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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tacagtactagcggcagtattgttctctctctctctctttatttaactattgtcatgatttgacatttcaagtcctaacaatactcatatgtgccgtcagATTACTTGCTAATCTTTCTTGAGGGCAGATGGCCGTTTCTTTTGCAAATGTCAACGCCGAGGCAGGGCTGAAAAAGCTTGATGAGTACCTTCTCACTCGC

Basic information

species Zea mays
transcript GRMZM2G153569_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G153569_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os07g42300.2 (Oryza sativa), 3'ss of exon 1
tacagtactagcggcagtattgttctctctctctctctttatttaactattgtcatgatttgacatttca---agtcctaacaatactcatatgtgccgtcagATTACTTGC--TAATCTTTCTTGAGGGC-AGATGGCCGTTTCTTTTGCAAATGTCAACGCCGAGGCAGGGCTGAAAAAGCTTGATGAGTACCTTCTCACTCGC
||||     ||   ||    || |       | |  | |   ||   |||||| |  ||| |   |||       |   |||||| ||| ||||||||  ||| | |||| |  |  | |||||||||||  ||||||| ||||||||  | || || | | | |||||||| || |||||||| ||||||||||||||||||   
tacaacttaagtaacatctatggttgtaaattgtaccatgcattggttattgtga--attagctcttttggttgattgaaacaattctc-tatgtgccaacagGTCACTTTCAGTCTTTTTTCTTGAGGGGGAGATGGCGGTTTCTTTCACCAACGTTAGCTCAGAGGCAGGCCTCAAAAAGCTCGATGAGTACCTTCTCACT---
















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|211378085|gb|FL329648.1|FL329648
EST:     CGCATCACGCCCCCGCCTCCGGTCCACCGCACACCGGCCGGTGACCCTAC                         ATTACTTGCTAATCTTTCTTGAGGGCAGATGGCCGTTTCTTTTGCAAATGT
genomic: CGCATCACGCCCCCGCCTCCGGTCCACCGCACACCGGCCGGTGACCCTACgtgcgtaccc ... gtgccgtcagATTACTTGCTAATCTTTCTTGAGGGCAGATGGCCGTTTCTTTTGCAAATGT
EST: gi|76285318|gb|DV024886.1|DV024886
EST:     CGCATCACGCCCCCGCCTCCGGTCCACCGCACACCGGCCGGTGACCCTAC                         ATTACTTGCTAATCTTTCTTGAGGGCAGATGGCCGTTTCTTTTGCAAATGT
genomic: CGCATCACGCCCCCGCCTCCGGTCCACCGCACACCGGCCGGTGACCCTACgtgcgtaccc ... gtgccgtcagATTACTTGCTAATCTTTCTTGAGGGCAGATGGCCGTTTCTTTTGCAAATGT
EST: gi|13237021|gb|BG355035.1|BG355035
EST:     CGCATCACGCCCCCGCCTCCGGTCCACCGCACACTGTTCGGTGACCCTAC                         ATTACTTGCTAATCTTTCTTGAGGGCAGATGGCCGTTTCTTTTGCAAATGT
genomic: CGCATCACGCCCCCGCCTCCGGTCCACCGCACACCGGCCGGTGACCCTACgtgcgtaccc ... gtgccgtcagATTACTTGCTAATCTTTCTTGAGGGCAGATGGCCGTTTCTTTTGCAAATGT
EST: gi|61117414|gb|DN558375.1|DN558375
EST:     CGCATCACGCCCTCGCCTCCGGTCCACCGCACACCGGCCGGTCACCCTGC                         ATTACTTGCTAATCTTTCTTGAGGGCAGATGGCCGTTTCTTTTGCAAATGT
genomic: CGCATCACGCCCCCGCCTCCGGTCCACCGCACACCGGCCGGTGACCCTACgtgcgtaccc ... gtgccgtcagATTACTTGCTAATCTTTCTTGAGGGCAGATGGCCGTTTCTTTTGCAAATGT
EST: gi|211291795|gb|FL131038.1|FL131038
EST:     YGCATCACGCCCTCGCCTCCGGTCCACCGCACACCGGCCGGTGACCCTGC                         ATTACTTGCTAATCTTTCTTGAGGGCAGATGGCCGTTTCTTTTGCAAATGT
genomic: CGCATCACGCCCCCGCCTCCGGTCCACCGCACACCGGCCGGTGACCCTACgtgcgtaccc ... gtgccgtcagATTACTTGCTAATCTTTCTTGAGGGCAGATGGCCGTTTCTTTTGCAAATGT
EST: gi|76926349|gb|DV170823.1|DV170823
EST:     CGCATCACGCCCCCGCCTCCGGTCCACCGCACACCGGCCGGTGACCCTAC                         ATTACTTGCTAATCTTTCTTGAGGGCAGATGGCCGTTTCTTTTGCAAATGT
genomic: CGCATCACGCCCCCGCCTCCGGTCCACCGCACACCGGCCGGTGACCCTACgtgcgtaccc ... gtgccgtcagATTACTTGCTAATCTTTCTTGAGGGCAGATGGCCGTTTCTTTTGCAAATGT
EST: gi|67012865|gb|CO441614.1|CO441614
EST:     CGCATCACGCCCCCGCCTCCGGTCCACCGCACACCGGCCGGTGACCCTAC                         ATTACTTGCTAATCTTTCTTGAGGGCAGATGGCCGTTTCTTTTGCAAATGT
genomic: CGCATCACGCCCCCGCCTCCGGTCCACCGCACACCGGCCGGTGACCCTACgtgcgtaccc ... gtgccgtcagATTACTTGCTAATCTTTCTTGAGGGCAGATGGCCGTTTCTTTTGCAAATGT
EST: gi|31557965|gb|CD527177.1|CD527177
EST:     CGCATCACGCCCCCGCCTCCGGTCCACCGCACACCGGCCGGTGACCCTAC                         ATTACTTGCTAATCTTTCTTGAGGGTTTATGGCCGTTTCTTTTGCAAATGT
genomic: CGCATCACGCCCCCGCCTCCGGTCCACCGCACACCGGCCGGTGACCCTACgtgcgtaccc ... gtgccgtcagATTACTTGCTAATCTTTCTTGAGGGCAGATGGCCGTTTCTTTTGCAAATGT
EST: gi|211291796|gb|FL131039.1|FL131039
EST:     CGCATCACGCCCTCGCCTCCGGTCCACCGCACACCGGCCGGTGACCCTGC                         ATTACTTGCTAATCTTTCTTGAGGGCAGATGGCCGTTTCTTTTGCAAATGT
genomic: CGCATCACGCCCCCGCCTCCGGTCCACCGCACACCGGCCGGTGACCCTACgtgcgtaccc ... gtgccgtcagATTACTTGCTAATCTTTCTTGAGGGCAGATGGCCGTTTCTTTTGCAAATGT
EST: gi|211437727|gb|FL330573.1|FL330573
EST:     CGCATCACGCCCCCGCCTCCGGTCCACCGCACACCGGCCGGTGACCCTAC                         ATTACTTGCTAATCTTTCTTGAGGGCAGATGGCCGTTTCTTTTGCAAATGT
genomic: CGCATCACGCCCCCGCCTCCGGTCCACCGCACACCGGCCGGTGACCCTACgtgcgtaccc ... gtgccgtcagATTACTTGCTAATCTTTCTTGAGGGCAGATGGCCGTTTCTTTTGCAAATGT
EST: gi|67037468|gb|CO464282.1|CO464282
EST:     CGCATCACGCCCTCGCCTCCGGTCCACCGCACACCGGCCGGTGACCCTGC                         ATTACTTGCTAATCTTTCTTGAGGGCAGATGGCCGTTTCTTTTGCAAATGT
genomic: CGCATCACGCCCCCGCCTCCGGTCCACCGCACACCGGCCGGTGACCCTACgtgcgtaccc ... gtgccgtcagATTACTTGCTAATCTTTCTTGAGGGCAGATGGCCGTTTCTTTTGCAAATGT
EST: gi|211535307|gb|FL356762.1|FL356762
EST:     CGCATCACGCCCCCGCCTCCGGTCCACCGCACACCGGCCGGTGACCCTAC                         ATTACTTGCTAATCTTTCTTGAGGGCAGATGGCCGTTTCTTTTGCAAATGT
genomic: CGCATCACGCCCCCGCCTCCGGTCCACCGCACACCGGCCGGTGACCCTACgtgcgtaccc ... gtgccgtcagATTACTTGCTAATCTTTCTTGAGGGCAGATGGCCGTTTCTTTTGCAAATGT
EST: gi|67016304|gb|CO445053.1|CO445053
EST:     CGCATCACGCCCCCGCCTCCGGTCCACCGCACACCGGCCGGTGACCCTAC                         ATTACTTGCTAATCTTTCTTGAGGGCAGATGGCCGTTTCTTTTGCAAATGT
genomic: CGCATCACGCCCCCGCCTCCGGTCCACCGCACACCGGCCGGTGACCCTACgtgcgtaccc ... gtgccgtcagATTACTTGCTAATCTTTCTTGAGGGCAGATGGCCGTTTCTTTTGCAAATGT
EST: gi|211255757|gb|FL351785.1|FL351785
EST:     CGCATCACGCCCCCGCCTCCGGTCCACCGCACACCGGCCGGTGACCCTAC                         ATTACTTGCTAATCTTTCTTGAGGGCAGATGGCCGTTTCTTTTGCAAATGT
genomic: CGCATCACGCCCCCGCCTCCGGTCCACCGCACACCGGCCGGTGACCCTACgtgcgtaccc ... gtgccgtcagATTACTTGCTAATCTTTCTTGAGGGCAGATGGCCGTTTCTTTTGCAAATGT
EST: gi|211232671|gb|FL320353.1|FL320353
EST:     CGCATCACGCCCCCGCCTCCGGTCCACCGCACACCGGCCGGTGACCCTAC                         ATTACTTGCTAATCTTTCTTGAGGGCAGATGGCCGTTTCTTTTGCAAATGT
genomic: CGCATCACGCCCCCGCCTCCGGTCCACCGCACACCGGCCGGTGACCCTACgtgcgtaccc ... gtgccgtcagATTACTTGCTAATCTTTCTTGAGGGCAGATGGCCGTTTCTTTTGCAAATGT
EST: gi|60359229|gb|DN226202.1|DN226202
EST:     CGCATCACGCCCCCGCCTCCGGTCCACCGCACACCGGCCGGTGACCCTAC                         ATTACTTGCTAATCTTTCTTGAGGGCAGATGGCCGTTTCTTTTGCAAATGT
genomic: CGCATCACGCCCCCGCCTCCGGTCCACCGCACACCGGCCGGTGACCCTACgtgcgtaccc ... gtgccgtcagATTACTTGCTAATCTTTCTTGAGGGCAGATGGCCGTTTCTTTTGCAAATGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actattgtcatgatttgacatttcaagtcctaacaatactcatatgtgccgtcagATTACTTGCTAATCTTTCTTGAGGGCAGATGGCCGTTTCTTTTGCAAATGTCAACGCCGAGGCAGGGCTGAAAAAGCTTGATGAGTACCTTCTCACTCGC
                           tcctaac  putative branch site (score: 1)
                              taacaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tacagtactagcggcagtattgttctctctctctctctttatttaactattgtcatgatttgacatttcaagtcctaacaatactcatatgtgccgtcagATTACTTGCTAATCTTTCTTGAGGGCAGATGGCCGTTTCTTTTGCAAATGTCAACGCCGAGGCAGGGCTGAAAAAGCTTGATGAGTACCTTCTCACTCGC

- - - - - gcggcag
- - - - - - - - - - - - - - - - - - - - - - - - - - -catgatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgacatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacaata