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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtcacctctgcacctgctgcttcaaaatttcaaggcaatttttgaggtttttatttttgataaaaaactgacatttatatgaaataattctttgcaccagTCCTCATTCAGAAAATGGTAAACAAAAACAAACAGCTAGAGGCAGTCAAATTCATTCAAGCTCTTAATATAGCGCACAAATACGCTTTGTTGCCTATTAT

Basic information

species Zea mays
transcript GRMZM2G032423_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G032423_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g09310.2 (Oryza sativa), 3'ss of exon 1
--gtcacctctgcacctgctgcttcaaaatttcaaggcaatttttgaggtttttatttttgataaaaaactgacatttatatgaaataattctttgcaccagTCCTCATTCAGAAAATGGTAAACAAAAACAAACAGCTAGAGGCAGTCAAATTCATTCAAGCTCTTAATATAGCGCACAAATACGCTTTGTTGCCTATTAT
       |        | |||||  | |  || || |   ||||     ||    | | |    |       ||||| | ||||||    ||||| |||||||  ||||||| | |||| |||| |||  ||||||||| ||||| || ||||||||||||||||||||| | | | | |||||  |||| |||||| || |
tccatggcatgatgttttctgctctaca--tttaatgtttttttgttctttgaggtatgtccgtatgtgtgaacattaacatgaaaactctctttccaccagTTTTCATTCATACAATGATAAAGAAAGGCAAACAGCTGGAGGCGGTTAAATTCATTCAAGCTCTTAATTTGGTGGAAAAATATCCTTTATTGCCTGTTCT
















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|76291847|gb|DV031415.1|DV031415
EST:     CGTTGATGCGTTCGTCGTCCTGGGCCTGGACCTCGACCAGCATATGCCAA                         TCCTCATTCAGAAAATGGTAAACAAAAACAAACAGCTAGAGGCAGTCAAAT
genomic: CGTTGATGCGTTCGTCGTCCTGGGCCTGGACCTCGACCAGCATATGCCAAgtaagtcaca ... tttgcaccagTCCTCATTCAGAAAATGGTAAACAAAAACAAACAGCTAGAGGCAGTCAAAT
EST: gi|91049336|gb|EB159754.1|EB159754
EST:     CGTTGATGCGTTCGTCGTCCTGGGCCTGGACCTCGACCAGCATATGCCAA                         TCCTCATTCAGAAAATGGTAAACAAAAACAAACAGCTAGAGGCAGTCAAAT
genomic: CGTTGATGCGTTCGTCGTCCTGGGCCTGGACCTCGACCAGCATATGCCAAgtaagtcaca ... tttgcaccagTCCTCATTCAGAAAATGGTAAACAAAAACAAACAGCTAGAGGCAGTCAAAT
EST: gi|149013864|gb|EE043348.2|EE043348
EST:     CGTTGATGCGTTCGTCGTCCTGGGCCTGGACCTCGACCAGCATATGCCAA                         TCCTCATTCAGAAAATGGTAAACAAAAACAAACAGCTAGAGGCAGTCAAAT
genomic: CGTTGATGCGTTCGTCGTCCTGGGCCTGGACCTCGACCAGCATATGCCAAgtaagtcaca ... tttgcaccagTCCTCATTCAGAAAATGGTAAACAAAAACAAACAGCTAGAGGCAGTCAAAT
EST: gi|91875202|gb|EB405159.1|EB405159
EST:     CGTTGATGCGTTCGTCGTCCTGGGCCTGGACCTCGACCAGCATATGCCAA                         TCCTCATTCAAAAAATGGGAAACAAAAACAAACAGCTAGAGGCAGTCAAAT
genomic: -GTTGATGCGTTCGTCGTCCTGGGCCTGGACCTCGACCAGCATATGCCAAgtaagtcaca ... tttgcaccagTCCTCATTCAGAAAATGGTAAACAAAAACAAACAGCTAGAGGCAGTCAAAT
EST: gi|148987143|gb|EE030971.2|EE030971
EST:     CGTTGATGCGTTCGTCGTCCTGGGCCTGGACCTCGACCAGCATATGCCAA                         TCCTCATTCAGAAAATGGTAAACAAAAACAAACAAGCTAGAGGCAGTCAAA
genomic: CGTTGATGCGTTCGTCGTCCTGGGCCTGGACCTCGACCAGCATATGCCAAgtaagtcaca ... tttgcaccagTCCTCATTCAGAAAATGGTAAACAAAAACAAACA-GCTAGAGGCAGTCAAA
EST: gi|71774896|gb|DR972774.1|DR972774
EST:     CGTTGATGCGTTCGTCGTCCTGGGCCTGGACCTCGACCAGCATATGCCAA                         TCCTCATTCAGAAAATGGTAAACAAAAACAAACAGCTAGAGGCAGTCAAAT
genomic: CGTTGATGCGTTCGTCGTCCTGGGCCTGGACCTCGACCAGCATATGCCAAgtaagtcaca ... tttgcaccagTCCTCATTCAGAAAATGGTAAACAAAAACAAACAGCTAGAGGCAGTCAAAT
EST: gi|89758269|gb|DY687513.1|DY687513
EST:     CGTTGATGCGTTCGTCGTCCTGGGCCTGGACCTCGACCAGCATATGCCAA                         TCCTCATTCAGAAAATGGTAAACAAAAACAAACAGCTAGAGGCAGTCAAAT
genomic: CGTTGATGCGTTCGTCGTCCTGGGCCTGGACCTCGACCAGCATATGCCAAgtaagtcaca ... tttgcaccagTCCTCATTCAGAAAATGGTAAACAAAAACAAACAGCTAGAGGCAGTCAAAT
EST: gi|148948642|gb|EC898556.2|EC898556
EST:     CGTTGATGCGTTCGTCGTCCTGGGCCTGGACCTCGACCAGCATATGCCAA                         TCCTCATTCAGAAAATGGTAAACAAAAACAAACAGCTAGAGGCAGTNCAA-
genomic: CGTTGATGCGTTCGTCGTCCTGGGCCTGGACCTCGACCAGCATATGCCAAgtaagtcaca ... tttgcaccagTCCTCATTCAGAAAATGGTAAACAAAAACAAACAGCTAGAGGCAGT-CAAA
EST: gi|211515655|gb|FL144144.1|FL144144
EST:     CGTTGATGCGTTCGTCGTCCTGGGGCTGGACCTCGACCAGCATATGCCAA                         TCCTCATTCAGAAAATGGTAAACAAAA
genomic: CGTTGATGCGTTCGTCGTCCTGGGCCTGGACCTCGACCAGCATATGCCAAgtaagtcaca ... tttgcaccagTCCTCATTCAGAAAATGGTAAACAAAA
EST: gi|76013592|gb|DT940762.1|DT940762
EST:     CGTTGATGCGTTCGTCGTCCTGGGCCTGGACCTCGACCAGCATATGCCAA                         TCCTCATTCAGAANATGGTAAACAAAAACAAACAGCTAGAGGCAGTCAAAT
genomic: CGTTGATGCGTTCGTCGTCCTGGGCCTGGACCTCGACCAGCATATGCCAAgtaagtcaca ... tttgcaccagTCCTCATTCAGAAAATGGTAAACAAAAACAAACAGCTAGAGGCAGTCAAAT
EST: gi|71426870|gb|DR807920.1|DR807920
EST:     CGTTGATGCGTTCGTCGTCCTGGGCCTGGACCTCGACCAGCATATGCCAA                         TCCTCATTCAGAAAATGGGTAA-CAAAAACAAACAGCTAGAGGCAGTCAAA
genomic: CGTTGATGCGTTCGTCGTCCTGGGCCTGGACCTCGACCAGCATATGCCAAgtaagtcaca ... tttgcaccagTCCTCATTCAGAAAATGG-TAAACAAAAACAAACAGCTAGAGGCAGTCAAA
EST: gi|148941362|gb|EC886271.2|EC886271
EST:     CGTTGATGCGTTCGTCGTCCTGGGCCTGGACCTCGACCAGCATATGCCAA                         TCCTCATTCAGAAAATGGTAAACAAAAACAAACAGCTAGAGGCAGTCAAAT
genomic: CGTTGATGCGTTCGTCGTCCTGGGCCTGGACCTCGACCAGCATATGCCAAgtaagtcaca ... tttgcaccagTCCTCATTCAGAAAATGGTAAACAAAAACAAACAGCTAGAGGCAGTCAAAT
EST: gi|211515654|gb|FL144143.1|FL144143
EST:     CGTTGATGCGTTCGTCGTCCTGGGCCTGGACCTCGACCAGCATATGCCAA                         TCCTCATTCAGAAAATGGTAAACAAAA-CAAACAGCTAGGAG-CAGTCAAA
genomic: CGTTGATGCGTTCGTCGTCCTGGGCCTGGACCTCGACCAGCATATGCCAAgtaagtcaca ... tttgcaccagTCCTCATTCAGAAAATGGTAAACAAAAACAAACAGCTAG-AGGCAGTCAAA
EST: gi|71307567|gb|DR790004.1|DR790004
EST:     CGTTGATGCGTTCGTCGTCCTGGGCCTGGACCTCGACCAGCATATGCCAA                         TCCTCATTCAGAAAATGGTAAACAAAAACA
genomic: CGTTGATGCGTTCGTCGTCCTGGGCCTGGACCTCGACCAGCATATGCCAAgtaagtcaca ... tttgcaccagTCCTCATTCAGAAAATGGTAAACAAAAACA
EST: gi|149081925|gb|EE171087.2|EE171087
EST:     CGGTGATGCGTTCGTCGTCCTGGGCCTGGACCTCGACCAGCATATGCCAA                         TCCTCATTCAGAAAATGGTAAACAAA
genomic: CGTTGATGCGTTCGTCGTCCTGGGCCTGGACCTCGACCAGCATATGCCAAgtaagtcaca ... tttgcaccagTCCTCATTCAGAAAATGGTAAACAAA
EST: gi|71770772|gb|DR968709.1|DR968709
EST:     CGTTGATGCGTTCGTCGTCCTGGGCCTGGACCTCGACCAGCATATGCCAA                         TCCTCATTCAGAAAATGGTAAACAAAAACAAACAGCTAGAGGCAGTCAAAT
genomic: CGTTGATGCGTTCGTCGTCCTGGGCCTGGACCTCGACCAGCATATGCCAAgtaagtcaca ... tttgcaccagTCCTCATTCAGAAAATGGTAAACAAAAACAAACAGCTAGAGGCAGTCAAAT
EST: gi|148940810|gb|EC885636.2|EC885636
EST:     CGTTGATGCGTTCGTCGTCCTGGGCCTGGACCTCGACCAGCATATGCCAA                         TCCTCATTCAGAAAATGGTAAACAAAAACAAACAGCTAGAGGCAGTCAAAT
genomic: CGTTGATGCGTTCGTCGTCCTGGGCCTGGACCTCGACCAGCATATGCCAAgtaagtcaca ... tttgcaccagTCCTCATTCAGAAAATGGTAAACAAAAACAAACAGCTAGAGGCAGTCAAAT
EST: gi|149004197|gb|EE039006.2|EE039006
EST:     CGTTGATGCGTTCGTCGTCCTGGGCCTGGACCTCGACCAGCATATGCCAA                         TCCTCATTCAGAAAATGGTAAACAAAAACAAACAGCTAGAGGCAGTCAAAT
genomic: CGTTGATGCGTTCGTCGTCCTGGGCCTGGACCTCGACCAGCATATGCCAAgtaagtcaca ... tttgcaccagTCCTCATTCAGAAAATGGTAAACAAAAACAAACAGCTAGAGGCAGTCAAAT

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), 49 (downstream exon)
Score: 109

ACCAGCGAGGTGCTTGATCTTGTCGTGTCGATCTCAGGTCGTGAGCGCGCCGTTGATGCGTTCGTCGTCCTGGGCCTGGACCTCGACCAGCATATGCCAAgtaagtcaca ... tttgcaccagTCCTCATTCAGAAAATGGTAAACAAAAACAAACAGCTAGAGGCAGTCAAATTCATTCAAGCTCTTAATATAGCGCACAAATACGCTTTGTTGCCTATTAT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 65

ACCAGCGAGGTGCTTGATCTTGTCGTGTCGATCTCAGGTCGTGAGCGCGCCGTTGATGCGTTCGTCGTCCTGGGCCTGGACCTCGACCAGCATATGCCAAgtaagtcaca ... tttgcaccagTCCTCATTCAGAAAATGGTAAACAAAAACAAACAGCTAGAGGCAGTCAAATTCATTCAAGCTCTTAATATAGCGCACAAATACGCTTTGTTGCCTATTAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 78

ACCAGCGAGGTGCTTGATCTTGTCGTGTCGATCTCAGGTCGTGAGCGCGCCGTTGATGCGTTCGTCGTCCTGGGCCTGGACCTCGACCAGCATATGCCAAgtaagtcaca ... tttgcaccagTCCTCATTCAGAAAATGGTAAACAAAAACAAACAGCTAGAGGCAGTCAAATTCATTCAAGCTCTTAATATAGCGCACAAATACGCTTTGTTGCCTATTAT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 135

ACCAGCGAGGTGCTTGATCTTGTCGTGTCGATCTCAGGTCGTGAGCGCGCCGTTGATGCGTTCGTCGTCCTGGGCCTGGACCTCGACCAGCATATGCCAAgtaagtcaca ... tttgcaccagTCCTCATTCAGAAAATGGTAAACAAAAACAAACAGCTAGAGGCAGTCAAATTCATTCAAGCTCTTAATATAGCGCACAAATACGCTTTGTTGCCTATTAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtttttatttttgataaaaaactgacatttatatgaaataattctttgcaccagTCCTCATTCAGAAAATGGTAAACAAAAACAAACAGCTAGAGGCAGTCAAATTCATTCAAGCTCTTAATATAGCGCACAAATACGCTTTGTTGCCTATTAT
                    aactgac  putative branch site (score: 135)
                                          ttctttgc  putative PPT
     ttatttttgataaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcacctctgcacctgctgcttcaaaatttcaaggcaatttttgaggtttttatttttgataaaaaactgacatttatatgaaataattctttgcaccagTCCTCATTCAGAAAATGGTAAACAAAAACAAACAGCTAGAGGCAGTCAAATTCATTCAAGCTCTTAATATAGCGCACAAATACGCTTTGTTGCCTATTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - -ctgcacc
- - - - - - - -gctgctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - taaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgacatt