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'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggggcaaagcaattattgaacaccatttcgttgctatttttcttctgagtgaattaactcatgccaagtgcatctacagGAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAG

Basic information

species Zea mays
transcript GRMZM2G164352_T04
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA02G10790.2 (Glycine max), 3'ss of exon 6
--gtgggggcaaagcaattattgaacaccatttcgttgctatttttcttctgagtgaattaactcatgccaagtgcatctacagGAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAG
  ||              | |||||   || |    ||   | | | | | |  | || ||  |     ||||    | | |||||||||||| | ||||| |  ||||||||||| || ||||| || || ||||| |||||||||||||| ||  | ||||||
gtgtctctttggttttggtcttgaaattcagtattctgaattatatttacaggctaaaatactttg---caag-atctttgcagGAATTGTCAACGGATTCTTTGCAGCATGTTCGCTCTGCTTTGGCTTCCGTGATAATGGGAATGGCTCCAGTGTTAGGAAAG

upper sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 6
---------------------------------------------------gtgggggcaaagc--aattattgaacaccatttcgtt--gctatttttcttctgagtgaattaactcatgccaagtg-catctacagGAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAG
                                                      | |||    |    || | |     || |||  |  | ||  ||| |  | |  |  |||| |  |   ||    | | | |||||||||||||||||||| || |||||||| || || ||||| || ||||| || |||||||||||||| ||  ||||||||
gtatacatctttggaaaagaaattataacacattaatattactgattatatacagaggctttccttggttttggtttgtcaattcagtaggataaatttatatttacaggtttaagttctttgaaacaacttttgcagGAATTGTCATCAGATTCTTCACAGCATGTCCGGTCTGCTTTGGCTTCAGTAATAATGGGAATGGCTCCAGTGTTGGGAAAG

upper sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 6
---------------------------------------------------gtgggggcaaagc--aattattgaacaccatttcgtt--gctatttttcttctgagtgaattaactcatgccaagtg-catctacagGAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAG
                                                      | |||    |    || | |     || |||  |  ||||  ||| |  | |  |  |||| |  |   ||    | | | |||||||||||||||||||| || |||||||| || || ||||| || ||||| || |||||||||||||| ||  ||||||||
gtatacatctttggaaaagaaattataacacattagtattactgattatatacagaggcttttcttggttttggttggtcaattcagtatgctaaatttatatttacaggtttaagttctttgaaacaacttttgcagGAATTGTCATCAGATTCTTCTCAGCATGTCCGGTCTGCTTTGGCTTCAGTAATAATGGGAATGGCTCCAGTGTTGGGAAAG

upper sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 6
lower sequence: Vv17s0000g03870.t01 (Vitis vinifera), 3'ss of exon 7
--------------------------------------------------------gtgggggcaaagcaattattgaacaccatttcgttgctatttttcttctgagtga--attaactcatgccaagtgcatctacagGAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAG
                                                         |    |    |    |||| | |||   ||   ||  || | ||||   | |    | ||  | |    | || | ||| |||||||| ||||||||||| ||||||||||||||||| ||||| || ||||| |||||||||||||| |||||  | ||||||
gtatacatgcttgcaaaagttttaagtttcattatgctatgaagtttcttatgggcttacatggtggggttctatttaccactgcttatctgtcatctgtcttaaaatttgtgactagattagaaaatgtccttctgcagGAATTATCATCAGATTCTTCCCAGCATGTTCGTTCTGCTTTGGCTTCAGTTATTATGGGAATGGCACCTGTTTTAGGAAAG

upper sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 6
lower sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 5
--------------------------------------gtgggggcaaagca-attattgaac--accatttcgttgctatttttcttctgag-tgaattaactcatgccaagtgcatct-acagGAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAG
                                       |   | |        ||   ||||  || |||  | |  | |    ||  |||| |   | ||    ||   |   ||| |   |||||||||||| |||||| ||||||||||| || || || || || |||||  | |||||||||||||| ||  | ||||||
gtgctcacgtttattaaaagagtgtttctctgtattatataatgtctccttttgttcacgaacttactattgagctaatgtgcacctgttgagctttctcaatatttggtgatgtcattttgtagGAATTGTCATTAGATTCGTCCCAGCATGTCCGCTCTGCCTTGGCTTCAGTTTTAATGGGAATGGCTCCCGTCTTAGGAAAG

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|87156353|gb|DY401142.1|DY401142
EST:     GCATATTAAATCCTCAGCTCTCAGTCCAACATATTCTTCCATGCGTTAAG                         GAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTG
genomic: GCATATTAAATCCTCAGCTCTCAGTCCAACATATTCTTCCATGCGTTAAGgtgggggcaa ... gcatctacagGAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTG
EST: gi|33091965|gb|CF051959.1|CF051959
EST:     GCATATTAAATCCTCAGCTCTCAGTCCAACATATTCTTCCATGCGTTAAG                         GAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTG
genomic: GCATATTAAATCCTCAGCTCTCAGTCCAACATATTCTTCCATGCGTTAAGgtgggggcaa ... gcatctacagGAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTG
EST: gi|87157118|gb|DY401907.1|DY401907
EST:     GCATATTAAATCCTCAGCTCTCAGTCCAACATATTCTTCCATGCGTTAAG                         GAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTG
genomic: GCATATTAAATCCTCAGCTCTCAGTCCAACATATTCTTCCATGCGTTAAGgtgggggcaa ... gcatctacagGAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTG
EST: gi|26558526|gb|CA830761.1|CA830761
EST:     GCATATTAAATCCTCAGCTCTCAGTCCAACATATTCTTCCATGCGTTAAG                         GAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTG
genomic: GCATATTAAATCCTCAGCTCTCAGTCCAACATATTCTTCCATGCGTTAAGgtgggggcaa ... gcatctacagGAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTG
EST: gi|32940030|gb|CF044849.1|CF044849
EST:     GCATATTAAATCCTCAGCTCTCAGTCCAACATATTCTTCCATGCGTTAAG                         GAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTG
genomic: GCATATTAAATCCTCAGCTCTCAGTCCAACATATTCTTCCATGCGTTAAGgtgggggcaa ... gcatctacagGAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTG
EST: gi|211403483|gb|FL417168.1|FL417168
EST:     GCATATTAAATCCTCAGCTCTCAGTCCAACATATTCTTCCATGCGTTAAG                         GAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTG
genomic: GCATATTAAATCCTCAGCTCTCAGTCCAACATATTCTTCCATGCGTTAAGgtgggggcaa ... gcatctacagGAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTG
EST: gi|32938569|gb|CF043388.1|CF043388
EST:     GCATATTAAATCCTCAGCTCTCAGTCCAACATATTCTTCCATGCGTTAAG                         GAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTG
genomic: GCATATTAAATCCTCAGCTCTCAGTCCAACATATTCTTCCATGCGTTAAGgtgggggcaa ... gcatctacagGAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTG
EST: gi|22546073|gb|BU098394.1|BU098394
EST:     GCATATTAAATCCTCAGCTCTCAGTCCAACATATTCTTCCATGCGTTAAG                         GAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTG
genomic: GCATATTAAATCCTCAGCTCTCAGTCCAACATATTCTTCCATGCGTTAAGgtgggggcaa ... gcatctacagGAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTG
EST: gi|31349427|gb|CD433784.1|CD433784
EST:     GCATATTAAATCCTCAGCTCTCAGTCCAACATATTCTTCCATGCGTTAAG                         GAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTG
genomic: GCATATTAAATCCTCAGCTCTCAGTCCAACATATTCTTCCATGCGTTAAGgtgggggcaa ... gcatctacagGAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTG
EST: gi|32847343|gb|CD987024.1|CD987024
EST:     GCATATTAAATCCTCAGCTCTCAGTCCAACATATTCTTCCATGCGTTAAG                         GAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTG
genomic: GCATATTAAATCCTCAGCTCTCAGTCCAACATATTCTTCCATGCGTTAAGgtgggggcaa ... gcatctacagGAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTG
EST: gi|31356642|gb|CD440999.1|CD440999
EST:     GCATATTAAATCCTCAGCTCTCAGTCCAACATATTCTTCCATGCGTTAAG                         GGATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTG
genomic: GCATATTAAATCCTCAGCTCTCAGTCCAACATATTCTTCCATGCGTTAAGgtgggggcaa ... gcatctacagGAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTG
EST: gi|42491785|gb|CK700831.1|CK700831
EST:     TTCCATGCGTTAAG                         GAATTGTCATCAGATNCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTG
genomic: TTCCATGCGTTAAGgtgggggcaa ... gcatctacagGAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTG
EST: gi|23357737|gb|BU645386.1|BU645386
EST:     GCATATTAAATCCTCAGCTCTCAGTCCAACATATTCTTCCATGCGTTAAG                         GAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTG
genomic: GCATATTAAATCCTCAGCTCTCAGTCCAACATATTCTTCCATGCGTTAAGgtgggggcaa ... gcatctacagGAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTG
EST: gi|32829962|gb|CD969640.1|CD969640
EST:     GCATATTAAATCCTCAGCTCTCAGTCCAACATATTCTTCCATGCGTTAAG                         GAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTG
genomic: GCATATTAAATCCTCAGCTCTCAGTCCAACATATTCTTCCATGCGTTAAGgtgggggcaa ... gcatctacagGAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTG
EST: gi|211315613|gb|FL415838.1|FL415838
EST:     GCATATTAAATCCTCAGCTCTCAGTCCAACATATTCTTCCATGCGTTAAG                         GAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTG
genomic: GCATATTAAATCCTCAGCTCTCAGTCCAACATATTCTTCCATGCGTTAAGgtgggggcaa ... gcatctacagGAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTG
EST: gi|26560084|gb|CA832319.1|CA832319
EST:     GCATATTAAATCCTCAGCTCTCAGTCCAACATATTCTTCCATGCGTTAAG                         GAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTG
genomic: GCATATTAAATCCTCAGCTCTCAGTCCAACATATTCTTCCATGCGTTAAGgtgggggcaa ... gcatctacagGAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTG
EST: gi|67039515|gb|CO465770.1|CO465770
EST:     GCATATTAAATCCTCAGCTCTCAGTCCAACATATTCTTCCATGCGTTAAG                         GAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTG
genomic: GCATATTAAATCCTCAGCTCTCAGTCCAACATATTCTTCCATGCGTTAAGgtgggggcaa ... gcatctacagGAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTG
EST: gi|31355734|gb|CD440091.1|CD440091
EST:     GCATATTAAATCCTCAGCTCTCAGTCCAACATATTCTTCCATGCGTTAAG                         GAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTG
genomic: GCATATTAAATCCTCAGCTCTCAGTCCAACATATTCTTCCATGCGTTAAGgtgggggcaa ... gcatctacagGAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttcgttgctatttttcttctgagtgaattaactcatgccaagtgcatctacagGAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAG
                           aattaac  putative branch site (score: 2)
          tatttttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgggggcaaagcaattattgaacaccatttcgttgctatttttcttctgagtgaattaactcatgccaagtgcatctacagGAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT