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'   		12  
 5'  3'   		13  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGATgtgagcttcctgtgccatgccgccttccgcttcttgaccacagcaccggctccgtgccggcagcatcggtccgtttgctgatgtgatgttttgggtccttttttcccccctttcgcttggggactggtgtcgctgtttgcag

Basic information

species Zea mays
transcript GRMZM2G437859_T04
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G437859_T03 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g55500.1 (Oryza sativa), 5'ss of exon 2
GCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGATgtgagcttcctgtgccatgccgccttccgcttcttgaccacagcaccggctccgtgccggcagcatcggtccgtttgctgatgtgatgttttgggtccttttttcccccctttcgcttggggactggtgtcgctgtttgcag
| ||||||||||||||||| |||||||||||||| |||||||||||||||||||||||||||||| | ||| |||| ||||||||||||||   ||| ||||||  |    |||  |  |||   | ||| ||||   |    ||   ||| |  || || || |  |  |||||   |     | || ||  | ||  | || |                                   
GGGAGGCGATCATACTGGGATTCCAGCACTACATCCTGGCGCTGGGCACGGCGGTGATGATCCCGGCGGTGCTGGTGCCCATGATGGGCGGGAGCGACgtgagcgcc----gccgcg--gccgcactcttgttgatttcc---cccaatccat-tcgccaccacccatg-gtttgagaactcacttttctgctttctgctgtcgcag---------------------------------

upper sequence: GRMZM2G437859_T03 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g55500.2 (Oryza sativa), 5'ss of exon 1
--GCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGATgtgagcttcctgtgccatgccgccttccgcttcttgaccacagcaccggctccgtgccggcagcatcggtccgtttgctgatgtgatgttttgggtccttttttcccccctttcgcttggggactggtgtcgctgtttgcag
  | ||||||||||||||||| |||||||||||||| |||||||||||||||||||||||||||||| | ||| |||| ||||||||||||||   ||| ||||||  |    |||  |  |||   | ||| ||||   |    ||   ||| |  || || || |  |  |||||   |     | || ||  | ||  | || |                                   
AGGGGAGGCGATCATACTGGGATTCCAGCACTACATCCTGGCGCTGGGCACGGCGGTGATGATCCCGGCGGTGCTGGTGCCCATGATGGGCGGGAGCGACgtgagcgcc----gccgcg--gccgcactcttgttgatttcc---cccaatccat-tcgccaccacccatg-gtttgagaactcacttttctgctttctgctgtcgcag---------------------------------
















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|211100341|gb|FL069922.1|FL069922
EST:     CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGAT                         GGGGACAGGGGTCAGGGTGGTGCAGACGCTGCCTGTTCGTGGACGGGGGAT
genomic: CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGATgtgagcttcc ... ctgtttgcagGGGGACAGGG-TCAGGGTGGTGCAGACGCTGC-TGTTCGTG-ACGGGG-AT
EST: gi|50339069|gb|CO534195.1|CO534195
EST:     CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGAT                         GGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCATGACGGGGATAAAC
genomic: CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGATgtgagcttcc ... ctgtttgcagGGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAAC
EST: gi|71449525|gb|DR830575.1|DR830575
EST:     CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGAT                         GGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAAC
genomic: CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGATgtgagcttcc ... ctgtttgcagGGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAAC
EST: gi|74244049|gb|DT651963.1|DT651963
EST:     CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGAT                         GGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAAC
genomic: CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGATgtgagcttcc ... ctgtttgcagGGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAAC
EST: gi|149001123|gb|EE038382.2|EE038382
EST:     CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGAT                         GGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAAC
genomic: CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGATgtgagcttcc ... ctgtttgcagGGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAAC
EST: gi|78084450|gb|DV512843.1|DV512843
EST:     CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGAT                         GGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAAC
genomic: CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGATgtgagcttcc ... ctgtttgcagGGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAAC
EST: gi|211102812|gb|FL069930.1|FL069930
EST:     CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGAT                         GGGGACAGGGTCAGGGTGGTGCAAACGCTGCTGTTCGTGA
genomic: CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGATgtgagcttcc ... ctgtttgcagGGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGA
EST: gi|211100342|gb|FL069923.1|FL069923
EST:     CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGAT                         GGGGACAGGGTCAGGGGTGGTGCAGACGCTGCTGTTCGTGACGG
genomic: CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGATgtgagcttcc ... ctgtttgcagGGGGACAGGGTCAGGG-TGGTGCAGACGCTGCTGTTCGTGACGG
EST: gi|71439895|gb|DR820945.1|DR820945
EST:     CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGAT                         GGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAAC
genomic: CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGATgtgagcttcc ... ctgtttgcagGGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAAC
EST: gi|50331687|gb|CO526813.1|CO526813
EST:     CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGAT                         GGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAAC
genomic: CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGATgtgagcttcc ... ctgtttgcagGGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAAC
EST: gi|74243489|gb|DT651403.1|DT651403
EST:     CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGAT                         GGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAAC
genomic: CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGATgtgagcttcc ... ctgtttgcagGGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAAC
EST: gi|76923378|gb|DV169457.1|DV169457
EST:     CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGAT                         GGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAAC
genomic: CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGATgtgagcttcc ... ctgtttgcagGGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAAC
EST: gi|74238882|gb|DT646796.1|DT646796
EST:     CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGAT                         GGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAAC
genomic: CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGATgtgagcttcc ... ctgtttgcagGGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAAC
EST: gi|149071736|gb|EE160129.2|EE160129
EST:     CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGAT                         GGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAAC
genomic: CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGATgtgagcttcc ... ctgtttgcagGGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAAC
EST: gi|74240437|gb|DT648351.1|DT648351
EST:     CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGAT                         GGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAAC
genomic: CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGATgtgagcttcc ... ctgtttgcagGGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAAC
EST: gi|91049745|gb|EB160163.1|EB160163
EST:     CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGAT                         GGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAAC
genomic: CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGATgtgagcttcc ... ctgtttgcagGGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAAC
EST: gi|211102809|gb|FL069927.1|FL069927
EST:     CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGAT                         GGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAAC
genomic: CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGATgtgagcttcc ... ctgtttgcagGGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAAC
EST: gi|211100340|gb|FL069921.1|FL069921
EST:     CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCCGCGACCAT                         GGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAAC
genomic: CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGATgtgagcttcc ... ctgtttgcagGGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAAC
EST: gi|211102808|gb|FL069926.1|FL069926
EST:     CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGAT                         GGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAA-C
genomic: CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGATgtgagcttcc ... ctgtttgcagGGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAAC
EST: gi|211100336|gb|FL069917.1|FL069917
EST:     CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGAT                         GGGGACAGGGTCAGGGTGGTGCAG
genomic: CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGATgtgagcttcc ... ctgtttgcagGGGGACAGGGTCAGGGTGGTGCAG
EST: gi|71310987|gb|DR791795.1|DR791795
EST:     CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGAT                         GGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAAC
genomic: CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGATgtgagcttcc ... ctgtttgcagGGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAAC
EST: gi|71431026|gb|DR812076.1|DR812076
EST:     CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGAT                         GGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAAC
genomic: CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGATgtgagcttcc ... ctgtttgcagGGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAAC
EST: gi|71438783|gb|DR819833.1|DR819833
EST:     CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGAT                         GGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAAC
genomic: CGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGATgtgagcttcc ... ctgtttgcagGGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAAC

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), 48 (downstream exon)
Score: 184

GCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGATgtgagcttcc ... ctgtttgcagGGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAACACGCTGCTGCAGTCCCTCTTCGGGACCCGGCTGCCGACGGTCATCGGCG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 35

GCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGATgtgagcttcc ... ctgtttgcagGGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAACACGCTGCTGCAGTCCCTCTTCGGGACCCGGCTGCCGACGGTCATCGGCG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 29

GCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGATgtgagcttcc ... ctgtttgcagGGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAACACGCTGCTGCAGTCCCTCTTCGGGACCCGGCTGCCGACGGTCATCGGCG


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 15

GCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGATgtgagcttcc ... ctgtttgcagGGGGACAGGGTCAGGGTGGTGCAGACGCTGCTGTTCGTGACGGGGATAAACACGCTGCTGCAGTCCCTCTTCGGGACCCGGCTGCCGACGGTCATCGGCG