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

GGCAAAAAACAGGGGGGCAGGAACTTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAGgtaaatttggggatcatatggcatgtgatagtcatattattgaattttgcatcttcaaaggatttgtagttattattaaacacacaaatatgaacaccatgtttcattgcagactgtttctcttgcag

Basic information

species Zea mays
transcript GRMZM2G023528_T05
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G023528_T03 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g03740.1 (Oryza sativa), 5'ss of exon 4
GGCAAAAAACAGGGGGGCAGGAACTTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAGgtaaatttggggatcatatggcatgt--gatagtcatattattgaattttgcatcttcaaaggatttgtagttattattaaacacacaaatatgaacaccatgtttcattgcagactgtttctcttgcag
| |||||| | || || ||||| ||| |||||||| |||||||||| |||||||| |||||||||||||| ||||||| |||| ||||| | |    |||  ||| | |  |  | |      |     ||| |  |  |  |   | |||||  |      |  ||||| ||     |   ||||||                
GCCAAAAATCCGGAGGTCAGGAGCTTATTGGAGGACTAGATTGTACTGTCCACCGGAACTTTTTTGGGAGCCAGgtaactttgaggatcgtgttctctgtttgatggccggagcagttttcactatcatttctattgtctcttcaattttattttatttttgag-atgaatac---actctcttgcag----------------

upper sequence: GRMZM2G023528_T03 (Zea mays), 5'ss of exon 4
lower sequence: Vv06s0004g03000.t01 (Vitis vinifera), 5'ss of exon 4
GGCAAAAAACAGGGGGGCAGGAACTTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAGgtaaatttggggatcatatggcatgtgatagtcatattattgaattttgcatcttcaaaggatttgtagttattattaaacacacaaatatgaacaccatgtttcattgcagactgtttctcttgcag
| || |||||||| ||||||||||| ||||| ||  | ||||||||||| ||||| ||||| ||||| ||||||||||   |    ||  | || | | |||   || | ||| ||    |  ||     |||   || ||| ||   |  |  || | |||| | || | ||   |    ||                   
GACAGAAAACAGGTGGGCAGGAACTAGTTGGGGGCCTTGATTGTACAGTTCACCGGAACTTCTTTGGCAGTCAGgtaatgatatacattctgtgtcct-tgact-tcgtcttactg----tcacaaagataaaatgtt-gta-ttgaaaacatgcaaaaaaat-taaaaatcaaactgatatg-------------------
















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|50327771|gb|CO522897.1|CO522897
EST:     TTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAG                         CTTCAAAGCTTTGAGACAGAGCTTTCCGTGCCAAAGCTTTCGGAGAAGGAA
genomic: TTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAGgtaaatttgg ... tctcttgcagCTTCAAAGCTTTGAGACAGAGCTTTCCGTGCCAAAGCTTTCGGAGAAGGAA
EST: gi|6020368|gb|AW065296.1|AW065296
EST:     TTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAG                         CTTCAAAGCTTTGAGACAGAGCTTTCCGTGCCAAAGCTTTCGGAGAAGGAA
genomic: TTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAGgtaaatttgg ... tctcttgcagCTTCAAAGCTTTGAGACAGAGCTTTCCGTGCCAAAGCTTTCGGAGAAGGAA
EST: gi|71318383|gb|DR795955.1|DR795955
EST:     TTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAG                         CTTCAAAGCTTTGAGACAGAGCTTTCCGTGCCAAAGCTTTCGGAGAAGGAA
genomic: TTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAGgtaaatttgg ... tctcttgcagCTTCAAAGCTTTGAGACAGAGCTTTCCGTGCCAAAGCTTTCGGAGAAGGAA
EST: gi|5895630|gb|AW036876.1|AW036876
EST:     TTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAG                         CTTCAAAGCTTTGAGACAGAGCTTTCCGTGCCAAAGCTTTCGGAGAAGGAA
genomic: TTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAGgtaaatttgg ... tctcttgcagCTTCAAAGCTTTGAGACAGAGCTTTCCGTGCCAAAGCTTTCGGAGAAGGAA
EST: gi|32934367|gb|CF039179.1|CF039179
EST:     CAGTCCACCGAAACTTTTTTGGGAGTCAG                         CTTCAAAGCTTTGAGACAGAGCTTTCGGTGCCAAAGCTTTCGGAGAAGGAA
genomic: CAGTCCACCGAAACTTTTTTGGGAGTCAGgtaaatttgg ... tctcttgcagCTTCAAAGCTTTGAGACAGAGCTTTCCGTGCCAAAGCTTTCGGAGAAGGAA
EST: gi|33467208|gb|CF244257.1|CF244257
EST:     TTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAG                         CTTCAAAGCTTTGAGACAGAGCTTTCCGTGCCAAAGCTTTCGGAGAAGGAA
genomic: TTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAGgtaaatttgg ... tctcttgcagCTTCAAAGCTTTGAGACAGAGCTTTCCGTGCCAAAGCTTTCGGAGAAGGAA
EST: gi|37382875|gb|CF628406.1|CF628406
EST:     ACCGAAAC-TTTTTGGGAGTCAG                         CTTCAAAGCTTTGAGACAGAGCTTTCGGTGCCAAAGCTTTCGGAGAAGGAA
genomic: ACCGAAACTTTTTTGGGAGTCAGgtaaatttgg ... tctcttgcagCTTCAAAGCTTTGAGACAGAGCTTTCCGTGCCAAAGCTTTCGGAGAAGGAA
EST: gi|74233030|gb|DT640944.1|DT640944
EST:     TTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAG                         CTTCAAAGCTTTGAGACAGAGCTTTCCGTGCCAAAGCTTTCGGAGAAGGAA
genomic: TTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAGgtaaatttgg ... tctcttgcagCTTCAAAGCTTTGAGACAGAGCTTTCCGTGCCAAAGCTTTCGGAGAAGGAA
EST: gi|31359368|gb|CD443725.1|CD443725
EST:     TTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAG                         CTTCAAAGCTTTGAGACAGAGCTTTCCGTGCCAAAGCTTTCGGAGAAGGAA
genomic: TTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAGgtaaatttgg ... tctcttgcagCTTCAAAGCTTTGAGACAGAGCTTTCCGTGCCAAAGCTTTCGGAGAAGGAA
EST: gi|40303169|gb|CK347556.1|CK347556
EST:     TTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAG                         CTTCAAAGCTTTGAGACAGAGCTTTCGGTGCCAAAGCTTTCGGAGAAGGAA
genomic: TTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAGgtaaatttgg ... tctcttgcagCTTCAAAGCTTTGAGACAGAGCTTTCCGTGCCAAAGCTTTCGGAGAAGGAA

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), 48 (downstream exon)
Score: 75

GGCAAAAAACAGGGGGGCAGGAACTTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAGgtaaatttgg ... tctcttgcagCTTCAAAGCTTTGAGACAGAGCTTTCCGTGCCAAAGCTTTCGGAGAAGGAAGGAGGGAATGATACATGCCGCGGTGTATTTATACGGGCACCTGCTATAT


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 178

GGCAAAAAACAGGGGGGCAGGAACTTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAGgtaaatttgg ... tctcttgcagCTTCAAAGCTTTGAGACAGAGCTTTCCGTGCCAAAGCTTTCGGAGAAGGAAGGAGGGAATGATACATGCCGCGGTGTATTTATACGGGCACCTGCTATAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 171

GGCAAAAAACAGGGGGGCAGGAACTTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAGgtaaatttgg ... tctcttgcagCTTCAAAGCTTTGAGACAGAGCTTTCCGTGCCAAAGCTTTCGGAGAAGGAAGGAGGGAATGATACATGCCGCGGTGTATTTATACGGGCACCTGCTATAT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 115

GGCAAAAAACAGGGGGGCAGGAACTTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAGgtaaatttgg ... tctcttgcagCTTCAAAGCTTTGAGACAGAGCTTTCCGTGCCAAAGCTTTCGGAGAAGGAAGGAGGGAATGATACATGCCGCGGTGTATTTATACGGGCACCTGCTATAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCAAAAAACAGGGGGGCAGGAACTTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAGgtaaatttggggatcatatggcatgtgatagtcatattattgaattttgcatcttcaaaggatttgtagttattattaaacacacaaatatgaacaccatgtttcattgcagactgtttctcttgcag

- - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - GAGGAT