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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaagttgtctatatgttcattctcctgagccatttttaaattcctgcatcattttccttttacattattctaattataattttaactgcaattaaatagAGTCTGTGGACAGCATCATGCAAGAGTCACATGAGCTTGATGGCACAACAGTAGTTGTTGATCGCGCGACTCCGAAG

Basic information

species Zea mays
transcript GRMZM2G030902_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G030902_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g71770.1 (Oryza sativa), 3'ss of exon 8
-aaaagttgtctat--atgttcattctcctgagccatttttaaattcctgcatcattttccttttacattattctaattataattttaactgcaattaaatagAGTCTGTGGACAGCATCATGCAAGAGTCACATGAGCTTGATGGCACAACAGTAGTTGTTGATCGCGCGACTCCGAAG
     ||| | ||   ||| |   | |  |   ||| ||| |  ||   || | || | | ||||  | |   || |||  |  |  ||||| |||   | ||| ||||||||||| ||||||||||| |||||||| || ||||||||||||||||||||||| ||||| ||||| |||
tctgtgttctttagggatgattgcttttttcc-ccagtttgatctttaagcttgatatgcattttgtaattaccttattcaa--tgcaactgtaatgttacagAATCTGTGGACAGTATCATGCAAGATTCACATGAACTGGATGGCACAACAGTAGTTGTTGACCGCGCCACTCCTAAG
















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|148936779|gb|EC880917.2|EC880917
EST:     TGGTTCAAAGGGGCATCGTGGAATTGGGTTTATCACGTTTCAGAGTGCAG                         AGTCTGTGGACAGCATCATGCAAGAGTCACATGAGCTTGATG
genomic: TGGTTCAAAGGGGCATCGTGGAATTGGGTTTATCACGTTTCAGAGTGCAGgtacgcttac ... aattaaatagAGTCTGTGGACAGCATCATGCAAGAGTCACATGAGCTTGATG
EST: gi|22545757|gb|BU098131.1|BU098131
EST:     TGGTTCAAAGGGGCATCGGGGAATTGGGTTTATCACGTTTCAGAGTGCAG                         AGTCTGTGGACAGCATCATGCAAGAGTCACATGAGCTTGATGGCACAACAG
genomic: TGGTTCAAAGGGGCATCGTGGAATTGGGTTTATCACGTTTCAGAGTGCAGgtacgcttac ... aattaaatagAGTCTGTGGACAGCATCATGCAAGAGTCACATGAGCTTGATGGCACAACAG
EST: gi|71769697|gb|DR967634.1|DR967634
EST:     TGGTTCAAAGGGGCATCGTGGAATTGGGTTTATCACGTTTCAGAGTGCAG                         AGTCTGTGGACAGCATCATGCAAGAGTCACATGAGCTTGATG
genomic: TGGTTCAAAGGGGCATCGTGGAATTGGGTTTATCACGTTTCAGAGTGCAGgtacgcttac ... aattaaatagAGTCTGTGGACAGCATCATGCAAGAGTCACATGAGCTTGATG
EST: gi|149096474|gb|EE182216.2|EE182216
EST:     TGGTTCAAAGGGGCATCGTGGAATTGGGTTTATCACGTTTCAGAGTGCAG                         AGTCTGTGGACAGCATCATGCAAGAGTCACATGAGCTTGATGGCACAACAG
genomic: TGGTTCAAAGGGGCATCGTGGAATTGGGTTTATCACGTTTCAGAGTGCAGgtacgcttac ... aattaaatagAGTCTGTGGACAGCATCATGCAAGAGTCACATGAGCTTGATGGCACAACAG
EST: gi|149000018|gb|EE037116.2|EE037116
EST:     TGGTTCAAAGGGGCATCGTGGAATTGGGTTTATCACGTTTCAGAGTGCAG                         AGTCTGTGGACAGCATCATGCAAGAGTCACATGAGCTGGATGGCACAACAG
genomic: TGGTTCAAAGGGGCATCGTGGAATTGGGTTTATCACGTTTCAGAGTGCAGgtacgcttac ... aattaaatagAGTCTGTGGACAGCATCATGCAAGAGTCACATGAGCTTGATGGCACAACAG
EST: gi|71304925|gb|DR788593.1|DR788593
EST:     TGGTTCAAAGGGGCATCGTGGAATTGGGTTTATCACGTTTCAGAGTGCAG                         AGTCTGTGGACAGCATCATGCAAGAGTCACATGAGCTTGATGGGCACA-CA
genomic: TGGTTCAAAGGGGCATCGTGGAATTGGGTTTATCACGTTTCAGAGTGCAGgtacgcttac ... aattaaatagAGTCTGTGGACAGCATCATGCAAGAGTCACATGAGCTTGATGG-CACAACA
EST: gi|211138007|gb|FL213712.1|FL213712
EST:     TGGTTCAAAGGGGCATCGTGGAATTGGGTTTATCACGTTTCAGAGTGCAG                         AGTCTGTGGACAGCATCATGCAAGATTCACATGAGCTTGATGGCACAACAG
genomic: TGGTTCAAAGGGGCATCGTGGAATTGGGTTTATCACGTTTCAGAGTGCAGgtacgcttac ... aattaaatagAGTCTGTGGACAGCATCATGCAAGAGTCACATGAGCTTGATGGCACAACAG
EST: gi|149080743|gb|EE169805.2|EE169805
EST:     TGGTTCAAAGGGGCATCGTGGAATTGGGTTTATCACGTTTCAGAGTGCAG                         AGTCTGTGGACAGCATCATGCAAGAGTCACATGAGCTTGATG
genomic: TGGTTCAAAGGGGCATCGTGGAATTGGGTTTATCACGTTTCAGAGTGCAGgtacgcttac ... aattaaatagAGTCTGTGGACAGCATCATGCAAGAGTCACATGAGCTTGATG
EST: gi|21432115|gb|BQ547605.1|BQ547605
EST:     TGGTTCAAAGGGGCATCGTGGAATTGGGTTTATCACGTTTCAGAGTGCAG                         AGTCTGTGGACAGCATCATGCAAGAGTCACATGAGCTTGATGGCACAACAG
genomic: TGGTTCAAAGGGGCATCGTGGAATTGGGTTTATCACGTTTCAGAGTGCAGgtacgcttac ... aattaaatagAGTCTGTGGACAGCATCATGCAAGAGTCACATGAGCTTGATGGCACAACAG
EST: gi|60350487|gb|DN217460.1|DN217460
EST:     TGGTTCAAAGGGGCATCGTGGAATTGGGTTTATCACGTTTCAGAGTGCAG                         AGTCTGTGGACAGCATC
genomic: TGGTTCAAAGGGGCATCGTGGAATTGGGTTTATCACGTTTCAGAGTGCAGgtacgcttac ... aattaaatagAGTCTGTGGACAGCATC
EST: gi|32847027|gb|CD986708.1|CD986708
EST:     TGGTTCAAAGGGGCATCGTGGAATTGGGTTTATCACGTTTCAGAGTGCAG                         AGTCTGTGGACAGCATCATGCAAGAGTCACATGAGCTTGATGGCACAACAG
genomic: TGGTTCAAAGGGGCATCGTGGAATTGGGTTTATCACGTTTCAGAGTGCAGgtacgcttac ... aattaaatagAGTCTGTGGACAGCATCATGCAAGAGTCACATGAGCTTGATGGCACAACAG
EST: gi|26558086|gb|CA830321.1|CA830321
EST:     GGTTCAAAGGGGCATCGTGGAATTGGGGTTTATCACGTTTCAGAGTGCAG                         AGTCTGTGGACAGCATCATGCAAGAGTCACATGAGCTTGATGGCACAACAG
genomic: GGTTCAAAGGGGCATCGTGGAATT-GGGTTTATCACGTTTCAGAGTGCAGgtacgcttac ... aattaaatagAGTCTGTGGACAGCATCATGCAAGAGTCACATGAGCTTGATGGCACAACAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcatcattttccttttacattattctaattataattttaactgcaattaaatagAGTCTGTGGACAGCATCATGCAAGAGTCACATGAGCTTGATGGCACAACAGTAGTTGTTGATCGCGCGACTCCGAAG
                                   ttttaac  putative branch site (score: 2)
             ttttacattattctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaagttgtctatatgttcattctcctgagccatttttaaattcctgcatcattttccttttacattattctaattataattttaactgcaattaaatagAGTCTGTGGACAGCATCATGCAAGAGTCACATGAGCTTGATGGCACAACAGTAGTTGTTGATCGCGCGACTCCGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT