Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTAGCGATAGATTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATTgtaagtaccctattctttttgtaacaaatcatgttactgaattatatgacattaccgcttaatgttttccttatttacag

Basic information

species Zea mays
transcript GRMZM2G106574_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G106574_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os08g34480.1 (Oryza sativa), 5'ss of exon 3
GCTAGCGATAGATTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATTgtaagtaccctattctttt---tgtaacaaatcatgttactga-attatatgacattaccgcttaatgttttccttatttacag
|||||||| || ||||||||||| ||||| ||||||||||||||||| |||||||| || |||||||||||||| |||  | |||||||||||     || |      |  |  |||   ||||  ||  | | ||  |  |||    | |   |||   |||||  |||
GCTAGCGACAGGTTCAACATAAATTCTCAACTTGAGCATCTTCAAGCGAAATATGTGGGCACAGGGCATGCTGACTTGAATCGATTgtaagtatatctttttccaaaataaacaaaaatgtgttgttgggaatgtagtaacttagtattgaggatttcttttatt-gcag

upper sequence: GRMZM2G106574_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA08G40200.1 (Glycine max), 5'ss of exon 2
GCTAGCGATAGATTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATTgtaagtaccctattctttttgtaacaaatcatgttactgaattatatgacattaccgcttaatgttttccttatttacag------------------
|| || ||||| || ||||| || || |||||||||||||| ||||||||||||||||| || || ||||| ||||||   ||||||| |||  |    ||| |   |        || ||       | | | | ||||    ||||   |||  || | |                      
GCCAGTGATAGGTTTAACATCAATTCCCAGCTTGAGCATCTCCAAGCCAAATATGTTGGAACTGGCCATGCCGATTTGAACAGATTgtgagtttctctctctctcccttttccccaattttttgtttatttttaaaattatttgttaaccgtttgtttttctttgtgtgcgtgtgtgtgtgcag

upper sequence: GRMZM2G106574_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA18G17590.1 (Glycine max), 5'ss of exon 2
GCTAGCGATAGATTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATTgtaagtaccctattctttttgtaacaaatcatgttactgaattatatgacattaccgcttaatgttttccttatttacag-----------------
||||| ||||| || ||||| || |||||||| |||||||| ||||||||||||||||| || || ||||||||||||   ||||||| |||   ||  ||| | |    ||| |  | ||  | | ||   | | | ||    ||||| ||||  || |||   |                 
GCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCAAATATGTTGGAACTGGCCATGCTGATTTGAACAGATTgtgagttttct-ctctctcttccccaattttttttgttaattt---taaaactatttattaatcttttttttcttttgcgtgggtgtgtgtctgcag

upper sequence: GRMZM2G106574_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT3G23325.1 (Arabidopsis thaliana), 5'ss of exon 2
GCTAGCGATAGATTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATTgtaagtaccctattctttttgt---aacaaatcatgttactgaattatatgacattaccgcttaatgttttccttatttacag-----
|| || ||||| || |||||||| ||||||||||||||||||||||| || |||||||||||||| ||||| ||||||   ||||||||||||   |   ||||||||    |    ||| | | |  || | | |||  |||  |   ||  ||||   | |||         
GCAAGTGATAGGTTTAACATAAATTCTCAGCTTGAGCATCTTCAAGCTAAGTATGTTGGTACAGGTCATGCAGATTTGAGCAGATTgtaagtatttttcactttttgtttggatttttcaggattccaaaat-tgtgaacttattg---aaaattttgaatgtttttgtgttag

upper sequence: GRMZM2G106574_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT4G14342.1 (Arabidopsis thaliana), 5'ss of exon 2
GCTAGCGATAGATTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATTgtaagtaccctattctttttgtaacaaatcatgttactgaattatatgacattaccgcttaat-gttttccttatttacag-------
|| || ||||| || ||||| || ||||||||||||||||||||||| ||||||||||| || || ||||||||||||  |||||||| |||  | | |  |||| ||    ||   | |   || ||| | |    |  |  || | | ||     |  |||| |        
GCAAGTGATAGGTTTAACATCAATTCTCAGCTTGAGCATCTTCAAGCTAAATATGTTGGAACCGGTCATGCTGATTTGAGTAGATTgtgagtttcttttgattttagtgttcaaatttttatatgcattgtttttattggctactaatttgtggaattggtttaaatggtacag

upper sequence: GRMZM2G106574_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv05s0049g01230.t01 (Vitis vinifera), 5'ss of exon 2
GCTAGCGATAGATTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATTgtaagtaccctattctttttgtaacaaatcatgttactgaatt-atatgacattaccgcttaatgttttccttatttacag----
|| || ||||| || || || ||||| |||||||||||||| ||||| ||||||||||| || || |||||||| |||  ||||||||||||| |||||| |||| |       |    | | |  ||| ||| |   ||    ||||   ||    || | |   |    
GCCAGTGATAGGTTTAATATTAACTCCCAGCTTGAGCATCTGCAAGCAAAATATGTTGGAACTGGTCATGCTGACTTGAATAGATTgtaagtaacctattattttagatttggttgtcatcattttatttataggtttttctttcttagatttgatgttttgtgtgggcag

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|32809029|gb|CD961263.1|CD961263
EST:     CATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT                         TGAATGGGCTGTAAACATCCAGAGAGACAGCTATGCCTCTTATATTGGGCA
genomic: CATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATTgtaagtaccc ... ttatttacagTGAATGGGCTGTAAACATCCAGAGAGACAGCTATGCCTCTTATATTGGGCA
EST: gi|14243476|gb|BG841204.2|BG841204
EST:     CATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT                         TGAATGGGCTGTAAACATCCAGAGAGACAGCTATGCCTCTTATATTGGGCA
genomic: CATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATTgtaagtaccc ... ttatttacagTGAATGGGCTGTAAACATCCAGAGAGACAGCTATGCCTCTTATATTGGGCA
EST: gi|76912105|gb|DV164577.1|DV164577
EST:     CATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT                         TGAATGGGCTGTAAACATCCAGAGAGACAGCTATGCCTCTTATATTGGGCA
genomic: CATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATTgtaagtaccc ... ttatttacagTGAATGGGCTGTAAACATCCAGAGAGACAGCTATGCCTCTTATATTGGGCA
EST: gi|4730361|gb|AI649527.1|AI649527
EST:     CATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT                         TGAATGGGCTGTAAACATCCAGAGAGACAGCTATGCCTCTTATATTGGGCA
genomic: CATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATTgtaagtaccc ... ttatttacagTGAATGGGCTGTAAACATCCAGAGAGACAGCTATGCCTCTTATATTGGGCA
EST: gi|32846502|gb|CD986183.1|CD986183
EST:     ACAGGGCATGCTGATTTGTCTAGATT                         TGAATGGGCTGTAAACATCCAGAGAGACAGCTATGCCTCTTATATTGGGCA
genomic: ACAGGGCATGCTGATTTGTCTAGATTgtaagtaccc ... ttatttacagTGAATGGGCTGTAAACATCCAGAGAGACAGCTATGCCTCTTATATTGGGCA
EST: gi|213169581|gb|FM186027.1|FM186027
EST:     CATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT                         TGAATGGGCTGTAAACATCCAGAGAGACAGCTATGCCTCTTATATTGGGCA
genomic: CATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATTgtaagtaccc ... ttatttacagTGAATGGGCTGTAAACATCCAGAGAGACAGCTATGCCTCTTATATTGGGCA
EST: gi|32855389|gb|CD995070.1|CD995070
EST:     CATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT                         TGAATGGGCTGTAAACATCCAGAGAGACAGCTATGCCTCTTATATTGGGCA
genomic: CATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATTgtaagtaccc ... ttatttacagTGAATGGGCTGTAAACATCCAGAGAGACAGCTATGCCTCTTATATTGGGCA
EST: gi|32809049|gb|CD961283.1|CD961283
EST:     CATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT                         TGAATGGGCTGTAAACATCCAGAGAGACAGCTATGCCTCTTATATTGGGCA
genomic: CATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATTgtaagtaccc ... ttatttacagTGAATGGGCTGTAAACATCCAGAGAGACAGCTATGCCTCTTATATTGGGCA
EST: gi|33285604|gb|CF075399.1|CF075399
EST:     CATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT                         TGAATGGGCTGTAAACATCCAGAGAGACAGCTATGCCTCTTATATTGGGCA
genomic: CATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATTgtaagtaccc ... ttatttacagTGAATGGGCTGTAAACATCCAGAGAGACAGCTATGCCTCTTATATTGGGCA
EST: gi|60338673|gb|DN205646.1|DN205646
EST:     CATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT                         TGAATGGGCTGTAAACATCCAGAGAGACAGCTATGCCTCTTATATTGGGCA
genomic: CATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATTgtaagtaccc ... ttatttacagTGAATGGGCTGTAAACATCCAGAGAGACAGCTATGCCTCTTATATTGGGCA
EST: gi|32806541|gb|CD958775.1|CD958775
EST:     CATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT                         TGAATGGGCTGTAAACATCCAGAGAGACAGCTATGCCTCTTATATTGGGCA
genomic: CATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATTgtaagtaccc ... ttatttacagTGAATGGGCTGTAAACATCCAGAGAGACAGCTATGCCTCTTATATTGGGCA
EST: gi|60358045|gb|DN225018.1|DN225018
EST:     CATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT                         TGAATGGGCTGTAAACATCCAGAGAGACAGCTATGCCTCTTATATTGGGCA
genomic: CATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATTgtaagtaccc ... ttatttacagTGAATGGGCTGTAAACATCCAGAGAGACAGCTATGCCTCTTATATTGGGCA
EST: gi|37391857|gb|CF633173.1|CF633173
EST:     CATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT                         TGAATGGGCTGTAAACATCCAGAGAGACAGCTATGCCTCTTATATTGGGCA
genomic: CATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATTgtaagtaccc ... ttatttacagTGAATGGGCTGTAAACATCCAGAGAGACAGCTATGCCTCTTATATTGGGCA
EST: gi|15080579|gb|BI389110.1|BI389110
EST:     CATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT                         TGAATGGGCTGTAAACATCCAGAGAGACAGCTATGCCTCTTATATTGGGCA
genomic: CATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATTgtaagtaccc ... ttatttacagTGAATGGGCTGTAAACATCCAGAGAGACAGCTATGCCTCTTATATTGGGCA
EST: gi|32907954|gb|CF012767.1|CF012767
EST:     CATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT                         TGAATGGGCTGTAAACATCCAGAGAGACAGCTATGCCTCTTATATTGGGCA
genomic: CATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATTgtaagtaccc ... ttatttacagTGAATGGGCTGTAAACATCCAGAGAGACAGCTATGCCTCTTATATTGGGCA
EST: gi|116819876|gb|EC863043.1|EC863043
EST:     CATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT                         TGAATGGGCTGTAAACATCCAGAGAGACAGCTATGCCTCTTATATTGGGCA
genomic: CATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATTgtaagtaccc ... ttatttacagTGAATGGGCTGTAAACATCCAGAGAGACAGCTATGCCTCTTATATTGGGCA
EST: gi|213179135|gb|FM184923.1|FM184923
EST:     CATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT                         TGAATGGGCTGTAAACATCCAGAGAGACAGCTATGCCTCTTATATTGGGCA
genomic: CATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATTgtaagtaccc ... ttatttacagTGAATGGGCTGTAAACATCCAGAGAGACAGCTATGCCTCTTATATTGGGCA
EST: gi|116829615|gb|EC870229.1|EC870229
EST:     CATCTTCAAGCCAAATATGTTGGTACAGGCCATGCTGATTTGTCTAGATT                         TGAATGGGCTGTAAACATCCAGAGAGACAGCTATGCCTCTTATATTGGGCA
genomic: CATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATTgtaagtaccc ... ttatttacagTGAATGGGCTGTAAACATCCAGAGAGACAGCTATGCCTCTTATATTGGGCA
EST: gi|211218119|gb|FL199938.1|FL199938
EST:     CATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT                         TGAATGGGCTGTAAACATCCAGAGAGACAGCTATGCCTCTTATATTGGGCA
genomic: CATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATTgtaagtaccc ... ttatttacagTGAATGGGCTGTAAACATCCAGAGAGACAGCTATGCCTCTTATATTGGGCA
EST: gi|116824059|gb|EC867648.1|EC867648
EST:     CATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT                         TGAATGGGCTGTAAACATCCAGAGAGACAGCTATGCCTCTTATATTGGGCA
genomic: CATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATTgtaagtaccc ... ttatttacagTGAATGGGCTGTAAACATCCAGAGAGACAGCTATGCCTCTTATATTGGGCA
EST: gi|211218118|gb|FL199937.1|FL199937
EST:     CATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT                         TGAATGGGCTGTAAACATCCAGAGAGACAGCTATGCCTCTTATATTGGGCA
genomic: CATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATTgtaagtaccc ... ttatttacagTGAATGGGCTGTAAACATCCAGAGAGACAGCTATGCCTCTTATATTGGGCA
EST: gi|32807783|gb|CD960017.1|CD960017
EST:     CATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT                         TGAATGGGCTGTAAACATCCAGAGAGACAGCTATGCCTCTTATATTGGGCA
genomic: CATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATTgtaagtaccc ... ttatttacagTGAATGGGCTGTAAACATCCAGAGAGACAGCTATGCCTCTTATATTGGGCA
EST: gi|32932016|gb|CF036828.1|CF036828
EST:     ACAGGGCATGCTGATTTGTCTAGATT                         TGAATGGGCTGTAAACATCCAGAGAGACAGCTATGCCTCTTATATTGGGCA
genomic: ACAGGGCATGCTGATTTGTCTAGATTgtaagtaccc ... ttatttacagTGAATGGGCTGTAAACATCCAGAGAGACAGCTATGCCTCTTATATTGGGCA
EST: gi|33095589|gb|CF055583.1|CF055583
EST:     ACAGGGCATGCTGATTTGTCTAGATT                         TGAATGGGCTGTAAACATCCAGAGAGACAGCTATGCCTCTTATATTGGGCA
genomic: ACAGGGCATGCTGATTTGTCTAGATTgtaagtaccc ... ttatttacagTGAATGGGCTGTAAACATCCAGAGAGACAGCTATGCCTCTTATATTGGGCA

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: 46 (upstream exon), 49 (downstream exon)
Score: 551

GCTAGCGATAGATTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATTgtaagtaccc ... ttatttacagTGAATGGGCTGTAAACATCCAGAGAGACAGCTATGCCTCTTATATTGGGCACTATCCAATGCTAGCATATTTTGCCATTGCTGAGAATGAATCGATCGGA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 420

GCTAGCGATAGATTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATTgtaagtaccc ... ttatttacagTGAATGGGCTGTAAACATCCAGAGAGACAGCTATGCCTCTTATATTGGGCACTATCCAATGCTAGCATATTTTGCCATTGCTGAGAATGAATCGATCGGA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 291

GCTAGCGATAGATTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATTgtaagtaccc ... ttatttacagTGAATGGGCTGTAAACATCCAGAGAGACAGCTATGCCTCTTATATTGGGCACTATCCAATGCTAGCATATTTTGCCATTGCTGAGAATGAATCGATCGGA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 502

GCTAGCGATAGATTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATTgtaagtaccc ... ttatttacagTGAATGGGCTGTAAACATCCAGAGAGACAGCTATGCCTCTTATATTGGGCACTATCCAATGCTAGCATATTTTGCCATTGCTGAGAATGAATCGATCGGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTAGCGATAGATTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATTgtaagtaccctattctttttgtaacaaatcatgttactgaattatatgacattaccgcttaatgttttccttatttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT