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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCACGTTCAAGCTGACTCTGCAATTTACAGAAGATTACCCCAACAAACCTCCGACTGTTCGGTTTGTTTCGAGGATGTTTCACCCAAACAgtatgttctctttagatgttaaggaactaaattattctcatattggcacctgagtacattgacaataagtggtttaataccaattctttttttccag

Basic information

species Zea mays
transcript GRMZM2G007260_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G007260_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os03g57790.2 (Oryza sativa), 5'ss of exon 3
GCACGTTCAAGCTGACTCTGCAATTTACAGAAGATTACCCCAACAAACCTCCGACTGTTCGGTTTGTTTCGAGGATGTTTCACCCAAACAgtatgttctct---ttagatgttaaggaactaaattattctcata--ttggcacctgagtacattgacaataagtggtttaatac-----caattctttttttccag--------------------
|||||||||||||||| || ||||||||||||||||| ||||||||||| ||   |||||||||||| || ||||||||||||||||| |||||||    |   ||     ||     |||  |||||  |   |   |   || | | | |   || | | | |  || || |      ||| |  || |||                        
GCACGTTCAAGCTGACACTACAATTTACAGAAGATTATCCCAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATAgtatgtctcataacttgataatttgaccacttcattatctttgcaagctactacattattcccaagagattgaattattgaagatatacacaactaattgtttttgttatccgttcagtttatgcag

upper sequence: GRMZM2G007260_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os03g57790.1 (Oryza sativa), 5'ss of exon 3
GCACGTTCAAGCTGACTCTGCAATTTACAGAAGATTACCCCAACAAACCTCCGACTGTTCGGTTTGTTTCGAGGATGTTTCACCCAAACAgtatgttctct---ttagatgttaaggaactaaattattct--catattggcacctgagtacattgacaataagtggtttaatac-----caattctttttttccag-----------
|||||||||||||||| || ||||||||||||||||| ||||||||||| ||   |||||||||||| || ||||||||||||||||| |||||||    |   ||     ||     |||  |||||  |  ||   |   || | | | |   || | | | |  || || |      ||| |  || |||               
GCACGTTCAAGCTGACACTACAATTTACAGAAGATTATCCCAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATAgtatgtctcataacttgataatttgaccacttcattatctttgcaagctactacattattcccaagagattgaattattgaagatatacacaactaattgtttttgttatccgttcag

upper sequence: GRMZM2G007260_T01 (Zea mays), 5'ss of exon 4
lower sequence: PP1S219_106V6.1 (Physcomitrella patens), 5'ss of exon 3
GCACGTTCAAGCTGACTCTGCAATTTACAGAAGATTACCCCAACAAACCTCCGACTGTTCGGTTTGTTTCGAGGATGTTTCACCCAAACAgtatgttctctttagatgttaaggaactaaattattctc--atattggcacctgagtacattgacaataagtggtttaataccaattctttttttc-cag
| ||||||||| ||||  |||||||||| || ||||| || ||||| ||||| || || || ||||| |||| |||||||||||| ||||||| |   | |    |||     | ||   |    ||    || |||     | ||      |    |    |||  |      |||    ||||  | |
GGACGTTCAAGTTGACGTTGCAATTTACCGAGGATTATCCGAACAAGCCTCCTACAGTGCGTTTTGTCTCGAAGATGTTTCACCCTAACAgtaagcgttttccgcatgcacttgtacacgaggggtcaaggatgttgattggttagggttggggtggtcgaaggtggagggtggattgggattttagctg

upper sequence: GRMZM2G007260_T01 (Zea mays), 5'ss of exon 4
lower sequence: PP1S91_87V6.1 (Physcomitrella patens), 5'ss of exon 3
GCACGTTCAAGCTGACTCTGCAATTTACAGAAGATTACCCCAACAAACCTCCGACTGTTCGGTTTGTTTCGAGGATGTTTCACCCAAACAgtatg--ttctctttagatgttaaggaactaaattattctcatattggcacctgagtacattgacaataagtggtttaataccaattctttttttccag-
| ||||||||| ||||  |||||||||| || |||||||| || || ||||| || || || ||||| || | |||||||||||| ||||||| |  ||  || |  || ||| ||  |       |       |||  ||  |   || |  | |   | ||  | |      | |  |        | 
GAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTCCCACAGTGCGCTTTGTCTCAAAGATGTTTCACCCTAACAgtaagcatttcctgtgaatattaggggtcgtggaggtagagtggttgagactggtccacctgaatacggaatgtgtgagggtgtacttgtggagagtgga

upper sequence: GRMZM2G007260_T01 (Zea mays), 5'ss of exon 4
lower sequence: EFJ17802 (Selaginella moellendorffii), 5'ss of exon 3
GCACGTTCAAGCTGACTCTGCAATTTACAGAAGATTACCCCAACAAACCTCCGACTGTTCGGTTTGTTTCGAGGATGTTTCACCCAAACAgtatgttctctttagatgttaaggaactaaattattctcatattggcacctgagtacattgacaataagtggtttaataccaattctttttttccag
| ||||| ||||||||  ||||||| ||||| || || |||||||||||||| || ||  |||||||||| | |||||| || || || |||  || | ||||     ||    || |   || || || || |  || ||   | ||                                       
GGACGTTTAAGCTGACATTGCAATTCACAGAGGACTATCCCAACAAACCTCCCACCGTGAGGTTTGTTTCCAAGATGTTCCATCCCAATAgtgagtcc-ctttcttctttctttaattttctttttttcttact--catctttttgcag--------------------------------------

upper sequence: GRMZM2G007260_T01 (Zea mays), 5'ss of exon 4
lower sequence: EFJ16328 (Selaginella moellendorffii), 5'ss of exon 3
GCACGTTCAAGCTGACTCTGCAATTTACAGAAGATTACCCCAACAAACCTCCGACTGTTCGGTTTGTTTCGAGGATGTTTCACCCAAACAgtatgttctctttagatgttaaggaactaaattattctcatattggcacctgagtacattgacaataagtggtttaataccaattctttttttccag
| ||||| ||||||||  ||||||| ||||| || || |||||||||||||| || ||  |||||||||| | |||||| || || || |||  || |  |     | |    ||  |   |  || || || |     ||  | |                                         
GGACGTTTAAGCTGACATTGCAATTCACAGAGGACTATCCCAACAAACCTCCCACCGTGAGGTTTGTTTCCAAGATGTTCCATCCCAATAgtgagtcccttgcttctttctttgagtttcttctttttcttactcatctcttcgcag----------------------------------------

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|211209634|gb|FL170002.1|FL170002
EST:     CAACAAACCTCCGACTGTTCGGTTTGTTTCGAGGATGTTTCACCCAAACA                         TTTATGCGGATGGAAGCATCTGTTTGGACATCCTACAAAACCAGTGGAGTC
genomic: CAACAAACCTCCGACTGTTCGGTTTGTTTCGAGGATGTTTCACCCAAACAgtatgttctc ... ttttttccagTTTATGCGGATGGAAGCATCTGTTTGGACATCCTACAAAACCAGTGGAGTC
EST: gi|22521069|gb|BU079880.1|BU079880
EST:     CAACAAACCTCCGACTGTTCGGTTTGTTTCGAGGATGTTTCACCCAAACA                         TTTATGCGGATGGAAGCATCTGTTTGGACATCCTACAAAACCAGTGGAGTC
genomic: CAACAAACCTCCGACTGTTCGGTTTGTTTCGAGGATGTTTCACCCAAACAgtatgttctc ... ttttttccagTTTATGCGGATGGAAGCATCTGTTTGGACATCCTACAAAACCAGTGGAGTC
EST: gi|211209639|gb|FL170007.1|FL170007
EST:     CAACAAACCTCCGACTGTTCGGTTTGTTTCGAGGATGTTTCACCCAAACA                         TTTATGCGGGATTGGAAGCATCTGTTTGGACATCCTACAAAACCAGTGGAG
genomic: CAACAAACCTCCGACTGTTCGGTTTGTTTCGAGGATGTTTCACCCAAACAgtatgttctc ... ttttttccagTTTATGCGG-AT-GGAAGCATCTGTTTGGACATCCTACAAAACCAGTGGAG
EST: gi|211212202|gb|FL170018.1|FL170018
EST:     CAACAAACCTCCGACTGTTCGGTTTGTTTCGAGGATGTTTCACCCAAACA                         TTTATGCGGATGGGAGCATCTGTTTGGACATCCTACAAAACCAGTGGAGTC
genomic: CAACAAACCTCCGACTGTTCGGTTTGTTTCGAGGATGTTTCACCCAAACAgtatgttctc ... ttttttccagTTTATGCGGATGGAAGCATCTGTTTGGACATCCTACAAAACCAGTGGAGTC
EST: gi|211209638|gb|FL170006.1|FL170006
EST:     CAACAAACCTCCGACTGTTCGGTTTGTTTCGAGGATGTTTCACCCAAACA                         TTTATGCGGATGGAAGCATCTGTTTGGACATCCTACAAAACCAGTGGAGTC
genomic: CAACAAACCTCCGACTGTTCGGTTTGTTTCGAGGATGTTTCACCCAAACAgtatgttctc ... ttttttccagTTTATGCGGATGGAAGCATCTGTTTGGACATCCTACAAAACCAGTGGAGTC
EST: gi|211209637|gb|FL170005.1|FL170005
EST:     CAACAAACCTCCGACTGTTCGGTTTGTTTMGAGGATGTTTCACCCAAACA                         TTTATGCGGATGGAAGCATCTGTTTGGAC
genomic: CAACAAACCTCCGACTGTTCGGTTTGTTTCGAGGATGTTTCACCCAAACAgtatgttctc ... ttttttccagTTTATGCGGATGGAAGCATCTGTTTGGAC
EST: gi|149074449|gb|EE162844.2|EE162844
EST:     CAACAAACCTCCGACTGTTCGGTTTGTTTCGAGGATGTTTCACCCAAACA                         TTTATGCGGATGGAAGCATCTGTTTGGACATCCTACAAAACCAGTGGAGTC
genomic: CAACAAACCTCCGACTGTTCGGTTTGTTTCGAGGATGTTTCACCCAAACAgtatgttctc ... ttttttccagTTTATGCGGATGGAAGCATCTGTTTGGACATCCTACAAAACCAGTGGAGTC
EST: gi|211209642|gb|FL170010.1|FL170010
EST:     CAACAAACCTCCGACTGTTCGGTTTGTTTCGAGGATGTTTCACCCAAACA                         TTTATGCGGATGGAAGCATCTGTTTGGACATCCTACAAAACCAGTGGAGTC
genomic: CAACAAACCTCCGACTGTTCGGTTTGTTTCGAGGATGTTTCACCCAAACAgtatgttctc ... ttttttccagTTTATGCGGATGGAAGCATCTGTTTGGACATCCTACAAAACCAGTGGAGTC
EST: gi|211212201|gb|FL170017.1|FL170017
EST:     CAACAAACCTCCGACTGTTCGGTTTGTTTCGAGGATGTTTCACCCAAACA                         TTTATGCGGATGGAAGCATCTGTTTGGACAT
genomic: CAACAAACCTCCGACTGTTCGGTTTGTTTCGAGGATGTTTCACCCAAACAgtatgttctc ... ttttttccagTTTATGCGGATGGAAGCATCTGTTTGGACAT
EST: gi|14701443|gb|BI233861.1|BI233861
EST:     CAACAAACCTCCGACTGTTCGGTTTGTTTCGAGGATGTTTCACCCAAACA                         TTTATGCGGATGGAAGCATCTGTTTGGACATCCTACAAAACCAGTGGAGTC
genomic: CAACAAACCTCCGACTGTTCGGTTTGTTTCGAGGATGTTTCACCCAAACAgtatgttctc ... ttttttccagTTTATGCGGATGGAAGCATCTGTTTGGACATCCTACAAAACCAGTGGAGTC
EST: gi|20803162|gb|BQ294212.1|BQ294212
EST:     CAACAAACCTCCGACTGTTCGGTTTGTTTCGAGGATGTTTCACCCAAACA                         TTTATGCGGATGGAAGCATCTGTTTGGACATCCTACAAAACCAGTGGAGTC
genomic: CAACAAACCTCCGACTGTTCGGTTTGTTTCGAGGATGTTTCACCCAAACAgtatgttctc ... ttttttccagTTTATGCGGATGGAAGCATCTGTTTGGACATCCTACAAAACCAGTGGAGTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCACGTTCAAGCTGACTCTGCAATTTACAGAAGATTACCCCAACAAACCTCCGACTGTTCGGTTTGTTTCGAGGATGTTTCACCCAAACAgtatgttctctttagatgttaaggaactaaattattctcatattggcacctgagtacattgacaataagtggtttaataccaattctttttttccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG