Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGAGTTTCAGCTGGCGCTGTTCAAGACTAATAAGAAGGAAAGTTTGTTTGCTGATCGGgtaaggctactttgcatactgtttctgttatgctctttgtactttgtagttgtccaatgaaaaatattgtagcactattagtagtattcagtcatgatca...

Basic information

species Zea mays
transcript GRMZM2G112672_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G112672_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g42840.1 (Oryza sativa), 5'ss of exon 3
GAGGAGTTTCAGCTGGCGCTGTTCAAGACTAATAAGAAGGAAAGTTTGTTTGCTGATCGGgtaaggctactttgcatactgtttctgttatgctctttgtactttgtagttgtcca-atgaaaaatattgtagcactattagtagtattcagtcatgatca
|||||||||||| |||||||||||||||| || |||||||| ||||| |||||||| || ||||| | |      |||    ||   |           ||   ||||  |||| | ||   || |    |   | ||| |      ||  || ||| || 
GAGGAGTTTCAGTTGGCGCTGTTCAAGACCAACAAGAAGGAGAGTTTATTTGCTGACCGTgtaagaccaacaataatataacttgcctaccatggaaaatatcctgtaactgtctacatttgaagtgaaatca-attatgaaattagtttggttatgctct

upper sequence: GRMZM2G112672_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA18G08230.1 (Glycine max), 5'ss of exon 5
GAGGAGTTTCAGCTGGCGCTGTTCAAGACTAATAAGAAGGAAAGTTTGTTTGCTGATCGGgtaaggctact-ttgcatactgtt-tctgttatgc---tctttgtactttgtagttgtccaatgaaaaatattgtagcactattag--tagtattcagtcatgatca
 | ||||||||| ||||  |||||||||| ||||| || |||||| |||||||||||||||||  |||    || | |  | || | | ||||||   | ||| ||| ||| ||      |||      |    | |  |||| ||  || ||| ||  ||      
-AAGAGTTTCAGTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTGCTGATCGGGtattgctttcatttctttttattgttttttatgcaaatatttttaccttgaagcatgaaaatctct--ttccatggtcctatcaggttaatatccacacaga----

upper sequence: GRMZM2G112672_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA08G44580.1 (Glycine max), 5'ss of exon 4
GAGGAGTTTCAGCTGGCGCTGTTCAAGACTAATAAGAAGGAAAGTTTGTTTGCTGATCGGgtaaggctactttgcatactgtttctgttatgctctttgtactttgtagttgtccaatgaaaaatattgtagcactattagtagtattcagt-catgatca-
|| ||||||||| ||||  |||||||||| ||||| || |||||| |||||||||||||||||  |||  ||||  |  | ||  |||| |  | |    |  |  |     |  |     |||   | |  || |  |  ||  |   |     || |   
GAAGAGTTTCAGTTGGCTTTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTGCTGATCGGgtattgct--tttgtttctttttattgtttttttatgcaaatatctttaccttgaagcatgaaaatctctttcattggtcataaaaaagaaagtctgtttgc

upper sequence: GRMZM2G112672_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT5G55990.1 (Arabidopsis thaliana), 5'ss of exon 5
GAGGAGTTTCAGCTGGCGCTGTTCAAGACTAATAAGAAGGAAAGTTTGTTTGCTGATCGGgtaaggctactttgcatactgtttctgttatgctctttgtactttgtagttgtccaatgaaaaatattgtagcactattagtagtattcagtcatgatca---
|| ||||||||| ||||  |||| ||||| ||||| || || ||||||||||| |||||||||| | | ||||    ||  | |  |   || ||||   |     |  ||||| ||    || | | | || | |  | | | |||    |  || |     
GAAGAGTTTCAGTTGGCTTTGTTTAAGACAAATAAAAAAGAGAGTTTGTTTGCAGATCGGgtaatgtttctttcttcacattataag---tgttctta--aacccatttttgtc-aagatcaagtttagaagaaatgct-gaaatatgtgattttgtttctag

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|5846848|gb|AI999931.1|AI999931
EST:     AGTTGGCGCTGTTCAAGACTAATAAGAAGGAAAGTTTGTTTGCTGATCGG                         GTATTTGACTTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAA
genomic: AGCTGGCGCTGTTCAAGACTAATAAGAAGGAAAGTTTGTTTGCTGATCGGgtaaggctac ... gttcttgcagGTATTTGACTTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAA
EST: gi|60354409|gb|DN221382.1|DN221382
EST:     AGCTGGCGCTGTTCAAGACTAATAAGAAGGAAAGTTTGTTTGCTGATCGG                         GTATTTGACTTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAA
genomic: AGCTGGCGCTGTTCAAGACTAATAAGAAGGAAAGTTTGTTTGCTGATCGGgtaaggctac ... gttcttgcagGTATTTGACTTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAA
EST: gi|6194508|gb|AW146612.1|AW146612
EST:     AGTTGGCGCTGTTCAAGACTAATAAGAAGGAAAGTTTGTTTGCTGATCGG                         GTATTTGACTTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAA
genomic: AGCTGGCGCTGTTCAAGACTAATAAGAAGGAAAGTTTGTTTGCTGATCGGgtaaggctac ... gttcttgcagGTATTTGACTTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAA
EST: gi|211071789|gb|FK958795.1|FK958795
EST:     AGTTGGCGCTGTTCAAGACTAATAAGAAGGAAAGTTTGTTTGCTGATCGG                         GTATTTGACTTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAA
genomic: AGCTGGCGCTGTTCAAGACTAATAAGAAGGAAAGTTTGTTTGCTGATCGGgtaaggctac ... gttcttgcagGTATTTGACTTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAA
EST: gi|9952360|gb|BE638943.1|BE638943
EST:     AGTTGGCGCTGTTCAAGACTAATAAGAAGGAAAGTTTGTTTGCTGATCGG                         GTATTTGACTTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAA
genomic: AGCTGGCGCTGTTCAAGACTAATAAGAAGGAAAGTTTGTTTGCTGATCGGgtaaggctac ... gttcttgcagGTATTTGACTTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAA
EST: gi|211483288|gb|FL326631.1|FL326631
EST:     TGTTTGCTGATCGG                         GTATTTGACTTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAA
genomic: TGTTTGCTGATCGGgtaaggctac ... gttcttgcagGTATTTGACTTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAA
EST: gi|211071790|gb|FK958796.1|FK958796
EST:     AGTTGGCGCTGTTCAAGACTAATAAGAAGGAAAGTTTGTTTGCTGATCGG                         GTATTTGACTTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAA
genomic: AGCTGGCGCTGTTCAAGACTAATAAGAAGGAAAGTTTGTTTGCTGATCGGgtaaggctac ... gttcttgcagGTATTTGACTTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAA
EST: gi|5325037|gb|AI783228.1|AI783228
EST:     AGTTGGCGCTGTTCAAGACTAATAAGAAGGAAAGTTTGTTTGCTGATCGG                         GTATTTGACTTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAA
genomic: AGCTGGCGCTGTTCAAGACTAATAAGAAGGAAAGTTTGTTTGCTGATCGGgtaaggctac ... gttcttgcagGTATTTGACTTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAA

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: 45 (upstream exon), 49 (downstream exon)
Score: 89

GAGGAGTTTCAGCTGGCGCTGTTCAAGACTAATAAGAAGGAAAGTTTGTTTGCTGATCGGgtaaggctac ... gttcttgcagGTATTTGACTTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAATTTGCTCGGGCGCTCTCAGTATTTCATCCCAATGCTCCCTTGGATGAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 126

GAGGAGTTTCAGCTGGCGCTGTTCAAGACTAATAAGAAGGAAAGTTTGTTTGCTGATCGGgtaaggctac ... gttcttgcagGTATTTGACTTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAATTTGCTCGGGCGCTCTCAGTATTTCATCCCAATGCTCCCTTGGATGAGA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 124

GAGGAGTTTCAGCTGGCGCTGTTCAAGACTAATAAGAAGGAAAGTTTGTTTGCTGATCGGgtaaggctac ... gttcttgcagGTATTTGACTTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAATTTGCTCGGGCGCTCTCAGTATTTCATCCCAATGCTCCCTTGGATGAGA


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 116

GAGGAGTTTCAGCTGGCGCTGTTCAAGACTAATAAGAAGGAAAGTTTGTTTGCTGATCGGgtaaggctac ... gttcttgcagGTATTTGACTTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAATTTGCTCGGGCGCTCTCAGTATTTCATCCCAATGCTCCCTTGGATGAGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGGAGTTTCAGCTGGCGCTGTTCAAGACTAATAAGAAGGAAAGTTTGTTTGCTGATCGGgtaaggctactttgcatactgtttctgttatgctctttgtactttgtagttgtccaatgaaaaatattgtagcactattagtagtattcagtcatgatca

- - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT