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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAAGCAAGGCTTTTCCTGGTCCTTCCTGATGCATTTTTGGATGCTTTTCTCATACTCTGGATTTTCACTTCTCTTTCCCGCACACTAGAGAAGCTACAGgtaagctaatttagtgcagtttaacaagtagaagcatttctaattgttctctctttatgtaaattcatacaatctaaactttgtagacttccacatgtaa...

Basic information

species Zea mays
transcript GRMZM2G064366_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G064366_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os11g34360.1 (Oryza sativa), 5'ss of exon 2
CAAAGCAAGGCTTTTCCTGGTCCTTCCTGATGCATTTTTGGATGCTTTTCTCATACTCTGGATTTTCACTTCTCTTTCCCGCACACTAGAGAAGCTACAGgtaagcta-atttagtgcagtttaacaagtagaagcatttctaat--tgttctctctttatgtaaattcatacaatctaaactttgtagacttccacatgtaa
||||||||||||||||| || ||||||||||| |||||||||||||| |||||||| ||||||||||||||||| ||||||||||| |||||| ||||||||||||| |||| || | ||| | || || ||| |||| || | ||| | || ||| || || || | | | | |
GAAAGCAAGGCTTTTCCTAGTTCTTCCTGATGCCTTTTTGGATGCTTTCCTCATACTTTGGATTTTCACTTCTCTCTCCCGCACACTTGAGAAGTTACAGgtaagctatatttgatgtaatttttcttgtct--gcttttataatgatgattactccctccgtcccaaaatataacaacttctacaccaacattctcttctc-

upper sequence: GRMZM2G064366_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv12s0034g01090.t01 (Vitis vinifera), 5'ss of exon 2
CAAAGCAAGGCTTTTCCTGGTCCTTCCTGATGCATTTTTGGATGCTTTTCTCATACTCTGGATTTTCACTTCTCTTTCCCGCACACTAGAGAAGCTACAGgtaagctaatttagtgcagtttaacaagtagaagcatttctaattgttctctctttatgtaaattca-tacaatctaaactttgtagacttccacatgtaa-----------------------------------------------------------------------
| ||||||||| ||| | ||||||||||||||||| ||||||| ||| | ||| | |||||||||||||| ||||| ||| ||||| | ||||||||| | || | || || | || | || | || || | || || | ||| | |||| | | ||
AAGAGCAAGGCTCTTCTTAGTCCTTCCTGATGCATTCCTGGATGCATTTTTGATATTGTGGATTTTCACTTCCCTTTCAAAGACATTAGAGCAACTACAGgta--tcagttcttcgtctactatcagttttgagttccagttgttaatatcagttaaaatagtggcaacaacatcagagcttttctttcctttttatcctttccttttcttttttactatttttatttttcattcattatcatattctgatgctataattatttgtgttcag
















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|67024546|gb|CO453295.1|CO453295
EST:     TCATACTCTGGATTTTCACTTCTCTTTCCCGCACACTAGAGAAGCTACAG                         GCAAGGAGGAGTTCTGTGAAATTGGATATATACAGAAAGTTCACAAATGCA
genomic: TCATACTCTGGATTTTCACTTCTCTTTCCCGCACACTAGAGAAGCTACAGgtaagctaat ... ctttcaccagGCAAGGAGGAGTTCTGTGAAATTGGATATATACAGAAAGTTCACAAATGCA
EST: gi|148967311|gb|EE018517.2|EE018517
EST:     TCATACTCTGGATTTTCACTTCTCTTTCCCGCACACTAGAGAAGCTACAG                         GCAAGGAGGAGTTCTGTGAAATTGGATATATACAGAAAGTTCACAAATGCA
genomic: TCATACTCTGGATTTTCACTTCTCTTTCCCGCACACTAGAGAAGCTACAGgtaagctaat ... ctttcaccagGCAAGGAGGAGTTCTGTGAAATTGGATATATACAGAAAGTTCACAAATGCA
EST: gi|76289905|gb|DV029473.1|DV029473
EST:     TCATACTCTGGATTTTCACTTCTCTTTCCCGCACACTAGAGAAGCTACAG                         GCAAGGAGGAGTTCTGTGAAATTGGATATATACAGAAAGTTCACAAATGCA
genomic: TCATACTCTGGATTTTCACTTCTCTTTCCCGCACACTAGAGAAGCTACAGgtaagctaat ... ctttcaccagGCAAGGAGGAGTTCTGTGAAATTGGATATATACAGAAAGTTCACAAATGCA
EST: gi|22491183|gb|BU051106.1|BU051106
EST:     TCATACTCTGGATTTTCACTTCTCTTTCCCGCACACTAGAGAAGCTACAG                         GCAAGGAGGAGTTCTGTGAAATTGGATATATACAGAAAGTTCACAAATGCA
genomic: TCATACTCTGGATTTTCACTTCTCTTTCCCGCACACTAGAGAAGCTACAGgtaagctaat ... ctttcaccagGCAAGGAGGAGTTCTGTGAAATTGGATATATACAGAAAGTTCACAAATGCA
EST: gi|83278764|gb|DV942772.1|DV942772
EST:     TCATACTCTGGATTTTCACTTCTCTTTCCCGCACACTAGAGAAGCTACAG                         GCAAGGAGGAGTTCTGTGAAATTGGATATATACAGAAAGTTCACAAATGCA
genomic: TCATACTCTGGATTTTCACTTCTCTTTCCCGCACACTAGAGAAGCTACAGgtaagctaat ... ctttcaccagGCAAGGAGGAGTTCTGTGAAATTGGATATATACAGAAAGTTCACAAATGCA
EST: gi|149112569|gb|EE295431.2|EE295431
EST:     TCATACTCTGGATTTTCACTTCTCTTTCCCGCACACTAGAGAAGCTACAG                         GCAAGGAGGAGTTCTGTGAAATTGGATATATACAGAAAGTTCACAAATGCA
genomic: TCATACTCTGGATTTTCACTTCTCTTTCCCGCACACTAGAGAAGCTACAGgtaagctaat ... ctttcaccagGCAAGGAGGAGTTCTGTGAAATTGGATATATACAGAAAGTTCACAAATGCA
EST: gi|211376336|gb|FL031209.1|FL031209
EST:     TCATACTCTGGATTTTCACTTCTCTTTCCCGCACACTAGAGAAGCTACAG                         GCAAGGAGGAGTTCTGTGAAATTGGATATATACAGAAAGTTCACAAATGCA
genomic: TCATACTCTGGATTTTCACTTCTCTTTCCCGCACACTAGAGAAGCTACAGgtaagctaat ... ctttcaccagGCAAGGAGGAGTTCTGTGAAATTGGATATATACAGAAAGTTCACAAATGCA
EST: gi|19272383|gb|BM888639.1|BM888639
EST:     TCATACTCTGGATTTTCACTTCTCTTTCCCGCACACTAGAGAAGCTACAG                         GCAAGGAGGAGTTCTGTGAAATTGGATATATACAGAAAGTTCACAAATGCA
genomic: TCATACTCTGGATTTTCACTTCTCTTTCCCGCACACTAGAGAAGCTACAGgtaagctaat ... ctttcaccagGCAAGGAGGAGTTCTGTGAAATTGGATATATACAGAAAGTTCACAAATGCA
EST: gi|19272497|gb|BM888753.1|BM888753
EST:     TCATACTCTGGATTTTCACTTCTCTTTCCCGCACACTAGAGAAGCTACAG                         GCAAGGAGGAGTTCTGTGAAATTGGATATATACAGAAAGTTCACAAATGCA
genomic: TCATACTCTGGATTTTCACTTCTCTTTCCCGCACACTAGAGAAGCTACAGgtaagctaat ... ctttcaccagGCAAGGAGGAGTTCTGTGAAATTGGATATATACAGAAAGTTCACAAATGCA
EST: gi|148959137|gb|EE010606.2|EE010606
EST:     TCATACTCTGGATTTTCACTTCTCTTTCCCGCACACTAGAGAAGCTACAG                         GCAAGGAGGAGTTCTGTGAAATTGGATATATACAGAAAGTTCACAAATGCA
genomic: TCATACTCTGGATTTTCACTTCTCTTTCCCGCACACTAGAGAAGCTACAGgtaagctaat ... ctttcaccagGCAAGGAGGAGTTCTGTGAAATTGGATATATACAGAAAGTTCACAAATGCA
EST: gi|211464044|gb|FL176493.1|FL176493
EST:     TCATACTCTGGATTTTCACTTCTCTTTCCCGCACACTAGAGAAGCTACAG                         GCAAGGAGGAGTTCTGTGAAATTGGATATATACAGAAAGTTCAMAAATGCA
genomic: TCATACTCTGGATTTTCACTTCTCTTTCCCGCACACTAGAGAAGCTACAGgtaagctaat ... ctttcaccagGCAAGGAGGAGTTCTGTGAAATTGGATATATACAGAAAGTTCACAAATGCA
EST: gi|148960354|gb|EE153613.2|EE153613
EST:     TCATACTCTGGATTTTCACTTCTCTTTCCCGCACACTAGAGAAGCTACAG                         GCAAGGAGGAGTTCTGTGAAATTGGATATATACAGAAAGTTCACAAATGCA
genomic: TCATACTCTGGATTTTCACTTCTCTTTCCCGCACACTAGAGAAGCTACAGgtaagctaat ... ctttcaccagGCAAGGAGGAGTTCTGTGAAATTGGATATATACAGAAAGTTCACAAATGCA
EST: gi|148971674|gb|EE022398.2|EE022398
EST:     TCATACTCTGGATTTTCACTTCTCTTTCCCGCACACTAGAGAAGCTACAG                         GCAAGGAGGAGTTCTGTGAAATTGGATATATACAGAAAGTTCACAAATGCA
genomic: TCATACTCTGGATTTTCACTTCTCTTTCCCGCACACTAGAGAAGCTACAGgtaagctaat ... ctttcaccagGCAAGGAGGAGTTCTGTGAAATTGGATATATACAGAAAGTTCACAAATGCA

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: 127

CAAAGCAAGGCTTTTCCTGGTCCTTCCTGATGCATTTTTGGATGCTTTTCTCATACTCTGGATTTTCACTTCTCTTTCCCGCACACTAGAGAAGCTACAGgtaagctaat ... ctttcaccagGCAAGGAGGAGTTCTGTGAAATTGGATATATACAGAAAGTTCACAAATGCATTGGCTGTTTCTGTGATAGCTTCAGTTGCCTGGATTGGTTATGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 180

CAAAGCAAGGCTTTTCCTGGTCCTTCCTGATGCATTTTTGGATGCTTTTCTCATACTCTGGATTTTCACTTCTCTTTCCCGCACACTAGAGAAGCTACAGgtaagctaat ... ctttcaccagGCAAGGAGGAGTTCTGTGAAATTGGATATATACAGAAAGTTCACAAATGCATTGGCTGTTTCTGTGATAGCTTCAGTTGCCTGGATTGGTTATGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 216

CAAAGCAAGGCTTTTCCTGGTCCTTCCTGATGCATTTTTGGATGCTTTTCTCATACTCTGGATTTTCACTTCTCTTTCCCGCACACTAGAGAAGCTACAGgtaagctaat ... ctttcaccagGCAAGGAGGAGTTCTGTGAAATTGGATATATACAGAAAGTTCACAAATGCATTGGCTGTTTCTGTGATAGCTTCAGTTGCCTGGATTGGTTATGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 340

CAAAGCAAGGCTTTTCCTGGTCCTTCCTGATGCATTTTTGGATGCTTTTCTCATACTCTGGATTTTCACTTCTCTTTCCCGCACACTAGAGAAGCTACAGgtaagctaat ... ctttcaccagGCAAGGAGGAGTTCTGTGAAATTGGATATATACAGAAAGTTCACAAATGCATTGGCTGTTTCTGTGATAGCTTCAGTTGCCTGGATTGGTTATGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAAGCAAGGCTTTTCCTGGTCCTTCCTGATGCATTTTTGGATGCTTTTCTCATACTCTGGATTTTCACTTCTCTTTCCCGCACACTAGAGAAGCTACAGgtaagctaatttagtgcagtttaacaagtagaagcatttctaattgttctctctttatgtaaattcatacaatctaaactttgtagacttccacatgtaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagtagaa