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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagagaatgctgtattttgagtaaatactggaagaatgctgtccctttccatgcttattgtcatactggtttgaaatattcatctacactttcagGTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATGTCTTCGAAATTGATTAATAGTGACAGTGATTTCTTTGCAACTTTG

Basic information

species Zea mays
transcript GRMZM2G039263_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G039263_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os04g46620.1 (Oryza sativa), 3'ss of exon 6
gtaagagaatgctgtattttgagtaaatactggaagaatgctgtccctttccatgcttattgtcatactggtttgaaatattcatctacactttcagGTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATGTCTTCGAAATTGATTAATAGTGACAGTGATTTCTTTGCAACTTTG
|||||||||| || | |  | | | ||||   | ||| | ||     | |  |  | |      | ||| ||       ||  ||| ||| ||||||||||| ||||||||||| || || ||||| |||| ||| || || |||||||| |||||  ||||||||||||||||||||||||| |||| | ||
gtaagagaatactatctgcttaatgaatagcagcagattact-----tcttgacacctg-----acactagt-------atctatcaacattttcagGTTGATAAACTTGGAAAGGATTCTCTTATAAACTGTGCGAAGACAAGCATGTCCTCGAAGCTGATTAATAGTGACAGTGATTTCTTCGCAAATCTG
















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|211250617|gb|FL215180.1|FL215180
EST:     TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAG                         GTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATG
genomic: TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAGgtaagagaat ... acactttcagGTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATG
EST: gi|149010855|gb|EE042239.2|EE042239
EST:     TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAG                         GTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATG
genomic: TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAGgtaagagaat ... acactttcagGTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATG
EST: gi|211250619|gb|FL215182.1|FL215182
EST:     TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAG                         GTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATG
genomic: TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAGgtaagagaat ... acactttcagGTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATG
EST: gi|21331562|gb|BQ486943.1|BQ486943
EST:     TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAG                         GTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATG
genomic: TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAGgtaagagaat ... acactttcagGTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATG
EST: gi|211248391|gb|FL215168.1|FL215168
EST:     TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAG                         GTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATG
genomic: TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAGgtaagagaat ... acactttcagGTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATG
EST: gi|19058770|gb|BM737437.1|BM737437
EST:     TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAG                         GTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATG
genomic: TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAGgtaagagaat ... acactttcagGTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATG
EST: gi|211250611|gb|FL215174.1|FL215174
EST:     TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAG                         GTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCNAAAACTAGCATG
genomic: TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAGgtaagagaat ... acactttcagGTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATG
EST: gi|211243922|gb|FL215142.1|FL215142
EST:     TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAG                         GTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGC
genomic: TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAGgtaagagaat ... acactttcagGTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGC
EST: gi|211378069|gb|FL215200.1|FL215200
EST:     TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAG                         GTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATG
genomic: TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAGgtaagagaat ... acactttcagGTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATG
EST: gi|149083358|gb|EE172656.2|EE172656
EST:     TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAG                         GTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATG
genomic: TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAGgtaagagaat ... acactttcagGTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATG
EST: gi|149074901|gb|EE163349.2|EE163349
EST:     TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAG                         GTTGACAAACTTGGAAAAGAATCCCCTTATCA-CTCTGCAAAAACTAGCAT
genomic: TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAGgtaagagaat ... acactttcagGTTGACAAACTTGGAAAAGAATCCC-TTATCAACTCTGCAAAAACTAGCAT
EST: gi|211383347|gb|FL215220.1|FL215220
EST:     TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAG                         GTTGACAAAACT-GGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCAT
genomic: TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAGgtaagagaat ... acactttcagGTTGACAAA-CTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCAT
EST: gi|149000083|gb|EE037198.2|EE037198
EST:     TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAG                         GTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATG
genomic: TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAGgtaagagaat ... acactttcagGTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATG
EST: gi|211248390|gb|FL215167.1|FL215167
EST:     TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAG                         GTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATG
genomic: TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAGgtaagagaat ... acactttcagGTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATG
EST: gi|60396669|gb|DN229537.1|DN229537
EST:     TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAG                         GTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATG
genomic: TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAGgtaagagaat ... acactttcagGTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATG
EST: gi|211250624|gb|FL215187.1|FL215187
EST:     TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAG                         GTTGACAAACTTG
genomic: TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAGgtaagagaat ... acactttcagGTTGACAAACTTG
EST: gi|211250622|gb|FL215185.1|FL215185
EST:     TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAG                         GTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATG
genomic: TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAGgtaagagaat ... acactttcagGTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATG
EST: gi|67021395|gb|CO450144.1|CO450144
EST:     TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAG                         GTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATG
genomic: TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAGgtaagagaat ... acactttcagGTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATG
EST: gi|211378065|gb|FL215196.1|FL215196
EST:     TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAG                         GTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATG
genomic: TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAGgtaagagaat ... acactttcagGTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATG
EST: gi|33092579|gb|CF052573.1|CF052573
EST:     TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAG                         GTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATG
genomic: TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAGgtaagagaat ... acactttcagGTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATG
EST: gi|211243912|gb|FL215132.1|FL215132
EST:     TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAG                         GTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATG
genomic: TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAGgtaagagaat ... acactttcagGTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATG
EST: gi|211248385|gb|FL215162.1|FL215162
EST:     TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAG                         GTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATG
genomic: TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAGgtaagagaat ... acactttcagGTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATG
EST: gi|71437844|gb|DR818894.1|DR818894
EST:     TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAG                         GTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATG
genomic: TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAGgtaagagaat ... acactttcagGTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATG
EST: gi|211243910|gb|FL215130.1|FL215130
EST:     TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAG                         GTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATG
genomic: TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAGgtaagagaat ... acactttcagGTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATG
EST: gi|31557915|gb|CD527127.1|CD527127
EST:     TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAG                         GGTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACT
genomic: TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAGgtaagagaat ... acactttcagGTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACT
EST: gi|211250613|gb|FL215176.1|FL215176
EST:     TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAG                         GTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATG
genomic: TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAGgtaagagaat ... acactttcagGTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATG
EST: gi|211383348|gb|FL215221.1|FL215221
EST:     TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAG                         GTTGACAAACTTGGAAAAGA-TCCCTTATCAACTCTGCAAAAACTAGCATG
genomic: TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAGgtaagagaat ... acactttcagGTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATG
EST: gi|33102590|gb|CF062550.1|CF062550
EST:     GCCTGCAAATATGTTGAGGAAAAATTAGCAGTCAAG                         GTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATG
genomic: GCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAGgtaagagaat ... acactttcagGTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATG
EST: gi|211378068|gb|FL215199.1|FL215199
EST:     TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAG                         GTTGACAAACTTGGAAAAGAATCCCTTATCA-CTCTGCAAAAACTAGCATG
genomic: TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAGgtaagagaat ... acactttcagGTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATG
EST: gi|211241686|gb|FL215128.1|FL215128
EST:     TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAG                         GTTGACAAACTTGGAAAAGAATCCCTTATCAAC
genomic: TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAGgtaagagaat ... acactttcagGTTGACAAACTTGGAAAAGAATCCCTTATCAAC
EST: gi|211250614|gb|FL215177.1|FL215177
EST:     TGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAAGT-AGCAGTCA-G                         GNTTGACAAACTTGGAAAAGAATCC
genomic: TGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAA-GTTAGCAGTCAAGgtaagagaat ... acactttcagG-TTGACAAACTTGGAAAAGAATCC
EST: gi|22490780|gb|BU050703.1|BU050703
EST:     TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAG                         GTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATG
genomic: TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAGgtaagagaat ... acactttcagGTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATG
EST: gi|61119168|gb|DN560129.1|DN560129
EST:     TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAG                         GTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATG
genomic: TTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAGgtaagagaat ... acactttcagGTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 554

CTTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAGgtaagagaat ... acactttcagGTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATGTCTTCGAAATTGATTAATAGTGACAGTGATTTCTTTGCAACTTTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 213

CTTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAGgtaagagaat ... acactttcagGTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATGTCTTCGAAATTGATTAATAGTGACAGTGATTTCTTTGCAACTTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 207

CTTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAGgtaagagaat ... acactttcagGTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATGTCTTCGAAATTGATTAATAGTGACAGTGATTTCTTTGCAACTTTG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 153

CTTGCTATGCGTGAAGCCTGCAAATATGTTGAGGAAAAGTTAGCAGTCAAGgtaagagaat ... acactttcagGTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATGTCTTCGAAATTGATTAATAGTGACAGTGATTTCTTTGCAACTTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtccctttccatgcttattgtcatactggtttgaaatattcatctacactttcagGTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATGTCTTCGAAATTGATTAATAGTGACAGTGATTTCTTTGCAACTTTG
                                              cactttc  CT-rich tract
                             tttgaaatattcat  TA-rich tract