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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctagaaaggccaaaacaacctataatttgggacacgccgagtaattattggagaacaagaaaaatgagatgataatacattggcagcatttggatttcagGAGAAGGCTCTTCACCATGATTAATAACCTGCCCACTGTTTATGAAGTTGTGACCGGGGTTGCTAAGAAGCAATCAAAAGCCCCCAACGGCAGCAGCAAA

Basic information

species Zea mays
transcript GRMZM2G107807_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107807_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g35600.1 (Oryza sativa), 3'ss of exon 3
ctagaaaggccaaaacaacctataatttgggacacgccgagtaattattggagaacaagaaaaatgagatgataatacattggcagcatttggatttcagGAGAAGGCTCTTCACCATGATTAATAACCTGCCCACTGTTTATGAAGTTGTGACCGGGGTTGCTAAGAAGCAATCAAAAGCCCCCAACGGCAGCAGCAAA
 ||     |  | |  | ||  |   |||  || |  | |  ||   |          | | ||   ||  ||| | |||     ||||||| ||||||||||| ||||||||||||||||||||   || |||||||| |||||||||||||| ||  |||| ||||||||| |||||| | |||||||||||||||||
ttatctgagtaatattatccagtgcattgtcactcaacaatcaacattatattgtttggtagaaaatgacaatagtccataactggcatttgaatttcagGAGACGGCTCTTCACCATGATTAATGGTCTTCCCACTGTATATGAAGTTGTGACGGGAATTGCCAAGAAGCAAACAAAAGTCTCCAACGGCAGCAGCAAA
















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|60342404|gb|DN209377.1|DN209377
EST:     GTTGCATTCTACTTTGGAGCTCGCTTTGGATTTGATAAAGATGCAAG                         GAGAAGGCTCTTCACCATGATTAATAACCTGCCCACTGTTTATGAAGTTGT
genomic: GTTGCATTCTACTTTGGAGCTCGCTTTGGATTTGATAAAGATGCAAGgtttgtgtat ... tggatttcagGAGAAGGCTCTTCACCATGATTAATAACCTGCCCACTGTTTATGAAGTTGT
EST: gi|211259582|gb|FL073576.1|FL073576
EST:     ATTCTACTTTGGAGCTCGCTTTGGATTTGATAAAGATGCAAG                         GAGAAGGCTCTTCACCATGATTAATAACCTGCCCACTGTTTATGAAGTTGT
genomic: ATTCTACTTTGGAGCTCGCTTTGGATTTGATAAAGATGCAAGgtttgtgtat ... tggatttcagGAGAAGGCTCTTCACCATGATTAATAACCTGCCCACTGTTTATGAAGTTGT
EST: gi|211262010|gb|FL073578.1|FL073578
EST:     TTGGATTTGATAAAGATGCAAG                         GAGAAGGCTCTTCACCATGATTAATAACCTGCCCACTGTTTATGAAGTTGT
genomic: TTGGATTTGATAAAGATGCAAGgtttgtgtat ... tggatttcagGAGAAGGCTCTTCACCATGATTAATAACCTGCCCACTGTTTATGAAGTTGT
EST: gi|47962533|gb|CN845242.1|CN845242
EST:     TCTGTTGCATTCTACTTTGGAGCTCGCTTTGGATTTGATAAAGATGCAAG                         GAGAAGGCTCTTCACCATGATTAATAACCTGCCCACTGTTTATGAAGTTGT
genomic: TCTGTTGCATTCTACTTTGGAGCTCGCTTTGGATTTGATAAAGATGCAAGgtttgtgtat ... tggatttcagGAGAAGGCTCTTCACCATGATTAATAACCTGCCCACTGTTTATGAAGTTGT
EST: gi|76285556|gb|DV025124.1|DV025124
EST:     GCTCGCTTTGGATTTGATAAAGATGCAAG                         GAGAAGGCTCTTCACCATGATTAATAACCTGCCCACTGTTTATGAAGTTGT
genomic: GCTCGCTTTGGATTTGATAAAGATGCAAGgtttgtgtat ... tggatttcagGAGAAGGCTCTTCACCATGATTAATAACCTGCCCACTGTTTATGAAGTTGT
EST: gi|71763520|gb|DR961457.1|DR961457
EST:     TCTGTTGCATTCTACTTTGGAGCTCGCTTTGGATTTGATAAAGATGCAAG                         GAGAAGGCTCTTCACCATGATTAATAACCTGCCCACTGTTTATGAAGTTGT
genomic: TCTGTTGCATTCTACTTTGGAGCTCGCTTTGGATTTGATAAAGATGCAAGgtttgtgtat ... tggatttcagGAGAAGGCTCTTCACCATGATTAATAACCTGCCCACTGTTTATGAAGTTGT
EST: gi|32921335|gb|CF026147.1|CF026147
EST:     TCTGTTGCATTCTACTTTGGAGCTCGCTTTGGATTTGATAAAGATGCAAG                         GAGAAGGCTCTTCACCATGATTAATAACCTGCCCACTGTTTATGAAGTTGT
genomic: TCTGTTGCATTCTACTTTGGAGCTCGCTTTGGATTTGATAAAGATGCAAGgtttgtgtat ... tggatttcagGAGAAGGCTCTTCACCATGATTAATAACCTGCCCACTGTTTATGAAGTTGT
EST: gi|76285557|gb|DV025125.1|DV025125
EST:     TCTGTTGCATTCTACTTTGGAGCTCGCTTTGGATTTGATAAAGATGCAAG                         GAGAAGGCTCTTCACCATGATTAATAACCTGCCCACTGTTTATGAAGTTGT
genomic: TCTGTTGCATTCTACTTTGGAGCTCGCTTTGGATTTGATAAAGATGCAAGgtttgtgtat ... tggatttcagGAGAAGGCTCTTCACCATGATTAATAACCTGCCCACTGTTTATGAAGTTGT
EST: gi|20301387|gb|BQ164330.1|BQ164330
EST:     TCTGTTGCATTCTACTTTGGAGCTCGCTTTGGATTTGATAAAGATGCATG                         GAGAAGGCTCTTCACCATGATTAATAACCTGCCCACTGTTTATGAAGTTGT
genomic: TCTGTTGCATTCTACTTTGGAGCTCGCTTTGGATTTGATAAAGATGCAAGgtttgtgtat ... tggatttcagGAGAAGGCTCTTCACCATGATTAATAACCTGCCCACTGTTTATGAAGTTGT
EST: gi|60394161|gb|DN227031.1|DN227031
EST:     TCTGTTGCATTCTACTTTGGAGCTCGCTTTGGATTTGATAAAGATGCAAG                         GAGAAGGCTCTTCACCATGATTAATAACCTGCCCACTGTTTATGAAGTTGT
genomic: TCTGTTGCATTCTACTTTGGAGCTCGCTTTGGATTTGATAAAGATGCAAGgtttgtgtat ... tggatttcagGAGAAGGCTCTTCACCATGATTAATAACCTGCCCACTGTTTATGAAGTTGT
EST: gi|60351249|gb|DN218222.1|DN218222
EST:     TCTGTTGCATTCTACTTTGGAGCTCGCTTTGGATTTGATAAAGATGCAAG                         GAGAAGGCTCTTCACCATGATTAATAACCTGCCCACTGTTTATGAAGTTGT
genomic: TCTGTTGCATTCTACTTTGGAGCTCGCTTTGGATTTGATAAAGATGCAAGgtttgtgtat ... tggatttcagGAGAAGGCTCTTCACCATGATTAATAACCTGCCCACTGTTTATGAAGTTGT
EST: gi|211262011|gb|FL073579.1|FL073579
EST:     GCTTTGGATTTGATAAAGATGCAAG                         GAGAAGGCTCTTCACCATGATTAATAACCTGCCCACTGTTTATGAAGTTGT
genomic: GCTTTGGATTTGATAAAGATGCAAGgtttgtgtat ... tggatttcagGAGAAGGCTCTTCACCATGATTAATAACCTGCCCACTGTTTATGAAGTTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattggagaacaagaaaaatgagatgataatacattggcagcatttggatttcagGAGAAGGCTCTTCACCATGATTAATAACCTGCCCACTGTTTATGAAGTTGTGACCGGGGTTGCTAAGAAGCAATCAAAAGCCCCCAACGGCAGCAGCAAA
                          ataatacatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctagaaaggccaaaacaacctataatttgggacacgccgagtaattattggagaacaagaaaaatgagatgataatacattggcagcatttggatttcagGAGAAGGCTCTTCACCATGATTAATAACCTGCCCACTGTTTATGAAGTTGTGACCGGGGTTGCTAAGAAGCAATCAAAAGCCCCCAACGGCAGCAGCAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - -aaaacaa
- - - - - - - - - - - - - - - - cacgccg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - aagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcagcat