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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caatatattcatgatgctatcatataagattgtggatttgttctgatttttttttcaatttctttttgtataataatgtatctgttggttgcatttgcagACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATTGTCTTCCAG

Basic information

species Zea mays
transcript GRMZM5G835235_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G835235_T04 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g14860.3 (Oryza sativa), 3'ss of exon 2
-------------------caatatattcatgatgc-tatcatataagattgtggatttgttctgattttt---ttttcaatttctttttgtataataatgtatctgttggttgcatttgcagACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATTGTCTTCCAG
                      |   ||||  |    |  ||| | |   |   ||| ||   |  ||  |   || | ||    | ||  | |   | ||    | |||| |    ||||||||||| ||||||||||||||||| |||||||| |||||||| ||||||||||||||||||
gtgatttcctgataccatgttgtgatttcagaacaaatgccatctgactgtcgcgatctgaaattgttcatcgattataaagcaatcttcatttctaattgatattcttggataatcttgcagACAGTTAGCTACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAG
















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|13490381|gb|BG517145.1|BG517145
EST:     GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAG                         ACAGTGAGCTACA
genomic: GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAGgcgagtgctt ... gcatttgcagACAGTGAGCTACA
EST: gi|67039601|gb|CO465856.1|CO465856
EST:     GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAG                         ACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATT
genomic: GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAGgcgagtgctt ... gcatttgcagACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATT
EST: gi|22819758|gb|BU499848.1|BU499848
EST:     GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAG                         ACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATT
genomic: GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAGgcgagtgctt ... gcatttgcagACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATT
EST: gi|211304795|gb|FL143344.1|FL143344
EST:     GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAG                         ACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATT
genomic: GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAGgcgagtgctt ... gcatttgcagACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATT
EST: gi|87156577|gb|DY401366.1|DY401366
EST:     GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAG                         ACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATT
genomic: GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAGgcgagtgctt ... gcatttgcagACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATT
EST: gi|211304794|gb|FL143343.1|FL143343
EST:     GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAG                         ACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATT
genomic: GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAGgcgagtgctt ... gcatttgcagACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATT
EST: gi|24773942|gb|CA409196.1|CA409196
EST:     GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAG                         ACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATT
genomic: GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAGgcgagtgctt ... gcatttgcagACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATT
EST: gi|26559736|gb|CA831971.1|CA831971
EST:     GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAG                         ACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATT
genomic: GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAGgcgagtgctt ... gcatttgcagACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATT
EST: gi|32865540|gb|CF005222.1|CF005222
EST:     GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAG                         ACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATT
genomic: GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAGgcgagtgctt ... gcatttgcagACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATT
EST: gi|32931957|gb|CF036769.1|CF036769
EST:     GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAG                         ACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATT
genomic: GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAGgcgagtgctt ... gcatttgcagACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATT
EST: gi|32933926|gb|CF038738.1|CF038738
EST:     GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAG                         ACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATT
genomic: GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAGgcgagtgctt ... gcatttgcagACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATT

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), 48 (downstream exon)
Score: 2083

GAAGTTGAAGCAACCATAATTAATGGGAAAGGGACCGAAACTGGGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAGgcgagtgctt ... gcatttgcagACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATTGTCTTCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 883

GAAGTTGAAGCAACCATAATTAATGGGAAAGGGACCGAAACTGGGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAGgcgagtgctt ... gcatttgcagACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATTGTCTTCCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 960

GAAGTTGAAGCAACCATAATTAATGGGAAAGGGACCGAAACTGGGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAGgcgagtgctt ... gcatttgcagACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATTGTCTTCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 774

GAAGTTGAAGCAACCATAATTAATGGGAAAGGGACCGAAACTGGGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAGgcgagtgctt ... gcatttgcagACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATTGTCTTCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttttttttcaatttctttttgtataataatgtatctgttggttgcatttgcagACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATTGTCTTCCAG
 ttctgat  putative branch site (score: 774)
     tttttcaatttctttt  TA-rich tract