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'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   		25  
 5'  3'   		26  
 5'  3'   		27  
 5'  3'   		28  
 5'  3'   		29  
 5'  3'   		30  
 5'  3'   		31  
 5'  3'   		32  
 5'  3'   		33  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattattacttttgctttactcttcagtatttctacaagtcctttttctgtcaacttgactttccaccttgtacagATAGGGATGGATTTCGACGATGTGAGGACAAAATCTTCAGTTATTCATGTTTTTCCATTTAACTCGGAGAAGAAACGTGGCGCTGTTGCAGTACAG

Basic information

species Zea mays
transcript GRMZM2G132712_T01
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G132712_T03 (Zea mays), 3'ss of exon 20
lower sequence: LOC_Os08g40530.2 (Oryza sativa), 3'ss of exon 4
-------------------------------------------------------------------------gtattattacttttgctttactcttcagtatttctacaagtcctttttctgtcaacttgactttccaccttgtacagATAGGGATGGATTTCGACGATGTGAGGACAAAATCTTCAGTTATTCATGTTTTTCCATTTAACTCGGAGAAGAAACGTGGCGCTGTTGCAGTACAG
                                                                              ||   ||   || |  |||  |  | ||   | |||  ||  |      ||| |   |||||| ||| ||||||||| ||||||||| | ||||   || ||||||||  | || ||||||| ||||||||||| ||||||||||| ||||| |  ||||||||||||
gtattaaccctttatctggcttccatactcaagtggttccttcaatggttgtgtacatccgttttggatgtagaggccatgttttaatctattttctaaaaaagttactccagtggttccttcaatgactagttcttccactttgaacagATAGGAATGGATTTCAATGATGCACGGTCAAAATCTCAAATTCTTCATGTCTTTCCATTTAATTCGGAGAAGAAGCGTGGTGGGGTTGCAGTACAG
















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|211422272|gb|FK992813.1|FK992813
EST:     AACTTACTGGTTCGCCTACTGAAAAGGCCATTCTTTCTTGGGGCCTTAAG                         ATAGGGATGGATTTCGACGACGTGAGGACAAAATCTTCAGTTATTCATGTT
genomic: AACTTACTGGTTCGCCTACTGAAAAGGCCATTCTTTCTTGGGGCCTTAAGgtattattac ... ccttgtacagATAGGGATGGATTTCGACGATGTGAGGACAAAATCTTCAGTTATTCATGTT
EST: gi|211422266|gb|FK992807.1|FK992807
EST:     AACTTACTGGTTCGCCTACTGAAAAGGCCATTCTTTCTTGGGGCCTTAAG                         ATAGGGATGGATTTCGACGACGTGAGGACAAAATCTTCAGTTATTCATGTT
genomic: AACTTACTGGTTCGCCTACTGAAAAGGCCATTCTTTCTTGGGGCCTTAAGgtattattac ... ccttgtacagATAGGGATGGATTTCGACGATGTGAGGACAAAATCTTCAGTTATTCATGTT
EST: gi|211422265|gb|FK992806.1|FK992806
EST:     AACTTACTGGTTCGCCTACTGAAAAGGCCATTCTTTCTTGGGGCCTTAAG                         ATAGGGATGGATTTCGACGACGTGAGGACAAAATCTTCAGTTATTCATGTT
genomic: AACTTACTGGTTCGCCTACTGAAAAGGCCATTCTTTCTTGGGGCCTTAAGgtattattac ... ccttgtacagATAGGGATGGATTTCGACGATGTGAGGACAAAATCTTCAGTTATTCATGTT
EST: gi|211422271|gb|FK992812.1|FK992812
EST:     AACTTACTGGTTCGCCTACTGAAAAGGCCATTCTTTCTTGGGGCCTTAAG                         ATAGGGATGGATTTCGACGACGTGAGGACAAAATCTTCAGTTATTCATGTT
genomic: AACTTACTGGTTCGCCTACTGAAAAGGCCATTCTTTCTTGGGGCCTTAAGgtattattac ... ccttgtacagATAGGGATGGATTTCGACGATGTGAGGACAAAATCTTCAGTTATTCATGTT
EST: gi|211422274|gb|FK992815.1|FK992815
EST:     AACTTACTGGTTCGCCTACTGAAAAGGCCATTCTTTCTTGGGGCCTTAAG                         ATAGGGATGGATTTCGACGACGTGAGGACAAAATCTTCAGTTATTCATGTT
genomic: AACTTACTGGTTCGCCTACTGAAAAGGCCATTCTTTCTTGGGGCCTTAAGgtattattac ... ccttgtacagATAGGGATGGATTTCGACGATGTGAGGACAAAATCTTCAGTTATTCATGTT
EST: gi|211422270|gb|FK992811.1|FK992811
EST:     AACTTACTGGTTCGCCTACTGAAAAGGCCATTCTTTCTTGGGGCCTTAAG                         ATAGGGATGGATTTCGACGACGTGAGGACAAAATCTTCAGTTATTCATGTT
genomic: AACTTACTGGTTCGCCTACTGAAAAGGCCATTCTTTCTTGGGGCCTTAAGgtattattac ... ccttgtacagATAGGGATGGATTTCGACGATGTGAGGACAAAATCTTCAGTTATTCATGTT
EST: gi|211422268|gb|FK992809.1|FK992809
EST:     AACTTACTGGTTCGCCTACTGAAAAGGCCATTCTTTCTTGGGGCCTTAAG                         ATAGGGATGGATTTCGACGACGTGAGGACAAAATCTTCAGTTATTCATGTT
genomic: AACTTACTGGTTCGCCTACTGAAAAGGCCATTCTTTCTTGGGGCCTTAAGgtattattac ... ccttgtacagATAGGGATGGATTTCGACGATGTGAGGACAAAATCTTCAGTTATTCATGTT
EST: gi|211422273|gb|FK992814.1|FK992814
EST:     AACTTACTGGTTCGCCTACTGAAAAGGCCATTCTTTCTTGGGGCCTTAAG                         ATAGGGATGGATTTCGACGACGTGAGGACAAAATCTTCAGTTATTCATGTT
genomic: AACTTACTGGTTCGCCTACTGAAAAGGCCATTCTTTCTTGGGGCCTTAAGgtattattac ... ccttgtacagATAGGGATGGATTTCGACGATGTGAGGACAAAATCTTCAGTTATTCATGTT
EST: gi|71443249|gb|DR824299.1|DR824299
EST:     AACTTACTGGTTCGCCTACTGAAAAGGCCATTCTTTCTTGGGGCCTTAAG                         ATAGGGATGGATTTCGACGATGTGAGGACAAAATCTTCAGTTATTCATGTT
genomic: AACTTACTGGTTCGCCTACTGAAAAGGCCATTCTTTCTTGGGGCCTTAAGgtattattac ... ccttgtacagATAGGGATGGATTTCGACGATGTGAGGACAAAATCTTCAGTTATTCATGTT
EST: gi|211422275|gb|FK992816.1|FK992816
EST:     AACTTACTGGTTCGCCTACTGAAAAGGCCATTCTTTCTTGGGGCCTTAAG                         ATAGGGATGGATTTCGACGACGTGAGGACAAAATCTTCAGTTATTCATGTT
genomic: AACTTACTGGTTCGCCTACTGAAAAGGCCATTCTTTCTTGGGGCCTTAAGgtattattac ... ccttgtacagATAGGGATGGATTTCGACGATGTGAGGACAAAATCTTCAGTTATTCATGTT
EST: gi|31350151|gb|CD434508.1|CD434508
EST:     AACTTACTGGTTCGCCTACTGAAAAGGCCATTCTTTCTTGGGGCCTTAAG                         ATAGGGATGGATTTCGACGACGTGAGGACAAAATCTTCAGTTATTCATGTT
genomic: AACTTACTGGTTCGCCTACTGAAAAGGCCATTCTTTCTTGGGGCCTTAAGgtattattac ... ccttgtacagATAGGGATGGATTTCGACGATGTGAGGACAAAATCTTCAGTTATTCATGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcagtatttctacaagtcctttttctgtcaacttgactttccaccttgtacagATAGGGATGGATTTCGACGATGTGAGGACAAAATCTTCAGTTATTCATGTTTTTCCATTTAACTCGGAGAAGAAACGTGGCGCTGTTGCAGTACAG
                                acttgac  putative branch site (score: 4)
                                      ctttccacctt  CT-rich tract
      tatttcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattattacttttgctttactcttcagtatttctacaagtcctttttctgtcaacttgactttccaccttgtacagATAGGGATGGATTTCGACGATGTGAGGACAAAATCTTCAGTTATTCATGTTTTTCCATTTAACTCGGAGAAGAAACGTGGCGCTGTTGCAGTACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT