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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcagttagggtcctaagaaacacattagaagtcttgagaactgatgctcatatacttcttgcttgcaaattgtctgatcagaagcattccttccttatagGATAAAAGAAGTAGGCGCAATGAGGAGTCATTTTCATTCACAAGCTCTAACAGAGAAAGTTGGGGCAGATGTTCATCTTTAGGAGCAGCCAGTGATGAAT

Basic information

species Zea mays
transcript GRMZM2G081642_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G081642_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os02g10440.1 (Oryza sativa), 3'ss of exon 12
tcagtta-gggtcctaagaaacacattagaagtcttgagaactgatgctcatatacttcttgcttgcaaattgtctgatcagaa---gcattccttccttatagGATAAAAGAAGTAGGCGCAATGAGGAGTCATTTTCATTCACAAGCTCTAACAGAGAAAGTTGGGGCAGATGTTCATCTTTAGGAGCAGCCAGTGATGAAT
 || ||     |  |    |||| |   |||       |    |||  || | ||| | |   |||     ||  |||| | ||   |  | | || ||||||||| |||  |||| ||| ||||||||| || |  ||||  |||||||||||||||||||||||||| |||||||| |||||||| | ||| ||||| || |
-caattgtatataattgtcaacagacaggaaaaac---gcttcgatattcctgtacctgtaagttgtgtgatgagtgatgacaatatgtctgcttttcttatagGACAAATCAAGTGGGCACAATGAGGAATCCTGCTCATGTACAAGCTCTAACAGAGAAAGTTGGGGTAGATGTTCCTCTTTAGGGGGAGCTAGTGACGACT

upper sequence: GRMZM2G081642_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA17G00770.1 (Glycine max), 3'ss of exon 12
tcagttagggtcctaagaaacacattagaagtcttgagaactgatgctcatatacttct-tgcttgcaaattgtctgatcagaagcattccttccttatagGATAAAAG---AAGTAGGCGCAATGAGGAGTCATTTTCATTCACAAGCTCTAACAGAGAAAGTTGGGGCAGATGTTCATCTTTAGGAGCAGCCAGTGATGAAT
| | || | ||    ||| |   | | ||    ||  ||  | |  || | |    | | | | | || ||| |   ||       |||      | ||||||||| |    || | |      ||| || |  |  || | ||| ||||| ||||||||||||||||| |||||||| || ||||||   | |||||||||| 
tgatttggtgtgaagagatattgacttgactagtttggagttaaaactgacaagtgtatgtccgtccacattttagcattcctt-tatttgaatttgatagGATAAGAAGCTAAATGGCGAGGGTGAAGATTGTTGCTCGTACACGAGCTCAAACAGAGAAAGTTGGGGAAGATGTTCTTCGTTAGGA---GGCAGTGATGAAG

upper sequence: GRMZM2G081642_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA07G40050.1 (Glycine max), 3'ss of exon 12
-----------------------------------------------------tcagttagggtcctaagaaacacattagaagtcttgagaactgatgctcatatacttcttgcttgcaaat---tgtctgatcaga----agcattccttcctt--------atagGATAAAAG---AAGTAGGCGCAATGAGGAGTCATTTTCATTCACAAGCTCTAACAGAGAAAGTTGGGGCAGATGTTCATCTTTAGGAGCAGCCAGTGATGAAT
                                                     | | |   |||| | || |     | |   |       |  |||      |  | ||    ||    | |   |||| |  || |    ||||||||||  ||        ||||||||| |    || | |      ||| || |  |  ||||  || ||||| |||||||||||||||||||||||||| |||||||||   | |||||||||| 
gtaatcttatcaaacactgtctctggaattaagaaaatgtgtcagacaaattattactggcggtcttgagtattggttgaatgggtgaataatttgactagtttggagttaaaactgaggagtgtatgtccgtccacattttagcattcctttatttgaatttgatagGATAAGAAGCTAAATGGCGAGGGTGAAGATTGTTGCTCATATACGAGCTCAAACAGAGAAAGTTGGGGCAGATGTTCTTCTTTAGGA---GGCAGTGATGAAG

upper sequence: GRMZM2G081642_T01 (Zea mays), 3'ss of exon 12
lower sequence: Vv00s0475g00050.t01 (Vitis vinifera), 3'ss of exon 5
tcagttagggtcctaagaaacacattagaagtcttgagaactga--tgctcatatact-tcttgcttgcaaattgtctgatcagaagcattccttccttat-----agGATAAAAGAAGTAGGCGCAATGAGGAGTCATTTTCATTCACAAGCTCTAACAGAGAAAGTTGGGGCAGATGTTCATCTTTAGGAGCAGCCAGTGATGAAT
             ||    || ||||    |  || |    | |  ||||  | |||  | |  |||  |    |  | |   ||    |||  |  | ||     |||||||   || | | |  ||||| || |  |  ||||  |||||||| || ||||| |||||||| ||||| |||||||||||||       ||| ||| 
--------aacaatacatgacccattgttggaattaaactttaaagtgcttttttaccatttcacttaaatgggggttcacttgagtttttcgattgtgatttcccagGATAAGCCAAATGGTCAGAATGATGAATGTTGCTCATATACAAGCTCAAATAGAGAGAGTTGGGGAAGATGCTCATCTTTAGGAGGCAGTGATGAAGAAA

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|149069964|gb|EE158363.2|EE158363
EST:     GAGATTGATAGTGATAGTGTTGGATCACGATTGCAG                         GATAAAAGAAGTAGGCGCAATGAGGAGTCATTTTCATTCACAAGCTCTAAC
genomic: GAGATTGATAGTGATAGTGTTGGATCACGATTGCAGgtaaagttca ... ttccttatagGATAAAAGAAGTAGGCGCAATGAGGAGTCATTTTCATTCACAAGCTCTAAC
EST: gi|32858949|gb|CD998630.1|CD998630
EST:     ACCACAGCCTGCCAGAGATTGATAGTGATAGTGTTGGATCACGATTGCAG                         GATAAAAGAAGTAGGCGCAATGAGGAGTCATTTTTATT-ATAAGCTCTAAC
genomic: ACCACAGCCTGCCAGAGATTGATAGTGATAGTGTTGGATCACGATTGCAGgtaaagttca ... ttccttatagGATAAAAGAAGTAGGCGCAATGAGGAGTCATTTTCATTCACAAGCTCTAAC
EST: gi|21481154|gb|BQ577837.1|BQ577837
EST:     ACCACAGCCTGCCAGAGATTGATAGTGATAGTGTTGGATCACGATTGCAG                         GATAAAAGAAGTAGGCGCAATGAGGAGTCATTTTCATTCACAAGCTCTAAC
genomic: ACCACAGCCTGCCAGAGATTGATAGTGATAGTGTTGGATCACGATTGCAGgtaaagttca ... ttccttatagGATAAAAGAAGTAGGCGCAATGAGGAGTCATTTTCATTCACAAGCTCTAAC
EST: gi|71757857|gb|DR955794.1|DR955794
EST:     AGAGATTGATAGTGATAGTGTTGGATCACGATTGCAG                         GATAAAAGAAGTAGGCGCAATGAGGAGTCATTTTCATTCACAAGCTCTAAC
genomic: AGAGATTGATAGTGATAGTGTTGGATCACGATTGCAGgtaaagttca ... ttccttatagGATAAAAGAAGTAGGCGCAATGAGGAGTCATTTTCATTCACAAGCTCTAAC
EST: gi|21329781|gb|BQ485162.1|BQ485162
EST:     ACCACAGCCTGCCAGAGATTGATAGTGATAGTGTTGGATCACGATTGCAG                         GATAAAAGAAGTAGGCGCAATGAGGAGTCATTTTCATTCACAAGCTCTAAC
genomic: ACCACAGCCTGCCAGAGATTGATAGTGATAGTGTTGGATCACGATTGCAGgtaaagttca ... ttccttatagGATAAAAGAAGTAGGCGCAATGAGGAGTCATTTTCATTCACAAGCTCTAAC
EST: gi|78125549|gb|DV543933.1|DV543933
EST:     ACCACAGCCTGCCAGAGATTGATAGTGATAGTGTTGGATCACGATTGCAG                         GATAAAAGAAGTAGGCGCAATGAGGAGTCATTTTCATTCACAAGCTCTAAC
genomic: ACCACAGCCTGCCAGAGATTGATAGTGATAGTGTTGGATCACGATTGCAGgtaaagttca ... ttccttatagGATAAAAGAAGTAGGCGCAATGAGGAGTCATTTTCATTCACAAGCTCTAAC
EST: gi|5804604|gb|AI979574.1|AI979574
EST:     CAGCCTGCCAGAGATTGATAGTGATAGTGTTGGATCACGATTGCAG                         GATAAAAGAAGTAGGCGCAATGAGGAGTCATTTTCATTCCCAAGCTCTAAC
genomic: CAGCCTGCCAGAGATTGATAGTGATAGTGTTGGATCACGATTGCAGgtaaagttca ... ttccttatagGATAAAAGAAGTAGGCGCAATGAGGAGTCATTTTCATTCACAAGCTCTAAC
EST: gi|211126998|gb|FL461335.1|FL461335
EST:     CCACAGCCTGCCCAAAGATTGATAGTGATAGTGTTGGACCACGATTGCAG                         GATAAAAGAAGTAGGCGCAATGAGGAGTCATTTTCATTCACAAGCTCTAAC
genomic: CCACAGCCTG-CCAGAGATTGATAGTGATAGTGTTGGATCACGATTGCAGgtaaagttca ... ttccttatagGATAAAAGAAGTAGGCGCAATGAGGAGTCATTTTCATTCACAAGCTCTAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctcatatacttcttgcttgcaaattgtctgatcagaagcattccttccttatagGATAAAAGAAGTAGGCGCAATGAGGAGTCATTTTCATTCACAAGCTCTAACAGAGAAAGTTGGGGCAGATGTTCATCTTTAGGAGCAGCCAGTGATGAAT
                          gtctgat  putative branch site (score: 4)
                                       cattccttccttat  putative PPT
     tatactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcagttagggtcctaagaaacacattagaagtcttgagaactgatgctcatatacttcttgcttgcaaattgtctgatcagaagcattccttccttatagGATAAAAGAAGTAGGCGCAATGAGGAGTCATTTTCATTCACAAGCTCTAACAGAGAAAGTTGGGGCAGATGTTCATCTTTAGGAGCAGCCAGTGATGAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG