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

ATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTTgtaagtcctccgctcctttcaaaacacccctcctcttccgcacttcctcagcctcggtcctcgtggtactgcgttgctttgcagtgatttcgtcggactg...

Basic information

species Zea mays
transcript GRMZM2G146670_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G146670_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA09G37570.1 (Glycine max), 5'ss of exon 2
ATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTTgtaagtcctccgctcctttcaaaacacccctcctcttccgcacttcctcagcctcggtcctcgtggtactgcgttgctttgcagtgatttcgtcggactg----
||||||||| |||||||||||| |  ||||| ||||||||| |||| ||||||    ||| ||| ||||| |||  |    |  |||  || |   |    | |   ||||   | ||      |   | |   |  ||  ||||| |   ||  | |  | |||       
ATCTGCTGTTCAAGGACTACCACAGTGACCAGAAGTTCACCATCACCACCTACTCACCCACTGGAGTTgtgagtgtttt--ttttttttaatctttcaatttttgtggcacaaacacaatgcatggaatgggtat-ttgttttgctgttgggtt-tgttattggatgttctt
















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:     ACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTT                         GCTGTCACTGCTACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATC
genomic: ACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTTgtaagtcctc ... tttcatgcagGCTGTCACTGCTACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATC
EST: gi|31354274|gb|CD438631.1|CD438631
EST:     ACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTC                         GCTGTCACTGCTACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATC
genomic: ACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTTgtaagtcctc ... tttcatgcagGCTGTCACTGCTACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATC
EST: gi|211283575|gb|FL005708.1|FL005708
EST:     ACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTC                         GCTGTCACTGCTACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATC
genomic: ACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTTgtaagtcctc ... tttcatgcagGCTGTCACTGCTACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATC
EST: gi|211283569|gb|FL005702.1|FL005702
EST:     ACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTC                         GCTGTCACTGCTACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATC
genomic: ACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTTgtaagtcctc ... tttcatgcagGCTGTCACTGCTACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATC
EST: gi|32910365|gb|CF015177.1|CF015177
EST:     ACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTT                         GCTGTCACTGCTACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATC
genomic: ACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTTgtaagtcctc ... tttcatgcagGCTGTCACTGCTACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATC
EST: gi|32945222|gb|CF050041.1|CF050041
EST:     ACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTT                         GCTGTCACTGCTACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATC
genomic: ACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTTgtaagtcctc ... tttcatgcagGCTGTCACTGCTACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATC
EST: gi|33093487|gb|CF053481.1|CF053481
EST:     ACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTT                         GCTGTCACTGCTACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATC
genomic: ACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTTgtaagtcctc ... tttcatgcagGCTGTCACTGCTACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATC
EST: gi|13562162|gb|BG550382.1|BG550382
EST:     ACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTT                         GCTGTCACTGTTACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATC
genomic: ACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTTgtaagtcctc ... tttcatgcagGCTGTCACTGCTACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATC
EST: gi|32915544|gb|CF020356.1|CF020356
EST:     ACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTT                         GCTGTCACTGCTACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATC
genomic: ACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTTgtaagtcctc ... tttcatgcagGCTGTCACTGCTACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATC
EST: gi|32917034|gb|CF021846.1|CF021846
EST:     ACCAGACGGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTT                         GCCGTCACTGCTACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATC
genomic: ACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTTgtaagtcctc ... tttcatgcagGCTGTCACTGCTACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATC
EST: gi|32913382|gb|CF018194.1|CF018194
EST:     ACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTT                         GCTGTCACTGCTACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATC
genomic: ACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTTgtaagtcctc ... tttcatgcagGCTGTCACTGCTACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATC
EST: gi|211283572|gb|FL005705.1|FL005705
EST:     ACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTT                         GCTGTCACTGCTACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATC
genomic: ACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTTgtaagtcctc ... tttcatgcagGCTGTCACTGCTACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATC
EST: gi|211283577|gb|FL005710.1|FL005710
EST:     ACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTT                         GCTGTCACTGCTACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATC
genomic: ACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTTgtaagtcctc ... tttcatgcagGCTGTCACTGCTACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATC
EST: gi|31354722|gb|CD439079.1|CD439079
EST:     ACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTC                         GCTGTCACTGCTACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATC
genomic: ACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTTgtaagtcctc ... tttcatgcagGCTGTCACTGCTACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATC
EST: gi|15208686|gb|BI430570.1|BI430570
EST:     ACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTC                         GCTGTCACTGCTACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATC
genomic: ACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTTgtaagtcctc ... tttcatgcagGCTGTCACTGCTACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATC
EST: gi|211283576|gb|FL005709.1|FL005709
EST:     ACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTC                         GCTGTCACTGCTACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATC
genomic: ACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTTgtaagtcctc ... tttcatgcagGCTGTCACTGCTACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATC
EST: gi|211281770|gb|FL005699.1|FL005699
EST:     ACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTC                         GCTGTCACTGCTACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATC
genomic: ACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTTgtaagtcctc ... tttcatgcagGCTGTCACTGCTACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATC
EST: gi|13557920|gb|BG549276.1|BG549276
EST:     ACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTT                         GCTGTCACTGTTTCTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATC
genomic: ACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTTgtaagtcctc ... tttcatgcagGCTGTCACTGCTACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATC
EST: gi|74243487|gb|DT651401.1|DT651401
EST:     ACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTT                         GCTGTCACTGCTACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATC
genomic: ACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTTgtaagtcctc ... tttcatgcagGCTGTCACTGCTACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATC
EST: gi|211283573|gb|FL005706.1|FL005706
EST:     ACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTC                         GCTGTCACTGCTACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATC
genomic: ACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTTgtaagtcctc ... tttcatgcagGCTGTCACTGCTACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATC
EST: gi|30307135|gb|CD001808.1|CD001808
EST:     ACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTT                         GCTGTCACTGCTACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATC
genomic: ACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTTgtaagtcctc ... tttcatgcagGCTGTCACTGCTACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATC
EST: gi|33094138|gb|CF054132.1|CF054132
EST:     ACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTT                         GCTGTCACTGCTACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATC
genomic: ACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTTgtaagtcctc ... tttcatgcagGCTGTCACTGCTACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATC
EST: gi|32910975|gb|CF015787.1|CF015787
EST:     ACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTT                         GCTGTCACTGCTACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATC
genomic: ACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTTgtaagtcctc ... tttcatgcagGCTGTCACTGCTACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATC
EST: gi|211283570|gb|FL005703.1|FL005703
EST:     ACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTC                         GCTGTCACTGCTACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATC
genomic: ACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTTgtaagtcctc ... tttcatgcagGCTGTCACTGCTACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATC
EST: gi|32912387|gb|CF017199.1|CF017199
EST:     ACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTT                         GCTGTCACTGCTACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATC
genomic: ACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTTgtaagtcctc ... tttcatgcagGCTGTCACTGCTACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATC
EST: gi|20208325|gb|BQ134414.1|BQ134414
EST:     ACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTT                         GCTGTCACTGCTACTAGCACAAAGATTGCTGACCTGATCTTCAGTGAGATC
genomic: ACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTTgtaagtcctc ... tttcatgcagGCTGTCACTGCTACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATC
EST: gi|31355357|gb|CD439714.1|CD439714
EST:     ACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTC                         GCTGTCACTGCTACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATC
genomic: ACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTTgtaagtcctc ... tttcatgcagGCTGTCACTGCTACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATC
EST: gi|211281772|gb|FL005701.1|FL005701
EST:     ACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTT                         GCTGTCACTGCTACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATC
genomic: ACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTTgtaagtcctc ... tttcatgcagGCTGTCACTGCTACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATC
EST: gi|32936145|gb|CF040957.1|CF040957
EST:     ACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTT                         GCTGTCACTGCTACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATC
genomic: ACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTTgtaagtcctc ... tttcatgcagGCTGTCACTGCTACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATC

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: 820

ATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTTgtaagtcctc ... tttcatgcagGCTGTCACTGCTACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATCCATTCACAGATAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 683

ATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTTgtaagtcctc ... tttcatgcagGCTGTCACTGCTACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATCCATTCACAGATAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 369

ATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTTgtaagtcctc ... tttcatgcagGCTGTCACTGCTACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATCCATTCACAGATAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 699

ATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTTgtaagtcctc ... tttcatgcagGCTGTCACTGCTACTAGCACAAAGAAAGCTGACCTGATCTTCAGTGAGATCCATTCACAGATAAAGAACAAGAACATGACCGTAGATGTGAAAGCAAACT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCTGCTGTACAAGGACTACCAGACAGACCACAAGTTCACCCTCACTACCTACAGCTCCAATGGCGTTgtaagtcctccgctcctttcaaaacacccctcctcttccgcacttcctcagcctcggtcctcgtggtactgcgttgctttgcagtgatttcgtcggactg

- - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctccgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cccctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctcagcc