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

gtaagcttgtacccttcttctgtatgcactgtttctttcttcatttgcttttatccaatttatgactagttgtataatgcagGTGATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAAAA

Basic information

species Zea mays
transcript GRMZM2G076826_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G076826_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os04g53240.4 (Oryza sativa), 3'ss of exon 2
gtaagcttgtaccc----ttcttctgtatgcactgtttctttcttcat--ttgcttttatccaatttatgactagtt--gtataatgcagGTGATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAAAA
|||||||||  |      ||  || || |    |||||| ||| |  |  ||  |||  || ||||| | ||   |    | ||||| |||||||||||||||| ||||| || ||||| |||||||||||||||||||||||
gtaagcttgctcttcatattgctcagt-tatgttgtttccttcattgtggtttttttgctctaatttgttacatatctaatgtaatgtagGTGATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAAAA

upper sequence: GRMZM2G076826_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv19s0090g00580.t01 (Vitis vinifera), 3'ss of exon 3
---gtaagcttgtacccttcttctgtatgcactgtttc----tttcttcatttgcttttatccaa------tttatgactagttgtataatgc-----agGTGATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAAAA
     || |||||  |  |    |  |   | | |||     | || |   ||   | | || ||      | | | | || || | |  |||     |||| ||||| ||||||||||| || |||||||| |||||||| |||||||| ||
gtatgaaacttgtgtctcttacatcaagaaagtttttggacgtctcatatgttatgtgtgtctaaatgttgtctttcattatttttctggtgccatatagGTTATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAGAA
















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|211035126|gb|FL190210.1|FL190210
EST:     GGCAGTCTGAGGCTAATCGGATCAGAGAGAAGTACCCTGACAGAATTCCA                         GTGATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAA
genomic: GGCAGTCTGAGGCTAATCGGATCAGAGAGAAGTACCCTGACAGAATTCCAgtaagcttgt ... tataatgcagGTGATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAA
EST: gi|211509914|gb|FL437411.1|FL437411
EST:     GGCAGTCTGAGGCTAATCGGATCAGAGAGAAGTACCCTGACAGAATTCCA                         GTGATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAA
genomic: GGCAGTCTGAGGCTAATCGGATCAGAGAGAAGTACCCTGACAGAATTCCAgtaagcttgt ... tataatgcagGTGATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAA
EST: gi|18165025|gb|BM334870.1|BM334870
EST:     GGCAGTCTGAGGCTAATCGGATCAGAGAGAAGTACCCTGACAGAATTCCA                         GTGATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGGCAAGAAA
genomic: GGCAGTCTGAGGCTAATCGGATCAGAGAGAAGTACCCTGACAGAATTCCAgtaagcttgt ... tataatgcagGTGATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAA
EST: gi|71441162|gb|DR822212.1|DR822212
EST:     GGCAGTCTGAGGCTAATCGGATCAGAGAGAAGTACCCTGACAGAATTCCA                         GTGATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAA
genomic: GGCAGTCTGAGGCTAATCGGATCAGAGAGAAGTACCCTGACAGAATTCCAgtaagcttgt ... tataatgcagGTGATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAA
EST: gi|91052588|gb|EB163006.1|EB163006
EST:     GGCAGTCTGAGGCTAATCGGATCAGAGAGAAGTACCCTGACAGAATTCCA                         GTGATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAA
genomic: GGCAGTCTGAGGCTAATCGGATCAGAGAGAAGTACCCTGACAGAATTCCAgtaagcttgt ... tataatgcagGTGATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAA
EST: gi|211192317|gb|FL065114.1|FL065114
EST:     GGCAGTCTGAGGCTAATCGGATCAGAGAGAAGTACCCTGACAGAATTCCA                         GTGATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAA
genomic: GGCAGTCTGAGGCTAATCGGATCAGAGAGAAGTACCCTGACAGAATTCCAgtaagcttgt ... tataatgcagGTGATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAA
EST: gi|18169711|gb|BM339551.1|BM339551
EST:     GGCTAATCGGATCAGAGAGAAGTACCCTGACAGAATTCCA                         GTGATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAA
genomic: GGCTAATCGGATCAGAGAGAAGTACCCTGACAGAATTCCAgtaagcttgt ... tataatgcagGTGATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAA
EST: gi|71434664|gb|DR815714.1|DR815714
EST:     GGCAGTCTGAGGCTAATCGGATCAGAGAGAAGTACCCTGACAGAATTCCA                         GTGATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAA
genomic: GGCAGTCTGAGGCTAATCGGATCAGAGAGAAGTACCCTGACAGAATTCCAgtaagcttgt ... tataatgcagGTGATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAA
EST: gi|211194714|gb|FL065125.1|FL065125
EST:     GGCAGTCTGAGGCTAATCGGATCAGAGAGAAGTACCCTGACAGAATTCCA                         GTGATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAA
genomic: GGCAGTCTGAGGCTAATCGGATCAGAGAGAAGTACCCTGACAGAATTCCAgtaagcttgt ... tataatgcagGTGATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAA
EST: gi|211192306|gb|FL065103.1|FL065103
EST:     GGCAGTCTGAGGCTAATCGGATCAGAGAGAAGTACCCTGACAGAATTCCA                         GTGATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAA
genomic: GGCAGTCTGAGGCTAATCGGATCAGAGAGAAGTACCCTGACAGAATTCCAgtaagcttgt ... tataatgcagGTGATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAA
EST: gi|32914236|gb|CF019048.1|CF019048
EST:     GGCAGTCTGAGGCTAATCGGATCAGAGAGAAGTACCCTGACAGAATTCCA                         GTGATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAA
genomic: GGCAGTCTGAGGCTAATCGGATCAGAGAGAAGTACCCTGACAGAATTCCAgtaagcttgt ... tataatgcagGTGATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAA
EST: gi|16926343|gb|BM079411.1|BM079411
EST:     AGTACCCTGACAGAATTCCA                         GTGATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAA
genomic: AGTACCCTGACAGAATTCCAgtaagcttgt ... tataatgcagGTGATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAA
EST: gi|91052589|gb|EB163007.1|EB163007
EST:     GGCAGTCTGAGGCTAATCGGATCAGAGAGAAGTACCCTGACAGAATTCCA                         GTGATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAA
genomic: GGCAGTCTGAGGCTAATCGGATCAGAGAGAAGTACCCTGACAGAATTCCAgtaagcttgt ... tataatgcagGTGATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAA
EST: gi|6194643|gb|AW146747.1|AW146747
EST:     GGCAGTCTGAGGCTAATCGGATCAGAGAGAAGTACCCTGACAGAATTCCA                         GTGATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAA
genomic: GGCAGTCTGAGGCTAATCGGATCAGAGAGAAGTACCCTGACAGAATTCCAgtaagcttgt ... tataatgcagGTGATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAA
EST: gi|93016973|gb|EB642493.1|EB642493
EST:     GGCAGTCTGAGGCTAATCGGATCAGAGAGAAGTACCCTGACAGAATTCCA                         GTGATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAA
genomic: GGCAGTCTGAGGCTAATCGGATCAGAGAGAAGTACCCTGACAGAATTCCAgtaagcttgt ... tataatgcagGTGATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAA
EST: gi|211194707|gb|FL065118.1|FL065118
EST:     GGCAGTCTGAGGCTAATCGGATCAGAGAGAAGTACCCTGACAGAATTCCA                         GTGATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAA
genomic: GGCAGTCTGAGGCTAATCGGATCAGAGAGAAGTACCCTGACAGAATTCCAgtaagcttgt ... tataatgcagGTGATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actgtttctttcttcatttgcttttatccaatttatgactagttgtataatgcagGTGATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAAAA
                     ttttatccaatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcttgtacccttcttctgtatgcactgtttctttcttcatttgcttttatccaatttatgactagttgtataatgcagGTGATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA