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'   		13  
 5'  3'   		14  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taataaaacacagctctcctgtgttttcgaggagaaaaaaattgttggccatttaacgcaagtataccatggctaatattgtaatctactcctaaaacagATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAG

Basic information

species Zea mays
transcript GRMZM2G181151_T02
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G181151_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 3'ss of exon 10
taataaaacacagctctcctgtgttttcgaggagaaaaaaattgttggccatttaa-cgcaagtat--accatggctaatattgtaat-ctactcctaaaacagATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAG
   |       | || | |  | | |   |  |   ||    || |     ||||  |  ||  |   |  |||  ||| |||||  |  | |  |  |||||||||| ||||| |||||||| || ||||| || |||||||| || ||||||||||||||||| |||||||| ||||||||||||
--ttgcgttggatctttaccatttatgttattacctaatgtgtgct--ttgtttagtcttaaacaataaatatgtttaacattgtgctgtttcatcctaaacagATATTACACATCCAACTCCTGATCTTACGGGGTACATTACCGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAG

upper sequence: GRMZM2G181151_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA10G42940.3 (Glycine max), 3'ss of exon 10
-taataaaacaca-gctctcctgtgttttcgaggagaaaaaaattgttggccatttaacgcaagtataccatggctaatattgtaatctactcctaaaacagATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAG
 |||| ||| | |     || |  | | ||  | |         || |||    ||||| |         |||  || |||| | | || ||      |||||||| || ||||||||||| || || || ||||| || |||||||| ||||||||||| || ||||||||  |||| ||||||
gtaatgaaatatacaagttcatcagctatcttgca---------tgatggtttcttaacactga------atgatta-tattttgaacttctgt----acagATATTACGCACCCAACTCCTGATCTAACAGGATATATCACTGAGGGGCAGATATACATCGACAGGCAGCTGTATAATAGACAG

upper sequence: GRMZM2G181151_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA09G38110.1 (Glycine max), 3'ss of exon 10
-taataaaacacagctctcctgtgttttcgaggagaaaaaaattgttggccatttaacgcaagtataccatggctaatattgtaatctactcctaaaacagATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAG
 | || ||| |      |  ||  | ||    |  |  |    |  ||  |  | ||  |          ||  |  | || |  |  ||| ||  | ||||||| ||||| |||||||| || ||||| ||||| |||||||||||||||||||| ||||| |||||| |  ||||||| |||
gtgatgaaatat-----tattgaatcttatcagctatcatgcataatgcactctcaattctgac------tgattgtttttct--tgaacttctgta-cagATATTACACATCCAACTCCTGATCTTACAGGATATATTACTGAGGGACAGATATATATTGACAGGCAGTTGTATAACAGGCAG

upper sequence: GRMZM2G181151_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 11
taataaaacacagctctcctgtgttttcgaggagaaaaaaattgttggccatttaacgcaagtataccatggctaat--attgtaatct--actcctaaaacagATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAG
                        |   ||     | ||  |  |  || || |  |  ||   |   |   || |   ||| || | |  ||| ||  | ||||||| || ||||||||||| || || || ||||| || |||||||| ||||||||||| || ||||||||  |||| ||||||
-----------------------gtaatgaaatatagaagttaatcagctatcttgcataatggttttaacactgaatgattatattttgaacttctgta-cagATATTACGCACCCAACTCCTGATCTAACAGGATATATCACTGAGGGGCAGATATACATCGACAGGCAGCTGTATAATAGACAG

upper sequence: GRMZM2G181151_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA18G48280.1 (Glycine max), 3'ss of exon 10
taataaaacacagctctcctgtgttttcgaggagaaaaaaattgttggccatttaacgcaagtataccatggctaatattgtaatctactcctaaaacagATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAG-
| || ||| |      |  ||  | ||  |  ||  |  |    ||   || |   | ||| | |  | ||  || | || |  |  ||| ||  | ||||||| || || |||||||| || ||||| ||||| |||||||||||||||||||| || || || ||| |  ||||||| ||| 
tgatgaaatat-----tattgaatctt--atcagctatcatgcattatgcact---ctcaattctgac-tgattatttttct--tgaacttctgta-cagaTATTACGCATCCAACTCCTGATCTTACAGGATATATTACTGAGGGACAGATATATATCGACAGACAGTTGTATAACAGGCAGG

upper sequence: GRMZM2G181151_T01 (Zea mays), 3'ss of exon 10
lower sequence: AT1G76030.1 (Arabidopsis thaliana), 3'ss of exon 10
taataaaacacagctctcctgtgttttcgaggagaaaaaaattgttggccatttaacgcaagtataccatggctaatattgtaatct-actcctaaaacagATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAG
   |||||  || || || |  |         |||    | || ||  |   || |   || |  |   |  ||    ||||  | | ||   |  | |||||||||| || ||||||||||| |||||||| ||||||||||| || |||||||| || |||||||| || || |||||||||
--gtaaaat-catctttcttaagccaatccctagattctattttttatc---ttgagaaaactcaattcttact--cgttgttgtttgacaaattgatcagATATCACTCATCCAACTCCGGATCTTACTGGTTACATTACTGAAGGTCAGATATATATCGATAGGCAACTTCACAACAGACAG

upper sequence: GRMZM2G181151_T01 (Zea mays), 3'ss of exon 10
lower sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 10
taataaaacacagctctcctgtgttttcgaggagaaaaaaattgttggccatttaacgcaagtataccatggctaatattgtaatctactcctaaaac--agATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAG
           |  | |  |     ||   |||    |    | |      |||   |    |  | ||  ||| ||| | |    |  |  ||||||  ||||||||| ||||| |||||||| |||||||| |||||||||||||| |||||||| ||||||||||| || || |||||||||
---------gtaattttttttatcgtttttggattccattcatatcaaatgttttttg---attaaacaaagctcataatatttcttgttattaaaactcagATATCACTCACCCTACTCCGGATCTTACTGGTTACATTACTGAGGGTCAGATATATATTGATAGGCAACTTCACAACAGACAG

upper sequence: GRMZM2G181151_T01 (Zea mays), 3'ss of exon 10
lower sequence: Vv18s0001g01020.t01 (Vitis vinifera), 3'ss of exon 10
-------taataaaacacagctctcctg-tgttttcgaggagaaaaaaattgttggccatttaacgcaagtataccatggctaatattgtaatctactcctaaaacagATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAG
       ||  |       | | ||  | | || |       | |  | || |||     | |  |  |  | ||  |  || | |        |  |  |  | ||||||| || || |||||||| || |||||||| || ||||||||||| |||||||||||||||||||| ||||| ||| | |||
gtaatgttagcattttcaggatgtctggctattcttccctgcacatcagttcttg-----taatagtgaacagacattacctgaaaccaattattttttgtccaccagATATTACGCATCCAACTCCAGATCTTACTGGTTATATTACTGAGGGCCAGATATACATTGATAGGCAACTCCACAACCGGCAG

upper sequence: GRMZM2G181151_T01 (Zea mays), 3'ss of exon 10
lower sequence: EFJ11911 (Selaginella moellendorffii), 3'ss of exon 9
taataaaacacagctctcctgtgttttcgaggagaaaaaaattgttggccatttaacgcaag-tataccatggctaatattgtaatctactcctaaaacagATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAG
                                                          | || | |   ||     | ||  |   ||          |||||||||| || || | |||||| || ||||| |||||||||||||||||||| ||  | ||  | || ||| | ||  | |||
-------------------------------------------------------gtacgagatgtctgatcatcgagatcatctactgacttactcgcagATATCACTCATCCGATTCCGGATCTCACTGGTTACATTACTGAGGGACAGATTTATGTGGACCGTCAACTCTACAATCGTCAG

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|16925493|gb|BM078561.1|BM078561
EST:     AGGGTCCA-TACCCCAAATTCCTATTCTGACAATGCCTAATGATG                         ATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGA
genomic: AGGGTCCATTA-CCCAAATTCCTATTCTGACAATGCCTAATGATGgtaagtaacc ... cctaaaacagATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGA
EST: gi|32945219|gb|CF050038.1|CF050038
EST:     AAGAACAGGGTCCATTACCCAAATTCCTATTCTGACAATGCCTAATGATG                         ATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGA
genomic: AAGAACAGGGTCCATTACCCAAATTCCTATTCTGACAATGCCTAATGATGgtaagtaacc ... cctaaaacagATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGA
EST: gi|30307204|gb|CD001877.1|CD001877
EST:     AAGAACAGGGTCCATTACCCAAATTCCTATTCTGACAATGCCTAATGATG                         ATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGA
genomic: AAGAACAGGGTCCATTACCCAAATTCCTATTCTGACAATGCCTAATGATGgtaagtaacc ... cctaaaacagATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGA
EST: gi|6973468|gb|AW438162.1|AW438162
EST:     AAGAACAGGGTCCATTACCCAAATTCCTATTCTGACAATGCCTAATGATG                         ATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGA
genomic: AAGAACAGGGTCCATTACCCAAATTCCTATTCTGACAATGCCTAATGATGgtaagtaacc ... cctaaaacagATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGA
EST: gi|67019767|gb|CO448516.1|CO448516
EST:     TTCTGACAATTCCTAATGATG                         ATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGA
genomic: TTCTGACAATGCCTAATGATGgtaagtaacc ... cctaaaacagATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGA
EST: gi|60352515|gb|DN219488.1|DN219488
EST:     AAGAACAGGGTCCATTACCCAAATTCCTATTCTGACAATGCCTAATGATG                         ATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGA
genomic: AAGAACAGGGTCCATTACCCAAATTCCTATTCTGACAATGCCTAATGATGgtaagtaacc ... cctaaaacagATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGA
EST: gi|33101769|gb|CF061729.1|CF061729
EST:     AAGAACAGGGTCCATTACCCAAATTCCTATTCTGACAATGCCTAATGATG                         ATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGA
genomic: AAGAACAGGGTCCATTACCCAAATTCCTATTCTGACAATGCCTAATGATGgtaagtaacc ... cctaaaacagATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGA
EST: gi|194716931|gb|FK934090.1|FK934090
EST:     AAGAACAGGGTCCATTACCCAAATTCCTATTCTGACAATGCCTAATGATG                         ATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGA
genomic: AAGAACAGGGTCCATTACCCAAATTCCTATTCTGACAATGCCTAATGATGgtaagtaacc ... cctaaaacagATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGA
EST: gi|31360502|gb|CD444859.1|CD444859
EST:     AAGAACAGGGTCCATTACCCAAATTCCTATTCTGACAATGCCTAATGATG                         ATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGA
genomic: AAGAACAGGGTCCATTACCCAAATTCCTATTCTGACAATGCCTAATGATGgtaagtaacc ... cctaaaacagATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGA
EST: gi|60394888|gb|DN227757.1|DN227757
EST:     AAGAACAGGGTCCATTACCCAAATTCCTATTCTGACAATGCCTAATGATG                         ATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGA
genomic: AAGAACAGGGTCCATTACCCAAATTCCTATTCTGACAATGCCTAATGATGgtaagtaacc ... cctaaaacagATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGA
EST: gi|67015926|gb|CO444675.1|CO444675
EST:     AAGAACAGGGTCCATTACCCAAATTCCTATTCTGACAATGCCTAATGATG                         ATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGA
genomic: AAGAACAGGGTCCATTACCCAAATTCCTATTCTGACAATGCCTAATGATGgtaagtaacc ... cctaaaacagATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGA
EST: gi|67028686|gb|CO457435.1|CO457435
EST:     AAGAACAGGGTCCATTACCCAAATTCCTATTCTGACNATGCCTAATGATG                         ATATCACACACCCAACTCCCGGAC-TTACTGGATACATTACTGAGGGAC
genomic: AAGAACAGGGTCCATTACCCAAATTCCTATTCTGACAATGCCTAATGATGgtaagtaacc ... cctaaaacagATATCACACACCCAACTCC-GGACCTTACTGGATACATTACTGAGGGAC
EST: gi|26557381|gb|CA829616.1|CA829616
EST:     AAGAACAGGGTCCATTACCCAAATTCCTATTCTGACAATGCCTAATGATG                         ATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGA
genomic: AAGAACAGGGTCCATTACCCAAATTCCTATTCTGACAATGCCTAATGATGgtaagtaacc ... cctaaaacagATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGA
EST: gi|33101431|gb|CF061391.1|CF061391
EST:     AAGAACAGGGTCCATTACCCAAATTCCTATTCTGACAATGCCTAATGATG                         ATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGA
genomic: AAGAACAGGGTCCATTACCCAAATTCCTATTCTGACAATGCCTAATGATGgtaagtaacc ... cctaaaacagATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGA
EST: gi|32944615|gb|CF049434.1|CF049434
EST:     AAGAACAGGGTCCATTACCCAAATTCCTATTCTGACAATGCCTAATGATG                         ATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGA
genomic: AAGAACAGGGTCCATTACCCAAATTCCTATTCTGACAATGCCTAATGATGgtaagtaacc ... cctaaaacagATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGA
EST: gi|37401251|gb|CF637988.1|CF637988
EST:     AAGAACAGGGTCCATTACCCAAATTCCTATTCTGACAATGCCTAATGATG                         ATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGA
genomic: AAGAACAGGGTCCATTACCCAAATTCCTATTCTGACAATGCCTAATGATGgtaagtaacc ... cctaaaacagATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGA
EST: gi|33094143|gb|CF054137.1|CF054137
EST:     AAGAACAGGGTCCATTACCCAAATTCCTATTCTGACAATGCCTAATGATG                         ATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGA
genomic: AAGAACAGGGTCCATTACCCAAATTCCTATTCTGACAATGCCTAATGATGgtaagtaacc ... cctaaaacagATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGA
EST: gi|32933748|gb|CF038560.1|CF038560
EST:     AGGGTCCATTACCCAAATTCCTATTCTGTCAATGCCTAATGATG                         ATATCACACACCCAACTCCGGTCCTTACTGGATACATTGCTGAGGGACAGA
genomic: AGGGTCCATTACCCAAATTCCTATTCTGACAATGCCTAATGATGgtaagtaacc ... cctaaaacagATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGA
EST: gi|32931582|gb|CF036394.1|CF036394
EST:     AAGAACAGGGTCCATTACCCAAATTCCTATTCTGACAATGCCTAATGATG                         ATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGA
genomic: AAGAACAGGGTCCATTACCCAAATTCCTATTCTGACAATGCCTAATGATGgtaagtaacc ... cctaaaacagATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggccatttaacgcaagtataccatggctaatattgtaatctactcctaaaacagATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAG
                                            tcctaaa  putative branch site (score: 2)
                                       tctactcct  CT-rich tract
                            taatattgtaatcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taataaaacacagctctcctgtgttttcgaggagaaaaaaattgttggccatttaacgcaagtataccatggctaatattgtaatctactcctaaaacagATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC