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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacggcatgcacgcatcccttcctccttgttcgtctgacgctgacggtgacaaacttggtcagGGGCTTCATGGAAGTTCCCAAATGGGGCGGCATGTACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGG

Basic information

species Zea mays
transcript GRMZM2G146463_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G146463_T03 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os07g26900.1 (Oryza sativa), 3'ss of exon 7
------------------------------gtacggcatgcac-gcatcccttcctccttgttcgtctgacg--ctgacggtgacaaacttggt---cagGGGCTTCATGGAAGTTCCCAAATGGGGCGGCATGTACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGG
                               ||     | |   |  | | || ||     ||  ||    |   |||   || |   | || |   |||||||   | | | ||  | |  ||||| |||  |||||||||||||||||||||||||||||||||||| ||| ||||| |  |
ctattaaaaaacaaatagagagatagtaaaatattttcttcgttgtttactttactaaacatttttcctgagatttgagcttggccggcgtgatcttcagGGGCCAGAGGAATGTGGCGACGTGGGGTGGCCAGTACGGCAACAGCTGGAGGACCACCGGCGACATCAATGACTCATGGGCCAG
















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|76930345|gb|DV172346.1|DV172346
EST:     CGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTACTCGCTTTGCGAATG                         GGGCTTCATGGAAGTTCCCCAATGGGGCGGCATGTACGGCAACAGCTGGAG
genomic: CGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTACTCGCTTTGCGAATGgtacggcatg ... acttggtcagGGGCTTCATGGAAGTTCCCAAATGGGGCGGCATGTACGGCAACAGCTGGAG
EST: gi|78113279|gb|DV531671.1|DV531671
EST:     CGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTACTCGCTTTGCGAATG                         GGGCTTCATGGAAGTTCCCAAATGGGGCGGCATGTACGGCAACAGCTGGAG
genomic: CGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTACTCGCTTTGCGAATGgtacggcatg ... acttggtcagGGGCTTCATGGAAGTTCCCAAATGGGGCGGCATGTACGGCAACAGCTGGAG
EST: gi|91054335|gb|EB164753.1|EB164753
EST:     CGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTACTCGCTTTGCGAATG                         GGGCTTCATGGAAGTTCCCAAATGGGGCGGCATGTACGGCAACAGCTGGAG
genomic: CGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTACTCGCTTTGCGAATGgtacggcatg ... acttggtcagGGGCTTCATGGAAGTTCCCAAATGGGGCGGCATGTACGGCAACAGCTGGAG
EST: gi|23199550|gb|BU582115.1|BU582115
EST:     CGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTACTCGCTTTGCGAATG                         GGGCTTCATGGAAGTTCCCAAATGGGGCGGCATGTACGGCAACAGCTGGAG
genomic: CGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTACTCGCTTTGCGAATGgtacggcatg ... acttggtcagGGGCTTCATGGAAGTTCCCAAATGGGGCGGCATGTACGGCAACAGCTGGAG
EST: gi|22472587|gb|BU037067.1|BU037067
EST:     CGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTACTCGCTTTGCGAATG                         GGGCTTCATGGAAGTTCCCAAATGGGGCGGCATGTACGGCAACAGCTGGAG
genomic: CGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTACTCGCTTTGCGAATGgtacggcatg ... acttggtcagGGGCTTCATGGAAGTTCCCAAATGGGGCGGCATGTACGGCAACAGCTGGAG
EST: gi|26560002|gb|CA832237.1|CA832237
EST:     CGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTACTCGCTTTGCGAATG                         GGGCTTCATGGAAGTTCCCAAATGGGGCGGCATGTACGGCAACAGCTGGAG
genomic: CGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTACTCGCTTTGCGAATGgtacggcatg ... acttggtcagGGGCTTCATGGAAGTTCCCAAATGGGGCGGCATGTACGGCAACAGCTGGAG
EST: gi|22935898|gb|BU572173.1|BU572173
EST:     CGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTACTCGCTTTGCGAATG                         GGGCTTCATGGAAGTTCCCAAATGGGGCGGCATGTACGGCAACAGCTGGAG
genomic: CGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTACTCGCTTTGCGAATGgtacggcatg ... acttggtcagGGGCTTCATGGAAGTTCCCAAATGGGGCGGCATGTACGGCAACAGCTGGAG
EST: gi|71431665|gb|DR812715.1|DR812715
EST:     CGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTACTCGCTTTGCGAATG                         GGGCTTCATGGAAGTTCCCAAATGGGGCGGCATGTACGGCAACAGCTGGAG
genomic: CGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTACTCGCTTTGCGAATGgtacggcatg ... acttggtcagGGGCTTCATGGAAGTTCCCAAATGGGGCGGCATGTACGGCAACAGCTGGAG
EST: gi|78108215|gb|DV526633.1|DV526633
EST:     CGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTACTCGCTTTGCGAATG                         GGGCTTCATGGAAGTTCCCAAATGGGGCGGCATGTACGGCAACAGCTGGAG
genomic: CGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTACTCGCTTTGCGAATGgtacggcatg ... acttggtcagGGGCTTCATGGAAGTTCCCAAATGGGGCGGCATGTACGGCAACAGCTGGAG
EST: gi|149055656|gb|EE156361.2|EE156361
EST:     CGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTACTCGCTTTGCGAATG                         GGGCTTCATGGAAGTTCCCAAATGGGGCGGCATGTACGGCAACAGCTGGAG
genomic: CGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTACTCGCTTTGCGAATGgtacggcatg ... acttggtcagGGGCTTCATGGAAGTTCCCAAATGGGGCGGCATGTACGGCAACAGCTGGAG
EST: gi|78075209|gb|DV503643.1|DV503643
EST:     CGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTACTCGCTTTGCGAATG                         GGGCTTCATGGAAGTTCCCAAATGGGGCGGCATGTACGGCAACAGCTGGAG
genomic: CGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTACTCGCTTTGCGAATGgtacggcatg ... acttggtcagGGGCTTCATGGAAGTTCCCAAATGGGGCGGCATGTACGGCAACAGCTGGAG
EST: gi|71442889|gb|DR823939.1|DR823939
EST:     CGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTACTCGCTTTGCGAATG                         GGGCTTCATGGAAGTTCCCAAATGGGGCGGCATGTACGGCAACAGCTGGAG
genomic: CGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTACTCGCTTTGCGAATGgtacggcatg ... acttggtcagGGGCTTCATGGAAGTTCCCAAATGGGGCGGCATGTACGGCAACAGCTGGAG
EST: gi|78088431|gb|DV516824.1|DV516824
EST:     CGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTACTCGCTTTGCGAATG                         GGGCTTCATGGAAGTTCCCAAATGGGGCGGCATGTACNGGCA-CAGCTGGA
genomic: CGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTACTCGCTTTGCGAATGgtacggcatg ... acttggtcagGGGCTTCATGGAAGTTCCCAAATGGGGCGGCATGTAC-GGCAACAGCTGGA
EST: gi|26559550|gb|CA831785.1|CA831785
EST:     CGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTACTCGCTTTGCGAATG                         GGGCTTCATGGAAGTTCCCAAATGGGGCGGCATGTACGGCAACAGCTGGAG
genomic: CGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTACTCGCTTTGCGAATGgtacggcatg ... acttggtcagGGGCTTCATGGAAGTTCCCAAATGGGGCGGCATGTACGGCAACAGCTGGAG
EST: gi|71443418|gb|DR824468.1|DR824468
EST:     CGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTACTCGCTTTGCGAATG                         GGGCTTCATGGAAGTTCCCAAATGGGGCGGCATGTACGGCAACAGCTGGAG
genomic: CGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTACTCGCTTTGCGAATGgtacggcatg ... acttggtcagGGGCTTCATGGAAGTTCCCAAATGGGGCGGCATGTACGGCAACAGCTGGAG
EST: gi|71443280|gb|DR824330.1|DR824330
EST:     CGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTACTCGCTTTGCGAATG                         GGGCTTCATGGAAGTTCCCAAATGGGGCGGCATGTACGGCAACAGCTGGAG
genomic: CGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTACTCGCTTTGCGAATGgtacggcatg ... acttggtcagGGGCTTCATGGAAGTTCCCAAATGGGGCGGCATGTACGGCAACAGCTGGAG
EST: gi|71318127|gb|DR795825.1|DR795825
EST:     CGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTACTCGCTTTGCGAATG                         GGGCTTCATGGAAGTTCCCAAATGGGGCGGCATGTACGGCAACAGCTGGAG
genomic: CGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTACTCGCTTTGCGAATGgtacggcatg ... acttggtcagGGGCTTCATGGAAGTTCCCAAATGGGGCGGCATGTACGGCAACAGCTGGAG
EST: gi|148940241|gb|EC885013.2|EC885013
EST:     CGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTACTCGCTTTGCGAATG                         GGGCTTCATGGAAGTTCCCAAATGGGGCGGCATGTACGGCAACAGCTGGAG
genomic: CGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTACTCGCTTTGCGAATGgtacggcatg ... acttggtcagGGGCTTCATGGAAGTTCCCAAATGGGGCGGCATGTACGGCAACAGCTGGAG
EST: gi|91875282|gb|EB405239.1|EB405239
EST:     CGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTACTCGCTTTGCGAATG                         GGGCTTCATGGAAGTTCCCAAATGGGGCGGCATGTACGGCAACAGCTGGAG
genomic: CGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTACTCGCTTTGCGAATGgtacggcatg ... acttggtcagGGGCTTCATGGAAGTTCCCAAATGGGGCGGCATGTACGGCAACAGCTGGAG
EST: gi|74238712|gb|DT646626.1|DT646626
EST:     GAGCGCTGGTGAACTCTGGCCCGCC-AATCTTCTACTCGCTTTGCGAATG                         GGGCTTCATGGAAGTT
genomic: GAGCGCTGGTGAACTCTGGCC-GCCCAATCTTCTACTCGCTTTGCGAATGgtacggcatg ... acttggtcagGGGCTTCATGGAAGTT
EST: gi|76011884|gb|DT939054.1|DT939054
EST:     CGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTACTCGCTTTGCGAATG                         GGGCTTCATGGAAGTTCCCAAATGGGGCGGCATGTACGGCAACAGCTGGAG
genomic: CGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTACTCGCTTTGCGAATGgtacggcatg ... acttggtcagGGGCTTCATGGAAGTTCCCAAATGGGGCGGCATGTACGGCAACAGCTGGAG
EST: gi|149009677|gb|EE041609.2|EE041609
EST:     CGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTACTCGCTTTGCGAATG                         GGGCTTCATGGAAGTTCCCAAATGGGGCGGCATGTACGGCAACAGCTGGAG
genomic: CGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTACTCGCTTTGCGAATGgtacggcatg ... acttggtcagGGGCTTCATGGAAGTTCCCAAATGGGGCGGCATGTACGGCAACAGCTGGAG
EST: gi|78110547|gb|DV528957.1|DV528957
EST:     CGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTACTCGCTTTGCGAATG                         GGGCTTCATGGAAGTTCCCAAATGGGGCGGCATGTACGGCAACAGCTGGAG
genomic: CGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTACTCGCTTTGCGAATGgtacggcatg ... acttggtcagGGGCTTCATGGAAGTTCCCAAATGGGGCGGCATGTACGGCAACAGCTGGAG
EST: gi|148973153|gb|EE024223.2|EE024223
EST:     CGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTACTCGCTTTGCGAATG                         GGGCTTCATGGAAGTTCCCAAATGGGGCGGCATGTACGGCAACAGCTGGAG
genomic: CGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTACTCGCTTTGCGAATGgtacggcatg ... acttggtcagGGGCTTCATGGAAGTTCCCAAATGGGGCGGCATGTACGGCAACAGCTGGAG
EST: gi|149013904|gb|EE043402.2|EE043402
EST:     CGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTACTCGCTTTGCGAATG                         GGGCTTCATGGAAGTTCCCAAATGGGGCGGCATGTACGGCAACAGCTGGAG
genomic: CGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTACTCGCTTTGCGAATGgtacggcatg ... acttggtcagGGGCTTCATGGAAGTTCCCAAATGGGGCGGCATGTACGGCAACAGCTGGAG
EST: gi|89763957|gb|DY690934.1|DY690934
EST:     CGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTACTCGCTTTGCGAATG                         GGGCTTCATGGAAGTTCCCAAATGGGGCGGCATGTACGGCAACAGCTGGAG
genomic: CGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTACTCGCTTTGCGAATGgtacggcatg ... acttggtcagGGGCTTCATGGAAGTTCCCAAATGGGGCGGCATGTACGGCAACAGCTGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcacgcatcccttcctccttgttcgtctgacgctgacggtgacaaacttggtcagGGGCTTCATGGAAGTTCCCAAATGGGGCGGCATGTACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGG
                              cgctgac  putative branch site (score: 3)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacggcatgcacgcatcccttcctccttgttcgtctgacgctgacggtgacaaacttggtcagGGGCTTCATGGAAGTTCCCAAATGGGGCGGCATGTACGGCAACAGCTGGAGGACCACCGGCGACATCAACGACACATGGTCAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA