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'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atatgcttataatggatttgagttttttgttatgattattagaaaaaaaaacagttactttaaatcaatcatacgtttgtttgttctttctttgcgtcagCATGCTAATGGTGAAAATGCGTGGGTTGGCATTGATGGAAGGAGTGGCGATATCGTTGATATGAAAGAGCGAAAG

Basic information

species Zea mays
transcript GRMZM2G175510_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G175510_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os06g34690.1 (Oryza sativa), 3'ss of exon 12
atatgcttataatggatttgagtttt----ttgttatgattattagaaaaaaaaacagttac-tttaaatcaatc----atacgtttgtttgttctttctttgcgtcagCATGCTAATGGTGAAAATGCGTGGGTTGGCATTGATGGAAGGAGTGGCGATATCGTTGATATGAAAGAGCGAAAG
         || |||  |  |  |||     ||     | || ||   | | ||  | ||   |||  || | |      ||| | | | |     |   ||   ||||||||| ||||||||||||||||||||||||||||| |||||||| || || || ||||| ||||||||||| |||
---------tactgggctctacctttgaacatgcaccaagtagtacttagagaagtaattgtatttgcattactttttgttacctgtttctaaatgtctgttttttcagCATGCAAATGGTGAAAATGCGTGGGTTGGCATTGACGGAAGGAGCGGTGACATTGTTGACATGAAAGAGCGGAAG
















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|74244740|gb|DT652654.1|DT652654
EST:     AAAATTGTGGTTTGAATGTTATTAGGATAATGACACAACTTCAGGGAAAG                         CATGCTAATGGTGAAAATGCGTGGGTTGGCATTGATGGAAGGAGTGGCGAT
genomic: AAAATTGTGGTTTGAATGTTATTAGGATAATGACACAACTTCAGGGAAAGgtaataatcc ... tttgcgtcagCATGCTAATGGTGAAAATGCGTGGGTTGGCATTGATGGAAGGAGTGGCGAT
EST: gi|33093301|gb|CF053295.1|CF053295
EST:     AAAATTGCGGTTTGAATGTTATTAGGATAATGACACAACTTCAGGGAAAG                         CATGCTAATGGTGAAAATGCGTGGGTTGGCATTGATGGAAGGAGTGGCGAT
genomic: AAAATTGTGGTTTGAATGTTATTAGGATAATGACACAACTTCAGGGAAAGgtaataatcc ... tttgcgtcagCATGCTAATGGTGAAAATGCGTGGGTTGGCATTGATGGAAGGAGTGGCGAT
EST: gi|4646563|gb|AI491301.2|AI491301
EST:     AAAATTGTGGTTTGAATGTTATTAGGATAATGACNCAACTTCAGGGAAAG                         CATGCTAATGGTGAAAATGCGTGGGTTGGCATTGATGGAAGGAGTGGCGAT
genomic: AAAATTGTGGTTTGAATGTTATTAGGATAATGACACAACTTCAGGGAAAGgtaataatcc ... tttgcgtcagCATGCTAATGGTGAAAATGCGTGGGTTGGCATTGATGGAAGGAGTGGCGAT
EST: gi|5895898|gb|AW037144.1|AW037144
EST:     AAAATTGCGGTTTGAATGTTATTAGGATAATGACACAACTTCAGGGAAAG                         CATGCTAATGGTGAAAATGCGTGGGTTGGCATTGATGGAAGGAGTGGCGAT
genomic: AAAATTGTGGTTTGAATGTTATTAGGATAATGACACAACTTCAGGGAAAGgtaataatcc ... tttgcgtcagCATGCTAATGGTGAAAATGCGTGGGTTGGCATTGATGGAAGGAGTGGCGAT
EST: gi|116813897|gb|EC856391.1|EC856391
EST:     AGGAT-ATGACACAACTTCAGGNAAAG                         CATGCTAATGGTGAAAATGCGTGGGTTGGCATTGATGGAAGGAGTGGCGAT
genomic: AGGATAATGACACAACTTCAGGGAAAGgtaataatcc ... tttgcgtcagCATGCTAATGGTGAAAATGCGTGGGTTGGCATTGATGGAAGGAGTGGCGAT
EST: gi|22489574|gb|BU049497.1|BU049497
EST:     AAAATTGTGGTTTGAATGTTATTAGGATAATGACACAACTTCAGGGAAAG                         CATGCTAATGGTGAAAATGCGTGGGTTGGCATTGATGGAAGGAGTGGCGAT
genomic: AAAATTGTGGTTTGAATGTTATTAGGATAATGACACAACTTCAGGGAAAGgtaataatcc ... tttgcgtcagCATGCTAATGGTGAAAATGCGTGGGTTGGCATTGATGGAAGGAGTGGCGAT
EST: gi|60349009|gb|DN215982.1|DN215982
EST:     AAAATTGTGGTTTGAATGTTATTAGGATAATGACACAACTTCAGGGAAAG                         CATGCTAATGGTGAAAATGCGTGGGTTGGCATTGATGGAAGGAGTGGCGAT
genomic: AAAATTGTGGTTTGAATGTTATTAGGATAATGACACAACTTCAGGGAAAGgtaataatcc ... tttgcgtcagCATGCTAATGGTGAAAATGCGTGGGTTGGCATTGATGGAAGGAGTGGCGAT
EST: gi|60354814|gb|DN221787.1|DN221787
EST:     AAAATTGTGGTTTGAATGTTATTAGGATAATGACACAACTTCAGGGAAAG                         CATGCTAATGGTGAAAATGCGTGGGTTGGCATTGATGGAAGGAGTGGCGAT
genomic: AAAATTGTGGTTTGAATGTTATTAGGATAATGACACAACTTCAGGGAAAGgtaataatcc ... tttgcgtcagCATGCTAATGGTGAAAATGCGTGGGTTGGCATTGATGGAAGGAGTGGCGAT
EST: gi|71428864|gb|DR809914.1|DR809914
EST:     AAAATTGTGGTTTGAATGTTATTAGGATAATGACCCAACTTCAGGGAAAG                         CATGCTAATGGTGAAAATGCGTGGGTTGGCATTGATGGAAGGAGTGGCGAT
genomic: AAAATTGTGGTTTGAATGTTATTAGGATAATGACACAACTTCAGGGAAAGgtaataatcc ... tttgcgtcagCATGCTAATGGTGAAAATGCGTGGGTTGGCATTGATGGAAGGAGTGGCGAT
EST: gi|18385090|gb|BM418289.1|BM418289
EST:     AAAATTGTGGTTTGAATGTTATTAGGATAATGACACAACTTCAGGGAAAG                         CATGCTAATGGTGAAAATGCGTGGGTTGGCATTGATGGAAGGAGTGGCGAT
genomic: AAAATTGTGGTTTGAATGTTATTAGGATAATGACACAACTTCAGGGAAAGgtaataatcc ... tttgcgtcagCATGCTAATGGTGAAAATGCGTGGGTTGGCATTGATGGAAGGAGTGGCGAT
EST: gi|71332447|gb|DR803182.1|DR803182
EST:     AAAATTGTGGTTTGAATGTTATTAGGATAATGACACAACTTCAGGGAAAG                         CATGCTAATGGTGAAAATGCGTGGGTTGGCATTGATGGAAGGAGTGGCGAT
genomic: AAAATTGTGGTTTGAATGTTATTAGGATAATGACACAACTTCAGGGAAAGgtaataatcc ... tttgcgtcagCATGCTAATGGTGAAAATGCGTGGGTTGGCATTGATGGAAGGAGTGGCGAT
EST: gi|71762722|gb|DR960659.1|DR960659
EST:     AAAATTGTGGTTTGAATGTTATTAGGATAATGACACAACTTCAGGGAAAG                         CATGCTAATGGTGAAAATGCGTGGGTTGGCATTGATGGAAGGAGTGGCGAT
genomic: AAAATTGTGGTTTGAATGTTATTAGGATAATGACACAACTTCAGGGAAAGgtaataatcc ... tttgcgtcagCATGCTAATGGTGAAAATGCGTGGGTTGGCATTGATGGAAGGAGTGGCGAT
EST: gi|78021982|gb|DV490369.1|DV490369
EST:     AAAATTGCGGTTTGAATGTTATTAGGATAATGACACAACTTCAGGGAAAG                         CATGCTAATGGTGAAAATGCGTGGGTTGGCATTGATGGAAGGAGTGGCGAT
genomic: AAAATTGTGGTTTGAATGTTATTAGGATAATGACACAACTTCAGGGAAAGgtaataatcc ... tttgcgtcagCATGCTAATGGTGAAAATGCGTGGGTTGGCATTGATGGAAGGAGTGGCGAT
EST: gi|211513338|gb|FL030354.1|FL030354
EST:     AAAATTGCGGTTTGAATGTTATTAGGATAATGACACAACTTCAGGGAAAG                         CATGCTAATGGTGAAAATGCGTGGGTTGGCATTGATGGAAGGAGTGGCGAT
genomic: AAAATTGTGGTTTGAATGTTATTAGGATAATGACACAACTTCAGGGAAAGgtaataatcc ... tttgcgtcagCATGCTAATGGTGAAAATGCGTGGGTTGGCATTGATGGAAGGAGTGGCGAT

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), 49 (downstream exon)
Score: 457

CTATGAAGCTGCTGCTCTAGCATTTGAGGCAATTCCAAGGACTTTGGCCCAAAATTGTGGTTTGAATGTTATTAGGATAATGACACAACTTCAGGGAAAGgtaataatcc ... tttgcgtcagCATGCTAATGGTGAAAATGCGTGGGTTGGCATTGATGGAAGGAGTGGCGATATCGTTGATATGAAAGAGCGAAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 202

CTATGAAGCTGCTGCTCTAGCATTTGAGGCAATTCCAAGGACTTTGGCCCAAAATTGTGGTTTGAATGTTATTAGGATAATGACACAACTTCAGGGAAAGgtaataatcc ... tttgcgtcagCATGCTAATGGTGAAAATGCGTGGGTTGGCATTGATGGAAGGAGTGGCGATATCGTTGATATGAAAGAGCGAAAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 135

CTATGAAGCTGCTGCTCTAGCATTTGAGGCAATTCCAAGGACTTTGGCCCAAAATTGTGGTTTGAATGTTATTAGGATAATGACACAACTTCAGGGAAAGgtaataatcc ... tttgcgtcagCATGCTAATGGTGAAAATGCGTGGGTTGGCATTGATGGAAGGAGTGGCGATATCGTTGATATGAAAGAGCGAAAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 174

CTATGAAGCTGCTGCTCTAGCATTTGAGGCAATTCCAAGGACTTTGGCCCAAAATTGTGGTTTGAATGTTATTAGGATAATGACACAACTTCAGGGAAAGgtaataatcc ... tttgcgtcagCATGCTAATGGTGAAAATGCGTGGGTTGGCATTGATGGAAGGAGTGGCGATATCGTTGATATGAAAGAGCGAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaaacagttactttaaatcaatcatacgtttgtttgttctttctttgcgtcagCATGCTAATGGTGAAAATGCGTGGGTTGGCATTGATGGAAGGAGTGGCGATATCGTTGATATGAAAGAGCGAAAG
                              tttgtttgttctttct  CT-rich tract
         ttactttaaatcaat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atatgcttataatggatttgagttttttgttatgattattagaaaaaaaaacagttactttaaatcaatcatacgtttgtttgttctttctttgcgtcagCATGCTAATGGTGAAAATGCGTGGGTTGGCATTGATGGAAGGAGTGGCGATATCGTTGATATGAAAGAGCGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- atgctta
- - - - - - - - - - - - ttttgtt
- - - - - - - - - - - - - - - - - - - - - aaaaaaa