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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggtgcccgtccatctcgccttccttccccacggattcctttcatcctctggggatcatgggtggagttcgctagtttattctcttttgttggtttggttatcattttcggttcgtttttttcgcagATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTT

Basic information

species Zea mays
transcript GRMZM2G146670_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G146670_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA18G49070.1 (Glycine max), 3'ss of exon 1
gtgggtgcccgtccatctcgccttccttccccacggattcctttcatcctctggggatcatgggtggagttcgctagtttattctcttttgttggtttggttatcattttcggttcgtttttttcgcagATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTT-
     |  |      | | |   | ||     | | |||  |||     | | |   |  |   |   |||    |||| || || |||  |   |    | ||   |||  ||| ||||  |  | ||||||||||| |||||||||||| |  ||||| ||||||||| |||| ||||||    | | ||| ||| 
tactctctctaattgtgttgaaattctaaattatg-atttttttgggggtgtagaatttttccctacggttaaa-agttgatgctttttgatgaatcctttaatgggtttttgtttgtttggt--gtagaTCTGCTGTTCAAGGACTACCACAGTGACCAGAAGTTCACCATCACCACCTACTCACCGACTGGAGTTG

upper sequence: GRMZM2G146670_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA09G37570.1 (Glycine max), 3'ss of exon 1
gtgggtgcccgtccatctcgccttccttccccacggattcctttcatcctctggggatcatgggtggagttcgctagt-----ttattctcttttgttggtttggttatcattttcggttcgtttttttcgcagATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTT
  |    | |   |   |    ||      | |   | |  |    |  | |||||   |    |     |  ||  |     ||  |   ||||| ||  |     ||   |||  ||| ||||  |  | ||||||||||| |||||||||||| |  ||||| ||||||||| |||| ||||||    ||| ||| |||
--gtactctctctctaattatgttgaaattctattaaattgtggt-ttttttggggggtagaatttttccttactgttaaaaattggtgctttttgatgaatcctaaatgggtttttgtttgtttggt--gtagATCTGCTGTTCAAGGACTACCACAGTGACCAGAAGTTCACCATCACCACCTACTCACCCACTGGAGTT
















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|32919820|gb|CF024632.1|CF024632
EST:     GAAGATGGTCGGACCAGGCCTCTACACCGAGATCGGCAAGAAGACCAGGG                         ATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCT
genomic: GAAGATGGTCGGACCAGGCCTCTACACCGAGATCGGCAAGAAGACCAGGGgtgggtgccc ... tttttcgcagATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCT
EST: gi|31354274|gb|CD438631.1|CD438631
EST:     GAAGATGGTCGGACCAGGCCTCTACACCGAGATCGGCAAGAAGACCAGGG                         ATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCT
genomic: GAAGATGGTCGGACCAGGCCTCTACACCGAGATCGGCAAGAAGACCAGGGgtgggtgccc ... tttttcgcagATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCT
EST: gi|211283575|gb|FL005708.1|FL005708
EST:     GAAGATGGTCGGACCAGGCCTCTACACCGAGATCGGCAAGAAGACCAGGG                         ATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCT
genomic: GAAGATGGTCGGACCAGGCCTCTACACCGAGATCGGCAAGAAGACCAGGGgtgggtgccc ... tttttcgcagATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCT
EST: gi|211283569|gb|FL005702.1|FL005702
EST:     GAAGATGGTCGGACCAGGCCTCTACACCGAGATCGGCAAGAAGACCAGGG                         ATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCT
genomic: GAAGATGGTCGGACCAGGCCTCTACACCGAGATCGGCAAGAAGACCAGGGgtgggtgccc ... tttttcgcagATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCT
EST: gi|32910365|gb|CF015177.1|CF015177
EST:     GAAGATGGTCGGACCAGGCCTCTACACCGAGATCGGCAAGAAGACCAGGG                         ATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCT
genomic: GAAGATGGTCGGACCAGGCCTCTACACCGAGATCGGCAAGAAGACCAGGGgtgggtgccc ... tttttcgcagATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCT
EST: gi|13562162|gb|BG550382.1|BG550382
EST:     GGACCAGGCCTCTACACCGAGATCGGCAAGAAGACCAGGG                         ATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCT
genomic: GGACCAGGCCTCTACACCGAGATCGGCAAGAAGACCAGGGgtgggtgccc ... tttttcgcagATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCT
EST: gi|32915544|gb|CF020356.1|CF020356
EST:     GAAGATGGTCGGACCAGGCCTCTACACCGAGATCGGCAAGAAGACCAGGG                         ATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCT
genomic: GAAGATGGTCGGACCAGGCCTCTACACCGAGATCGGCAAGAAGACCAGGGgtgggtgccc ... tttttcgcagATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCT
EST: gi|32917034|gb|CF021846.1|CF021846
EST:     GAAGATGGTCGGACCAGGCCTCTACACCGAGATCGGCAAGAAGACCAGGG                         ATCTGCTGTACAAGGACTACCAGACGGACCACAAGTTCACCCTCACTACCT
genomic: GAAGATGGTCGGACCAGGCCTCTACACCGAGATCGGCAAGAAGACCAGGGgtgggtgccc ... tttttcgcagATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCT
EST: gi|32913382|gb|CF018194.1|CF018194
EST:     GAAGATGGTCGGACCAGGCCTCTACACCGAGATCGGCAAGAAGACCAGGG                         ATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCT
genomic: GAAGATGGTCGGACCAGGCCTCTACACCGAGATCGGCAAGAAGACCAGGGgtgggtgccc ... tttttcgcagATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCT
EST: gi|211283571|gb|FL005704.1|FL005704
EST:     GAAGATGGTCGGACCAGGCCTCTACACCGAGATCGGCAAGAAGACCAGGG                         ATCTGCTGTACAAGKGACTACCAGACAGACCACAAGTTCACCCTCACTACC
genomic: GAAGATGGTCGGACCAGGCCTCTACACCGAGATCGGCAAGAAGACCAGGGgtgggtgccc ... tttttcgcagATCTGCTGTACAAG-GACTACCAGACAGACCACAAGTTCACCCTCACTACC
EST: gi|211283572|gb|FL005705.1|FL005705
EST:     GAAGATGGTCGGACCAGGCCTCTACACCGAGATCGGCAAGAAGACCAGGG                         ATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCT
genomic: GAAGATGGTCGGACCAGGCCTCTACACCGAGATCGGCAAGAAGACCAGGGgtgggtgccc ... tttttcgcagATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCT
EST: gi|211283577|gb|FL005710.1|FL005710
EST:     GAAGATGGTCGGACCAGGCCTCTACACCGAGATCGGCAAGAAGACCAGGG                         ATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCT
genomic: GAAGATGGTCGGACCAGGCCTCTACACCGAGATCGGCAAGAAGACCAGGGgtgggtgccc ... tttttcgcagATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCT
EST: gi|31354722|gb|CD439079.1|CD439079
EST:     GAAGATGGTCGGACCAGGCCTCTACACCGAGATCGGCAAGAAGACCAGGG                         ATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCT
genomic: GAAGATGGTCGGACCAGGCCTCTACACCGAGATCGGCAAGAAGACCAGGGgtgggtgccc ... tttttcgcagATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCT
EST: gi|211283576|gb|FL005709.1|FL005709
EST:     GAAGATGGTCGGACCAGGCCTCTACACCGAGATCGGCAAGAAGACCAGGG                         ATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCT
genomic: GAAGATGGTCGGACCAGGCCTCTACACCGAGATCGGCAAGAAGACCAGGGgtgggtgccc ... tttttcgcagATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCT
EST: gi|211281770|gb|FL005699.1|FL005699
EST:     GAAGATGGTCGGACCAGGCCTCTACACCGAGATCGGCAAGAAGACCAGGG                         ATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCT
genomic: GAAGATGGTCGGACCAGGCCTCTACACCGAGATCGGCAAGAAGACCAGGGgtgggtgccc ... tttttcgcagATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCT
EST: gi|13557920|gb|BG549276.1|BG549276
EST:     GAAGATGGTCGGACCAGGCCTCTACACCGAGATCGGCAAGAAGACCAGGG                         ATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCT
genomic: GAAGATGGTCGGACCAGGCCTCTACACCGAGATCGGCAAGAAGACCAGGGgtgggtgccc ... tttttcgcagATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCT
EST: gi|74243487|gb|DT651401.1|DT651401
EST:     AGAAGACCAGGG                         ATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCT
genomic: AGAAGACCAGGGgtgggtgccc ... tttttcgcagATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCT
EST: gi|211283573|gb|FL005706.1|FL005706
EST:     GAAGATGGTCGGACCAGGCCTCTACACCGAGATCGGCAAGAAGACCAGGG                         ATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCT
genomic: GAAGATGGTCGGACCAGGCCTCTACACCGAGATCGGCAAGAAGACCAGGGgtgggtgccc ... tttttcgcagATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCT
EST: gi|30307135|gb|CD001808.1|CD001808
EST:     GAAGATGGTCGGACCAGGCCTCTACACCGAGATCGGCAAGAAGACCAGGG                         ATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCT
genomic: GAAGATGGTCGGACCAGGCCTCTACACCGAGATCGGCAAGAAGACCAGGGgtgggtgccc ... tttttcgcagATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCT
EST: gi|32910975|gb|CF015787.1|CF015787
EST:     GAAGATGGTCGGACCAGGCCTCTACACCGAGATCGGCAAGAAGACCAGGG                         ATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCT
genomic: GAAGATGGTCGGACCAGGCCTCTACACCGAGATCGGCAAGAAGACCAGGGgtgggtgccc ... tttttcgcagATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCT
EST: gi|211283570|gb|FL005703.1|FL005703
EST:     GAAGATGGTCGGACCAGGCCTCTACACCGAGATCGGCAAGAAGACCAGGG                         ATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCT
genomic: GAAGATGGTCGGACCAGGCCTCTACACCGAGATCGGCAAGAAGACCAGGGgtgggtgccc ... tttttcgcagATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCT
EST: gi|32912387|gb|CF017199.1|CF017199
EST:     GAAGATGGTCGGACCAGGCCTCTACACCGAGATCGGCAAGAAGACCAGGG                         ATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCT
genomic: GAAGATGGTCGGACCAGGCCTCTACACCGAGATCGGCAAGAAGACCAGGGgtgggtgccc ... tttttcgcagATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCT
EST: gi|31355357|gb|CD439714.1|CD439714
EST:     GAAGATGGTCGGACCAGGCCTCTACACCGAGATCGGCAAGAAGACCAGGG                         ATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCT
genomic: GAAGATGGTCGGACCAGGCCTCTACACCGAGATCGGCAAGAAGACCAGGGgtgggtgccc ... tttttcgcagATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCT
EST: gi|211281772|gb|FL005701.1|FL005701
EST:     GAAGATGGTCGGACCAGGCCTCTACACCGAGATCGGCAAGAAGACCAGGG                         ATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCT
genomic: GAAGATGGTCGGACCAGGCCTCTACACCGAGATCGGCAAGAAGACCAGGGgtgggtgccc ... tttttcgcagATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCT
EST: gi|32936145|gb|CF040957.1|CF040957
EST:     GAAGATGGTCGGACCAGGCCTCTACACCGAGATCGGCAAGAAGACCAGGG                         ATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCT
genomic: GAAGATGGTCGGACCAGGCCTCTACACCGAGATCGGCAAGAAGACCAGGGgtgggtgccc ... tttttcgcagATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCT

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: 949

GCAGCATCTCCACGCCGCCACACCTCGTCGCGTCGCGTCGTCTCCGCCGAGAAGATGGTCGGACCAGGCCTCTACACCGAGATCGGCAAGAAGACCAGGGgtgggtgccc ... tttttcgcagATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 618

GCAGCATCTCCACGCCGCCACACCTCGTCGCGTCGCGTCGTCTCCGCCGAGAAGATGGTCGGACCAGGCCTCTACACCGAGATCGGCAAGAAGACCAGGGgtgggtgccc ... tttttcgcagATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 307

GCAGCATCTCCACGCCGCCACACCTCGTCGCGTCGCGTCGTCTCCGCCGAGAAGATGGTCGGACCAGGCCTCTACACCGAGATCGGCAAGAAGACCAGGGgtgggtgccc ... tttttcgcagATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 914

GCAGCATCTCCACGCCGCCACACCTCGTCGCGTCGCGTCGTCTCCGCCGAGAAGATGGTCGGACCAGGCCTCTACACCGAGATCGGCAAGAAGACCAGGGgtgggtgccc ... tttttcgcagATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtttattctcttttgttggtttggttatcattttcggttcgtttttttcgcagATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTT
                                       ttcgtttttttcgc  CT-rich tract
                          ttatcatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgggtgcccgtccatctcgccttccttccccacggattcctttcatcctctggggatcatgggtggagttcgctagtttattctcttttgttggtttggttatcattttcggttcgtttttttcgcagATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC