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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgatagaagctaacacctctctctctctcccccccctccctctcgctatccctgtggctctccctttctctgttgtatgtgtggactcaccgactcaggcacacgtgtgcaaaacagaattatttaaattcatcatggatttatgtttttgacagATGACGTGGATACACGTGCTATAACACGAAGATTAAGAGAAGACGGCAGTCTTATTGGTGTCTTGAGTACTGATCAGTCTCAGACAGACAATGAGTTGTT

Basic information

species Zea mays
transcript GRMZM2G147450_T03
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147450_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g47850.3 (Oryza sativa), 3'ss of exon 6
gtaagtgatagaagctaacacctctctctctctcccccccctccctctcgctatccctgtggctctccctttctctgttgtatgtgtggactcaccgactcaggcacacgtgtgcaaaacagaattatttaaattcatcatggatttatgtttttgacagATGACGTGGATACACGTGCTATAACACGAAGATTAAGAGAAGACGGCAGTCTTATTGGTGTCTTGAGTACTGATCAGTCTCAGACAGACAATGAGTTGTT
                                                                         |  ||  | |     ||  ||  |           ||     | |||| ||  |   | |  || |||  ||||   || |   ||||||| ||||| ||||| || |||||||| |||||| ||||||| || ||||| ||||||||||| ||||||||||| |||| ||| ||  ||||||||||
------------------------------------------------------------------------gtaagtattgtcacctgatacattgctctctatgtccg-acaaacaacaaaagcaacaataaacaccatcaatttgctttatatgcagATGATGTGGACACACGCGCCATAACACGGAGATTACGAGAAGATGGTAGTCTAATTGGTGTCTTAAGTACTGATCAATCTCGGACCGATGATGAGTTGTT

upper sequence: GRMZM2G147450_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA05G32190.1 (Glycine max), 3'ss of exon 5
gtaagtgatagaagctaacacctctctctctctcccccccctccctctcgctatccctgtggctctccctttctctgttgtatgtgtggactcaccgactcaggcacacgtgtgcaaaacagaattatttaaattcatcatggatttatgtttttgacagATGACGTGGATACACGTGCTATAACACGAAGATTAAGAGAAGACGGCAGTCTTATTGGTGTCTTGAGTACTGATCAGTCTCAGACAGACAATGAGTTGTT
                                                                 |       |    |  || | |  | ||   ||   |  |     | || | ||| | |   |||   || | | | | |     | |   ||||||||||| || ||||| ||||| || || |||||| |  || | ||||| ||||||||||| |||||||||||  | ||| | |||||  | ||  |  |
----------------------------------------------------------------gtaagaaatttatataaatatata-attctttgagaaaatctactctctgtacaactgcaagttttgcctttaaccttggtg---atatgcaacagATGACGTTGACACACGGGCTATCACGCGCAGATTACGGCAAAAAGGCAGCCTTATTGGTGTGTTGAGTACTGACAATTCTAAAACAGAGGAGGAACTACT
















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|22472307|gb|BU036787.1|BU036787
EST:     GAAACACTTGAAGAGTATCTGACTAAGAGGAACATCATGGGAATAT                         ATGACGTGGATACACGTGCTATAACACGAAGATTAAGAGAAGACGGCAGTC
genomic: GAAACACTTGAAGAGTATCTGACTAAGAGGAACATCATGGGAATATgtaagtgata ... tttttgacagATGACGTGGATACACGTGCTATAACACGAAGATTAAGAGAAGACGGCAGTC
EST: gi|26457213|gb|CA828796.1|CA828796
EST:     CAAAGAAACACTTGAAGAGTATCTGACTAAGAGGAACATCATGGGAATAT                         ATGACGTGGATACACGTGCTATAACACGAAGATTAAGAGAAGACGGCAGTC
genomic: CAAAGAAACACTTGAAGAGTATCTGACTAAGAGGAACATCATGGGAATATgtaagtgata ... tttttgacagATGACGTGGATACACGTGCTATAACACGAAGATTAAGAGAAGACGGCAGTC
EST: gi|148969716|gb|EE020588.2|EE020588
EST:     CAAAGAAACACTTGAAGAGTATCTGACTAAGAGGAACATCATGGGAATAT                         ATGACGTGGATACACGTGCTATAACACGAAGATTAAGAGAAGACGGCAGTC
genomic: CAAAGAAACACTTGAAGAGTATCTGACTAAGAGGAACATCATGGGAATATgtaagtgata ... tttttgacagATGACGTGGATACACGTGCTATAACACGAAGATTAAGAGAAGACGGCAGTC
EST: gi|14569352|gb|BI097675.1|BI097675
EST:     CAAAGAAACACTTGAAGAGTATCTGACTAAGAGGAACATCATGGGAATAT                         ATGACGTGGATACACGTGCTATAACACGAAGATTAAGAGAAGACGGCAGTC
genomic: CAAAGAAACACTTGAAGAGTATCTGACTAAGAGGAACATCATGGGAATATgtaagtgata ... tttttgacagATGACGTGGATACACGTGCTATAACACGAAGATTAAGAGAAGACGGCAGTC

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: 117

TACTTCCAACTGGCGATGCAAAGAAACACTTGAAGAGTATCTGACTAAGAGGAACATCATGGGAATATgtaagtgata ... tttttgacagATGACGTGGATACACGTGCTATAACACGAAGATTAAGAGAAGACGGCAGTCTTATTGGTGTCTTGAGTACTGATCAGTCTCAGACAGACAATGAGTTGTT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 195

TACTTCCAACTGGCGATGCAAAGAAACACTTGAAGAGTATCTGACTAAGAGGAACATCATGGGAATATgtaagtgata ... tttttgacagATGACGTGGATACACGTGCTATAACACGAAGATTAAGAGAAGACGGCAGTCTTATTGGTGTCTTGAGTACTGATCAGTCTCAGACAGACAATGAGTTGTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 93

TACTTCCAACTGGCGATGCAAAGAAACACTTGAAGAGTATCTGACTAAGAGGAACATCATGGGAATATgtaagtgata ... tttttgacagATGACGTGGATACACGTGCTATAACACGAAGATTAAGAGAAGACGGCAGTCTTATTGGTGTCTTGAGTACTGATCAGTCTCAGACAGACAATGAGTTGTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 79

TACTTCCAACTGGCGATGCAAAGAAACACTTGAAGAGTATCTGACTAAGAGGAACATCATGGGAATATgtaagtgata ... tttttgacagATGACGTGGATACACGTGCTATAACACGAAGATTAAGAGAAGACGGCAGTCTTATTGGTGTCTTGAGTACTGATCAGTCTCAGACAGACAATGAGTTGTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acacgtgtgcaaaacagaattatttaaattcatcatggatttatgtttttgacagATGACGTGGATACACGTGCTATAACACGAAGATTAAGAGAAGACGGCAGTCTTATTGGTGTCTTGAGTACTGATCAGTCTCAGACAGACAATGAGTTGTT
                                           tgttttt  CT-rich tract
                 aattatttaaattcat  TA-rich tract