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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttcgtcaatcatgtttattcgtcaatctttgactgttctctttcaaaattcctgcccttcttattttttcagTTATGATGTTTACTCGTTTTCTGTGATTCCGACTATTGGAGAGCTGGTTGCTGGTGATCGGCAGTCGTACCAATACTTGGTTGAGAGCATCCGTCGGTTT

Basic information

species Zea mays
transcript GRMZM2G438673_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G438673_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g74520.2 (Oryza sativa), 3'ss of exon 5
-------------------gtaagtttcgtcaatcatgtttattcgtcaatctttgactgttctctttcaaaattcctgcccttctta----ttttttcagTTATGATGTTTACTCGTTTTCTGTGATTCCGACTATTGGAGAGCTGGTTGCTGGTGATCGGCAGTCGTACCAATACTTGGTTGAGAGCATCCGTCGGTTT
                    |   ||  ||  || ||  ||    || |   ||  | || ||| ||   || ||  ||    | ||     ||| ||||||||||||||||| || ||||||||||||||| || | ||||| || || || |||||||| ||||| |||||||||||||||||||| ||||| ||||||
aaatcaacagaaatagcatatctattatgtgtat-atagttgccagttacctttccattgatctattgacaagttgttgattcttttggccttttcttcagTTATGATGTTTATTCATTTTCTGTGATTCCGGCTGTGGGAGAACTAGTGGCCGGTGATCGCCAGTCATACCAATACTTGGTTGAGAGTATCCGCCGGTTT

upper sequence: GRMZM2G438673_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA08G22890.1 (Glycine max), 3'ss of exon 6
----------------------gtaagtttcgtc-aatcatgtttattcgtcaatctttgactgttctctttcaaaat--tcctgcccttcttattttttcagTTATGATGTTTACTCGTTTTCTGTGATTCCGACTATTGGAGAGCTGGTTGCTGGTGATCGGCAGTCGTACCAATACTTGGTTGAGAGCATCCGTCGGTTT
                        || |  | |  |||||||    | | | |||  |||| | |   ||||||   |  |  | | | ||||  | || ||| |||||   ||| || || || || |||||    || || ||||||||||||||||| ||||| || || || ||||| |||||||| ||||| || || 
tctaccctaaccacagaaactgtcaactgccatagaatcatggcc-tcctttaatacttgaat-tcaactttcagtttaatgttactcatctt-ctcttgcagGTATGACTATTATTCTTTCTCAGTTATTCCATACATGGGTGAGCTGGTTGCTGGTGACCGGCAATCCTATCAGTACTTAGTTGAGAGTATCCGGCGTTTC
















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|5296335|gb|AI783105.1|AI783105
EST:     TTCCTATGCTTGGAGTTGAGTCATGTGGATGTCCCTGTTTTTAAAGAGAT                         TTATGATGTTTACTCGTTTTCTGTGATTCCGACTATTGGAGAGCTGGNTGC
genomic: TTCCTATGCTTGGAGTTGAGTCATGTGGATGTCCCTGTTTTTAAAGAGATgtaagtttcg ... attttttcagTTATGATGTTTACTCGTTTTCTGTGATTCCGACTATTGGAGAGCTGGTTGC
EST: gi|50339054|gb|CO534180.1|CO534180
EST:     TTCCTATGCTTGGAGTTGAGTCATGTGGATGTCCCTGTTTTTAAAGAGAT                         TTATGATGTTTACTCGTTTTCTGTGATTCCGACTATTGGAGAGCTGGTTGC
genomic: TTCCTATGCTTGGAGTTGAGTCATGTGGATGTCCCTGTTTTTAAAGAGATgtaagtttcg ... attttttcagTTATGATGTTTACTCGTTTTCTGTGATTCCGACTATTGGAGAGCTGGTTGC
EST: gi|101385922|gb|EB815009.1|EB815009
EST:     TTCCTATGCTTGGAGTTGAGTCATGTGGATGTCCCTGTTTTTAAAGAGAT                         TTATGATGTTTACTCGTTTTCTGTGATTCCGACTATTGGAGAGCTGGTTGC
genomic: TTCCTATGCTTGGAGTTGAGTCATGTGGATGTCCCTGTTTTTAAAGAGATgtaagtttcg ... attttttcagTTATGATGTTTACTCGTTTTCTGTGATTCCGACTATTGGAGAGCTGGTTGC
EST: gi|76012774|gb|DT939944.1|DT939944
EST:     TTCCTATGCTTGGAGTTGAGTCATGTGGATGTCCCTGTTTTTAAAGAGAT                         TTATGATGTTTACTCGTTTTCTGTGATTCCGACTATTGGAGAGCTGGTTGC
genomic: TTCCTATGCTTGGAGTTGAGTCATGTGGATGTCCCTGTTTTTAAAGAGATgtaagtttcg ... attttttcagTTATGATGTTTACTCGTTTTCTGTGATTCCGACTATTGGAGAGCTGGTTGC
EST: gi|20811204|gb|BQ295682.1|BQ295682
EST:     TTCCTATGCTTGGAGTTGAGTCATGTGGATGTCCCTGTTTTTAAAGAGAT                         TTATGATGTTTACTCGTTTTCTGTGATTCCGACTATTGGAGAGCTGGTTGC
genomic: TTCCTATGCTTGGAGTTGAGTCATGTGGATGTCCCTGTTTTTAAAGAGATgtaagtttcg ... attttttcagTTATGATGTTTACTCGTTTTCTGTGATTCCGACTATTGGAGAGCTGGTTGC
EST: gi|13557789|gb|BG549145.1|BG549145
EST:     TTCCTATGCTTGGAGTTGAGTCATGTGGATGTCCCTGTTTTTAAAGAGAT                         TTATGATGTTTACTCGTTTTCTGTGATTCCGACTATTGGAGAGCTGGTTGC
genomic: TTCCTATGCTTGGAGTTGAGTCATGTGGATGTCCCTGTTTTTAAAGAGATgtaagtttcg ... attttttcagTTATGATGTTTACTCGTTTTCTGTGATTCCGACTATTGGAGAGCTGGTTGC
EST: gi|16380081|gb|BI993303.1|BI993303
EST:     TTCCTATGCTTGGAGTTGAGTCATGTGGATGTCCCTGTTTTTAAAGAGAT                         TTATGATGTTTACTCGTTTTCTGTGATTCCGACTATTGGAGAGCTGGTTGC
genomic: TTCCTATGCTTGGAGTTGAGTCATGTGGATGTCCCTGTTTTTAAAGAGATgtaagtttcg ... attttttcagTTATGATGTTTACTCGTTTTCTGTGATTCCGACTATTGGAGAGCTGGTTGC
EST: gi|5846957|gb|AW000036.1|AW000036
EST:     TTCCTATGCTTGGAGTTGAGTCATGTGGATGTCCCTGTTTTTAAAGAGAT                         TTATGATGTTTACTCGTTTTCTGTGATTCCGACTATTGGAGAGCTGGTTGC
genomic: TTCCTATGCTTGGAGTTGAGTCATGTGGATGTCCCTGTTTTTAAAGAGATgtaagtttcg ... attttttcagTTATGATGTTTACTCGTTTTCTGTGATTCCGACTATTGGAGAGCTGGTTGC
EST: gi|76919519|gb|DV167756.1|DV167756
EST:     TTCCTATGCTTGGAGTTGAGTCATGTGGATGTCCCTGTTTTTAAAGAGAT                         TTATGATGTTTACTCGTTTTCTGTGATTCCGACTATTGGAGAGCTGGTTGC
genomic: TTCCTATGCTTGGAGTTGAGTCATGTGGATGTCCCTGTTTTTAAAGAGATgtaagtttcg ... attttttcagTTATGATGTTTACTCGTTTTCTGTGATTCCGACTATTGGAGAGCTGGTTGC
EST: gi|13557788|gb|BG549144.1|BG549144
EST:     TTCCTATGCTTGGAGTTGAGTCATGTGGATGTCCCTGTTTTTAAAGAGAT                         TTATGATGTTTACTCGTTTTCTGTGATTCCGACTATTGGAGAGCTGGTTGC
genomic: TTCCTATGCTTGGAGTTGAGTCATGTGGATGTCCCTGTTTTTAAAGAGATgtaagtttcg ... attttttcagTTATGATGTTTACTCGTTTTCTGTGATTCCGACTATTGGAGAGCTGGTTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcgtcaatctttgactgttctctttcaaaattcctgcccttcttattttttcagTTATGATGTTTACTCGTTTTCTGTGATTCCGACTATTGGAGAGCTGGTTGCTGGTGATCGGCAGTCGTACCAATACTTGGTTGAGAGCATCCGTCGGTTT
         ctttgac  putative branch site (score: 4)
                               ttcctgcccttcttat  putative PPT
                                        ttcttattttttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttcgtcaatcatgtttattcgtcaatctttgactgttctctttcaaaattcctgcccttcttattttttcagTTATGATGTTTACTCGTTTTCTGTGATTCCGACTATTGGAGAGCTGGTTGCTGGTGATCGGCAGTCGTACCAATACTTGGTTGAGAGCATCCGTCGGTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA