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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccacacatattatttgcttctgctgtttttgttatcatgtgttatatatcctatcgtatgtagttgaagcatactcacatatatgcaaatatcttttcagCAAAAATCCCCTTTCCATTGACTCAGAGATTCAGGGGAATGCTGCAAAATGGGATTGACCTGAGCACTGTTGATGTCAGCTATGTTAGTAGCCGGTCATG

Basic information

species Zea mays
transcript GRMZM2G014313_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G014313_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os09g32220.1 (Oryza sativa), 3'ss of exon 4
ccacacatattatttgcttctgctgtttttgttatcatgtgttatatatcctatcgtatgtagttgaagcat---actcacatatatgcaaatatcttttcagCAAAAATCCCCTTTCCATTGACTCAGAGATTCAGGGGAATGCTGCAAAATGGGATTGACCTGAGCACTGTTGATGTCAGCTATGTTAGTAGCCGGTCATG
 || || | | ||   ||| |  ||||||||| ||||| ||| | | || | || | ||||| |||   |     |||||||||| | |   | |||||||||| || || |||||||||||||||| | |||||||||||||||||||||| ||||| |||||||| ||||||||||| ||||||||||| ||||| |||||
-catacgtgtcatccacttattttgtttttgtaatcatatgt-aca-attcaatggcatgtacttgtgtccctggactcacatatttcctgctctcttttcagCTAAGATTCCCTTTCCATTGACTCCGCGATTCAGGGGAATGCTGCAAAACGGGATAGACCTGAGTACTGTTGATGTGAGCTATGTTAGCAGCCGTTCATG

upper sequence: GRMZM2G014313_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA18G08370.1 (Glycine max), 3'ss of exon 2
ccacacatattatttgcttctgctgtttttgttatca-tgtgttatatatcctatcgtatgtagttgaagcatactcacatatatgcaaatatctttt---cagCAAAAATCCCCTTTCCATTGACTCAGAGATTCAGGGGAATGCTGCAAAATGGGATTGACCTGAGCACTGTTGATGTCAGCTATGTTAGTAGCCGGTCATG
 || |||| |  ||  ||| || |  |  | |  |          |       ||    | || |     | | ||   | || |  |||  | |  |   |||| || || |||||||||||||| ||||| || |||  |||||| || ||||| || ||||| ||||| || ||||| |||||||| || || || || | 
-catacatgt-gttgacttatgatagtcatctgcttggcacaaccttggattcattacttttactatttacct-cttgaaaatgtttaaaactttcatgcacaGCCAAGATACCCTTTCCATTGACACAGAGGTTTAGGTCAATGCTACAGAATGGAATAGACCTTAGCACCGTAGATGTTAGCTATGTCAGCAGTCGCTCTT-
















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|211291996|gb|FL370573.1|FL370573
EST:     ACACTTACATTTGCATGGGTGAACTTTTTCTTTTCAGGTTTCGTTGCAG                         CAAAA-TCCCCTTTCCATTGACTCAGAG
genomic: ACACTTACATTTGCATGGGTGAACTTTTTCTTTTCAGGTTTCGTTGCAGgtatgttcat ... atcttttcagCAAAAATCCCCTTTCCATTGACTCAGAG
EST: gi|211064386|gb|FL218050.1|FL218050
EST:     ACACTTACATTTGCATGGGTGAACTTTTTCTTTTCAGGTTTCGTTGCAG                         CAAAA-TCCCCTTTCC
genomic: ACACTTACATTTGCATGGGTGAACTTTTTCTTTTCAGGTTTCGTTGCAGgtatgttcat ... atcttttcagCAAAAATCCCCTTTCC
EST: gi|14202406|gb|BG836083.1|BG836083
EST:     ACACTTACATTTGCATGGGTGAACTTTTTCTTTTCAGGTTTCGTTGCAG                         CAAAAATCCCCTTTCCATTGACTCAGAGATTCAGGGGAATGCTGCAAAATG
genomic: ACACTTACATTTGCATGGGTGAACTTTTTCTTTTCAGGTTTCGTTGCAGgtatgttcat ... atcttttcagCAAAAATCCCCTTTCCATTGACTCAGAGATTCAGGGGAATGCTGCAAAATG
EST: gi|15053265|gb|BI358810.1|BI358810
EST:     ACACTTACATTTGCATGGGTGAACTTTTTCTTTTCAGGTTTCGTTGCAG                         CAAAAATCCCCTTTCCATTGACTCAGAGATTCAGGGGAATGCTGCAAAATG
genomic: ACACTTACATTTGCATGGGTGAACTTTTTCTTTTCAGGTTTCGTTGCAGgtatgttcat ... atcttttcagCAAAAATCCCCTTTCCATTGACTCAGAGATTCAGGGGAATGCTGCAAAATG
EST: gi|211069863|gb|FL218071.1|FL218071
EST:     ACACTTACATTTGCATGGGTGAACTTTTTCTTTTCAGGTTTCGTTGCAG                         CAAAAATCCCCTTTCCATTGACTCAGAGATTCAGGGGAATGCTGCAAAATG
genomic: ACACTTACATTTGCATGGGTGAACTTTTTCTTTTCAGGTTTCGTTGCAGgtatgttcat ... atcttttcagCAAAAATCCCCTTTCCATTGACTCAGAGATTCAGGGGAATGCTGCAAAATG
EST: gi|211498980|gb|FL377920.1|FL377920
EST:     ACACTTACATTTGCATGGGTGAACTTTTTCTTTTCAGGTTTCGTTGCAG                         CAAAAATCCCCTTT
genomic: ACACTTACATTTGCATGGGTGAACTTTTTCTTTTCAGGTTTCGTTGCAGgtatgttcat ... atcttttcagCAAAAATCCCCTTT
EST: gi|211291993|gb|FL370570.1|FL370570
EST:     ACACTTACATTTGCATGGGTGAACTTTTTCTTTTCAGGTTTCGTTGCAG                         CAAAAATCCCCTTTTCATTGACTCAGAGA
genomic: ACACTTACATTTGCATGGGTGAACTTTTTCTTTTCAGGTTTCGTTGCAGgtatgttcat ... atcttttcagCAAAAATCCCCTTTCCATTGACTCAGAGA
EST: gi|211069861|gb|FL218069.1|FL218069
EST:     ACACTTACATTTGCATGGGTGAACTTTTTCTTTTCAGGTTTCGTTGCAG                         CAAAAATCCCCTTTCCATTGACTCAGAGATTCAGGGGAATGCTGCAAAATG
genomic: ACACTTACATTTGCATGGGTGAACTTTTTCTTTTCAGGTTTCGTTGCAGgtatgttcat ... atcttttcagCAAAAATCCCCTTTCCATTGACTCAGAGATTCAGGGGAATGCTGCAAAATG
EST: gi|211497850|gb|FL218033.1|FL218033
EST:     ACACTTACATTTGCATGGGTGAACTTTTTCTTTTCAGGTTTCGTTGCAG                         CAAAAATCCCCCTTTC
genomic: ACACTTACATTTGCATGGGTGAACTTTTTCTTTTCAGGTTTCGTTGCAGgtatgttcat ... atcttttcagCAAAAATCCCC-TTTC
EST: gi|50337385|gb|CO532511.1|CO532511
EST:     ACACTTACATTTGCATGGGTGAACTTTTTCTTTTCAGGTTTCGTTGCAG                         CAAAAATCCCCTTTCCATTGACTCAGAGATTCAGGGGAATGCTGCAAAATG
genomic: ACACTTACATTTGCATGGGTGAACTTTTTCTTTTCAGGTTTCGTTGCAGgtatgttcat ... atcttttcagCAAAAATCCCCTTTCCATTGACTCAGAGATTCAGGGGAATGCTGCAAAATG
EST: gi|94477440|gb|EB706398.1|EB706398
EST:     ACACTTACATTTGCATGGGTGAACTTTTTCTTTTCAGGTTTCGTTGCAG                         CAAAAATCCCCTTTCCATTGACTCAGAGATTCAGGGGAATGCTGCAAAATG
genomic: ACACTTACATTTGCATGGGTGAACTTTTTCTTTTCAGGTTTCGTTGCAGgtatgttcat ... atcttttcagCAAAAATCCCCTTTCCATTGACTCAGAGATTCAGGGGAATGCTGCAAAATG
EST: gi|211067129|gb|FL218060.1|FL218060
EST:     ACACTTACATTTGCATGGGTGAACTTTTTCTTTTCAGGTTTCGTTGCAG                         CAAAAATCCCCTTTCCATTGACTCAGAGATTCAG
genomic: ACACTTACATTTGCATGGGTGAACTTTTTCTTTTCAGGTTTCGTTGCAGgtatgttcat ... atcttttcagCAAAAATCCCCTTTCCATTGACTCAGAGATTCAG
EST: gi|32936209|gb|CF041021.1|CF041021
EST:     ACACTTACATTTGCATGGGTGAACTTTTTCTTTTCAGGTTTCGTTGCAG                         CAAAAATCCCCTTTCCATTGACTCAGAGATTCAGGGGAATGCTGCAAAATG
genomic: ACACTTACATTTGCATGGGTGAACTTTTTCTTTTCAGGTTTCGTTGCAGgtatgttcat ... atcttttcagCAAAAATCCCCTTTCCATTGACTCAGAGATTCAGGGGAATGCTGCAAAATG
EST: gi|211011987|gb|FL416045.1|FL416045
EST:     ACACTTACATTTGCATGGGTGAACTTTTTCTTTTCAGGTTTCGTTGCAG                         CAAAA-TCCCCTTTTCATTGACTCAGAGATTCA
genomic: ACACTTACATTTGCATGGGTGAACTTTTTCTTTTCAGGTTTCGTTGCAGgtatgttcat ... atcttttcagCAAAAATCCCCTTTCCATTGACTCAGAGATTCA
EST: gi|15545720|gb|BI643514.1|BI643514
EST:     ACACTTACATTTGCATGGGTGAACTTTTTCTTTTCAGGTTTCGTTGCAG                         CAAAAATCCCCTTTCCATTGACTCAGAGATTCAGGGGAATGCTGCAAAATG
genomic: ACACTTACATTTGCATGGGTGAACTTTTTCTTTTCAGGTTTCGTTGCAGgtatgttcat ... atcttttcagCAAAAATCCCCTTTCCATTGACTCAGAGATTCAGGGGAATGCTGCAAAATG
EST: gi|211482792|gb|FL423815.1|FL423815
EST:     ACACTTACATTTGCATGGGTGAACTTTTTCTTTTCAGGTTTCGTTGCAG                         CAAAAATCCCCTTTCCATTGACT
genomic: ACACTTACATTTGCATGGGTGAACTTTTTCTTTTCAGGTTTCGTTGCAGgtatgttcat ... atcttttcagCAAAAATCCCCTTTCCATTGACT
EST: gi|211064385|gb|FL218049.1|FL218049
EST:     ACACTTACATTTGCATGGGTGAACTTTTTCTTTTCAGGTTTCGTTGCAG                         CAAAAATCCCCTTTCCATTGACTCAGAGATTCAGGGGAATGCTGCAAAATG
genomic: ACACTTACATTTGCATGGGTGAACTTTTTCTTTTCAGGTTTCGTTGCAGgtatgttcat ... atcttttcagCAAAAATCCCCTTTCCATTGACTCAGAGATTCAGGGGAATGCTGCAAAATG
EST: gi|211064387|gb|FL218051.1|FL218051
EST:     ACACTTACATTTGCATGGGTGAACTTTTTCTTTTCAGGTTTCGTTGCAG                         CAAAAATCCCCTTTCCATTGACTCAGAGATTCAGGGGAATGCTGCAAAATG
genomic: ACACTTACATTTGCATGGGTGAACTTTTTCTTTTCAGGTTTCGTTGCAGgtatgttcat ... atcttttcagCAAAAATCCCCTTTCCATTGACTCAGAGATTCAGGGGAATGCTGCAAAATG
EST: gi|15590500|gb|BI675116.1|BI675116
EST:     ACACTTACATTTGCATGGGTGAACTTTTTCTTTTCAGGTTTCGTTGCAG                         CAAAAATCCCCTTTCCATTGACTCAGAGATTCAGGGGAATGCTGCAAAATG
genomic: ACACTTACATTTGCATGGGTGAACTTTTTCTTTTCAGGTTTCGTTGCAGgtatgttcat ... atcttttcagCAAAAATCCCCTTTCCATTGACTCAGAGATTCAGGGGAATGCTGCAAAATG
EST: gi|211069864|gb|FL218072.1|FL218072
EST:     ACACTTACATTTGCATGGGTGAACTTTTTCTTTTCAGGTTTCGTTGCAG                         CAAAAATCCCCTTTCCATTGACTCAGAGATTCAGGGGAATGCTGCAAAATG
genomic: ACACTTACATTTGCATGGGTGAACTTTTTCTTTTCAGGTTTCGTTGCAGgtatgttcat ... atcttttcagCAAAAATCCCCTTTCCATTGACTCAGAGATTCAGGGGAATGCTGCAAAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatcctatcgtatgtagttgaagcatactcacatatatgcaaatatcttttcagCAAAAATCCCCTTTCCATTGACTCAGAGATTCAGGGGAATGCTGCAAAATGGGATTGACCTGAGCACTGTTGATGTCAGCTATGTTAGTAGCCGGTCATG
                          tactcac  putative branch site (score: 1)
                                            tatcttttc  putative PPT
                                 atatatgcaaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccacacatattatttgcttctgctgtttttgttatcatgtgttatatatcctatcgtatgtagttgaagcatactcacatatatgcaaatatcttttcagCAAAAATCCCCTTTCCATTGACTCAGAGATTCAGGGGAATGCTGCAAAATGGGATTGACCTGAGCACTGTTGATGTCAGCTATGTTAGTAGCCGGTCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
ccacaca
- - - - - - - - - tctgctg
- - - - - - - - - - - - - ttttgtt
- - - - - - - - - - - - - - - - - -catgtgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatgcaa