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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggtctacattaaccacaccaagacaccaagtacacttgcttgttttcatgattcttgttgctcatagtggccaattgacttctacagGAACTTGGAGGGTAGGTGGTGTACTTGCGATGTCTCGGGCATTTGGCAACCGTCTCTTAAAACAATTTGTTATTGCAGACCCTGAAATTCAG

Basic information

species Zea mays
transcript GRMZM2G412937_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G412937_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os05g50970.1 (Oryza sativa), 3'ss of exon 6
-----------------------------------------------------------------------------------------gtaaggtctacattaaccacaccaagacaccaagtacacttgcttgttttcatgattcttgttgctcatagtggccaattgacttctacagGAACTTGGAGGGTAGGTGGTGTACTTGCGATGTCTCGGGCATTTGGCAACCGTCTCTTAAAACAATTTGTTATTGCAGACCCTGAAATTCAG
| | | | | ||| | | || | |||||| || | || | ||||| || ||| ||| ||||| | ||||||||||||||||||||||||||||||| ||||||||||||||||||||||| | || || ||||||||| ||||||| ||||| ||||||
gtaagtcctgcttccatcaacacctagagtaccacacaatactacaatatctgtgttctaatctgagttgccatagatcgtgcctgtttattttggagaagtcactgacatacataggtggaggagacttgcaaattgcgactatcatc-ttgctgatgatggtaaatggacttttgcagGAACTTGGAGGGTAGGTGGTGTACTTGCAATGTCTCGGGCATTTGGCAACCGCTTGTTGAAGCAATTTGTTGTTGCAGATCCTGAGATTCAG
















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|13149578|gb|BG319900.1|BG319900
EST:     TGATGAGAGGAATCGAATTGAGAGTGCTGGTGGGATAGTTATGTGGGCAG                         GAACTTGGAGGGTAGGTGGTGTACTTGCGATGTCTCGGGCATTTGGCAACC
genomic: TGATGAGAGGAATCGAATTGAGAGTGCTGGTGGGATAGTTATGTGGGCAGgtaaggtcta ... acttctacagGAACTTGGAGGGTAGGTGGTGTACTTGCGATGTCTCGGGCATTTGGCAACC
EST: gi|7227483|gb|AW566124.1|AW566124
EST:     TGATGAGAGGAATCGAATTGAGAGTGCTGGTGGGATAGTTATGTGGGCAG                         GAACTTGGAGGGTAGGTGGTGTACTTGCGATGTCTCGGGCATTTGGCAACC
genomic: TGATGAGAGGAATCGAATTGAGAGTGCTGGTGGGATAGTTATGTGGGCAGgtaaggtcta ... acttctacagGAACTTGGAGGGTAGGTGGTGTACTTGCGATGTCTCGGGCATTTGGCAACC
EST: gi|67013545|gb|CO442294.1|CO442294
EST:     ATTGATAGTGCTGGTGGGATAGTTATGTGGGCAG                         GAACTTGGAGGGTAGGTGGTGTACTTGCGATGTCTCGGGCATTTGGCAACC
genomic: ATTGAGAGTGCTGGTGGGATAGTTATGTGGGCAGgtaaggtcta ... acttctacagGAACTTGGAGGGTAGGTGGTGTACTTGCGATGTCTCGGGCATTTGGCAACC
EST: gi|211041804|gb|FL481852.1|FL481852
EST:     TGATGAGAGGAATCGAATTGAGAGTGCTGGTGGGATAGTTATGTGGGCAG                         GAACTTGGAGGGTAGGTGGTGTACTTGCGATGTCTCGGGCATTTGGCAACC
genomic: TGATGAGAGGAATCGAATTGAGAGTGCTGGTGGGATAGTTATGTGGGCAGgtaaggtcta ... acttctacagGAACTTGGAGGGTAGGTGGTGTACTTGCGATGTCTCGGGCATTTGGCAACC

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: 48 (upstream exon), 49 (downstream exon)
Score: 95

CTATTGCGCTCTCTGAAGATCACAAGCCAAACAGAAGTGATGAGAGGAATCGAATTGAGAGTGCTGGTGGGATAGTTATGTGGGCAGgtaaggtcta ... acttctacagGAACTTGGAGGGTAGGTGGTGTACTTGCGATGTCTCGGGCATTTGGCAACCGTCTCTTAAAACAATTTGTTATTGCAGACCCTGAAATTCAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 97

CTATTGCGCTCTCTGAAGATCACAAGCCAAACAGAAGTGATGAGAGGAATCGAATTGAGAGTGCTGGTGGGATAGTTATGTGGGCAGgtaaggtcta ... acttctacagGAACTTGGAGGGTAGGTGGTGTACTTGCGATGTCTCGGGCATTTGGCAACCGTCTCTTAAAACAATTTGTTATTGCAGACCCTGAAATTCAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 71

CTATTGCGCTCTCTGAAGATCACAAGCCAAACAGAAGTGATGAGAGGAATCGAATTGAGAGTGCTGGTGGGATAGTTATGTGGGCAGgtaaggtcta ... acttctacagGAACTTGGAGGGTAGGTGGTGTACTTGCGATGTCTCGGGCATTTGGCAACCGTCTCTTAAAACAATTTGTTATTGCAGACCCTGAAATTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 90

CTATTGCGCTCTCTGAAGATCACAAGCCAAACAGAAGTGATGAGAGGAATCGAATTGAGAGTGCTGGTGGGATAGTTATGTGGGCAGgtaaggtcta ... acttctacagGAACTTGGAGGGTAGGTGGTGTACTTGCGATGTCTCGGGCATTTGGCAACCGTCTCTTAAAACAATTTGTTATTGCAGACCCTGAAATTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacttgcttgttttcatgattcttgttgctcatagtggccaattgacttctacagGAACTTGGAGGGTAGGTGGTGTACTTGCGATGTCTCGGGCATTTGGCAACCGTCTCTTAAAACAATTTGTTATTGCAGACCCTGAAATTCAG
                                        aattgac  putative branch site (score: 90)
 cttctac  CT-rich tract
 ttgtttt  TA-rich tract