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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACGGATCACTCCAAGGTCATTGGACATATTAACTAAAGGACCTCCTGTTTGTGGAGACCTTGCTGTATCATTATCTCAAGCAGGACCTCAGTTTACCCAAgtgagcttgttctttgctcttattgatagcttctttttcgcctgagctaatgcatcttccctaattgttttag

Basic information

species Zea mays
transcript GRMZM2G150772_T02
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G150772_T02 (Zea mays), 5'ss of exon 20
lower sequence: LOC_Os09g24260.1 (Oryza sativa), 5'ss of exon 20
ACGGATCACTCCAAGGTCATTGGACATATTAACTAAAGGACCTCCTGTTTGTGGAGACCTTGCTGTATCATTATCTCAAGCAGGACCTCAGTTTACCCAAgtgagcttgttctttgctcttattgatagctt----ctttttcgcctgagctaatgcatcttccctaattgttttag
|||  |||||||||||||| ||||||||||| |||||||||| |||||||||||||| |||||||||||| |||| |||||||| ||||||||||||||||| |||||  ||| ||||| || | ||   ||    || ||| || ||| ||||| | |  | ||  |||||||   
ACGTGTCACTCCAAGGTCACTGGACATATTAGCTAAAGGACCCCCTGTTTGTGGAGATCTTGCTGTATCACTATCCCAAGCAGGCCCTCAGTTTACCCAAgtaagcttaatctgtgctcataatcatccttttgttctcttttgcttgatctaatactttcttccatattgtttag-

upper sequence: GRMZM2G150772_T02 (Zea mays), 5'ss of exon 20
lower sequence: GLYMA01G39110.1 (Glycine max), 5'ss of exon 21
ACGGATCACTCCAAGGTCATTGGACATATTAACTAAAGGACCTCCTGTTTGTGGAGACCTTGCTGTATCATTATCTCAAGCAGGACCTCAGTTTACCCAAgtgagcttgttctttgctcttattgatagcttctttttcgcctgagctaat--gcatcttccctaattgttttag
 || || || || ||||| ||||||||  || ||| |||  ||||||||||||||||| | ||||| ||||||||||||  ||| || || || ||||| || || |  |    | ||||   |  |   || |  |    |||| ||  |  | || ||   |  |    | ||
GCGCATAACACCTAGGTCTTTGGACATCCTAGCTAGAGGTTCTCCTGTTTGTGGAGACTTAGCTGTGTCATTATCTCAATTAGGTCCACATTTCACCCAGgtaag-tgatagaattctctgtctttttagttttggtctatctgatcttctaaggatgttgagttttgacatcag

upper sequence: GRMZM2G150772_T02 (Zea mays), 5'ss of exon 20
lower sequence: AT3G50590.1 (Arabidopsis thaliana), 5'ss of exon 22
ACGGATCACTCCAAGGTCATTGGACATATTAACTAAAGGACCTCCTGTTTGTGGAGACCTTGCTGTATCATTATCTCAAGCAGGACCTCAGTTTACCCAAgtgagctt-gttctttgctcttattgatagcttctttttcgcctgagctaatgcatcttccctaattgttttag---------
 || || |||||||| ||  | || ||  |  ||| | |  |||| || |||||||| |||||||||||| || |||||||||| ||||| || | ||| |||||    ||||  |     |  |||      || |  | |   || |      |||| |  ||  |||||           
GCGAATTACTCCAAGATCTCTTGATATTCTTGCTAGAAGCGCTCCAGTATGTGGAGATCTTGCTGTATCACTAGCTCAAGCAGGCCCTCAATTCAACCAGgtgagtcgagttcagtagatcttatgaccagaactctcccccagaagatgtgttctcttactaaacggttttgaaaaaattag

upper sequence: GRMZM2G150772_T02 (Zea mays), 5'ss of exon 20
lower sequence: Vv00s1501g00010.t01 (Vitis vinifera), 5'ss of exon 4
ACGGATCACTCCAAGGTCATTGGACATATTAACTAAAGGACCTCCTGTTTGTGGAGACCTTGCTGTATCATTATCTCAAGCAGGACCTCAGTTTACCCAAgtgagct-tgttctttgctctta--ttgatagcttctttttcgcctgagctaatgcatcttccctaattgttttag----------
 || || ||||| |||||  | || ||  |   || ||| ||||||||||||||||| || ||||| |||||||| |||||| | || ||||| || || ||| ||| || | | ||   | |  ||  |  | | ||||  |  |    |  |  |  |||   | ||||| |            
GCGTATTACTCCGAGGTCTCTTGATATTCTTGGTAGAGGCCCTCCTGTTTGTGGAGATCTAGCTGTGTCATTATCCCAAGCAAGTCCACAGTTCACTCAGgtgggctatggtttgtgtgttaagtttttttccatgttttatgaatttttttttttagtttctgaatttgttgtgaataaaatcag

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|13315888|gb|BG410236.1|BG410236
EST:     GTGGAGACCTTGCTGTATCATTATCTCAAGCAGGACCTCAGTTTACCCAA                         ATCATGCGCTGCAATTATGCAATCAAAGCTCTCCGGTTCTCTACTGCGCTG
genomic: GTGGAGACCTTGCTGTATCATTATCTCAAGCAGGACCTCAGTTTACCCAAgtgagcttgt ... attgttttagATCATGCGCTGCAATTATGCAATCAAAGCTCTCCGGTTCTCTACTGCGCTG
EST: gi|149014442|gb|EE044051.2|EE044051
EST:     GTGGAGACCTTGCTGTATCATTATCTCAAGCAGGACCTCAGTTTACCCAA                         ATCATGCGCTGCAATTATGCAATCAAAGCTCTCCGGTTCTCTACTGCGCTG
genomic: GTGGAGACCTTGCTGTATCATTATCTCAAGCAGGACCTCAGTTTACCCAAgtgagcttgt ... attgttttagATCATGCGCTGCAATTATGCAATCAAAGCTCTCCGGTTCTCTACTGCGCTG
EST: gi|32837707|gb|CD977385.1|CD977385
EST:     GTGGAGACCTTGCTGTATCATTATCTCAAGCAGGACCTCAGTTTACCCAA                         ATCATGCGCTGCAATTATGCAATCAAAGCTCTCCGGTTCTCTACTGCGCTG
genomic: GTGGAGACCTTGCTGTATCATTATCTCAAGCAGGACCTCAGTTTACCCAAgtgagcttgt ... attgttttagATCATGCGCTGCAATTATGCAATCAAAGCTCTCCGGTTCTCTACTGCGCTG
EST: gi|32838041|gb|CD977719.1|CD977719
EST:     TGGAGACC-TGNCTGTATCATTATCTCAAGCAGGACCTCAGTTTACCCAA                         ATCATGCGCTGCAATTATGCAATCAAAGCTCTCCGGTTCTCTACTGCGCTG
genomic: TGGAGACCTTG-CTGTATCATTATCTCAAGCAGGACCTCAGTTTACCCAAgtgagcttgt ... attgttttagATCATGCGCTGCAATTATGCAATCAAAGCTCTCCGGTTCTCTACTGCGCTG

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: 355

ACGGATCACTCCAAGGTCATTGGACATATTAACTAAAGGACCTCCTGTTTGTGGAGACCTTGCTGTATCATTATCTCAAGCAGGACCTCAGTTTACCCAAgtgagcttgt ... attgttttagATCATGCGCTGCAATTATGCAATCAAAGCTCTCCGGTTCTCTACTGCGCTGTCAATTTTGAAAGATGAGTTCCTGCGCTCCAGAGATTATCCTCAATGCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 293

ACGGATCACTCCAAGGTCATTGGACATATTAACTAAAGGACCTCCTGTTTGTGGAGACCTTGCTGTATCATTATCTCAAGCAGGACCTCAGTTTACCCAAgtgagcttgt ... attgttttagATCATGCGCTGCAATTATGCAATCAAAGCTCTCCGGTTCTCTACTGCGCTGTCAATTTTGAAAGATGAGTTCCTGCGCTCCAGAGATTATCCTCAATGCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 278

ACGGATCACTCCAAGGTCATTGGACATATTAACTAAAGGACCTCCTGTTTGTGGAGACCTTGCTGTATCATTATCTCAAGCAGGACCTCAGTTTACCCAAgtgagcttgt ... attgttttagATCATGCGCTGCAATTATGCAATCAAAGCTCTCCGGTTCTCTACTGCGCTGTCAATTTTGAAAGATGAGTTCCTGCGCTCCAGAGATTATCCTCAATGCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 385

ACGGATCACTCCAAGGTCATTGGACATATTAACTAAAGGACCTCCTGTTTGTGGAGACCTTGCTGTATCATTATCTCAAGCAGGACCTCAGTTTACCCAAgtgagcttgt ... attgttttagATCATGCGCTGCAATTATGCAATCAAAGCTCTCCGGTTCTCTACTGCGCTGTCAATTTTGAAAGATGAGTTCCTGCGCTCCAGAGATTATCCTCAATGCC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACGGATCACTCCAAGGTCATTGGACATATTAACTAAAGGACCTCCTGTTTGTGGAGACCTTGCTGTATCATTATCTCAAGCAGGACCTCAGTTTACCCAAgtgagcttgttctttgctcttattgatagcttctttttcgcctgagctaatgcatcttccctaattgttttag

- - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA