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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattgctagtaacattggtggaaacaagtcacattataaactcaaaaaaaggcatctgtcaatagttataagactggatgtttctccaatgctgttatagctgctgccacaattaatcatttctccctcatgttttctcccatctacatgtcatagatgtaaaatatgatatgatctgtttcatctggcagATTCAATGTCTGTTTGGAACCTATTAAGAGAGTTCCGGATCAGGCAGGTTCATATGGCAGTGGTCCTCAATGAATATGGTGGAACTATTGGT

Basic information

species Zea mays
transcript GRMZM2G153928_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G153928_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g39640.1 (Oryza sativa), 3'ss of exon 9
gtaattgctagtaacattggtggaaacaagtcacattataaactcaaaaaaaggcatctgtcaatagttataagactggatgtttctccaatgctgttatagctgctgccacaattaatcatttctccctcatgttttctcccatctacatgtcatagatgtaaaatatgatatgatctgtttcatctggcagATTCAATGTCTGTTTGGAACCTATTAAGAGAGTTCCGGATCAGGCAGGTTCATATGGCAGTGGTCCTCAATGAATATGGTGGAACTATTGGT
                                                                                      || ||| | | | |   |   ||       | || ||    | | |||||| |||   || |||||||||| |||||||| |||  ||  | ||| |    || ||||||||||||||||||||||| |  |||||||||| || |||||||||||||||||||||||||||||||| ||||||||||| |||||||||
--------------------------------------------------------------------------------------tcaaatccagatttgtgtagggcattg--cattctttatgtcttaatgtttcctctggtccacatgtcatatatgtaaaa-atgtgatattttgtct----tgacagATTCAATGTCTGTTTGGAACTTGCTAAGAGAGTTTCGCATCAGGCAGGTTCATATGGCAGTGGTCCTCAACGAATATGGTGGGACTATTGGT

upper sequence: GRMZM2G153928_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA14G01920.1 (Glycine max), 3'ss of exon 9
gtaattgctagtaacattggtggaaacaagtcacattataaactcaaaaaaaggcatctgtcaatagttataagactggatgtttctccaatgctgttatagctgctgccacaattaatcatttctccctcatgttttctcccatctacatgtcatagatgtaaaatatgatatgatctgtttcatctg----gcagATTCAATGTCTGTTTGGAACCTATTAAGAGAGTTCCGGATCAGGCAGGTTCATATGGCAGTGGTCCTCAATGAATATGGTGGAACTATTGGT
                                                                                                 |  |  || |       || ||  | |||     | |  | |  | || |   |    | | || | ||| | | || |  ||||    |||    ||||||||||||||||||||||| ||  | ||||||||| | |||||| ||||||| |||||||| || || ||||| |||||||||||| | || 
-----------------------------------------------------------------------------------------------aattgaattgttaaactggttgatt-tgtctgggataggaatacatctatatcttttaacttggtgcagaatgtta-ataaattgttattactgatttgcagATTCAATGTCTGTTTGGAATCTTCTTAGAGAGTTCAGAATCAGGAAGGTTCACATGGCAGTTGTTCTTAATGAGTATGGTGGAACTGTGGGG

upper sequence: GRMZM2G153928_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA02G46780.1 (Glycine max), 3'ss of exon 9
gtaattgctagtaacattggtggaaacaagtcacattataaactcaaaaaaaggcatctgtcaatagttataagactggatgtttctccaatgctgttatagctgctgccacaattaatcatttctccctcatgttttctcccatctacatgtca-tagatgtaaaatatgatatgatctgtttcatctggcagATTCAATGTCTGTTTGGAACCTATTAAGAGAGTTCCGGATCAGGCAGGTTCATATGGCAGTGGTCCTCAATGAATATGGTGGAACTATTGGT
                                                                                          |||    |  |  || |       || | | | |||     | |  | |  | || |   | | | | | || | ||| | |    |||    | || || |||||||||||||||||||||| ||  | ||||||||| | |||||| ||||||| ||||| || || || || || |||||||||||| | || 
------------------------------------------------------------------------------------------atgggaattgaattgttaaactggttgaac-tgtctgggataggaatacatctatatctgtttaacttggtgcagaatgttaataaatcc--ctgatttg-cagATTCAATGTCTGTTTGGAATCTTCTTAGAGAGTTCAGAATCAGGAAGGTTCACATGGCGGTTGTTCTTAACGAGTATGGTGGAACTGTGGGG

upper sequence: GRMZM2G153928_T02 (Zea mays), 3'ss of exon 3
lower sequence: AT1G55930.1 (Arabidopsis thaliana), 3'ss of exon 9
gtaattgctagtaacattggtggaaacaagtcacattataaactcaaaaaaaggcatctgtcaatagttataagactggatgtttctccaatgctgttatagctgctgccacaattaatcatttctccctcatgttttctcccatctacatgt-catagatgtaaaatatgatatgatctgtttcatctggcagATTCAATGTCTGTTTGGAACCTATTAAGAGAGTTCCGGATCAGGCAGGTTCATATGGCAGTGGTCCTCAATGAATATGGTGGAACTATTGGT
                                                                                            |   | |||| |||   || |  |  | || |    |  ||   ||   |  |||   |   ||| ||  |||  | |||| | || |   | || || ||||||| ||||| |||||||| ||  | ||||||||  | || ||  ||||||| |||||||| || || ||||||||||||||||| || || 
--------------------------------------------------------------------------------------------gtaatcatagatgcattca-atcttttaatctaatacatatacctttgacattctttgttcacatgga-ataatctttgatgttatgtcaataatttg-cagATTCGATGTCAGTTTGGAATCTTCTTAGAGAGTTTAGAATAAGAAAGGTTCACATGGCAGTTGTTCTTAATGAATATGGTGGAACCATCGGA

upper sequence: GRMZM2G153928_T02 (Zea mays), 3'ss of exon 3
lower sequence: AT3G13070.1 (Arabidopsis thaliana), 3'ss of exon 9
gtaattgctagtaacattggtggaaacaagtcacattataaactcaaaaaaaggcatctgtca-atagttataagactggatgtttctccaatgctgttatagctgctgccacaattaatcatttctccctcatgttttctcccatctacatgtcatagatgtaaaatatgatatgatctgtttcatctggcagATTCAATGTCTGTTTGGAACCTATTAAGAGAGTTCCGGATCAGGCAGGTTCATATGGCAGTGGTCCTCAATGAATATGGTGGAACTATTGGT
||||||   | |     || | |      |  |  ||   ||   |   |   | ||   ||| ||  ||     | | |  | ||     || ||||||||     | ||   ||||| ||    | | |||   |   |      || |      |||    |||| | ||   || |||| ||  | ||||||||||||||||||||||| ||  | ||||| ||||| || ||  ||||||| |||||||| ||||| || |||||||||||||| || || 
gtaattatcaatg----tgtttgcttttggatatgttgccaaactaggcatttgaatgcttcagattttttctgcattcg--gattaaattatactgttata----ttaccgacattaaacacgaattcttcacactgaattat---tatactctgaaga----aaatctaatgatatatgttacactttgcagATTCAATGTCTGTTTGGAATCTTCTTAGAGAATTCCGAATAAGAAAGGTTCACATGGCAGTTGTCCTTAACGAATATGGTGGAACGATCGGA

upper sequence: GRMZM2G153928_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv19s0090g01820.t01 (Vitis vinifera), 3'ss of exon 9
gtaattgctagtaacattggtggaaacaagtcacattataaactcaaaaaaaggcatctgtcaatagttataagactggatgtttctccaatgctgttatagctgctgccacaattaatcatttctccctcatgttttctcccatctacatgtcatagatgtaaaatatgatatgatctgtttcatctggcagATTCAATGTCTGTTTGGAACCTATTAAGAGAGTTCCGGATCAGGCAGGTTCATATGGCAGTGGTCCTCAATGAATATGGTGGAACTATTGGT
                                                                                   || ||   |||| | || | |     |  ||    ||       ||  ||   | |||  | | ||    | | ||   ||  ||| | || |        || | ||||||||||||||||| ||||| ||  ||||||| || || |||||| |||| || ||||| || || |||||||| |||||||||||| | || 
-----------------------------------------------------------------------------------ttgtct--tgctttcattgatttgaacctaagacctcccactcgccaaataagtgctctaaccaactgagctttgaataaacttataacatca--------attttgcagATTCAATGTCTGTCTGGAATCTTCTAAGAGAATTTCGCATCAGGAAGGTCCACATGGCTGTTGTTCTCAATGAGTATGGTGGAACTGTGGGA

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|87155760|gb|DY400549.1|DY400549
EST:     TGCAATCACTGTGAAGGAAATCGCACATATGCCTACATACTTTGTTCCAG                         ATTCAATGTCTGTTTGGAACCTATTAAGAGAGTTCCGGATCAGGCAGGTTC
genomic: TGCAATCACTGTGAAGGAAATCGCACATATGCCTACATACTTTGTTCCAGgtaattgcta ... catctggcagATTCAATGTCTGTTTGGAACCTATTAAGAGAGTTCCGGATCAGGCAGGTTC
EST: gi|26558918|gb|CA831153.1|CA831153
EST:     TGCAATCACTGTGAAGGAAATCGCACATATGCCTACATACTTTGTTCCAG                         ATTCAATGTCTGTTTGGAACCTATTAAGAGAGTTCCGGATCAGGCAGGTTC
genomic: TGCAATCACTGTGAAGGAAATCGCACATATGCCTACATACTTTGTTCCAGgtaattgcta ... catctggcagATTCAATGTCTGTTTGGAACCTATTAAGAGAGTTCCGGATCAGGCAGGTTC
EST: gi|22473287|gb|BU037767.1|BU037767
EST:     TGCAATCACTG-GAAGGAAATCGCACATATGCCTACATACTTTGTTCCAG                         ATTCAATGTCTGTTTGGAACCTATTAAGAGAGTTCCGGATCAGGCAGGTTC
genomic: TGCAATCACTGTGAAGGAAATCGCACATATGCCTACATACTTTGTTCCAGgtaattgcta ... catctggcagATTCAATGTCTGTTTGGAACCTATTAAGAGAGTTCCGGATCAGGCAGGTTC
EST: gi|31356399|gb|CD440756.1|CD440756
EST:     TGCAATCACTGTGAAGGAAATCGCACATATGCCTACATACTTTGTTCCAG                         ATTCAATGTCTGTTTGGAACCTATTAAGAGAGTTCCGGATCAGGCAGGTTC
genomic: TGCAATCACTGTGAAGGAAATCGCACATATGCCTACATACTTTGTTCCAGgtaattgcta ... catctggcagATTCAATGTCTGTTTGGAACCTATTAAGAGAGTTCCGGATCAGGCAGGTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcccatctacatgtcatagatgtaaaatatgatatgatctgtttcatctggcagATTCAATGTCTGTTTGGAACCTATTAAGAGAGTTCCGGATCAGGCAGGTTCATATGGCAGTGGTCCTCAATGAATATGGTGGAACTATTGGT
                                      tctgtttc  CT-rich tract
                    atgtaaaatatgatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattgctagtaacattggtggaaacaagtcacattataaactcaaaaaaaggcatctgtcaatagttataagactggatgtttctccaatgctgttatagctgctgccacaattaatcatttctccctcatgttttctcccatctacatgtcatagatgtaaaatatgatatgatctgtttcatctggcagATTCAATGTCTGTTTGGAACCTATTAAGAGAGTTCCGGATCAGGCAGGTTCATATGGCAGTGGTCCTCAATGAATATGGTGGAACTATTGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA