAGCTGCAGCTACAAGGAATCGTCATCTTTGTGAGgttcttatca ... tttacgacagAGCCTTGCAGACAGTTGCTTTCCTATTAATCAAGGTCTTGCTGCCAGCCGT
EST: gi|71773093|gb|DR971011.1|DR971011
EST:     NNNGTAAATGCAATGCAGCTGCAGCTACAAGGAATCGTCATCTTTGTGAG                         AGCCTTGCAGACAGTTGCTTTCCTATTAATCAAGGTCTTGCTGCCAGCCGT
genomic: AAAGTAAATGCAATGCAGCTGCAGCTACAAGGAATCGTCATCTTTGTGAGgttcttatca ... tttacgacagAGCCTTGCAGACAGTTGCTTTCCTATTAATCAAGGTCTTGCTGCCAGCCGT
EST: gi|78115630|gb|DV534018.1|DV534018
EST:     AA-GTAAATGCAATGCAGCTGCAGCTACCAGGAATCGTCATCTTTGTGAG                         AGCCTTGCAGACAGTTGCTTTCCTATTAATCAAGGTCTTGCTGCCAGCCGT
genomic: AAAGTAAATGCAATGCAGCTGCAGCTACAAGGAATCGTCATCTTTGTGAGgttcttatca ... tttacgacagAGCCTTGCAGACAGTTGCTTTCCTATTAATCAAGGTCTTGCTGCCAGCCGT

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: 48 (upstream exon), 48 (downstream exon)
Score: 42

TCTATGCGGCGCACTACATTGTGATCTGATGATGCAGTTCAAAAAACCAAAAAGTAAATGCAATGCAGCTGCAGCTACAAGGAATCGTCATCTTTGTGAGgttcttatca ... tttacgacagAGCCTTGCAGACAGTTGCTTTCCTATTAATCAAGGTCTTGCTGCCAGCCGTCTTCATGGTAAGTGGAATGTGAGTGAATGTAATGATCATTCACTCATAT


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 48

TCTATGCGGCGCACTACATTGTGATCTGATGATGCAGTTCAAAAAACCAAAAAGTAAATGCAATGCAGCTGCAGCTACAAGGAATCGTCATCTTTGTGAGgttcttatca ... tttacgacagAGCCTTGCAGACAGTTGCTTTCCTATTAATCAAGGTCTTGCTGCCAGCCGTCTTCATGGTAAGTGGAATGTGAGTGAATGTAATGATCATTCACTCATAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 55

TCTATGCGGCGCACTACATTGTGATCTGATGATGCAGTTCAAAAAACCAAAAAGTAAATGCAATGCAGCTGCAGCTACAAGGAATCGTCATCTTTGTGAGgttcttatca ... tttacgacagAGCCTTGCAGACAGTTGCTTTCCTATTAATCAAGGTCTTGCTGCCAGCCGTCTTCATGGTAAGTGGAATGTGAGTGAATGTAATGATCATTCACTCATAT


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 17

TCTATGCGGCGCACTACATTGTGATCTGATGATGCAGTTCAAAAAACCAAAAAGTAAATGCAATGCAGCTGCAGCTACAAGGAATCGTCATCTTTGTGAGgttcttatca ... tttacgacagAGCCTTGCAGACAGTTGCTTTCCTATTAATCAAGGTCTTGCTGCCAGCCGTCTTCATGGTAAGTGGAATGTGAGTGAATGTAATGATCATTCACTCATAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctacatgtgtttgtgagatagcaagcaacatgtaactccctacatttacgacagAGCCTTGCAGACAGTTGCTTTCCTATTAATCAAGGTCTTGCTGCCAGCCGTCTTCATGGTAAGTGGAATGTGAGTGAATGTAATGATCATTCACTCATAT
                              atgtaac  putative branch site (score: 17)
 tacattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actttgtttcatatggcaaacaataaatgtgttatttagctagcttctacatgtgtttgtgagatagcaagcaacatgtaactccctacatttacgacagAGCCTTGCAGACAGTTGCTTTCCTATTAATCAAGGTCTTGCTGCCAGCCGTCTTCATGGTAAGTGGAATGTGAGTGAATGTAATGATCATTCACTCATAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA