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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_T01
intron # 4
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|37397476|gb|CF636037.1|CF636037
EST:     CAACAAACCTCCGACTGTTCGGTTTGTTTCGAGGATGTTTCACCCAAACA                         TTTATGCGGATGGAAGCATCTGTTTGGACATCCTACAAAACCAGTGGAGTC
genomic: CAACAAACCTCCGACTGTTCGGTTTGTTTCGAGGATGTTTCACCCAAACAgtatgttctc ... ttttttccagTTTATGCGGATGGAAGCATCTGTTTGGACATCCTACAAAACCAGTGGAGTC
EST: gi|110947584|gb|EE167741.1|EE167741
EST:     CAACAAACCTCCGACTGTTCGGTTTGTTTCGAGGATGTTTCACCCAAACA                         TTTATGCGGATGGAAGCATCTGTTTGGACATCCTACAAAACCAGTGGAGTC
genomic: CAACAAACCTCCGACTGTTCGGTTTGTTTCGAGGATGTTTCACCCAAACAgtatgttctc ... ttttttccagTTTATGCGGATGGAAGCATCTGTTTGGACATCCTACAAAACCAGTGGAGTC
EST: gi|18168064|gb|BM337904.1|BM337904
EST:     CAACAAACCTCCGACTGTTCGGTTTGTTTCGAGGATGTTTCACCCAAACA                         TTTATGCGGATGGAAGCATCTGTTTGGACATCCTACAAAACCAGTGGAGTC
genomic: CAACAAACCTCCGACTGTTCGGTTTGTTTCGAGGATGTTTCACCCAAACAgtatgttctc ... ttttttccagTTTATGCGGATGGAAGCATCTGTTTGGACATCCTACAAAACCAGTGGAGTC
EST: gi|37377294|gb|CF625238.1|CF625238
EST:     CAACAAACCTCCGACTGTTCGGTTTGTTTCGAGGATGTTTCACCCAAACA                         TTTATGCGGATGGAAGCATCTGTTTGGACATCCTACAAAACCAGTGGAGTC
genomic: CAACAAACCTCCGACTGTTCGGTTTGTTTCGAGGATGTTTCACCCAAACAgtatgttctc ... ttttttccagTTTATGCGGATGGAAGCATCTGTTTGGACATCCTACAAAACCAGTGGAGTC
EST: gi|12972475|gb|BG268000.1|BG268000
EST:     CAACAAACCTCCGACTGTTCGGTTTGTTTCGAGGATGTTTCACCCAAACA                         TTTATGCGGATGGAAGCATCTGTTTGGACATCCTACAAAACCAGTGGAGTC
genomic: CAACAAACCTCCGACTGTTCGGTTTGTTTCGAGGATGTTTCACCCAAACAgtatgttctc ... ttttttccagTTTATGCGGATGGAAGCATCTGTTTGGACATCCTACAAAACCAGTGGAGTC
EST: gi|18168754|gb|BM338594.1|BM338594
EST:     CAACAAACCTCCGACTGTTCGGTTTGTTTCGAGGATGTTTCACCCAAACA                         TTTATGCGGATGGAAGCATCTGTTTGGACATCCTACAAAACCAGTGGAGTC
genomic: CAACAAACCTCCGACTGTTCGGTTTGTTTCGAGGATGTTTCACCCAAACAgtatgttctc ... ttttttccagTTTATGCGGATGGAAGCATCTGTTTGGACATCCTACAAAACCAGTGGAGTC
EST: gi|94474209|gb|EB703167.1|EB703167
EST:     CAACAAACCTCCGACTGTTCGGTTTGTTTCGAGGATGTTTCACCCAAACA                         TTTATGCGGATGGAAGCATCTGTTTGGACATCCTACAAAACCAGTGGAGTC
genomic: CAACAAACCTCCGACTGTTCGGTTTGTTTCGAGGATGTTTCACCCAAACAgtatgttctc ... ttttttccagTTTATGCGGATGGAAGCATCTGTTTGGACATCCTACAAAACCAGTGGAGTC
EST: gi|149112232|gb|EE191288.2|EE191288
EST:     CAACAAACCTCCGACTGTTCGGTTTGTTTCGAGGATGTTTCACCCAAACA                         TTTATGCGGATGGAAGCATCTGTTTGGACATCCTACAAAACCAGTGGAGTC
genomic: CAACAAACCTCCGACTGTTCGGTTTGTTTCGAGGATGTTTCACCCAAACAgtatgttctc ... ttttttccagTTTATGCGGATGGAAGCATCTGTTTGGACATCCTACAAAACCAGTGGAGTC
EST: gi|94474208|gb|EB703166.1|EB703166
EST:     CAACAAACCTCCGACTGTTCGGTTTGTTTTGAGGATGTTTCACCCAAACA                         TTTATGCGGATGGAAGCATCTGTTTGGACATCCTACAAAACCAGTGGAGTC
genomic: CAACAAACCTCCGACTGTTCGGTTTGTTTCGAGGATGTTTCACCCAAACAgtatgttctc ... ttttttccagTTTATGCGGATGGAAGCATCTGTTTGGACATCCTACAAAACCAGTGGAGTC
EST: gi|113703398|gb|EE680902.1|EE680902
EST:     CAACAAACCTCCGACTGTTCGGTTTGTTTCGAGGATGTTTCACCCAAACA                         TTTATGCGGATGGAAGCATCTGTTTGGACATCCTACAAAACCAGTGGAGTC
genomic: CAACAAACCTCCGACTGTTCGGTTTGTTTCGAGGATGTTTCACCCAAACAgtatgttctc ... ttttttccagTTTATGCGGATGGAAGCATCTGTTTGGACATCCTACAAAACCAGTGGAGTC
EST: gi|18179315|gb|BM380525.1|BM380525
EST:     CAACAAACCTCCGACTGTTCGGTTTGTTTCGAGGATGTTTCACCCAAACA                         TTTATGCGGATGGAAGCATCTGTTTGGACATCCTACAAAACCAGTGGAGTC
genomic: CAACAAACCTCCGACTGTTCGGTTTGTTTCGAGGATGTTTCACCCAAACAgtatgttctc ... ttttttccagTTTATGCGGATGGAAGCATCTGTTTGGACATCCTACAAAACCAGTGGAGTC
EST: gi|78122431|gb|DV540815.1|DV540815
EST:     TGTTCGGTTTGTTTCGAGGATGTTTCACCCAACCA                         TTTATGCGGATGGAAGCATCTGTTTGGACATCCTCCAAAACCAGTGGAGTC
genomic: TGTTCGGTTTGTTTCGAGGATGTTTCACCCAAACAgtatgttctc ... 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