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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagagatataccccctataactactggtcataccatagcttcttactaaggtttgtgggcttctggtgtagattgatttatgtgcttatttgcaatttcttcaaacttctaatgtcaacatacctattagattattgtaacagccatctcatcaagtggttgcatcatgcagGCGATCTTGTTGCACACATAAAGTTCACTGTGCTGCTGATGCCCAATGGATCAGATAAGATAACATCACATCCTCTACAGGAGTTAAAGCCCACCAAATC

Basic information

species Zea mays
transcript AC233895.1_FGT001
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC233895.1_FGT001 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os05g28280.1 (Oryza sativa), 3'ss of exon 8
gtagagatataccccctataactactggtcataccatagcttcttactaaggtttgtgggcttctggtgtagattgatttatgtgcttatttgcaatttcttcaaacttctaatgtcaacatacc-tattagattattgtaacagccatctcatcaagtggttgcatcatgcagGCGATCTTGTTGCACACATAAAGTTCACTGTGCTGCTGATGCCCAATGGATCAGATAAGATAACATCACATCCTCTACAGGAGTTAAAGCCCACCAAATC
                                                                        ||| |||| |||   | | | |||     |     |  | |   | |||| || ||||      || ||   |   | | |  |  ||||||  |  ||||||||| |||||||||||||| ||||| |||||||| ||| ||||   ||| ||| | | | ||||||| ||| | || ||||||||  ||||||| |||||
------------------------------------------------------------------------att-atttgtgtttatttgtacaaaccgcttctgttgattactgctacatgccatatttctcgtttctagtggttgtattaatagttggttgt-ttgtgcagGCGACCTTGTTGCACACATCAAGTTTACTGTGCTTCTGCTGCCATCTGGTTCACAGAGGGTAACATCGCATTCACTTCAGGAGTTGCAGCCCACTAAATC

upper sequence: AC233895.1_FGT001 (Zea mays), 3'ss of exon 7
lower sequence: PP1S264_34V6.1 (Physcomitrella patens), 3'ss of exon 7
--------------------gtagagatataccccctataactactggtcatacca-tagcttcttactaaggtttgtg--ggcttctggtgtagattgatttatgtgcttatttgcaatttcttcaaacttctaatgtcaacatacctattagattattgtaacagccatctcatcaagtggttgcatcatgcagGCGATCTTGTTGCACACATAAAGTTCACTGTGCTGCTGATGCCCAATGGATCAGATAAGATAACATCACATCCTCTACAGGAGTTAAAGCCCACCAAATC
                    |   |  |    |  || ||     || | ||  || ||||| |||     |   |||   |||| |  |  |    ||    | |||  | || |||  || ||      ||   ||       |   |||| || ||| | ||  | | |   ||   || ||  |    ||||| ||    || || ||||| |||||||||||  |||| |||||||| ||||| |||||||||||    |  || || || || |   || | ||||||  
gtatgtaaccctctatcgctgaccatgtgggacaactgtagtacatgatgatggcactagctgcttggcgtgtcctgttttggctacgtgcattctctg-cacaggtgtatgtt-gcatctttttttg--ctcaggtggagtacgatgcattaaataattcttact-caagcatgtcccatg-ttttactg-gcagGTGACTGCGTAGCCCACATTAAGTTCACTGTATTGCTCATGCCCAACGGATCCGATAAGATAACTGGTCTGCCACTTCAAGAATGTCAGTCGACCAAAGT
















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|14569289|gb|BI097612.1|BI097612
EST:     CATGAACCATGAACTATTGCAGCCGTACCCTGTACTTCATGAGAAGCCAG                         GCGATCTTGTTGCACACATAAAGTTCACTGTGCTGCTGATGCCCAATGGAT
genomic: CATGAACCATGAACTATTGCAGCCGTACCCTGTACTTCATGAGAAGCCAGgtagagatat ... catcatgcagGCGATCTTGTTGCACACATAAAGTTCACTGTGCTGCTGATGCCCAATGGAT
EST: gi|84980121|gb|DW530470.1|DW530470
EST:     CATGAACCATGAACTATTGCAGCCGTACCCTGTACTTCATGAGAAGCCAG                         GCGATCTTGTTGCACACATAAAGTTCACTGTGCTGCTGATGCCCAATGGAT
genomic: CATGAACCATGAACTATTGCAGCCGTACCCTGTACTTCATGAGAAGCCAGgtagagatat ... catcatgcagGCGATCTTGTTGCACACATAAAGTTCACTGTGCTGCTGATGCCCAATGGAT
EST: gi|15208836|gb|BI430720.1|BI430720
EST:     CATGAACCATGAACTATTGCAGCCGTACCCTGTACTTCATGAGAAGCCAG                         GCGATCTTGTTGCACACATAAAGTTCACTGTGCTGCTGATGCCCAATGGAT
genomic: CATGAACCATGAACTATTGCAGCCGTACCCTGTACTTCATGAGAAGCCAGgtagagatat ... catcatgcagGCGATCTTGTTGCACACATAAAGTTCACTGTGCTGCTGATGCCCAATGGAT

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: 533

GGCATTAGAAGAGAAGCGTGCGCGTTTAGGCTTGGTGGAATGCATGAACCATGAACTATTGCAGCCGTACCCTGTACTTCATGAGAAGCCAGgtagagatat ... catcatgcagGCGATCTTGTTGCACACATAAAGTTCACTGTGCTGCTGATGCCCAATGGATCAGATAAGATAACATCACATCCTCTACAGGAGTTAAAGCCCACCAAATC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 413

GGCATTAGAAGAGAAGCGTGCGCGTTTAGGCTTGGTGGAATGCATGAACCATGAACTATTGCAGCCGTACCCTGTACTTCATGAGAAGCCAGgtagagatat ... catcatgcagGCGATCTTGTTGCACACATAAAGTTCACTGTGCTGCTGATGCCCAATGGATCAGATAAGATAACATCACATCCTCTACAGGAGTTAAAGCCCACCAAATC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 419

GGCATTAGAAGAGAAGCGTGCGCGTTTAGGCTTGGTGGAATGCATGAACCATGAACTATTGCAGCCGTACCCTGTACTTCATGAGAAGCCAGgtagagatat ... catcatgcagGCGATCTTGTTGCACACATAAAGTTCACTGTGCTGCTGATGCCCAATGGATCAGATAAGATAACATCACATCCTCTACAGGAGTTAAAGCCCACCAAATC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 359

GGCATTAGAAGAGAAGCGTGCGCGTTTAGGCTTGGTGGAATGCATGAACCATGAACTATTGCAGCCGTACCCTGTACTTCATGAGAAGCCAGgtagagatat ... catcatgcagGCGATCTTGTTGCACACATAAAGTTCACTGTGCTGCTGATGCCCAATGGATCAGATAAGATAACATCACATCCTCTACAGGAGTTAAAGCCCACCAAATC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatacctattagattattgtaacagccatctcatcaagtggttgcatcatgcagGCGATCTTGTTGCACACATAAAGTTCACTGTGCTGCTGATGCCCAATGGATCAGATAAGATAACATCACATCCTCTACAGGAGTTAAAGCCCACCAAATC
                 ttgtaac  putative branch site (score: 359)
       tattagattattgtaa  TA-rich tract