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

...ttgtttaactccaaattatgtcatgcctcatgcaatgttatcttttattacctggatgattctgacactctttctgctgtttgatgtttctgtttgacagCATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG

Basic information

species Zea mays
transcript GRMZM2G121456_T03
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G121456_T03 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g19510.1 (Oryza sativa), 3'ss of exon 6
ttgtttaactccaaattatgtcatgcctcatgcaatgttatcttttattacctggat---gattctgacactc-tttctgctgtttgatgtttctgtttgacagCATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
    |    |   |||  | || |    |   | || ||  |||   || | | |||   | || || ||||| |||   ||||||  | |  || |||| ||| |||||||||||||| |||||||||||||| ||||
---gtacttttggaatgctctcttttagctatccatcttgccttaagttgcattgatttcggttatg-cactcattttcactgttttgtttccctttttggcagTATGGGAGCTTTTCTGCTTAGTGCTGGGACAAAAG

upper sequence: GRMZM2G121456_T03 (Zea mays), 3'ss of exon 6
lower sequence: AT1G02560.1 (Arabidopsis thaliana), 3'ss of exon 6
ttgtttaactccaaattatgtcatgcctcatg--caatgttatcttttattacctggatgattctgacactct-ttctgctgtttgatgtttctgtttgacagCATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
 |||||  ||| |||  | |  || | |  |   |  |||  |    | || ||| ||| ||     |   || || | |||| |    |||||  |  |||| |||||||||||||| ||||||||||| |||||||
-tgttt--ctcgaaaacacggaatccttttttatctgtgtggttgaatgtttcctagattatgacatcctcctctttttctgtgttggttttcttatgaacagTATGGGAGCTTTTCTGCTTAGTGCTGGAACCAAAG
















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|19769319|gb|BQ034040.1|BQ034040
EST:     TGTATCCCCTGTTTGTATTGGACTAGCTGCAAG                         CATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
genomic: TGTATCCACTGTTTGTATTGGACTAGCTGCAAGgtactgaaca ... tgtttgacagCATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
EST: gi|110519563|gb|EE023896.1|EE023896
EST:     AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGCACTAGCTGCAAG                         CATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
genomic: AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAGgtactgaaca ... tgtttgacagCATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
EST: gi|74237088|gb|DT645002.1|DT645002
EST:     AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAG                         CATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
genomic: AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAGgtactgaaca ... tgtttgacagCATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
EST: gi|78092088|gb|DV520462.1|DV520462
EST:     AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAG                         CATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
genomic: AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAGgtactgaaca ... tgtttgacagCATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
EST: gi|19821991|gb|BQ048015.1|BQ048015
EST:     AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAG                         CATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
genomic: AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAGgtactgaaca ... tgtttgacagCATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
EST: gi|71436538|gb|DR817588.1|DR817588
EST:     AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAG                         CATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
genomic: AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAGgtactgaaca ... tgtttgacagCATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
EST: gi|148939986|gb|EC884717.2|EC884717
EST:     AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAG                         CATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
genomic: AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAGgtactgaaca ... tgtttgacagCATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
EST: gi|32942454|gb|CF047273.1|CF047273
EST:     AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCCGCAAG                         CATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
genomic: AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAGgtactgaaca ... tgtttgacagCATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
EST: gi|211478511|gb|FL023987.1|FL023987
EST:     AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAG                         CATGGGAGCTTTTTCTACTTAGTGCTGGGACCAAAG
genomic: AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAGgtactgaaca ... tgtttgacagCATGGGAGCTTTT-CTACTTAGTGCTGGGACCAAAG
EST: gi|20208074|gb|BQ134163.1|BQ134163
EST:     AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAG                         CATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
genomic: AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAGgtactgaaca ... tgtttgacagCATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
EST: gi|26456147|gb|CA827730.1|CA827730
EST:     AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAG                         CATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
genomic: AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAGgtactgaaca ... tgtttgacagCATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
EST: gi|149088221|gb|EE177331.2|EE177331
EST:     AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAG                         CATGGGAACTTTTCTACTTAGTGCTGGGACCAAAG
genomic: AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAGgtactgaaca ... tgtttgacagCATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
EST: gi|101399114|gb|EB821430.1|EB821430
EST:     AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAG                         CATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
genomic: AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAGgtactgaaca ... tgtttgacagCATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
EST: gi|78111070|gb|DV529467.1|DV529467
EST:     AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAG                         CATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
genomic: AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAGgtactgaaca ... tgtttgacagCATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
EST: gi|78544613|gb|DV622111.1|DV622111
EST:     AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAG                         CATGGGAGCTTTTTTACTTAGTGCTGGGACCAAAG
genomic: AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAGgtactgaaca ... tgtttgacagCATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
EST: gi|76919121|gb|DV167599.1|DV167599
EST:     AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAG                         CATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
genomic: AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAGgtactgaaca ... tgtttgacagCATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
EST: gi|71427481|gb|DR808531.1|DR808531
EST:     AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAG                         CATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
genomic: AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAGgtactgaaca ... tgtttgacagCATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
EST: gi|71445134|gb|DR826184.1|DR826184
EST:     AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAG                         CATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
genomic: AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAGgtactgaaca ... tgtttgacagCATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
EST: gi|74245787|gb|DT653701.1|DT653701
EST:     AAGCATATCAGGCCTGATGTATCCACTGTTTGTATCGGACTAGCTGCAAG                         CATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
genomic: AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAGgtactgaaca ... tgtttgacagCATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
EST: gi|148939985|gb|EC884716.2|EC884716
EST:     AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAG                         CATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
genomic: AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAGgtactgaaca ... tgtttgacagCATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
EST: gi|78090189|gb|DV518563.1|DV518563
EST:     AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAG                         CATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
genomic: AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAGgtactgaaca ... tgtttgacagCATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
EST: gi|148938546|gb|EC882867.2|EC882867
EST:     AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAG                         CATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
genomic: AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAGgtactgaaca ... tgtttgacagCATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
EST: gi|19822147|gb|BQ048171.1|BQ048171
EST:     AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAG                         CATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
genomic: AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAGgtactgaaca ... tgtttgacagCATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
EST: gi|50338176|gb|CO533302.1|CO533302
EST:     AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAG                         CATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
genomic: AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAGgtactgaaca ... tgtttgacagCATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
EST: gi|58029811|gb|CX725238.1|CX725238
EST:     AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAG                         CATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
genomic: AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAGgtactgaaca ... tgtttgacagCATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
EST: gi|101400189|gb|EB821914.1|EB821914
EST:     AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAG                         CATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
genomic: AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAGgtactgaaca ... tgtttgacagCATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
EST: gi|93282145|gb|EB674409.1|EB674409
EST:     AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAG                         CATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
genomic: AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAGgtactgaaca ... tgtttgacagCATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
EST: gi|76012850|gb|DT940020.1|DT940020
EST:     AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAG                         CATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
genomic: AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAGgtactgaaca ... tgtttgacagCATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
EST: gi|211478510|gb|FL023986.1|FL023986
EST:     AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAG                         CATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
genomic: AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAGgtactgaaca ... tgtttgacagCATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
EST: gi|93282646|gb|EB674910.1|EB674910
EST:     AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAG                         CATGGGAGCTTTTCTACTTAGTGCTGGGACCCAAG
genomic: AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAGgtactgaaca ... tgtttgacagCATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
EST: gi|9254470|gb|BE344938.1|BE344938
EST:     AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAG                         CATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
genomic: AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAGgtactgaaca ... tgtttgacagCATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
EST: gi|148934818|gb|EC878864.2|EC878864
EST:     AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAG                         CATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
genomic: AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAGgtactgaaca ... tgtttgacagCATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
EST: gi|113702266|gb|EE679770.1|EE679770
EST:     AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAG                         CATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
genomic: AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAGgtactgaaca ... tgtttgacagCATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
EST: gi|101399344|gb|EB821545.1|EB821545
EST:     AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAG                         CATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
genomic: AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAGgtactgaaca ... tgtttgacagCATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
EST: gi|71307773|gb|DR790105.1|DR790105
EST:     AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAG                         CATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
genomic: AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAGgtactgaaca ... tgtttgacagCATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
EST: gi|26455779|gb|CA827362.1|CA827362
EST:     AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAG                         CATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
genomic: AAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAGgtactgaaca ... tgtttgacagCATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattacctggatgattctgacactctttctgctgtttgatgtttctgtttgacagCATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG
                                         tttctgttt  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtttaactccaaattatgtcatgcctcatgcaatgttatcttttattacctggatgattctgacactctttctgctgtttgatgtttctgtttgacagCATGGGAGCTTTTCTACTTAGTGCTGGGACCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT