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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagagcgatctttgttctgtgtttcttgatgataacttgcactttggtgtgtgatccatgctctggttgctgacacctcccaaattcctgaagGGTGCTATATGCTTGGCGCGAAGTTTCAAGATAATCAACGAATCGTTGACGTCCCTTGACCTGGGTTTCAATGAGATTCGA

Basic information

species Zea mays
transcript GRMZM2G110289_T01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G110289_T01 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os06g13050.1 (Oryza sativa), 3'ss of exon 15
gtaagagcgatctttgttctgtgtttcttgatgataacttgcactttggtgtgtgatccatgctctggttgctgacacctcccaaattcctgaagGGTGCTATATGCTTGGCGCGAAGTTTCAAGATAATCAACGAATCGTTGACGTCCCTTGACCTGGGTTTCAATGAGATTCGA
||| |  | ||||| |||   | ||  ||    ||||||||| ||||| |   | | ||||||  |     ||||  | || |   ||  ||||||||||||| |||||||| |||||||||||||| ||||| ||||| ||||| || ||||||||||| || ||||||||| ||
gtatgcacaatcttcgttgaattttattt----ataacttgcgctttgattcat-acccatgcctt-----ctgatccttctc---tttttgaagGGTGCTATCTGCTTGGCTCGAAGTTTCAAGATCATCAATGAATCTTTGACTTCACTTGACCTGGGCTTTAATGAGATTAGA
















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|60354010|gb|DN220983.1|DN220983
EST:     ACACAACGTTATCGACATTGGATCTGCGGGCAAACGGGCTTGGAAACGAT                         GGTGCTATATGCTTGGCGCGAAGTTTCAAGATAATCAACGAATCGTTGACG
genomic: ACACAACGTTATCGACATTGGATCTGCGGGCAAACGGGCTTGGAAACGATgtaagagcga ... attcctgaagGGTGCTATATGCTTGGCGCGAAGTTTCAAGATAATCAACGAATCGTTGACG
EST: gi|67010636|gb|CO439385.1|CO439385
EST:     ACACAACGTTATCGACATTGGATCTGCGGGCAAACGGGCTTGGAAACGAT                         GGTGCTATATGCTTGGCGCGAAGTTTCAAGATAATCAACGAATCGTTGACG
genomic: ACACAACGTTATCGACATTGGATCTGCGGGCAAACGGGCTTGGAAACGATgtaagagcga ... attcctgaagGGTGCTATATGCTTGGCGCGAAGTTTCAAGATAATCAACGAATCGTTGACG
EST: gi|60346680|gb|DN213653.1|DN213653
EST:     ACACAACGTTATCGACATTGGATCTGCGGGCAAACGGGCTTGGAAACGAT                         GGTGCTATATGCTTGGCGCGAAGTTTCAAGATAATCAACGAATCGTTGACG
genomic: ACACAACGTTATCGACATTGGATCTGCGGGCAAACGGGCTTGGAAACGATgtaagagcga ... attcctgaagGGTGCTATATGCTTGGCGCGAAGTTTCAAGATAATCAACGAATCGTTGACG
EST: gi|71763770|gb|DR961707.1|DR961707
EST:     ACACAACGTTATCGACATTGGATCTGCGGGCAAACGGGCTTGGAAACGAT                         GGTGCTATATGCTTGGCGCGAAGTTTCAAGATAATCAACGAATCGTTGACG
genomic: ACACAACGTTATCGACATTGGATCTGCGGGCAAACGGGCTTGGAAACGATgtaagagcga ... attcctgaagGGTGCTATATGCTTGGCGCGAAGTTTCAAGATAATCAACGAATCGTTGACG
EST: gi|60355903|gb|DN222876.1|DN222876
EST:     ACACAACGTTATCGACATTGGATCTGCGGGCAAACGGGCTTGGAAACGAT                         GGTGCTATATGCTTGGCGCGAAGTTTCAAGATAATCAACGAATCGTTGACG
genomic: ACACAACGTTATCGACATTGGATCTGCGGGCAAACGGGCTTGGAAACGATgtaagagcga ... attcctgaagGGTGCTATATGCTTGGCGCGAAGTTTCAAGATAATCAACGAATCGTTGACG
EST: gi|32937038|gb|CF041857.1|CF041857
EST:     GCGGGCAAACGGGCTTGGAAACGAT                         GGTGCTATATGCTTGGCGCGAAGTTTCAAGATAATCAACGAATCGTTGACG
genomic: GCGGGCAAACGGGCTTGGAAACGATgtaagagcga ... attcctgaagGGTGCTATATGCTTGGCGCGAAGTTTCAAGATAATCAACGAATCGTTGACG
EST: gi|60341143|gb|DN208116.1|DN208116
EST:     ACACAACGTTATCGACATTGGATCTGCGGGCAAACGGGCTTGGAAACGAT                         GGTGCTATATGCTTGGCGCGAAGTTTCAAGATAATCAACGAATCGTTGACG
genomic: ACACAACGTTATCGACATTGGATCTGCGGGCAAACGGGCTTGGAAACGATgtaagagcga ... attcctgaagGGTGCTATATGCTTGGCGCGAAGTTTCAAGATAATCAACGAATCGTTGACG

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: 47 (upstream exon), 49 (downstream exon)
Score: 90

ATAGGCATGGAAGGTGCAGAGTGTATTGCCGACTGTCTCAAGTACAACACAACGTTATCGACATTGGATCTGCGGGCAAACGGGCTTGGAAACGATgtaagagcga ... attcctgaagGGTGCTATATGCTTGGCGCGAAGTTTCAAGATAATCAACGAATCGTTGACGTCCCTTGACCTGGGTTTCAATGAGATTCGA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 155

ATAGGCATGGAAGGTGCAGAGTGTATTGCCGACTGTCTCAAGTACAACACAACGTTATCGACATTGGATCTGCGGGCAAACGGGCTTGGAAACGATgtaagagcga ... attcctgaagGGTGCTATATGCTTGGCGCGAAGTTTCAAGATAATCAACGAATCGTTGACGTCCCTTGACCTGGGTTTCAATGAGATTCGA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 108

ATAGGCATGGAAGGTGCAGAGTGTATTGCCGACTGTCTCAAGTACAACACAACGTTATCGACATTGGATCTGCGGGCAAACGGGCTTGGAAACGATgtaagagcga ... attcctgaagGGTGCTATATGCTTGGCGCGAAGTTTCAAGATAATCAACGAATCGTTGACGTCCCTTGACCTGGGTTTCAATGAGATTCGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 103

ATAGGCATGGAAGGTGCAGAGTGTATTGCCGACTGTCTCAAGTACAACACAACGTTATCGACATTGGATCTGCGGGCAAACGGGCTTGGAAACGATgtaagagcga ... attcctgaagGGTGCTATATGCTTGGCGCGAAGTTTCAAGATAATCAACGAATCGTTGACGTCCCTTGACCTGGGTTTCAATGAGATTCGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcactttggtgtgtgatccatgctctggttgctgacacctcccaaattcctgaagGGTGCTATATGCTTGGCGCGAAGTTTCAAGATAATCAACGAATCGTTGACGTCCCTTGACCTGGGTTTCAATGAGATTCGA
                             tgctgac  putative branch site (score: 103)
                                              ttcct  putative PPT
                                           aaatt  TA-rich tract