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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgctttcttttttttatgagacatgaattttgaattgtctcagcaattgtggtactaggatgttttcttttgtaacatcatttgttcatatttccttcagGTGGCAAGGATATTTTTGTTCATGTATGTATTTTACCACATCTATTTGCATTACGGTCAG

Basic information

species Zea mays
transcript GRMZM2G016184_T03
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G016184_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os03g46410.1 (Oryza sativa), 3'ss of exon 7
tgctttcttttttttatgagacatgaattttgaattgtctcagcaattgtggtactaggatgttttct-tttgtaacatcatttgttcatatttccttcagGTGGCAAGGATATTTTTGTTCATGTATGTATTTTACCACATCTATTTGCATTACGGTCAG
  | |     |   || |  |  | | || |||      |         ||||   |   |  |  || ||| |   | |  |  | | | ||||  |||||| ||||||||| || ||||||| || ||||| || |||||||||||||| ||| |||||
-tcatgtacctgactaagctattttagttgtgagacaatttcttttccttggtgtcatacttctggctctttatcttagcgatcttacttctttcaatcagGTTGCAAGGATACTTCTGTTCATTTACGTATTCTATCACATCTATTTGCACTACAGTCAG
















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|6466756|gb|AW191416.1|AW191416
EST:     AATCAAGTGCTTACTTGGTTAATGGAATTCTGATGTTTGTTGCATGGCTG                         GTGGCAAGGATATTTTTGTTCATGTATGTATTTTACCACATCTATTTGCAT
genomic: AATCAAGTGCTTACTTGGTTAATGGAATTCTGATGTTTGTTGCATGGCTGgtatgcacca ... tttccttcagGTGGCAAGGATATTTTTGTTCATGTATGTATTTTACCACATCTATTTGCAT
EST: gi|71760532|gb|DR958469.1|DR958469
EST:     AATCAAGTGCTTACTTGGTTAATGGAATTCTGATGTTTGTTGCATGGCTG                         GTGGCAAGGATATTTTTGTTCATGTATGTATTTTACCACATCTATTTGCAT
genomic: AATCAAGTGCTTACTTGGTTAATGGAATTCTGATGTTTGTTGCATGGCTGgtatgcacca ... tttccttcagGTGGCAAGGATATTTTTGTTCATGTATGTATTTTACCACATCTATTTGCAT
EST: gi|50338097|gb|CO533223.1|CO533223
EST:     GATGTTTGTTGCATGGCTG                         GTGGCAAGGATATTTTTGTTCATGTATGTATTTTACCACATCTATTTGCAT
genomic: GATGTTTGTTGCATGGCTGgtatgcacca ... tttccttcagGTGGCAAGGATATTTTTGTTCATGTATGTATTTTACCACATCTATTTGCAT
EST: gi|6526808|gb|AW216077.1|AW216077
EST:     AATCAAGTGCTTACTTGGGTAATGGAATTCTGATGTTTGTTGCATGGCTG                         GTGGCAAGGATATTTTTGTTCATGTATGTATTTTACCACATCTATTTGCAT
genomic: AATCAAGTGCTTACTTGGTTAATGGAATTCTGATGTTTGTTGCATGGCTGgtatgcacca ... tttccttcagGTGGCAAGGATATTTTTGTTCATGTATGTATTTTACCACATCTATTTGCAT
EST: gi|50322745|gb|CO517871.1|CO517871
EST:     AATCAAGTGCTTACTTGGTTAATGGAATTCTGATGTTTGTTGCATGGCTG                         GTGGCAAGGATATTTTTGTTCATGTATGTATTTTACCACATCTATTTGCAT
genomic: AATCAAGTGCTTACTTGGTTAATGGAATTCTGATGTTTGTTGCATGGCTGgtatgcacca ... tttccttcagGTGGCAAGGATATTTTTGTTCATGTATGTATTTTACCACATCTATTTGCAT
EST: gi|211033261|gb|FL440337.1|FL440337
EST:     AATCAAGTGCTTACTTGGTTAATGGAATTCTGATGTTTGTTGCATGGCTG                         GTGGCAAGGATATTTTTGTTCATGTATGTATTTTACCACATCTATTTGCAT
genomic: AATCAAGTGCTTACTTGGTTAATGGAATTCTGATGTTTGTTGCATGGCTGgtatgcacca ... tttccttcagGTGGCAAGGATATTTTTGTTCATGTATGTATTTTACCACATCTATTTGCAT
EST: gi|12972667|gb|BG268096.1|BG268096
EST:     AATCAAGTGCTTACTTGGTTAATGGAATTCTGATGTTTGTTGCATGGCTG                         GTGGCAAGGATATTTTTGTTCATGTATGTATTTTACCACATGCTATTTGCA
genomic: AATCAAGTGCTTACTTGGTTAATGGAATTCTGATGTTTGTTGCATGGCTGgtatgcacca ... tttccttcagGTGGCAAGGATATTTTTGTTCATGTATGTATTTTACCACAT-CTATTTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgtggtactaggatgttttcttttgtaacatcatttgttcatatttccttcagGTGGCAAGGATATTTTTGTTCATGTATGTATTTTACCACATCTATTTGCATTACGGTCAG
                        ttgtaac  putative branch site (score: 2)
                                       ttcatatttccttc  putative PPT
                                  atttgttcatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgctttcttttttttatgagacatgaattttgaattgtctcagcaattgtggtactaggatgttttcttttgtaacatcatttgttcatatttccttcagGTGGCAAGGATATTTTTGTTCATGTATGTATTTTACCACATCTATTTGCATTACGGTCAG

tgctttc
- - - - - - - - - - acatgaa
- - - - - - - - - - - - - - - tgaattg
- - - - - - - - - - - - - - - - - - - - - - - - -tggtact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacatca