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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTGTTGAAGAAATACCCATCCAAGTTCGTTGGTTGCTGTCTTGCGAATCCTGCAGACGATGGGACTGGGATTAAACAGCTTGAACATCTGATTGTACAAgtaacctcttggaattttcttctgacacaaaaggaatgacccattctgctagtttctaacatgcagtcccttcgtttatccccag

Basic information

species Zea mays
transcript GRMZM2G155962_T03
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G155962_T03 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os04g32150.1 (Oryza sativa), 5'ss of exon 4
TGTGTTGAAGAAATACCCATCCAAGTTCGTTGGTTGCTGTCTTGCGAATCCTGCAGACGATGGGACTGGGATTAAACAGCTTGAACATCTGATTGTACAAgta-acctcttggaattttcttctgacacaaaaggaatgacccattctgctagtttctaacatgcagtcccttcgtttatccccag
 ||||||||||||||||||||||| ||| |||||||||||||||| ||||||||||| ||||| |  || |||||||||||||||||||| |||||||||||| |   ||||||| ||||     | ||  ||  | ||   ||  |    |||  || | ||    | | || | || || | ||
CGTGTTGAAGAAATACCCATCCAAATTCATTGGTTGCTGTCTTGCTAATCCTGCAGATGATGGAAGCGGCATTAAACAGCTTGAACATCTAATTGTACAAgtacataccttggaactttccc---aaacctaaaaactggttcaaacctacagt--ctgatatatgattcatttgcttctcactag

upper sequence: GRMZM2G155962_T03 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA02G10680.1 (Glycine max), 5'ss of exon 6
TGTGTTGAAGAAATACCCATCCAAGTTCGTTGGTTGCTGTCTTGCGAATCCTGCAGACGATGGGACTGGGATTAAACAGCTTGAACATCTGATTGTACAAgtaacctcttggaattttcttctgacacaaaaggaatgacccattctgctagtttctaacatgcagtcccttcgtttatccccag
  | ||||||||||||||  |||| || |||||||| |||||| | ||||| ||||| ||||| | |||| |||| ||| ||||| ||||  || |  | ||    |  |||| | ||||| |    ||| |   || |     |  |  ||    | | ||    ||  ||  | | |      
CATTTTGAAGAAATACCCGACCAAATTTGTTGGTTGTTGTCTTACTAATCCAGCAGATGATGGAAGTGGGCTTAAGCAGTTTGAAGATCTTGTTTTGAAGgt---ttaatggattattcttttttatcaagatagattattttattagaaagcaattgaaattt--tctttttatctgtgttag-

upper sequence: GRMZM2G155962_T03 (Zea mays), 5'ss of exon 4
lower sequence: AT2G35450.1 (Arabidopsis thaliana), 5'ss of exon 4
TGTGTTGAAGAAATACCCATCCAAGTTCGTTGGTTGCTGTCTTGCGAATCCTGCAGACGATGGGACTGGGATTAAACAGCTTGAACATCTGATTGTACAAgtaacctcttggaattttcttctga-ca-caaaaggaatgacccattctgctagtttctaacatgcagtcccttcgtttatccccag
|||  |||||| ||||||||| ||||| || ||||| || ||||| ||||||||||| ||||| | ||| ||||  || |||||  ||||  || || | ||   | |||  | | ||  ||  | || |   |   || |   || |  ||  ||||| | | | | |    || ||| |    ||
TGTTCTGAAGAGATACCCATCAAAGTTTGTCGGTTGTTGCCTTGCTAATCCTGCAGAAGATGGCAGTGGAATTACGCACCTTGAGAATCTTGTTTTAGAGgtcttccctttcactgttactcaaagcatctccaaatattatatatgcatctcatttctgaga-gtacttaaatc-tttttttgtag

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|93284051|gb|EB676315.1|EB676315
EST:     CTGCAGACGATGGGACTGGGATTAAACAGCTTGAACATCTGATTGTACAA                         GAAAAATACCGTGCTGTGAGGTTCAACCCAAACTTATGGCCATCTGGTCAA
genomic: CTGCAGACGATGGGACTGGGATTAAACAGCTTGAACATCTGATTGTACAAgtaacctctt ... ttatccccagGAAAAATACCGTGCTGTGAGGTTCAACCCAAACTTATGGCCATCTGGTCAA
EST: gi|60397566|gb|DN230382.1|DN230382
EST:     CTGCAGACGATGGGACTGGGATTAAACAGCTTGAACATCTGATTGTACAA                         GAAAAATACCGTGCTGTGAGGTTCAACCCAAACTTATGGCCATCTGGTCAA
genomic: CTGCAGACGATGGGACTGGGATTAAACAGCTTGAACATCTGATTGTACAAgtaacctctt ... ttatccccagGAAAAATACCGTGCTGTGAGGTTCAACCCAAACTTATGGCCATCTGGTCAA
EST: gi|211322966|gb|FL249424.1|FL249424
EST:     CTGCAGACGATGGGACTGGGATTAAACAGCTTGAACATCTGATTGTACAA                         GAAAAATACCGTGCTGTGAGGTTCAACC-AAACTTATGGCCATCTGGT
genomic: CTGCAGACGATGGGACTGGGATTAAACAGCTTGAACATCTGATTGTACAAgtaacctctt ... ttatccccagGAAAAATACCGTGCTGTGAGGTTCAACCCAAACTTATGGCCATCTGGT
EST: gi|20507977|gb|BQ279847.1|BQ279847
EST:     CTGCAGACGATGGGACTGGGATTAAACAGCTTGAACATCTGATTGTACAA                         GAAAAATACCGTGCTGTGAGGTTCAACCCAAACTTATGGCCATCTGGTCAA
genomic: CTGCAGACGATGGGACTGGGATTAAACAGCTTGAACATCTGATTGTACAAgtaacctctt ... ttatccccagGAAAAATACCGTGCTGTGAGGTTCAACCCAAACTTATGGCCATCTGGTCAA
EST: gi|211322963|gb|FL249421.1|FL249421
EST:     CTGCAGACGATGGGACTGGGATTAAACAGCTTGAACATCTGATTGTACMA                         GAAAAATACCGTGCTGTGAGGTTCAACCCA
genomic: CTGCAGACGATGGGACTGGGATTAAACAGCTTGAACATCTGATTGTACAAgtaacctctt ... ttatccccagGAAAAATACCGTGCTGTGAGGTTCAACCCA
EST: gi|21987683|gb|BQ779211.1|BQ779211
EST:     CTGCAGACGATGGGACTGGGATTAAACAGCTTGAACATCTGATTGGACCA                         GAAAAAATACCGTGCTGTGAGGTTCAACCCAAACTTATGGCCATCTGGTCA
genomic: CTGCAGACGATGGGACTGGGATTAAACAGCTTGAACATCTGATTGTACAAgtaacctctt ... ttatccccagGAAAAA-TACCGTGCTGTGAGGTTCAACCCAAACTTATGGCCATCTGGTCA
EST: gi|76909087|gb|DV163216.1|DV163216
EST:     CTGCAGACGATGGGACTGGGATTAAACAGCTTGAACATCTGATTGTACAA                         GAAAAATACCGTGCTGTGAGGTTCAACCCAAACTTATGGCCATCTGGTCAA
genomic: CTGCAGACGATGGGACTGGGATTAAACAGCTTGAACATCTGATTGTACAAgtaacctctt ... ttatccccagGAAAAATACCGTGCTGTGAGGTTCAACCCAAACTTATGGCCATCTGGTCAA
EST: gi|101390398|gb|EB817133.1|EB817133
EST:     CTGCAGACGATGGGACTGGGATTAAACAGCTTGAACATCTGATTGTACAA                         GAAAAATACCGTGCTGTGAGGTTCAACCCAAACTTATGGCCATCTGGTCAA
genomic: CTGCAGACGATGGGACTGGGATTAAACAGCTTGAACATCTGATTGTACAAgtaacctctt ... ttatccccagGAAAAATACCGTGCTGTGAGGTTCAACCCAAACTTATGGCCATCTGGTCAA
EST: gi|211322965|gb|FL249423.1|FL249423
EST:     CTGCAGACGATGGGACTGGGATTAAACAGCTTGAACATCTGATTGTACAA                         GAAAAATACCGTGCTGTGAGGTTCAACCCAAACTTATGGCCATCTGGT
genomic: CTGCAGACGATGGGACTGGGATTAAACAGCTTGAACATCTGATTGTACAAgtaacctctt ... ttatccccagGAAAAATACCGTGCTGTGAGGTTCAACCCAAACTTATGGCCATCTGGT
EST: gi|211322961|gb|FL249419.1|FL249419
EST:     CTGCAGACGATGGGACTGGGATTAAACAGCTTGAACATCTGATTGTACAA                         GAAAAATACCGTGCTGTGAGGT
genomic: CTGCAGACGATGGGACTGGGATTAAACAGCTTGAACATCTGATTGTACAAgtaacctctt ... ttatccccagGAAAAATACCGTGCTGTGAGGT
EST: gi|26456812|gb|CA828395.1|CA828395
EST:     CTGCAGACGATGGGACTGGGATTAAACAGCTTGAACATCTGATTGTACAA                         GAAAAATACCGTGCTGTGAGGTTCAACCCAAACTTATGGCCATCTGGTCAA
genomic: CTGCAGACGATGGGACTGGGATTAAACAGCTTGAACATCTGATTGTACAAgtaacctctt ... ttatccccagGAAAAATACCGTGCTGTGAGGTTCAACCCAAACTTATGGCCATCTGGTCAA
EST: gi|211322964|gb|FL249422.1|FL249422
EST:     CTGCAGACGATGGGACTGGGATTAAACAGCTTGAACATCTGATTGTACAA                         GAAAAATACCGTGCTGTGAGGTTCAACCCAAACTTATGGCCATCTGGTCAA
genomic: CTGCAGACGATGGGACTGGGATTAAACAGCTTGAACATCTGATTGTACAAgtaacctctt ... ttatccccagGAAAAATACCGTGCTGTGAGGTTCAACCCAAACTTATGGCCATCTGGTCAA
EST: gi|78090807|gb|DV519181.1|DV519181
EST:     CTGCAGACGATGGGACTGGGATTAAACAGCTTGAACATCTGATTGTACAA                         GAAAAATACCGTGCTGTGAGGTTCAACCCAAACTTATGGCCATCTGGTCAA
genomic: CTGCAGACGATGGGACTGGGATTAAACAGCTTGAACATCTGATTGTACAAgtaacctctt ... ttatccccagGAAAAATACCGTGCTGTGAGGTTCAACCCAAACTTATGGCCATCTGGTCAA
EST: gi|26558292|gb|CA830527.1|CA830527
EST:     CTGCAGACGATGGGACTGGGATTAAACAGCTTGAACATCTGATTGTACAA                         GAAAAATACCGTGCTGTGAGGTTCAACCCAAACTTATGGCCATCTGGTCAA
genomic: CTGCAGACGATGGGACTGGGATTAAACAGCTTGAACATCTGATTGTACAAgtaacctctt ... ttatccccagGAAAAATACCGTGCTGTGAGGTTCAACCCAAACTTATGGCCATCTGGTCAA
EST: gi|76909089|gb|DV163217.1|DV163217
EST:     CTGCAGACGATGGGACTGGGATTAAACAGCTTGAACATCTGATTGTACAA                         GAAAAATACCGTGCTGTGAGGTTCAACCCAAACTTATGGCCATCTGGTCAA
genomic: CTGCAGACGATGGGACTGGGATTAAACAGCTTGAACATCTGATTGTACAAgtaacctctt ... ttatccccagGAAAAATACCGTGCTGTGAGGTTCAACCCAAACTTATGGCCATCTGGTCAA
EST: gi|60357568|gb|DN224541.1|DN224541
EST:     CTGCAGACGATGGGACTGGGATTAAACAGCTTGAACATCTGATTGTACAA                         GAAAAATACCGTGCTGTGAGGTTCAACCCAAACTTATGGCCATCTGGTCAA
genomic: CTGCAGACGATGGGACTGGGATTAAACAGCTTGAACATCTGATTGTACAAgtaacctctt ... ttatccccagGAAAAATACCGTGCTGTGAGGTTCAACCCAAACTTATGGCCATCTGGTCAA
EST: gi|211320798|gb|FL249415.1|FL249415
EST:     CTGCAGACGATGGGACTGGGATTAAACAGCTTGAACATCTGATTGTACAA                         GAAAAATACCGTGCTGTGAGGTTCAACCCAAACTTATGGCCATCTGGTCAA
genomic: CTGCAGACGATGGGACTGGGATTAAACAGCTTGAACATCTGATTGTACAAgtaacctctt ... ttatccccagGAAAAATACCGTGCTGTGAGGTTCAACCCAAACTTATGGCCATCTGGTCAA
EST: gi|211320801|gb|FL249418.1|FL249418
EST:     CTGCAGACGATGGGACTGGGATTAAACAGCTTGAACATCTGATTGTACAA                         GAAAAATACCGTGCTGTGAGGTTCAACCCAAACTTATGGSCATCTGGTCAA
genomic: CTGCAGACGATGGGACTGGGATTAAACAGCTTGAACATCTGATTGTACAAgtaacctctt ... ttatccccagGAAAAATACCGTGCTGTGAGGTTCAACCCAAACTTATGGCCATCTGGTCAA
EST: gi|211320800|gb|FL249417.1|FL249417
EST:     CTGCAGACGATGGGACTGGGATTAAACAGCTTGAACATCTGATTGTACAA                         GAAAAATACCGTGCTGTGAGGTTCAACCCAAACTTATGG
genomic: CTGCAGACGATGGGACTGGGATTAAACAGCTTGAACATCTGATTGTACAAgtaacctctt ... ttatccccagGAAAAATACCGTGCTGTGAGGTTCAACCCAAACTTATGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTGTTGAAGAAATACCCATCCAAGTTCGTTGGTTGCTGTCTTGCGAATCCTGCAGACGATGGGACTGGGATTAAACAGCTTGAACATCTGATTGTACAAgtaacctcttggaattttcttctgacacaaaaggaatgacccattctgctagtttctaacatgcagtcccttcgtttatccccag

- - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG