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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacattaccaccactggaataaatttgtggacatcttacagtgctaaaccgttgcatattctaatgcagGACACATTGATGAGGATATGCTGTGCCATGCTCATCCTAGTCCGAAAGCGTCTCTTAGCTGGAGACTTCACCGCCAATGTCCAGCTGCTGCAACATTACC

Basic information

species Zea mays
transcript GRMZM2G122935_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G122935_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os11g28990.1 (Oryza sativa), 3'ss of exon 8
-----------gtacattaccaccactggaataaatttgtggacatcttac--------------agtgctaaaccgttgcatattctaatgcagGACACATTGATGAGGATATGCTGTGCCATGCTCATCCTAGTCCGAAAGCGTCTCTTAGCTGGAGACTTCACCGCCAATGTCCAGCTGCTGCAACATTACC
            |  | ||   || |   | ||  ||||  | ||| ||||               | |||||  | |||||| ||||  |||||||||| ||| | || ||||||||||||||||||||||| ||||| | ||| ||| |||||||||||||||| |||||  ||||||||||||| || || |
gtatgtaacctctggactaa-gcctccaaactaggtttgcagccatgttacttgtacaactgcagggggctaatgctttgcatgttcttgtgcagGACACGTTGCTAAGAATATGCTGTGCCATGCTCATCCTTGTCCGGAGGCGCCTCCTAGCTGGAGACTTCACTGCCAACATCCAGCTGCTGCAGCACTATC
















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|32856562|gb|CD996243.1|CD996243
EST:     TGTGTGTACATATCTGGGATGCTATCTTGGGTGATCCAGAAGGCCCATCG                         GACACATTGATGAGGATATGCTGTGCCATGCTCATCCTAGTCCGAAAGCGT
genomic: TGTGTATACATATCTGGGATGCTATCTTGGGTGATCCAGAAGGCCCATCGgtacattacc ... tctaatgcagGACACATTGATGAGGATATGCTGTGCCATGCTCATCCTAGTCCGAAAGCGT
EST: gi|44900278|gb|CK826823.1|CK826823
EST:     TGTGTATACATATCTGGGATGCTATCTTGGGTGATCCAGAAGGCCCCTCG                         GACACATTGATGAGGATATGCTGTGCCATGCTCATCCTAGTCCGAAAGCGT
genomic: TGTGTATACATATCTGGGATGCTATCTTGGGTGATCCAGAAGGCCCATCGgtacattacc ... tctaatgcagGACACATTGATGAGGATATGCTGTGCCATGCTCATCCTAGTCCGAAAGCGT
EST: gi|60339344|gb|DN206317.1|DN206317
EST:     TGTGTATACATATCTGGGATGCTATCCTGGGTGATCCAGAAGGCCCATCG                         GACACATTGATGAGGATATGCTGTGCCATGCTCATCCTAGTCCGAAAGCGT
genomic: TGTGTATACATATCTGGGATGCTATCTTGGGTGATCCAGAAGGCCCATCGgtacattacc ... tctaatgcagGACACATTGATGAGGATATGCTGTGCCATGCTCATCCTAGTCCGAAAGCGT
EST: gi|78110295|gb|DV528710.1|DV528710
EST:     TGTGTATACATATCTGGGATGCTATCTTGGGTGATCCAGAAGGCCCATCG                         GACACATTGATGAGGATATGCTGTGCCATGCTCATCCTAGTCCGAAAGCGT
genomic: TGTGTATACATATCTGGGATGCTATCTTGGGTGATCCAGAAGGCCCATCGgtacattacc ... tctaatgcagGACACATTGATGAGGATATGCTGTGCCATGCTCATCCTAGTCCGAAAGCGT
EST: gi|74232771|gb|DT640685.1|DT640685
EST:     TGTGTATACATATCTGGGATGCTATCTTGGGTGATCCAGAAGGCCCATCG                         GACACATTGATGAGGATATGCTGTGCCATGCTCATCCTAGTCCGAAAGCGT
genomic: TGTGTATACATATCTGGGATGCTATCTTGGGTGATCCAGAAGGCCCATCGgtacattacc ... tctaatgcagGACACATTGATGAGGATATGCTGTGCCATGCTCATCCTAGTCCGAAAGCGT
EST: gi|148981603|gb|EE027761.2|EE027761
EST:     TGTGTATACATATCTGGGATGCTATCTTGGGTGATCCAGAAGGCCCATCG                         GACACATTGATGAGGATATGCTGTGCCATGCTCATCCTAGTCCGAAAGCGT
genomic: TGTGTATACATATCTGGGATGCTATCTTGGGTGATCCAGAAGGCCCATCGgtacattacc ... tctaatgcagGACACATTGATGAGGATATGCTGTGCCATGCTCATCCTAGTCCGAAAGCGT
EST: gi|76014384|gb|DT941554.1|DT941554
EST:     TGTGTATACATATCTGGGATGCTATCTTGGGTGATCCAGAAGGCCCATCG                         GACACATTGATGAGGATATGCTGTGCCATGCTCATCCTAGTCCGAAAGCGT
genomic: TGTGTATACATATCTGGGATGCTATCTTGGGTGATCCAGAAGGCCCATCGgtacattacc ... tctaatgcagGACACATTGATGAGGATATGCTGTGCCATGCTCATCCTAGTCCGAAAGCGT
EST: gi|76011673|gb|DT938843.1|DT938843
EST:     TGTGTATACATATTTGGGATGCTATCTTGGGTGATCCAGAAGGCCCATCG                         GACACATTGATGAGGATATGCTGTGCCATGCTCATCCTAGTCCGAAAGCGT
genomic: TGTGTATACATATCTGGGATGCTATCTTGGGTGATCCAGAAGGCCCATCGgtacattacc ... tctaatgcagGACACATTGATGAGGATATGCTGTGCCATGCTCATCCTAGTCCGAAAGCGT
EST: gi|71425450|gb|DR806680.1|DR806680
EST:     TGTGTATACATATCTGGGATGCTATCTTGGGTGATCCAGAAGGCCCTTCG                         GACACATTGATGAGGATATGCTGTGCCATGCTCATCCTAGTCCGAAAGCGT
genomic: TGTGTATACATATCTGGGATGCTATCTTGGGTGATCCAGAAGGCCCATCGgtacattacc ... tctaatgcagGACACATTGATGAGGATATGCTGTGCCATGCTCATCCTAGTCCGAAAGCGT
EST: gi|32928604|gb|CF033416.1|CF033416
EST:     TGTGTATACATATCTGGGATGCTATCTTGGGTGATCCAGAAGGCCCATCG                         GACACATTGATGAGGATATGCTGTGCCATGCTCATCCTAGTCCGAAAGCGT
genomic: TGTGTATACATATCTGGGATGCTATCTTGGGTGATCCAGAAGGCCCATCGgtacattacc ... tctaatgcagGACACATTGATGAGGATATGCTGTGCCATGCTCATCCTAGTCCGAAAGCGT
EST: gi|31628335|gb|CD526557.1|CD526557
EST:     TGTGTATACATATCTGGGATGCTATCTTGGGTGATCCAGAAGGCCCATCG                         GACACATTGATGAGGATATGCTGTGCCATGCTCATCCTAGTCCGAAAGCGT
genomic: TGTGTATACATATCTGGGATGCTATCTTGGGTGATCCAGAAGGCCCATCGgtacattacc ... tctaatgcagGACACATTGATGAGGATATGCTGTGCCATGCTCATCCTAGTCCGAAAGCGT
EST: gi|83278661|gb|DV942669.1|DV942669
EST:     TGTGTATACATATCTGGGATGCTATCTTGGGTGATCCAGAAGGCCCATCG                         GACACATTGATGAGGATATGCTGTGCCATGCTCATCCTAGTCCGAAAGCGT
genomic: TGTGTATACATATCTGGGATGCTATCTTGGGTGATCCAGAAGGCCCATCGgtacattacc ... tctaatgcagGACACATTGATGAGGATATGCTGTGCCATGCTCATCCTAGTCCGAAAGCGT
EST: gi|38687663|gb|CK144694.1|CK144694
EST:     TGTGTATACATATCTGGGATGCTATCTTGGGTGATCCAGAAGGCCCATCG                         GACACATTGATGAGGATATGCTGTGCCATGCTCATCCTAGTCCGAAAGCGT
genomic: TGTGTATACATATCTGGGATGCTATCTTGGGTGATCCAGAAGGCCCATCGgtacattacc ... tctaatgcagGACACATTGATGAGGATATGCTGTGCCATGCTCATCCTAGTCCGAAAGCGT
EST: gi|149089684|gb|EE178941.2|EE178941
EST:     TGTGTATACATATTTGGGATGCTATCTTGGGTGATCCAGAAGGCCCATCG                         GACACATTGATGAGGATATGCTGTGCCATGCTCATCCTAGTCCGAAAGCGT
genomic: TGTGTATACATATCTGGGATGCTATCTTGGGTGATCCAGAAGGCCCATCGgtacattacc ... tctaatgcagGACACATTGATGAGGATATGCTGTGCCATGCTCATCCTAGTCCGAAAGCGT
EST: gi|32928506|gb|CF033318.1|CF033318
EST:     TGTGTATACATATCTGGGATGCTATCTTGGGTGATCCAGAAGGCCCATCG                         GACACATTGATGAGGATATGCTGTGCCATGCTCATCCTAGTCCGAAAGCGT
genomic: TGTGTATACATATCTGGGATGCTATCTTGGGTGATCCAGAAGGCCCATCGgtacattacc ... tctaatgcagGACACATTGATGAGGATATGCTGTGCCATGCTCATCCTAGTCCGAAAGCGT
EST: gi|74241509|gb|DT649423.1|DT649423
EST:     TGTGTATACATATCTGGGATGCTATCTTGGGTGATCCAGAAGGCCCATCG                         GACACATTGATGAGGATATGCTGTGCCATGCTCATCCTAGTCCGAAAGCGT
genomic: TGTGTATACATATCTGGGATGCTATCTTGGGTGATCCAGAAGGCCCATCGgtacattacc ... tctaatgcagGACACATTGATGAGGATATGCTGTGCCATGCTCATCCTAGTCCGAAAGCGT
EST: gi|32928299|gb|CF033111.1|CF033111
EST:     TGTGTATACATATCTGGGATGCTATCTTGGGTGATCCAGAAGGCCCATCG                         GACACATTGATGAGGATATGCTGTGCCATGCTCATCCTAGTCCGAAAGCGT
genomic: TGTGTATACATATCTGGGATGCTATCTTGGGTGATCCAGAAGGCCCATCGgtacattacc ... tctaatgcagGACACATTGATGAGGATATGCTGTGCCATGCTCATCCTAGTCCGAAAGCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggaataaatttgtggacatcttacagtgctaaaccgttgcatattctaatgcagGACACATTGATGAGGATATGCTGTGCCATGCTCATCCTAGTCCGAAAGCGTCTCTTAGCTGGAGACTTCACCGCCAATGTCCAGCTGCTGCAACATTACC
                                            ttctaat  putative branch site (score: 2)
                                         atattctaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacattaccaccactggaataaatttgtggacatcttacagtgctaaaccgttgcatattctaatgcagGACACATTGATGAGGATATGCTGTGCCATGCTCATCCTAGTCCGAAAGCGTCTCTTAGCTGGAGACTTCACCGCCAATGTCCAGCTGCTGCAACATTACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC