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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtttttctgttttacagtccaatatatatttgttttcagttctttaattcttttcgtttggttaataaaagacaaacctcataatctgtagGAGCAAGGTCTCTTGATAAAGAGGGATATGCTGAAGAAGATGATGGTGATGCTAATGCAGCCATTTTTGTCAAGTATGATAGAATGCTCCATGGTCAGGA

Basic information

species Zea mays
transcript GRMZM2G100639_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G100639_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os05g39850.1 (Oryza sativa), 3'ss of exon 9
gtagtttttctgttttacagtccaatata-tatttgttttcagttctttaattcttttcgtttggttaataaaagacaaacctcataatctgtagGAGCAAGGTCTCTTGATAAAGAGGGATATGCTGAAGAAGATGATGGTGATGCTAATGCAGCCATTTTTGTCAAGTATGATAGAATGCTCCATGGTCAGGA
   || ||| ||| ||  | | ||| | | |      ||||||   ||| | |  ||   |||| ||||   || |||||| |  ||| ||| ||||||||| ||||||||||||   |||||||||||||||||||||||||||| |||||||||||| ||||| || |||||||||||||||||||| |||||
---gtatttttgtgttttattacaacaaagtgagatatttcagccttttcagttattctatttgcttaactgaaaacaaacat-gtaaactgcagGAGCAAGATCTCTTGATAAAACAGGATATGCTGAAGAAGATGATGGTGATGTTAATGCAGCCATATTTGTTAAATATGATAGAATGCTCCATGGGCAGGA
















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|60398614|gb|DN231430.1|DN231430
EST:     AATCTCAGAACATGTTGCCCGAATGCATAGATATTGCACTGACGATGGAG                         GAGCAAGGTCTCTTGATAAAGAGGGATATGCTGAAGAAGATGATGGTGATG
genomic: AATCTCAGAACATGTTGCCCGAATGCATAGATATTGCACTGACGATGGAGgtagtttttc ... taatctgtagGAGCAAGGTCTCTTGATAAAGAGGGATATGCTGAAGAAGATGATGGTGATG
EST: gi|32933016|gb|CF037828.1|CF037828
EST:     AATCTCAGAACATGTTGCCCGAATGCATAGATATTGCACTGACGATGGAG                         GAGCAAGGTCTCTTGATAAAGAGGGATATGCTGAAGAAGATGATGGTGATG
genomic: AATCTCAGAACATGTTGCCCGAATGCATAGATATTGCACTGACGATGGAGgtagtttttc ... taatctgtagGAGCAAGGTCTCTTGATAAAGAGGGATATGCTGAAGAAGATGATGGTGATG
EST: gi|5895653|gb|AW036899.1|AW036899
EST:     AATCTCAGAACACGTTGCACGAATGCATAGATATTGCACTGACGATGGAG                         GAGCAAGGTCTCTTGATAAAGAGGGATATGCTGAAGAAGATGATGGTGATG
genomic: AATCTCAGAACATGTTGCCCGAATGCATAGATATTGCACTGACGATGGAGgtagtttttc ... taatctgtagGAGCAAGGTCTCTTGATAAAGAGGGATATGCTGAAGAAGATGATGGTGATG
EST: gi|166615896|gb|EG152005.1|EG152005
EST:     AATCTCAGAACATGTTGCCCGAATGCATAGATATTGCACTGACGATGGAG                         GAGCAAGGTCTCTTGATAAAGAGGGATATGC
genomic: AATCTCAGAACATGTTGCCCGAATGCATAGATATTGCACTGACGATGGAGgtagtttttc ... taatctgtagGAGCAAGGTCTCTTGATAAAGAGGGATATGC
EST: gi|32934580|gb|CF039392.1|CF039392
EST:     AATCTCAGAACATGTTGCCCGAATGCATAGATATTGCACTGACGATGGAG                         GAGCAAGGTCTCTTGATAAAGAGGGATATGCTGAAGAAGATGATGGTGATG
genomic: AATCTCAGAACATGTTGCCCGAATGCATAGATATTGCACTGACGATGGAGgtagtttttc ... taatctgtagGAGCAAGGTCTCTTGATAAAGAGGGATATGCTGAAGAAGATGATGGTGATG
EST: gi|32945489|gb|CF050308.1|CF050308
EST:     AATCTCAGAACATGTTGCCCGAATGCATAGATATTGCACTGACGATGGAG                         GAGCAAGGTCTCTTGATAAAGAGGGATATGCTGAAGAAGATGATGGTGATG
genomic: AATCTCAGAACATGTTGCCCGAATGCATAGATATTGCACTGACGATGGAGgtagtttttc ... taatctgtagGAGCAAGGTCTCTTGATAAAGAGGGATATGCTGAAGAAGATGATGGTGATG
EST: gi|60341724|gb|DN208697.1|DN208697
EST:     AATCTCAGAACATGTTGCCCGAATGCATAGATATTGCACTGACGATGGAG                         GAGCAAGGTCTCTTGATAAAGAGGGATATGCTGAAGAAGATGATGGTGATG
genomic: AATCTCAGAACATGTTGCCCGAATGCATAGATATTGCACTGACGATGGAGgtagtttttc ... taatctgtagGAGCAAGGTCTCTTGATAAAGAGGGATATGCTGAAGAAGATGATGGTGATG
EST: gi|32930876|gb|CF035688.1|CF035688
EST:     AATCTCAGAACATGTTGCCCGAATGCATAGATATTGCACTGACGATGGAG                         GAGCAAGGTCTCTTGATAAAGAGGGATATGCTGAAGAAGATGATGGTGATG
genomic: AATCTCAGAACATGTTGCCCGAATGCATAGATATTGCACTGACGATGGAGgtagtttttc ... taatctgtagGAGCAAGGTCTCTTGATAAAGAGGGATATGCTGAAGAAGATGATGGTGATG

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: 182

GATTTACTTTTTATTGTTCTTGATCAAATGGACCCTGAGATTGACCGGCAAATCTCAGAACATGTTGCCCGAATGCATAGATATTGCACTGACGATGGAGgtagtttttc ... taatctgtagGAGCAAGGTCTCTTGATAAAGAGGGATATGCTGAAGAAGATGATGGTGATGCTAATGCAGCCATTTTTGTCAAGTATGATAGAATGCTCCATGGTCAGGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 59

GATTTACTTTTTATTGTTCTTGATCAAATGGACCCTGAGATTGACCGGCAAATCTCAGAACATGTTGCCCGAATGCATAGATATTGCACTGACGATGGAGgtagtttttc ... taatctgtagGAGCAAGGTCTCTTGATAAAGAGGGATATGCTGAAGAAGATGATGGTGATGCTAATGCAGCCATTTTTGTCAAGTATGATAGAATGCTCCATGGTCAGGA


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 21

GATTTACTTTTTATTGTTCTTGATCAAATGGACCCTGAGATTGACCGGCAAATCTCAGAACATGTTGCCCGAATGCATAGATATTGCACTGACGATGGAGgtagtttttc ... taatctgtagGAGCAAGGTCTCTTGATAAAGAGGGATATGCTGAAGAAGATGATGGTGATGCTAATGCAGCCATTTTTGTCAAGTATGATAGAATGCTCCATGGTCAGGA


Block sizes: 47 (upstream exon), 42 (downstream exon)
Score: 10

GATTTACTTTTTATTGTTCTTGATCAAATGGACCCTGAGATTGACCGGCAAATCTCAGAACATGTTGCCCGAATGCATAGATATTGCACTGACGATGGAGgtagtttttc ... taatctgtagGAGCAAGGTCTCTTGATAAAGAGGGATATGCTGAAGAAGATGATGGTGATGCTAATGCAGCCATTTTTGTCAAGTATGATAGAATGCTCCATGGTCAGGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagttctttaattcttttcgtttggttaataaaagacaaacctcataatctgtagGAGCAAGGTCTCTTGATAAAGAGGGATATGCTGAAGAAGATGATGGTGATGCTAATGCAGCCATTTTTGTCAAGTATGATAGAATGCTCCATGGTCAGGA
                       ggttaat  putative branch site (score: 10)
                         ttaataaaagacaaa  TA-rich tract