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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgtcgttgcctgtttttgtttgtttgttttttttttttcaaacacaatgctgcgccgcggatcgaattgtattattgtacgactgccgggcccgtcgatcgatgtgtctccaataatttctccgccggtgcatgatgcacgcagCTGCGCTTCGACGGCGACGGCGGCGCCGGGAGCGTGAGCGTCGGCGGGAAGCTGTACACGCTGAAGCAGGTGCACTGGCACTCGCCTTCCGAGCACACCG

Basic information

species Zea mays
transcript GRMZM5G807267_T04
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G807267_T04 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os04g33660.1 (Oryza sativa), 3'ss of exon 2
gtctgtcgttgcctgtttttgtttgtttgttttttttttttcaaacacaatgctgcgccgcggatcgaat-tgtattattgtacgactgccgggcccgtcgatcgat-gtgtctccaataatttctccgccggtgcatgatgcacgcagCTGCGCTTCGACGGCGACGGCGGCGCCGGGAGCGTGAGCGTCGGCGGGAAGCTGTACACGCTGAAGCAGGTGCACTGGCACTCGCCTTCCGAGCACACCG------
                                                     |  |    | | | ||  | |   | || || ||| |   | || ||    ||| |||    |      |  |  | || |   || | |   |||||||| | ||| |     ||| ||   |||    ||||| |   ||||  |  |||||||||||||||| ||||||||||||| |||||||||||||||       
----------------------------------------------------gtttgttctgaaccaaacctcttgcactgaac-actactctgtccctcctctgattgtgcagtcttctgatagttagtcgtttt-tgtttccttcagCTGCGGTACGAAGA----GGCAGCA--GGGGTTCTGAGCATTAACGGGGTGAAGTACACGCTGAAGCAGATGCACTGGCACTCTCCTTCCGAGCACACCATCAACG
















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|74239799|gb|DT647713.1|DT647713
EST:     ACTACACCGTGGCCAACGCCACCCTCGTCGACAACGTCGTCAACGTCGCG                         CTGCGCTTCGACGGCGACGGCGGCGCCGGGAGCGTGAGCGTCGGCGGGAAG
genomic: ACTACACCGTGGCCAACGCCACCCTCGTCGACAACGTCGTCAACGTCGCGgtctgtcgtt ... atgcacgcagCTGCGCTTCGACGGCGACGGCGGCGCCGGGAGCGTGAGCGTCGGCGGGAAG
EST: gi|71417345|gb|DR804018.1|DR804018
EST:     ACTACACCGTGGCCAACGCCACCCTCGTCGACAACGTCATCAACGTCGCG                         CTGCGCTTCGACGGCGACGGCGGCGCCGGGAGCGTGAGCGTCGGCGGGAAG
genomic: ACTACACCGTGGCCAACGCCACCCTCGTCGACAACGTCGTCAACGTCGCGgtctgtcgtt ... atgcacgcagCTGCGCTTCGACGGCGACGGCGGCGCCGGGAGCGTGAGCGTCGGCGGGAAG
EST: gi|78112701|gb|DV531095.1|DV531095
EST:     ACTACACCGTGGCCAACGCCACCCTCGTCGACAACGTCGTCAACGTCGCG                         CTGCGCTTCGACGGCGACGGCGGCGCCGGGAGCGTGAGCGTCGGCGGGAAG
genomic: ACTACACCGTGGCCAACGCCACCCTCGTCGACAACGTCGTCAACGTCGCGgtctgtcgtt ... atgcacgcagCTGCGCTTCGACGGCGACGGCGGCGCCGGGAGCGTGAGCGTCGGCGGGAAG
EST: gi|148933555|gb|EC877415.2|EC877415
EST:     ACTACACCGTGGCCAACGCCACCCTCGTCGACAACGTCGTCAACGTCGCG                         CTGCGCTTCGACGGCGACGGCGGCGCCGGGAGCGTGAGCGTCGGCGGGAAG
genomic: ACTACACCGTGGCCAACGCCACCCTCGTCGACAACGTCGTCAACGTCGCGgtctgtcgtt ... atgcacgcagCTGCGCTTCGACGGCGACGGCGGCGCCGGGAGCGTGAGCGTCGGCGGGAAG
EST: gi|76014111|gb|DT941281.1|DT941281
EST:     ACTACACCGTGGCCAACGCCACCCTCGTCGACAACGTCGTCAACGTCGCG                         CTGCGCTTCGACGGCGACGGCGGCGCCGGGAGCGTGAGCGTCGGCGGGAAG
genomic: ACTACACCGTGGCCAACGCCACCCTCGTCGACAACGTCGTCAACGTCGCGgtctgtcgtt ... atgcacgcagCTGCGCTTCGACGGCGACGGCGGCGCCGGGAGCGTGAGCGTCGGCGGGAAG
EST: gi|76288688|gb|DV028256.1|DV028256
EST:     ACTACACCGTGGCCAACGCCACCCTCGTCGACAACGTCGTCAACGTCGCG                         CTGCGCTTCGACGGCGACGGCGGCGCCGGGAGCGTGAGCGTCGGCGGGAAG
genomic: ACTACACCGTGGCCAACGCCACCCTCGTCGACAACGTCGTCAACGTCGCGgtctgtcgtt ... atgcacgcagCTGCGCTTCGACGGCGACGGCGGCGCCGGGAGCGTGAGCGTCGGCGGGAAG
EST: gi|91871059|gb|EB401220.1|EB401220
EST:     ACTACACCGTGGCCAACGCCACCCTCGTCGACAACGTCGTCAACGTCGCG                         CTGCGCTTCGACGGCGACGGCGGCGCCGGGAGCGTGAGCGTCGGCGGGAAG
genomic: ACTACACCGTGGCCAACGCCACCCTCGTCGACAACGTCGTCAACGTCGCGgtctgtcgtt ... atgcacgcagCTGCGCTTCGACGGCGACGGCGGCGCCGGGAGCGTGAGCGTCGGCGGGAAG
EST: gi|71316204|gb|DR794778.1|DR794778
EST:     ACTACACCGTGGCCAACGCCACCCTCGTCGACAACGTCGTCAACGTCGCG                         CTGCGCTTCGACGGCGACGGCGGCGCCGGGAGCGTGAGCGTCGGCGGGAAG
genomic: ACTACACCGTGGCCAACGCCACCCTCGTCGACAACGTCGTCAACGTCGCGgtctgtcgtt ... atgcacgcagCTGCGCTTCGACGGCGACGGCGGCGCCGGGAGCGTGAGCGTCGGCGGGAAG
EST: gi|50324602|gb|CO519728.1|CO519728
EST:     ACTACACCGTGGCCAACGCCACCCTCGTCGACAACGTCGTCAACGTCGCG                         CTGCGCTTCGACGGCGACGGCGGCGCCGGGAGCGTGAGCGTCGGCGGGAAG
genomic: ACTACACCGTGGCCAACGCCACCCTCGTCGACAACGTCGTCAACGTCGCGgtctgtcgtt ... atgcacgcagCTGCGCTTCGACGGCGACGGCGGCGCCGGGAGCGTGAGCGTCGGCGGGAAG
EST: gi|89758326|gb|DY687544.1|DY687544
EST:     ACTACACCGTGGCCAACGCCACCCTCGTCGACAACGTCGTCAACGTCGCG                         CTGCGCTTCGACGGCGACGGCGGCGCCGGGAGCGTGAGCGTCGGCGGGAAG
genomic: ACTACACCGTGGCCAACGCCACCCTCGTCGACAACGTCGTCAACGTCGCGgtctgtcgtt ... atgcacgcagCTGCGCTTCGACGGCGACGGCGGCGCCGGGAGCGTGAGCGTCGGCGGGAAG
EST: gi|74244873|gb|DT652787.1|DT652787
EST:     ACTACACCGTGGCCAACGCCACCCTCGTCGACAACGTCGTCAACGTCGCG                         CTGCGCTTCGACGGCGACGGCGGCGCCGGGAGCGTGAGCGTCGGCGGGAAG
genomic: ACTACACCGTGGCCAACGCCACCCTCGTCGACAACGTCGTCAACGTCGCGgtctgtcgtt ... atgcacgcagCTGCGCTTCGACGGCGACGGCGGCGCCGGGAGCGTGAGCGTCGGCGGGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcccgtcgatcgatgtgtctccaataatttctccgccggtgcatgatgcacgcagCTGCGCTTCGACGGCGACGGCGGCGCCGGGAGCGTGAGCGTCGGCGGGAAGCTGTACACGCTGAAGCAGGTGCACTGGCACTCGCCTTCCGAGCACACCG
                      aataatttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgtcgttgcctgtttttgtttgtttgttttttttttttcaaacacaatgctgcgccgcggatcgaattgtattattgtacgactgccgggcccgtcgatcgatgtgtctccaataatttctccgccggtgcatgatgcacgcagCTGCGCTTCGACGGCGACGGCGGCGCCGGGAGCGTGAGCGTCGGCGGGAAGCTGTACACGCTGAAGCAGGTGCACTGGCACTCGCCTTCCGAGCACACCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC