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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttcgaatgaatcttcattgatttcgtttccatagttttatgtatcagaagttcagtaatttgttgctttgttaaaatcatgctttaatgtggaatgacagATGAGAGGGAGTGACACATCAACTGCTGAGTCTGGTTCAGAAGCTGATGATGCTGTGTCCCCCAAAGCTCTCAGAAGTTACATATCACATCCTAAGTTGA

Basic information

species Zea mays
transcript GRMZM2G073571_T02
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G073571_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os02g04020.1 (Oryza sativa), 3'ss of exon 10
gtaagtttcgaatgaatcttcattgatttcgtttccatagttttatgtatcagaagttcagtaatttgttgctttgttaaaatcatgctttaatgtggaatgacagATGAGAGGGAGTGACACATCAACTGCTGAGTCTGGTTCAGAAGCTGATGATGCTGTGTCCCCCAAAGCTCTCAGAAGTTACATATCACATCCTAAGTTGA
||| || ||  |  | ||   | |  |||    || || | ||| | |  |    | ||  |     |   | |     ||||| ||||||| | |||| ||  ||||  ||||||| || ||||| |||||||||||||| || || ||||| |||| |  ||| || ||||  || ||||||||||| || |||||||||||||
gtatgtctc--acaactcagtactatttt----tctattgctttctttgccttgtgctctatg--cagaaacct-----aaatcttgctttattctggattgctagATACGAGGGAGCGATACATCCACTGCTGAGTCTGGATCTGAGGCTGAAGATGTTACGTCTCCAAAAGTACTGAGAAGTTACATCTCCCATCCTAAGTTGA
















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|8383108|gb|BE055991.1|BE055991
EST:     CCAATGGTGAGGAAAAATTTATTACTTACGCCAAACCGAAGCGCCACGCA                         ATGAGAGGGAGTGACACATCAACTGCTGAGTCTGGTTCAGAAGCTGATGAT
genomic: CCAATGGTGAGGAAAAATTTATTACTTACGCCAAACCGAAGCGCCACGCAgtaagtttcg ... ggaatgacagATGAGAGGGAGTGACACATCAACTGCTGAGTCTGGTTCAGAAGCTGATGAT
EST: gi|15177587|gb|BI398526.1|BI398526
EST:     CCAATGGTGAGGAAAAATTTATTACTTACGCCAAACCGAAGCGCCACGCA                         ATGAGAGGGAGTGACACATCAACTGCTGAGTCTGGTTCAGAAGCTGATGAT
genomic: CCAATGGTGAGGAAAAATTTATTACTTACGCCAAACCGAAGCGCCACGCAgtaagtttcg ... ggaatgacagATGAGAGGGAGTGACACATCAACTGCTGAGTCTGGTTCAGAAGCTGATGAT
EST: gi|16137338|gb|BI894203.1|BI894203
EST:     CCAATGGTGAGGAAAAATTTATTACTTACGCCAAACCGAAGCGCCACGCA                         ATGAGAGGGAGTGACACATCAACTGCTGAGTCTGGTTCAGAAGCTGATGAT
genomic: CCAATGGTGAGGAAAAATTTATTACTTACGCCAAACCGAAGCGCCACGCAgtaagtttcg ... ggaatgacagATGAGAGGGAGTGACACATCAACTGCTGAGTCTGGTTCAGAAGCTGATGAT
EST: gi|3172014|gb|AJ006545.1|AJ006545
EST:     CCAATGGTGAGGAAAAATTTATTACTTACGCCAAACCGAACCGCCACACA                         ATGAGAGGGAGTGACACATCAACTGCTGAGTCTGGTTCAGAAGCTGATGAT
genomic: CCAATGGTGAGGAAAAATTTATTACTTACGCCAAACCGAAGCGCCACGCAgtaagtttcg ... ggaatgacagATGAGAGGGAGTGACACATCAACTGCTGAGTCTGGTTCAGAAGCTGATGAT
EST: gi|15177586|gb|BI398525.1|BI398525
EST:     CCAATGGTGAGGAAAAATTTATTACTTACGCCAAACCGAAGCGCCACGCA                         ATGAGAGGGAGTGACACATCAACTGCTGAGTCTGGTTCAGAAGCTGATGAT
genomic: CCAATGGTGAGGAAAAATTTATTACTTACGCCAAACCGAAGCGCCACGCAgtaagtttcg ... ggaatgacagATGAGAGGGAGTGACACATCAACTGCTGAGTCTGGTTCAGAAGCTGATGAT
EST: gi|15188204|gb|BI417181.1|BI417181
EST:     CCAATGGTGAGGAAAAATTTATTACTTACGCCAAACCGAAGCGCCACGCA                         ATGAGAGGGAGTGACACATCAACTGTTGAGTCTGGTTCAGAAGCTGATGAT
genomic: CCAATGGTGAGGAAAAATTTATTACTTACGCCAAACCGAAGCGCCACGCAgtaagtttcg ... ggaatgacagATGAGAGGGAGTGACACATCAACTGCTGAGTCTGGTTCAGAAGCTGATGAT
EST: gi|15323597|gb|BI478855.1|BI478855
EST:     CCAATGGTGAGGAAAAATTTATTACTTACGCCAAACCGAAGCGCCACGCA                         ATGAGAGGGAGTGACACATCAACTGCTGAGTCTGGTTCAGAAGCTGATGAT
genomic: CCAATGGTGAGGAAAAATTTATTACTTACGCCAAACCGAAGCGCCACGCAgtaagtttcg ... ggaatgacagATGAGAGGGAGTGACACATCAACTGCTGAGTCTGGTTCAGAAGCTGATGAT
EST: gi|15323596|gb|BI478854.1|BI478854
EST:     CCAATGGTGAGGAAAAATTTATTACTTACGCCAAACCGAAGCGCCACGCA                         ATGAGAGGGAGTGACACATCAACTGCTGAGTCTGGTTCAGAAGCTGATGAT
genomic: CCAATGGTGAGGAAAAATTTATTACTTACGCCAAACCGAAGCGCCACGCAgtaagtttcg ... ggaatgacagATGAGAGGGAGTGACACATCAACTGCTGAGTCTGGTTCAGAAGCTGATGAT
EST: gi|32832349|gb|CD972027.1|CD972027
EST:     CCAATGGTGAGGAAAAATTTATTACTTACGCCAAACCGAACCGCCACGCA                         ATGAGAGGGAGTGACACATCAACTGCTGAGTCTGGTTCAGAAGCTGATGAT
genomic: CCAATGGTGAGGAAAAATTTATTACTTACGCCAAACCGAAGCGCCACGCAgtaagtttcg ... ggaatgacagATGAGAGGGAGTGACACATCAACTGCTGAGTCTGGTTCAGAAGCTGATGAT
EST: gi|32847771|gb|CD987452.1|CD987452
EST:     CCAATGGTGAGGAAAAATTTATTACTTACGCCAAACCGAACCGCCACGCA                         ATGAGAGGGAGTGACACATCAACTGCTGAGTCTGGTTCAGAAGCTGATGAT
genomic: CCAATGGTGAGGAAAAATTTATTACTTACGCCAAACCGAAGCGCCACGCAgtaagtttcg ... ggaatgacagATGAGAGGGAGTGACACATCAACTGCTGAGTCTGGTTCAGAAGCTGATGAT

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: 198

ATAGTCCAAAGTGGTGGGGTTCATTGTGCTCGTCAAATTGTAACTATTTCCAATGGTGAGGAAAAATTTATTACTTACGCCAAACCGAAGCGCCACGCAgtaagtttcg ... ggaatgacagATGAGAGGGAGTGACACATCAACTGCTGAGTCTGGTTCAGAAGCTGATGATGCTGTGTCCCCCAAAGCTCTCAGAAGTTACATATCACATCCTAAGTTGA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 98

ATAGTCCAAAGTGGTGGGGTTCATTGTGCTCGTCAAATTGTAACTATTTCCAATGGTGAGGAAAAATTTATTACTTACGCCAAACCGAAGCGCCACGCAgtaagtttcg ... ggaatgacagATGAGAGGGAGTGACACATCAACTGCTGAGTCTGGTTCAGAAGCTGATGATGCTGTGTCCCCCAAAGCTCTCAGAAGTTACATATCACATCCTAAGTTGA


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 127

ATAGTCCAAAGTGGTGGGGTTCATTGTGCTCGTCAAATTGTAACTATTTCCAATGGTGAGGAAAAATTTATTACTTACGCCAAACCGAAGCGCCACGCAgtaagtttcg ... ggaatgacagATGAGAGGGAGTGACACATCAACTGCTGAGTCTGGTTCAGAAGCTGATGATGCTGTGTCCCCCAAAGCTCTCAGAAGTTACATATCACATCCTAAGTTGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 132

ATAGTCCAAAGTGGTGGGGTTCATTGTGCTCGTCAAATTGTAACTATTTCCAATGGTGAGGAAAAATTTATTACTTACGCCAAACCGAAGCGCCACGCAgtaagtttcg ... ggaatgacagATGAGAGGGAGTGACACATCAACTGCTGAGTCTGGTTCAGAAGCTGATGATGCTGTGTCCCCCAAAGCTCTCAGAAGTTACATATCACATCCTAAGTTGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaagttcagtaatttgttgctttgttaaaatcatgctttaatgtggaatgacagATGAGAGGGAGTGACACATCAACTGCTGAGTCTGGTTCAGAAGCTGATGATGCTGTGTCCCCCAAAGCTCTCAGAAGTTACATATCACATCCTAAGTTGA
                                    ctttaat  putative branch site (score: 132)
                     tttgttaaaatcat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttcgaatgaatcttcattgatttcgtttccatagttttatgtatcagaagttcagtaatttgttgctttgttaaaatcatgctttaatgtggaatgacagATGAGAGGGAGTGACACATCAACTGCTGAGTCTGGTTCAGAAGCTGATGATGCTGTGTCCCCCAAAGCTCTCAGAAGTTACATATCACATCCTAAGTTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT