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

...tttggcttctctatagtatatttctctctcttttttagtgttccctgttttactctgtaatattaagtgatattgaagtgtccctgttatctctgttcagTTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGCGATGATGAAGATGATGCATCTGCTATTTTCTCG

Basic information

species Zea mays
transcript GRMZM2G156734_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G156734_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g36740.5 (Oryza sativa), 3'ss of exon 5
-tttggcttctctatagtatatttctctctcttttttagtgttccctgttttactctgtaatattaagtgata-ttgaagtgtccctgttatctctgttcagTTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGCGATGATGAAGATGATGCATCTGCTATTTTCTCG
 |     | ||   |  | |  || | |     | | | ||  | |  | ||| |   |   |||   |||||  ||| |||||| || | | ||| | ||| | ||||| ||| | ||| | ||||||||||| ||||||||||  || |||||||||||||| ||||||||||||||||||
atccctttacttctttctttcattgtttaatactgtcattgcccaccatgttaat--attggattggatgataactgatgtgtccttgctttgtctatccagCTAATGGCTCTTCTACTCTTAAGGCATACACTAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCG

upper sequence: GRMZM2G156734_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g36740.7 (Oryza sativa), 3'ss of exon 5
-tttggcttctctatagtatatttctctctcttttttagtgttccctgttttactctgtaatattaagtgata-ttgaagtgtccctgttatctctgttcagTTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGCGATGATGAAGATGATGCATCTGCTATTTTCTCG-------------------
 |     | ||   |  | |  || | |     | | | ||  | |  | ||| |   |   |||   |||||  ||| |||||| || | | ||| | ||| | ||||| ||| | ||| | ||||||||||| ||||||||||  || |||||||||||||| ||||||||||||||||||                   
atccctttacttctttctttcattgtttaatactgtcattgcccaccatgttaat--attggattggatgataactgatgtgtccttgctttgtctatccagCTAATGGCTCTTCTACTCTTAAGGCATACACTAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCGGTAAGTTAGATTTTTTTTT
















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|33101150|gb|CF061110.1|CF061110
EST:     CTGCAACAAACAACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATT                         TTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGTGAT
genomic: CTGCAACAAACAACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATTgtgagttttg ... ctctgttcagTTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGCGAT
EST: gi|76909618|gb|DV163452.1|DV163452
EST:     CTGCAACAAACAACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATT                         TTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGCGAT
genomic: CTGCAACAAACAACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATTgtgagttttg ... ctctgttcagTTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGCGAT
EST: gi|60357633|gb|DN224606.1|DN224606
EST:     CTGCAACAAACAACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATT                         TTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGCGAT
genomic: CTGCAACAAACAACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATTgtgagttttg ... ctctgttcagTTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGCGAT
EST: gi|78545094|gb|DV622592.1|DV622592
EST:     CTGCAACAAACAACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATT                         TTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGTGAT
genomic: CTGCAACAAACAACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATTgtgagttttg ... ctctgttcagTTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGCGAT
EST: gi|5871396|gb|AW017867.1|AW017867
EST:     GCTGCTGCATTTTGCCGCTCTATATTTCTGATT                         TTGATGGCCCTTTTGCTCCTGAGGCATACCCTGACCATTACTAACAGTGAT
genomic: GCTGCTGCATTTTGCCGCTCTATATTTCTGATTgtgagttttg ... ctctgttcagTTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGCGAT
EST: gi|6031346|gb|AW076203.1|AW076203
EST:     CTGCAACAAACAACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATT                         TTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGTGAT
genomic: CTGCAACAAACAACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATTgtgagttttg ... ctctgttcagTTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGCGAT
EST: gi|32924962|gb|CF029774.1|CF029774
EST:     CTGCAACAAACAACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATT                         TTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGTGAT
genomic: CTGCAACAAACAACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATTgtgagttttg ... ctctgttcagTTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGCGAT
EST: gi|29130457|gb|CB381161.1|CB381161
EST:     TGCAACAAACAACAACGCTGCTGCATTTTTGCCGCTCTATATTTCTGATT                         TTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGCGAT
genomic: TGCAACAAACAACAACGCTGCTGCATTTT-GCCGCTCTATATTTCTGATTgtgagttttg ... ctctgttcagTTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGCGAT
EST: gi|32924741|gb|CF029553.1|CF029553
EST:     CTGCAACAAACAACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATT                         TTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGTGAT
genomic: CTGCAACAAACAACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATTgtgagttttg ... ctctgttcagTTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGCGAT
EST: gi|5770167|gb|AI973341.1|AI973341
EST:     ACAACGTTGCTGCATTTTGCCGCTCTATATTTCTGATT                         TTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGTGAT
genomic: ACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATTgtgagttttg ... ctctgttcagTTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGCGAT
EST: gi|32925907|gb|CF030719.1|CF030719
EST:     CTGCAACAAACAACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATT                         TTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGTGAT
genomic: CTGCAACAAACAACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATTgtgagttttg ... ctctgttcagTTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGCGAT
EST: gi|28390336|gb|CB250165.1|CB250165
EST:     CTGCAACAAACAACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATT                         TTGATGGNCCTTTTGCTCCTGAGGCATACACTGACCATTTACTAACAGCGA
genomic: CTGCAACAAACAACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATTgtgagttttg ... ctctgttcagTTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATT-ACTAACAGCGA
EST: gi|78125041|gb|DV543425.1|DV543425
EST:     CTGCAACAAACAACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATT                         TTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGCGAT
genomic: CTGCAACAAACAACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATTgtgagttttg ... ctctgttcagTTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGCGAT
EST: gi|32925165|gb|CF029977.1|CF029977
EST:     CTGCAACAAACAACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATT                         TTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGTGAT
genomic: CTGCAACAAACAACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATTgtgagttttg ... ctctgttcagTTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGCGAT
EST: gi|5325050|gb|AI783241.1|AI783241
EST:     CTGCAACAAACAACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATT                         TTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGTGAT
genomic: CTGCAACAAACAACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATTgtgagttttg ... ctctgttcagTTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGCGAT
EST: gi|78074789|gb|DV503223.1|DV503223
EST:     CTGCAACAAACAACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATT                         TTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGCGAT
genomic: CTGCAACAAACAACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATTgtgagttttg ... ctctgttcagTTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGCGAT
EST: gi|32926687|gb|CF031499.1|CF031499
EST:     CTGCAACAAACAACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATT                         TTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGTGAT
genomic: CTGCAACAAACAACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATTgtgagttttg ... ctctgttcagTTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGCGAT
EST: gi|60358023|gb|DN224996.1|DN224996
EST:     CTGCAACAAACAACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATT                         TTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGCGAT
genomic: CTGCAACAAACAACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATTgtgagttttg ... ctctgttcagTTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGCGAT
EST: gi|28361582|gb|CB239938.1|CB239938
EST:     CTGCAACAAACAACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATT                         TTGATGGCCCTTTTGCTCCTGAGGCATAACACTGACCATTACTAACAGCGA
genomic: CTGCAACAAACAACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATTgtgagttttg ... ctctgttcagTTGATGGCCCTTTTGCTCCTGAGGCATA-CACTGACCATTACTAACAGCGA
EST: gi|71332392|gb|DR803152.1|DR803152
EST:     CTGCAACAAACAACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATT                         TTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGCGAT
genomic: CTGCAACAAACAACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATTgtgagttttg ... ctctgttcagTTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGCGAT
EST: gi|6031347|gb|AW076204.1|AW076204
EST:     CTGCAACAAACAACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATT                         TTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGTGAT
genomic: CTGCAACAAACAACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATTgtgagttttg ... ctctgttcagTTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGCGAT
EST: gi|32925763|gb|CF030575.1|CF030575
EST:     CTGCAACAAACAACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATT                         TTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGTGAT
genomic: CTGCAACAAACAACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATTgtgagttttg ... ctctgttcagTTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGCGAT
EST: gi|16378881|gb|BI992655.1|BI992655
EST:     AACGCTGCTGCATTTTGCCGCTCTATATTTCTGATT                         TTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGCGAT
genomic: AACGCTGCTGCATTTTGCCGCTCTATATTTCTGATTgtgagttttg ... ctctgttcagTTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGCGAT
EST: gi|76013718|gb|DT940888.1|DT940888
EST:     CTGCAACACACAACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATT                         TTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGCGAT
genomic: CTGCAACAAACAACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATTgtgagttttg ... ctctgttcagTTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGCGAT
EST: gi|86469928|gb|DY236298.1|DY236298
EST:     CTGCAACAAACAACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATT                         TTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGCGAT
genomic: CTGCAACAAACAACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATTgtgagttttg ... ctctgttcagTTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGCGAT
EST: gi|101402591|gb|EB822839.1|EB822839
EST:     CTGCAACAAACAACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATT                         TTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGCGAT
genomic: CTGCAACAAACAACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATTgtgagttttg ... ctctgttcagTTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGCGAT
EST: gi|5846862|gb|AI999945.1|AI999945
EST:     CTGCAACAAACAACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATT                         TTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGTGAT
genomic: CTGCAACAAACAACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATTgtgagttttg ... ctctgttcagTTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGCGAT
EST: gi|32926380|gb|CF031192.1|CF031192
EST:     CTGCAACAAACAACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATT                         TTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGTGAT
genomic: CTGCAACAAACAACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATTgtgagttttg ... ctctgttcagTTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGCGAT
EST: gi|32924716|gb|CF029528.1|CF029528
EST:     CTACAACAAACAACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATT                         TTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGTGAT
genomic: CTGCAACAAACAACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATTgtgagttttg ... ctctgttcagTTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGCGAT
EST: gi|60395273|gb|DN228142.1|DN228142
EST:     CTGCAACAAACAACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATT                         TTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGCGAT
genomic: CTGCAACAAACAACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATTgtgagttttg ... ctctgttcagTTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGCGAT
EST: gi|32840136|gb|CD979817.1|CD979817
EST:     CTGCAACAAACAACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATT                         TTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGTGAT
genomic: CTGCAACAAACAACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATTgtgagttttg ... ctctgttcagTTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGCGAT
EST: gi|60336732|gb|DN203705.1|DN203705
EST:     CTGCAACAAACAACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATT                         TTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGCGAT
genomic: CTGCAACAAACAACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATTgtgagttttg ... ctctgttcagTTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGCGAT
EST: gi|76936722|gb|DV174850.1|DV174850
EST:     CTGCAACAAACAACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATT                         TTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGCGAT
genomic: CTGCAACAAACAACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATTgtgagttttg ... ctctgttcagTTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGCGAT
EST: gi|211013250|gb|FL462098.1|FL462098
EST:     CTGCAACAAACAACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATT                         TTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGTGAT
genomic: CTGCAACAAACAACAACGCTGCTGCATTTTGCCGCTCTATATTTCTGATTgtgagttttg ... ctctgttcagTTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGCGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttttactctgtaatattaagtgatattgaagtgtccctgttatctctgttcagTTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGCGATGATGAAGATGATGCATCTGCTATTTTCTCG
                                   tccctgttatctct  CT-rich tract
            taatattaagtgatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttggcttctctatagtatatttctctctcttttttagtgttccctgttttactctgtaatattaagtgatattgaagtgtccctgttatctctgttcagTTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGCGATGATGAAGATGATGCATCTGCTATTTTCTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - gcttctc