Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgccatcgctgtttatgaattattatgatgttcttaaaccatctgtgctgatggctacagtgcgtgtgtgtgactaacctgaggtttgtgccatttgcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCCCGCATGTTCAGCGAGAACAAGCGAGAGTACAACCGCAAAGTTCGGGAGG

Basic information

species Zea mays
transcript GRMZM2G110983_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G110983_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g08960.1 (Oryza sativa), 3'ss of exon 5
tgccat-cgctgtttatgaattattatgatgttcttaaaccatctgtg--ctgatggctacagtgcgtgtgtgtgactaacctgaggtttgtgccatttgcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCCCGCATGTTCAGCGAGAACAAGCGAGAGTACAACCGCAAAGTTCGGGAGG
  | || |    || ||| | |   | ||  ||   | |  |   |     | || | |  |     |  ||    |||      | |||||   |||| |||||  || | |||||||||||||| ||||| || || ||||||||||| |||||| | ||||| ||||||||||| || |||||||| |||||||| ||| 
-acaatgcatatttcatggact--caagacattgacatattacaggcaatttcattgatttaactgttcagtacttctatttcctgctttgtattatttccagTCGCTGCTTTGCGATCCAAACCCAAATTCACCTGCCAACTCTGAAGCTGCCCGCCTATTCAGTGAGAACAAGCGGGAATACAACCGAAAAGTTCGTGAGA

upper sequence: GRMZM2G110983_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g08960.2 (Oryza sativa), 3'ss of exon 5
tgccatcgctgtttatgaattattatgatgttcttaaaccatctgtgctgatggctacagtgcgtgtgtgtgactaacctgaggtttgtgccatttgcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCCCGCATGTTCAGCGAGAACAAGCGAGAGTACAACCGCAAAGTTCGGGAGG----------------------------------------------
                                             |     ||  |  | ||     ||    |||      | |||||   |||| |||||  || | |||||||||||||| ||||| || || ||||||||||| |||||| | ||||| ||||||||||| || |||||||| |||||||| |||                                               
---------------------------------------------tttcattgatttaactgttca-gtacttctatttcctgctttgtattatttccagtcgctgctttgcgatccaaacccaaattcacctgccaactctgaagCTGCCCGCCTATTCAGTGAGAACAAGCGGGAATACAACCGAAAAGTTCGTGAGATAGTGGAGCAGAGCTGGACCGCGGACTGATCCACTCCATCTAACCA

upper sequence: GRMZM2G110983_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA17G10640.2 (Glycine max), 3'ss of exon 5
tgccatcgctgtttatgaattattatgatgttcttaaacc-----atctgtgctgatggctacagtgcgtgtgtgtgactaacct----gaggtttgtgccattt----gcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCCCGCATGTTCAGCGAGAACAAGCGAGAGTACAACCGCAAAGTTCGGGAGG
            ||||  |||||  | ||| |  ||  |      |||  || |      ||    || ||| | | | ||   |     || |   |   | |     |||||||||| | || ||||| ||||| ||||| || || ||||| ||||| || || ||||| || ||||||||||| |||||||| || | |||| | ||  
------------ttatatattatcttcatgattctactctttggtatccctgttatatagtagtcagcatgt-tataattattttctgaaagatacatattactctgcggcagTCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCAGAAGCAGCTCGAATGTTTAGTGAGAACAAGCGGGAGTACAATCGAAGAGTTAGAGAAA

upper sequence: GRMZM2G110983_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA18G16160.1 (Glycine max), 3'ss of exon 6
------tgccatcgctgtttatgaattattatgatgttcttaaaccatctgtgctgatggctacagtgcgtgtgtgtgactaacctgaggtttgtgccatttgcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCCCGCATGTTCAGCGAGAACAAGCGAGAGTACAACCGCAAAGTTCGGGAGG
      | |  |  || ||  | ||     || ||  | || |    |   |     ||| | |  |||   | | | | |||  ||   ||  ||    |||||||||||| |||| ||||||||||| ||||| || || || |||||||| || || |||||||| || |||||||| || |||||| | | ||| || ||| 
agtgtgttcttttactcttcctcaacaggaat-atagtgttgacttgtacattgctctggattct-tgctattttttcattaaattggctttcttg----ttgcagTCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCTCGGATGTTCAGTGAAAACAAGCGTGAATACAACAGAAGAGTACGTGAGA

upper sequence: GRMZM2G110983_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA06G20310.1 (Glycine max), 3'ss of exon 4
tgccatcgctgtttatgaattattatgatgttcttaaaccatctgtgctgatggctacagtgcgtgtgtgtga-ctaacctgaggtttgtgccatttgcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCCCGCATGTTCAGCGAGAACAAGCGAGAGTACAACCGCAAAGTTCGGGAGG
    ||  |     || ||| |     ||       | ||  || ||| |  | |  || |   |   | |   ||||   |   |||    | ||||||||||||| | || ||||| ||||| ||||| || || ||||||||||| || || ||||| || ||||||||||| |||||||| || | |||  ||||  
-tttatttcctgaaataaataaaatatatagcaagtatcctgctatgcagtagtcatcattttataattattttctaaaaggtaattttcctcctttgcagTCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCTGAAGCAGCTCGAATGTTTAGTGAGAACAAGCGTGAGTACAATCGAAGAGTGAGGGAAA

upper sequence: GRMZM2G110983_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA08G40860.1 (Glycine max), 3'ss of exon 5
tgccatcgctgt-ttatgaattattatgatgttcttaaaccatctgtgc--tgatggctacagtgcgtgtgtgtgactaacctgaggtttgtgccatttgcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCCCGCATGTTCAGCGAGAACAAGCGAGAGTACAACCGCAAAGTTCGGGAGG
     | | | |  | |   | | ||  ||  | |||    || ||| |  || |    |   |   | | | | |||||  || | |   | |   ||||||||||||||||| ||||||||||| ||||| || || || |||||||| || || ||||||||||| |||||||| || |||||| | ||||| || ||| 
--gtgttgttttactcttcctcaatagaatagtgttagttgatttgtacattgctctggattcttgttatttatcactaaattg-gctgctttcttgttgcagTCATTGTTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCTCGGATGTTCAGCGAAAACAAGCGCGAATACAACAGAAAAGTACGCGAGA

upper sequence: GRMZM2G110983_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA18G16160.3 (Glycine max), 3'ss of exon 6
-----tgccatcgctgtttatgaattattatgatgttcttaaaccatctgtgctgatggctacagtgcgtgtgtgtgactaacctgaggtttgtgccatttgcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCCCGCATGTTCAGCGAGAACAAGCGAGAGTACAACCGCAAAGTTCGGGAGG-
     | |  |  || ||  | ||     || ||  | || |    |   |     ||| | |  |||   | | | | |||  ||   ||  ||    |||||||||||| |||| ||||||||||| ||||| || || || |||||||| || || |||||||| || |||||||| || |||||| | | ||| || |||  
gtgtgttcttttactcttcctcaacaggaat-atagtgttgacttgtacattgctctggattct-tgctattttttcattaaattggctttcttg----ttgcagtCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCTCGGATGTTCAGTGAAAACAAGCGTGAATACAACAGAAGAGTACGTGAGAT

upper sequence: GRMZM2G110983_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA05G01270.1 (Glycine max), 3'ss of exon 5
tgccatcgctgtttatg--aattattatgatgttcttaaaccatctgtgctgatggctacagtgcgtgtgtgtgactaacctgaggtttgtgccatttg-cagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCCCGCATGTTCAGCGAGAACAAGCGAGAGTACAACCGCAAAGTTCGGGAGG
   ||| |     |||   | || || |  |  | || |    | | |  |  |    |   |     | | |  || |   |   ||  | |  | || ||||||||| | || ||||| ||||| ||||| || || ||||| ||||| || || ||||| || ||||||||||| |||||||| || | |||  | ||  
-atcattggcacatatatcagttgttttacttgtattca-tggtgtatagtagtcagcatgttataattatttt-ctgaaaggtaattattactctgtggcagTCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCAGAAGCAGCTCGAATGTTTAGTGAGAACAAGCGTGAGTACAATCGAAGAGTGAGAGAAA

upper sequence: GRMZM2G110983_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA04G34170.2 (Glycine max), 3'ss of exon 5
tgccatcgctgtttatgaattat-tatgatgttcttaaaccatc-tgtgctgatggctacagtgcgtgtgtgtgactaacctgaggtttgtgccatttgcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCCCGCATGTTCAGCGAGAACAAGCGAGAGTACAACCGCAAAGTTCGGGAGG
 |  ||        || ||  |  |||   |   |||  |     |||  | ||    |   |     | | |  ||||   |   |||    | ||||||||||||| | || ||||| ||||| ||||| || || ||||||||||| || || ||||| |||||||||||||| || ||||| || | |||  ||||  
-gaaataaaaaaaaataaaaaaagtatatagcatttatcctgctatgtagtaatcatcatgctctaattatttt-ctaaaaggtaattttcctcctttgcagTCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCTGAAGCAGCTCGAATGTTTAGCGAGAACAAGCGTGAATACAATCGAAGAGTGAGGGAAA

upper sequence: GRMZM2G110983_T03 (Zea mays), 3'ss of exon 3
lower sequence: Vv14s0108g00140.t01 (Vitis vinifera), 3'ss of exon 6
tgccatcgctgtttatgaattattatg-atgttcttaaaccatctgtgctgatggctacagtgcgtgtgtgtgactaacctgaggtttgtgccatt--tgcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCCCGCATGTTCAGCGAGAACAAGCGAGAGTACAACCGCAAAGTTCGGGAGG
    ||   ||   |  |   |  ||  ||||| |    ||| | || ||  ||     | |   |   ||||     |   |   ||||    ||  | |||||| || | || ||||| ||||| || ||||||||||| || ||||| || || ||||| || ||||||||||| ||||||||| | | ||| || ||  
---gatgtttgaacagaatcaaacatatatgttttggttccagcagtccttttgatattactagcttgatgtggtcttctgaatccttgttttgttatttcagTCACTGCTTTGTGATCCCAACCCAAACTCGCCCGCTAATTCAGAAGCTGCACGGATGTTTAGTGAGAACAAGCGCGAGTACAACAGAAGAGTCCGTGAAA

upper sequence: GRMZM2G110983_T03 (Zea mays), 3'ss of exon 3
lower sequence: Vv08s0032g00310.t01 (Vitis vinifera), 3'ss of exon 4
tgccatcgctgtttatgaattattatgatgttc-ttaaaccatctgtgctgatggctacagtgcgtgtgtgtgactaacctgaggttt---gtgccatttgcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCCCGCATGTTCAGCGAGAACAAGCGAGAGTACAACCGCAAAGTTCGGGAGG
 | ||||  |  | |  |     | | || |   ||| |  || | ||    | ||    | | |  | |   | |   |  || | |    ||   | | |||||  || | || ||||||||||| || || || || |||||||||||||| ||||||||||| ||||| ||||| || |||||| | | ||| || ||  
-gacatc--tagtgagcagcagctttaatttcagttacaatattt-tgtcagttgcctgtgagggcatattctaatgggcatagttcttaaatgttttatccagTCCCTGCTCTGTGATCCAAACCCAAACTCACCTGCAAACTCTGAAGCCGCACGCATGTTCAGTGAGAATAAGCGGGAATACAACAGAAGAGTGCGTGAAA

upper sequence: GRMZM2G110983_T03 (Zea mays), 3'ss of exon 3
lower sequence: PP1S91_87V6.1 (Physcomitrella patens), 3'ss of exon 4
-tgccatcgctgtttatgaattattatgatgttcttaaaccatctgtgctgatggctacagtgcgt-gtgtgtgactaacctgaggtttgtgccatttgcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCCCGCATGTTCAGCGAGAACAAGCGAGAGTACAACCGCAAAGTTCGGGAGG
          || |       |  | ||   ||      |    |  |  || | | ||  ||||| | | | || ||  || |     |       ||||||| ||| ||||||| |||||||||||||| || || ||||| || || |||||||||| |||||||||   ||| ||||||||||| |  || || ||| 
agcttgagattggtcggcgtcttctttggcatttgcgg-ctgaatacgtcgacgacaacgatgcgtagagcgagatta-tctaatacacggctttgatgcagTCTTTGCTGTGCGACCCAAACCCGAATTCACCAGCGAACTCGGAGGCTGCCCGCATGTACAGCGAGAATCGGCGTGAGTACAACCGGAGGGTACGCGAGA

upper sequence: GRMZM2G110983_T03 (Zea mays), 3'ss of exon 3
lower sequence: PP1S219_106V6.1 (Physcomitrella patens), 3'ss of exon 4
tgccatcgctgtttatgaattattatgatgttcttaaaccatct--gtgctgatggctacagtgcgtgtgtgtgactaacctgaggtttgtgccatttgcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCCCGCATGTTCAGCGAGAACAAGCGAGAGTACAACCGCAAAGTTCGGGAGG
 || |  |  | |      || ||     ||    |  | | |   | | ||||| | ||  ||||||   |    |   || |    ||       ||||||| ||| | ||||| |||||||||||||| || || ||||| || || || ||||||| ||||||||||  ||| || || ||||| |  || || ||| 
-gcgagagtggatggcttcttctt-cagcgtgtgcagccgaacacagcgatgatgacgacgatgcgtgaaagctgtttctctaacacgtggctttggtgcagTCTTTGCTATGCGACCCAAACCCGAATTCACCAGCAAACTCGGAGGCTGCTCGCATGTACAGCGAGAACCGGCGTGAATATAACCGGAGGGTACGCGAGA

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|211368006|gb|FL470437.1|FL470437
EST:     ATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAG                         TCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCC
genomic: ATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAGgtacaaccat ... ccatttgcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCC
EST: gi|149108750|gb|EE189816.2|EE189816
EST:     ATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAG                         TCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCC
genomic: ATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAGgtacaaccat ... ccatttgcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCC
EST: gi|16920335|gb|BM074609.1|BM074609
EST:     CCGATATATGATGTAGCTGCGATACTCACGTCAATCCAG                         TCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCC
genomic: CCGATATATGATGTAGCTGCGATACTCACGTCAATCCAGgtacaaccat ... ccatttgcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCC
EST: gi|37393932|gb|CF634233.1|CF634233
EST:     CACGTCAATCCAG                         TCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCC
genomic: CACGTCAATCCAGgtacaaccat ... ccatttgcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCC
EST: gi|14244483|gb|BG842475.2|BG842475
EST:     ATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAG                         TCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCC
genomic: ATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAGgtacaaccat ... ccatttgcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCC
EST: gi|18166104|gb|BM335943.1|BM335943
EST:     CCGATATATGATGTAGCTGCGATACTCACGTCAATCCAG                         TCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCC
genomic: CCGATATATGATGTAGCTGCGATACTCACGTCAATCCAGgtacaaccat ... ccatttgcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCC
EST: gi|211248410|gb|FL329620.1|FL329620
EST:     TCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAG                         TCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCC
genomic: TCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAGgtacaaccat ... ccatttgcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCC
EST: gi|7216375|gb|AW562497.1|AW562497
EST:     AGCTGCGATACTCACGTCAATCCAG                         TCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCC
genomic: AGCTGCGATACTCACGTCAATCCAGgtacaaccat ... ccatttgcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCC
EST: gi|40334943|gb|CK369013.1|CK369013
EST:     ATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAG                         TCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCC
genomic: ATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAGgtacaaccat ... ccatttgcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctgatggctacagtgcgtgtgtgtgactaacctgaggtttgtgccatttgcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCCCGCATGTTCAGCGAGAACAAGCGAGAGTACAACCGCAAAGTTCGGGAGG
                          gactaac  putative branch site (score: 1)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgccatcgctgtttatgaattattatgatgttcttaaaccatctgtgctgatggctacagtgcgtgtgtgtgactaacctgaggtttgtgccatttgcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCCCGCATGTTCAGCGAGAACAAGCGAGAGTACAACCGCAAAGTTCGGGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG