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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaacggagcgagtacaatgtttttcacagtcatcctttttcatctcaaaaaagatcataggcagacatccagtgcaaagatttctctcttgacatgcagGTGAACGAGAACTCCGAGAATCCATACTGGAAAGCGATAGGATACAGCGTGGACGAGCCACGGGAGGATCGGGCTCGGACGGCGACACCGTCGCCGTCCC

Basic information

species Zea mays
transcript GRMZM2G143883_T06
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G143883_T06 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os10g33540.1 (Oryza sativa), 3'ss of exon 1
aaaacggagcgagtacaatgtttttcacagtcatcctttttcatctcaaaaaagatcataggcagacatccagtgcaaagatttctctcttgacatgcagGTGAACGAGAACTCCGAGAATCCATACTGGAAAGCGATAGGATACAGCGTGGACGAGCCACGGGAGGATCGGGCTCGGACGGCGACACCGTCGCCGTCCC
|| || ||   |   |    |   | |        |   |  ||||  |||   | |           |    ||||||  |   |       ||||||||||||||||||||| |||||||||||||||||||| ||||||||||| ||||| ||||| ||    ||||| ||   | ||  | |  || || || |  
aagaccgattaatatctgaatgaatgatcaaagaacaaatgtatctgcaaatcaaacgatcatttctgtaacttgcaaatttcctttgtccatcatgcagGTGAACGAGAACTCGGAGAATCCATACTGGAAAGCAATAGGATACAGAGTGGAAGAGCCCCGACGTGATCGAGCAGAGTCGATGCCGTCGCCGTCGCCAT
















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|148948203|gb|EC893719.2|EC893719
EST:     TCGCCTTCGCCATCGTCAAGATCCTCTGCCACTACGTCTTCTACGCCATG                         GTGAACGAGAACTCCGAGAATCCATACTGGAAAGCGATAGGATACCGCGTG
genomic: TCGCCTTCGCCATCGTCAAGATCCTCTGCCACTACGTCTTCTACGCCATGgtacgccggc ... tgacatgcagGTGAACGAGAACTCCGAGAATCCATACTGGAAAGCGATAGGATACAGCGTG
EST: gi|148973859|gb|EE025001.2|EE025001
EST:     TCGCCTTCGCCATCGTCAAGATCCTCTGCCACTACGTCTTCTACGCCATG                         GTGAACGAGAACTCCGAGAATCCATACTGGAAAGCG
genomic: TCGCCTTCGCCATCGTCAAGATCCTCTGCCACTACGTCTTCTACGCCATGgtacgccggc ... tgacatgcagGTGAACGAGAACTCCGAGAATCCATACTGGAAAGCG
EST: gi|71328928|gb|DR801150.1|DR801150
EST:     TCGCCTTCGCCATCGTCAAGATCCTCTGCCACTACGTCTTCTACGCCATG                         GTGAACGAGAACTCCGAGAATCCATACTGGAAAGCGATAGGATACAGCGTG
genomic: TCGCCTTCGCCATCGTCAAGATCCTCTGCCACTACGTCTTCTACGCCATGgtacgccggc ... tgacatgcagGTGAACGAGAACTCCGAGAATCCATACTGGAAAGCGATAGGATACAGCGTG
EST: gi|148951656|gb|EC897401.2|EC897401
EST:     TCGCCTTCGCCATCGTCAAGATCCTCTGCCACTACGTCTTCTACGCCATG                         GTGAACGAGAACTCCGAGAATCCATACTGGAAAGCGATAGGATACAG
genomic: TCGCCTTCGCCATCGTCAAGATCCTCTGCCACTACGTCTTCTACGCCATGgtacgccggc ... tgacatgcagGTGAACGAGAACTCCGAGAATCCATACTGGAAAGCGATAGGATACAG
EST: gi|76281721|gb|DV021289.1|DV021289
EST:     TCGCCTTCGCCATCGTCAAGATCCTCTGCCACTACCTCTTCTACGCCATG                         GTGAACGAGAACTCCGAGAATCCATACTGGAAAG
genomic: TCGCCTTCGCCATCGTCAAGATCCTCTGCCACTACGTCTTCTACGCCATGgtacgccggc ... tgacatgcagGTGAACGAGAACTCCGAGAATCCATACTGGAAAG
EST: gi|78083349|gb|DV511742.1|DV511742
EST:     TCGCCTTCGCCATCGTCAAGATCCTCTGCCACTACGTCTTCTACGCCATG                         GTGAACGAGAACTCCGAGAATCCATACTGGAAAGCGATAGGATACAGCGTG
genomic: TCGCCTTCGCCATCGTCAAGATCCTCTGCCACTACGTCTTCTACGCCATGgtacgccggc ... tgacatgcagGTGAACGAGAACTCCGAGAATCCATACTGGAAAGCGATAGGATACAGCGTG
EST: gi|71438157|gb|DR819207.1|DR819207
EST:     TCGCCTTCGCCATCGTCAAGATCCTCTGCCACTACGTCTTCTACGCCATG                         GTGAACGAGAACTCCGAGAATCCATACTGGAAAGCGATAGGATACAGCGTG
genomic: TCGCCTTCGCCATCGTCAAGATCCTCTGCCACTACGTCTTCTACGCCATGgtacgccggc ... tgacatgcagGTGAACGAGAACTCCGAGAATCCATACTGGAAAGCGATAGGATACAGCGTG
EST: gi|93014896|gb|EB640416.1|EB640416
EST:     TCGCCTTCGCCATCGTCAAGATCCTCTGCCACTACGTCTTCTACGCCATG                         GTGAACGAGAACTCCGAGAATCCATACTGGAAAGCGATAGGATACAGCGTG
genomic: TCGCCTTCGCCATCGTCAAGATCCTCTGCCACTACGTCTTCTACGCCATGgtacgccggc ... tgacatgcagGTGAACGAGAACTCCGAGAATCCATACTGGAAAGCGATAGGATACAGCGTG
EST: gi|149020921|gb|EE045762.2|EE045762
EST:     TCGCCTTCGCCATCGTCAAGATCCTCTGCCACTACGTCTTCTACGCCATG                         GTGAACGAGAACTCCGAGAATCCATACTGGAAAGCGATAGGATACAGC
genomic: TCGCCTTCGCCATCGTCAAGATCCTCTGCCACTACGTCTTCTACGCCATGgtacgccggc ... tgacatgcagGTGAACGAGAACTCCGAGAATCCATACTGGAAAGCGATAGGATACAGC
EST: gi|149085834|gb|EE175357.2|EE175357
EST:     TCGCCTTCGCCATCGTCAAGATCCTCTGCCACTACGTCTTCTACGCCATG                         GTGAACGAGAACTCCGAGAATCCATACTGGAAAGCGATAGGATACAGCGTG
genomic: TCGCCTTCGCCATCGTCAAGATCCTCTGCCACTACGTCTTCTACGCCATGgtacgccggc ... tgacatgcagGTGAACGAGAACTCCGAGAATCCATACTGGAAAGCGATAGGATACAGCGTG
EST: gi|50327417|gb|CO522543.1|CO522543
EST:     TCGCCTTCGCCATCGTCAAGATCCTCTGCCACTACGTCTTCTACGCCATG                         GTGAACGAGAACTCCGAGAATCCATACTGGAAAGCGATAGGATACAGCGTG
genomic: TCGCCTTCGCCATCGTCAAGATCCTCTGCCACTACGTCTTCTACGCCATGgtacgccggc ... tgacatgcagGTGAACGAGAACTCCGAGAATCCATACTGGAAAGCGATAGGATACAGCGTG
EST: gi|78075545|gb|DV503979.1|DV503979
EST:     TCGCCTTCGCCATCGTCAAGATCCTCTGCCACTACGTCTTCTACGCCATG                         GTGAACGAGAACTCCGAGAATCCATA
genomic: TCGCCTTCGCCATCGTCAAGATCCTCTGCCACTACGTCTTCTACGCCATGgtacgccggc ... tgacatgcagGTGAACGAGAACTCCGAGAATCCATA
EST: gi|149084377|gb|EE173826.2|EE173826
EST:     TCGCCTTCGCCATCGTCAAGATCCTCTGCCACTACGTCTTCTACGCCATG                         GTGAACGAGAACTCCGAGAATCCATACTGGAAAGCGATAGGATACAGCGTG
genomic: TCGCCTTCGCCATCGTCAAGATCCTCTGCCACTACGTCTTCTACGCCATGgtacgccggc ... tgacatgcagGTGAACGAGAACTCCGAGAATCCATACTGGAAAGCGATAGGATACAGCGTG
EST: gi|76926142|gb|DV170732.1|DV170732
EST:     TCGCCTTCGCCATCGTCAAGATCCTCTGCCACTACGTCTTCTACGCCATG                         GTGAACGAGAACTCCGAGAATCCATACTGGAAAGCGATAGGATACAGCGTG
genomic: TCGCCTTCGCCATCGTCAAGATCCTCTGCCACTACGTCTTCTACGCCATGgtacgccggc ... tgacatgcagGTGAACGAGAACTCCGAGAATCCATACTGGAAAGCGATAGGATACAGCGTG
EST: gi|78087753|gb|DV516146.1|DV516146
EST:     TCGCCTTCGCCATCGTCAAGATCCTCTGCCACTACGTCTTCTACGCCATG                         GTGAACGAGAACTCCGAGAATCCATACTGGAAAGCGATAGGATACAGCGTG
genomic: TCGCCTTCGCCATCGTCAAGATCCTCTGCCACTACGTCTTCTACGCCATGgtacgccggc ... tgacatgcagGTGAACGAGAACTCCGAGAATCCATACTGGAAAGCGATAGGATACAGCGTG
EST: gi|149086895|gb|EE176439.2|EE176439
EST:     TCGCCTTCGCCATCGTCAAGATCCTCTGCCACTACGTCTTCTACGCCATG                         GTGAACGAGAACTCCGAGAATCCATACTGGAAAGCGATAGGATACAGCGTG
genomic: TCGCCTTCGCCATCGTCAAGATCCTCTGCCACTACGTCTTCTACGCCATGgtacgccggc ... tgacatgcagGTGAACGAGAACTCCGAGAATCCATACTGGAAAGCGATAGGATACAGCGTG
EST: gi|148931643|gb|EC874791.2|EC874791
EST:     TCGCCTTCGCCATCGTCAAGATCCTCTGCCACTACGTCTTCTACGCCATG                         GTGAACGAGAACTCCGAGAATCCATACTGGAAAGCGATAGGATACAGCGTG
genomic: TCGCCTTCGCCATCGTCAAGATCCTCTGCCACTACGTCTTCTACGCCATGgtacgccggc ... tgacatgcagGTGAACGAGAACTCCGAGAATCCATACTGGAAAGCGATAGGATACAGCGTG
EST: gi|71769980|gb|DR967917.1|DR967917
EST:     TCGCCTTCGCCATCGTCAAGATCCTCTGCCACTACGTCTTCTACGCCATG                         GTGAACGAGAACTCCGAGAATCCATACTGGAA
genomic: TCGCCTTCGCCATCGTCAAGATCCTCTGCCACTACGTCTTCTACGCCATGgtacgccggc ... tgacatgcagGTGAACGAGAACTCCGAGAATCCATACTGGAA

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: 142

GGCGGCCCTGCGGCGCTGGAACCGGGTGCGCTGGCTCTTCCCGCTCCGCATCGCCTTCGCCATCGTCAAGATCCTCTGCCACTACGTCTTCTACGCCATGgtacgccggc ... tgacatgcagGTGAACGAGAACTCCGAGAATCCATACTGGAAAGCGATAGGATACAGCGTGGACGAGCCACGGGAGGATCGGGCTCGGACGGCGACACCGTCGCCGTCCC


Block sizes: 43 (upstream exon), 45 (downstream exon)
Score: 12

GGCGGCCCTGCGGCGCTGGAACCGGGTGCGCTGGCTCTTCCCGCTCCGCATCGCCTTCGCCATCGTCAAGATCCTCTGCCACTACGTCTTCTACGCCATGgtacgccggc ... tgacatgcagGTGAACGAGAACTCCGAGAATCCATACTGGAAAGCGATAGGATACAGCGTGGACGAGCCACGGGAGGATCGGGCTCGGACGGCGACACCGTCGCCGTCCC


Block sizes: 36 (upstream exon), 44 (downstream exon)
Score: 4

GGCGGCCCTGCGGCGCTGGAACCGGGTGCGCTGGCTCTTCCCGCTCCGCATCGCCTTCGCCATCGTCAAGATCCTCTGCCACTACGTCTTCTACGCCATGgtacgccggc ... tgacatgcagGTGAACGAGAACTCCGAGAATCCATACTGGAAAGCGATAGGATACAGCGTGGACGAGCCACGGGAGGATCGGGCTCGGACGGCGACACCGTCGCCGTCCC


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 66

GGCGGCCCTGCGGCGCTGGAACCGGGTGCGCTGGCTCTTCCCGCTCCGCATCGCCTTCGCCATCGTCAAGATCCTCTGCCACTACGTCTTCTACGCCATGgtacgccggc ... tgacatgcagGTGAACGAGAACTCCGAGAATCCATACTGGAAAGCGATAGGATACAGCGTGGACGAGCCACGGGAGGATCGGGCTCGGACGGCGACACCGTCGCCGTCCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaaaaaagatcataggcagacatccagtgcaaagatttctctcttgacatgcagGTGAACGAGAACTCCGAGAATCCATACTGGAAAGCGATAGGATACAGCGTGGACGAGCCACGGGAGGATCGGGCTCGGACGGCGACACCGTCGCCGTCCC
                                          tcttgac  putative branch site (score: 66)
                                    tttctctctt  CT-rich tract
                               aaagattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaacggagcgagtacaatgtttttcacagtcatcctttttcatctcaaaaaagatcataggcagacatccagtgcaaagatttctctcttgacatgcagGTGAACGAGAACTCCGAGAATCCATACTGGAAAGCGATAGGATACAGCGTGGACGAGCCACGGGAGGATCGGGCTCGGACGGCGACACCGTCGCCGTCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT