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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCAAGACAATTAGGCGCTGTAGAAGGGTGGTATTTATTGGTTGTGGAACAAGTTACAATGCTGCCTTAGCTGCAAGACCTTTTGTGGAAGAACTGACTGgtaagaccaatcaattaattactccagctgtattgcctataccaagaaaagtttggaatttgtcgaagcaatcagaccttagttaatgatcctttaggtttaacctttctccttgctttatttggatgacag

Basic information

species Zea mays
transcript GRMZM2G005849_T02
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G005849_T03 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os11g03900.1 (Oryza sativa), 5'ss of exon 6
CTCAAGACAATTAGGCGCTGTAGAAGGGTGGTATTTATTGGTTGTGGAACAAGTTACAATGCTGCCTTAGCTGCAAGACCTTTTGTGGAAGAACTGACTGgtaagaccaatcaattaattactccagctgtattgcctataccaagaaaagtttggaatttgtcgaagcaatcagaccttagttaatgatcctttaggtttaac-ctttctccttgctttatttggatgacag
||||| || ||||||||| |||||||| | || || ||||| ||||| |||||||||||||||||||| |||||||||||||||||||| ||| | ||||||| |      ||| | |||   |   ||   ||   || |      | |  |    ||  ||     |||| |    |||| ||    |   ||       |  |||  ||||||| |||||||||  | ||
CTCAAAACTATTAGGCGCAGTAGAAGGTTAGTTTTCATTGGCTGTGGTACAAGTTACAATGCTGCCTTGGCTGCAAGACCTTTTGTGGAGGAATTAACTGgtatg-----ccaacttattgtcctgactcc-ttatgtagatattttagatgtcaacatcagt---gacaat-atgtattagctacctgtttcttgacccagatacttcatccttgcattatttggacaatag

upper sequence: GRMZM2G005849_T03 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os12g03720.1 (Oryza sativa), 5'ss of exon 6
CTCAAGACAATTAGGCGCTGTAGAAGGGTGGTATTTATTGGTTGTGGAACAAGTTACAATGCTGCCTTAGCTGCAAGACCTTTTGTGGAAGAACTGACTGgtaagaccaatcaattaattactccagctgtattgcctataccaagaaaagtttggaatt--tgtcgaagcaatcagaccttagttaatgatcctttaggtttaac-ctttctccttgctttatttggatgacag
||||| || ||||||||| |||||||| | || || ||||| ||||| |||||||||||||||||||| |||||||||||||||||||| ||| | ||||||| |      ||| | |||   |   ||       |  ||   |||||  || |   |     ||   |  |  |    |||| ||    |   ||       |  |||  ||||||| |||||||||  | ||
CTCAAAACTATTAGGCGCAGTAGAAGGTTAGTTTTCATTGGCTGTGGTACAAGTTACAATGCTGCCTTGGCTGCAAGACCTTTTGTGGAGGAATTAACTGgtatg-----ccaacttattgtcctgact-------ccttatgtagaaattttagatgtcaacatcagtgacaatatgtattagctacctgtttcttgacccagatacttcttccttgcattatttggacaatag

upper sequence: GRMZM2G005849_T03 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA09G38460.1 (Glycine max), 5'ss of exon 6
CTCAAGACAATTAGGCGCTGTAGAAGGGTGGTATTTATTGGTTGTGGAACAAGTTACAATGCTGCCTTAGCTGCAAGACCTTTTGTGGAAGAACTGACTGgtaagaccaatcaattaattactccagctgtattgcctataccaagaaaagtttggaatttgtcgaagcaatcagaccttagttaatgatcctttaggtttaacctttctccttgctttatttggatgacag
||||| |||||||||||  |||||||| |  | || ||||||||||| |||||||| |||||||| || || || |||||  |  ||||||||||  ||||| ||  |  |  ||    || |  |   || ||||  ||      |||||| || |  || | | |    |      |   ||| | ||  ||   |                                  
CTCAAAACAATTAGGCGAAGTAGAAGGATACTTTTCATTGGTTGTGGTACAAGTTATAATGCTGCTTTGGCAGCTAGACCCATCTTGGAAGAACTTTCTGgtcagtgctgt--atcctgtattttaa--gttttgctgat-----taaaagtatgcacattcttgcaatgttttattatattttatttattattatag----------------------------------

upper sequence: GRMZM2G005849_T03 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA18G47860.1 (Glycine max), 5'ss of exon 7
-CTCAAGACAATTAGGCGCTGTAGAAGGGTGGTATTTATTGGTTGTGGAACAAGTTACAATGCTGCCTTAGCTGCAAGACCTTTTGTGGAAGAACTGACTGgtaagaccaatcaattaattactccagctgtattgcctataccaagaaaagtttggaatttgtcga--agcaatcagaccttagttaatgatcctttaggtttaacctttctccttgctttatttggatgacag
 ||||| |||||||||||  |||||||| |  | || ||||||||||| |||||||| |||||||| || || || |||||  |  ||||||||||  | ||| ||                     |||||||    |||  |||      |||    || |  ||  |  ||  |  ||     | |  ||  ||||  ||| |  ||   | ||  | ||            
CCTCAAAACAATTAGGCGAAGTAGAAGGATACTTTTCATTGGTTGTGGTACAAGTTATAATGCTGCTTTGGCAGCTAGACCCATATTGGAAGAACTTTCAggtcagt--------------------gctgtatcctgtatgacaaatcttttttaagtttggctgattaaaaagtatgcccattcttacaatgtttta--ttttattttatacattattata------------

upper sequence: GRMZM2G005849_T03 (Zea mays), 5'ss of exon 5
lower sequence: Vv13s0064g00050.t01 (Vitis vinifera), 5'ss of exon 6
CTCAAGACAATTAGGCGCTGTAGAAGGGTGGTATTTATTGGTTGTGGAACAAGTTACAATGCTGCCTTAGCTGCAAGACCTTTTGTGGAAGAACTGACTGgtaag-accaatcaattaattactccagctgtattgcctataccaagaaaagtttggaatttgtcgaagcaatcagaccttagttaatgatcctttaggtttaacctttctccttgctttatttggatgacag
|| || || |||||| |  | || ||  | || |||||||||||||| |||||||| |||||||| ||||||||||||||  || ||||||||||  | |||||  ||  |   | |  |   | | || |  ||| |  |  |  | |  | ||    ||   |         | | | |||                                                  
CTGAAAACTATTAGGAGAAGCAGGAGAATTGTTTTTATTGGTTGTGGCACAAGTTATAATGCTGCTTTAGCTGCAAGACCCATTTTGGAAGAACTTTCAGgtaattactgaatgactgttgggttctgcagatttgacattttcttgtactgattt---ttccccctgatctggaaaacatag--------------------------------------------------

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|211507109|gb|FK960923.1|FK960923
EST:     AAGTTACAATGCTGCCTTAGCTGCAAGAMCTTTTGTGGAAGAACTGACTG                         GTATTCCTGTGACTATGGAGGTTGCAAGTGACTTGCTGGACAGACAAGGTC
genomic: AAGTTACAATGCTGCCTTAGCTGCAAGACCTTTTGTGGAAGAACTGACTGgtaagaccaa ... tggatgacagGTATTCCTGTGACTATGGAGGTTGCAAGTGACTTGCTGGACAGACAAGGTC
EST: gi|211509470|gb|FK960935.1|FK960935
EST:     AAGTTACAATGCTGCCTTAGCTGCAAGACCTTTTGTGGAAGAACTGACTG                         GTATTCCTGTGACTATGGAGGTTGCAAGTGACTTGCTGGACAGACAAGGTC
genomic: AAGTTACAATGCTGCCTTAGCTGCAAGACCTTTTGTGGAAGAACTGACTGgtaagaccaa ... tggatgacagGTATTCCTGTGACTATGGAGGTTGCAAGTGACTTGCTGGACAGACAAGGTC
EST: gi|71771454|gb|DR969391.1|DR969391
EST:     AAGTTACAATGCTGCCTTAGCTGCAAGACCTTTTGTGGAAGAACTGACTG                         GTATTCCTGTGACTATGGAGGTTGCAAGTGACTTGCTGGACAGACAAGGTC
genomic: AAGTTACAATGCTGCCTTAGCTGCAAGACCTTTTGTGGAAGAACTGACTGgtaagaccaa ... tggatgacagGTATTCCTGTGACTATGGAGGTTGCAAGTGACTTGCTGGACAGACAAGGTC
EST: gi|211507117|gb|FK960931.1|FK960931
EST:     AAGTTACAATGCTGCCTTAGCTGCAAGACCTTTTGTGGAAGAACTGACTG                         GTATTCCTGTGACTATGGAGGTTGCAAGTGACTTGCTGGACAGACAAGGTC
genomic: AAGTTACAATGCTGCCTTAGCTGCAAGACCTTTTGTGGAAGAACTGACTGgtaagaccaa ... tggatgacagGTATTCCTGTGACTATGGAGGTTGCAAGTGACTTGCTGGACAGACAAGGTC
EST: gi|211507113|gb|FK960927.1|FK960927
EST:     AAGTTACAATGCTGCCTTAGCTGCAAGACCTTTTGTGGAAGAACTGACTG                         GTATTCCTGTGACTATGGAGGTTGCAAGTKACTTGCTGGACAGACAAGGTC
genomic: AAGTTACAATGCTGCCTTAGCTGCAAGACCTTTTGTGGAAGAACTGACTGgtaagaccaa ... tggatgacagGTATTCCTGTGACTATGGAGGTTGCAAGTGACTTGCTGGACAGACAAGGTC
EST: gi|211509469|gb|FK960934.1|FK960934
EST:     AAGTTACAATGCTGCCTTAGCTGCAAGACCTTTTGTGGAAGAACTGACTG                         GTATTCCTGTGACTATGGAGGTTGCAAGTGACTTGCTGGACAGACAAGGTC
genomic: AAGTTACAATGCTGCCTTAGCTGCAAGACCTTTTGTGGAAGAACTGACTGgtaagaccaa ... tggatgacagGTATTCCTGTGACTATGGAGGTTGCAAGTGACTTGCTGGACAGACAAGGTC
EST: gi|211507106|gb|FK960920.1|FK960920
EST:     AAGTTACAATGCTGCCTTAGCTGCAAGACCTTTTGTGGAAGAACTGACTG                         GTATTCCTGTGACTATGGAGGTTGCAAGTGACTTGCTGGACAGACAAGGTC
genomic: AAGTTACAATGCTGCCTTAGCTGCAAGACCTTTTGTGGAAGAACTGACTGgtaagaccaa ... tggatgacagGTATTCCTGTGACTATGGAGGTTGCAAGTGACTTGCTGGACAGACAAGGTC
EST: gi|211509467|gb|FK960932.1|FK960932
EST:     AAGTTACAATGCTGCCTTAGCTGCAAGACCTTTTGTGGAAGAACTGACTG                         GTATTCCTGTGACTATGGAGGTTGCAAGTGACTTGCTGGACAGACAAGGTC
genomic: AAGTTACAATGCTGCCTTAGCTGCAAGACCTTTTGTGGAAGAACTGACTGgtaagaccaa ... tggatgacagGTATTCCTGTGACTATGGAGGTTGCAAGTGACTTGCTGGACAGACAAGGTC
EST: gi|463302|gb|T18269.1|T18269
EST:     GCTGCCTTAGCTGCAAGACCTTTTGTGGAAGAACTGACTG                         GTATTCCTGTGACTATGGAGGTTGCAAGTNACTTGCTGGACAGACAAGGTC
genomic: GCTGCCTTAGCTGCAAGACCTTTTGTGGAAGAACTGACTGgtaagaccaa ... tggatgacagGTATTCCTGTGACTATGGAGGTTGCAAGTGACTTGCTGGACAGACAAGGTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCAAGACAATTAGGCGCTGTAGAAGGGTGGTATTTATTGGTTGTGGAACAAGTTACAATGCTGCCTTAGCTGCAAGACCTTTTGTGGAAGAACTGACTGgtaagaccaatcaattaattactccagctgtattgcctataccaagaaaagtttggaatttgtcgaagcaatcagaccttagttaatgatcctttaggtttaacctttctccttgctttatttggatgacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC