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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctgcaaaaacttctgtcaaaatcgtttgtgattgcaattttattatgttagctaacaaaagcatgtgattcctgcagGTTCATGACATTACCCACTCACCTTTTGCTGAAAGGGAACTTATGCTTATTAAGGTTTCTGTCAACACTGCTGCTCGGAAGGAAATCCTAGATATTGCTG

Basic information

species Zea mays
transcript GRMZM2G407044_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G407044_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os02g39570.5 (Oryza sativa), 3'ss of exon 9
gtaagctgcaaaaacttctgtcaaaatcgtttgtgattgcaattttattatgttagctaacaaaagcatgtgattcctgcagGTTCATGACATTACCCACTCACCTTTTGCTGAAAGGGAACTTATGCTTATTAAGGTTTCTGTCAACACTGCTGCTCGGAAGGAAATCCTAGATATTGCTG
||||     |   | || |   | |   ||   |  | | | |    |    |||  | | ||||   | |||||  |||||||||| || || || ||||  |||||||||||||| |||||||||||||| ||||||||||| ||||||||||||||||  || || |||||||||||||
gtaaatcatatgcagtttt-caagagcagtcaattgtggtagtaaagtcgcattaattcaaaaaa---tatgatttgtgcagGTTCAAGATATAACTCACTTGCCTTTTGCTGAAAGAGAACTTATGCTTATCAAGGTTTCTGTGAACACTGCTGCTCGGAGAGACATACTAGATATTGCTG
















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|89253086|gb|DY624872.1|DY624872
EST:     CCATTGAGAAGTTAGTTCAGCAGCTTTACAAGCTTATTGATGTGCACGAA                         GTTCATGACATTACCCACTCACCTTTTGCTGAAAGGGAACTTATGCTTATT
genomic: CCATTGAGAAGTTAGTTCAGCAGCTTTACAAGCTTATTGATGTGCACGAAgtaagctgca ... attcctgcagGTTCATGACATTACCCACTCACCTTTTGCTGAAAGGGAACTTATGCTTATT
EST: gi|211452062|gb|FL278247.1|FL278247
EST:     CCATTGASAAGTTAGTTCAGCAGCTTTACAAGCTTATTGATGTGCACGAA                         GTTCATGACATTACCCACTCACCTTTTGCTGAAAGGGAACTTATGCTTATT
genomic: CCATTGAGAAGTTAGTTCAGCAGCTTTACAAGCTTATTGATGTGCACGAAgtaagctgca ... attcctgcagGTTCATGACATTACCCACTCACCTTTTGCTGAAAGGGAACTTATGCTTATT
EST: gi|211122006|gb|FL444944.1|FL444944
EST:     CCATTGAGAAGTTAGTTCAGCAGCTTTACAAGCTTATTGATGTGCACGAA                         GTTCATGACATTACCCACTCACCTTTTGCTGAAAGGGAACTTATGCTTATT
genomic: CCATTGAGAAGTTAGTTCAGCAGCTTTACAAGCTTATTGATGTGCACGAAgtaagctgca ... attcctgcagGTTCATGACATTACCCACTCACCTTTTGCTGAAAGGGAACTTATGCTTATT
EST: gi|24934868|gb|CA453086.1|CA453086
EST:     CCATTGAGAAGTTAGTTCAGCAGCTTTACAAGCTTATTGATGTGCACGAA                         GTTCATGACATTACCCACTCACCTTTTGCTGAAAGGGAACTTATGCTTATT
genomic: CCATTGAGAAGTTAGTTCAGCAGCTTTACAAGCTTATTGATGTGCACGAAgtaagctgca ... attcctgcagGTTCATGACATTACCCACTCACCTTTTGCTGAAAGGGAACTTATGCTTATT
EST: gi|60338155|gb|DN205128.1|DN205128
EST:     CCATTGAGAAGTTAGTTCAGCAGCTTTACAAGCTTATTGATGTGCACGAA                         GTTCATGACATTACCCACTCACCTTTTGCTGAAAGGGAACTTATGCTTATT
genomic: CCATTGAGAAGTTAGTTCAGCAGCTTTACAAGCTTATTGATGTGCACGAAgtaagctgca ... attcctgcagGTTCATGACATTACCCACTCACCTTTTGCTGAAAGGGAACTTATGCTTATT
EST: gi|211132732|gb|FL016680.1|FL016680
EST:     CCATTGAGAAGTTAGTTCAGCAGCTTTACAAGCTTATTGATGTGCACGAA                         GTTCATGACATTACCCACTCACCTTTTGCTGAAAGGGAACTTATGCTTATT
genomic: CCATTGAGAAGTTAGTTCAGCAGCTTTACAAGCTTATTGATGTGCACGAAgtaagctgca ... attcctgcagGTTCATGACATTACCCACTCACCTTTTGCTGAAAGGGAACTTATGCTTATT
EST: gi|149087823|gb|EE287139.2|EE287139
EST:     CCATTGAGAAGTTAGTTCAGCAGCTTTACAAGCTTATTGATGTGCACGAA                         GTTCATGACATTACCCACTCACCTTTTGCTGAAAGGGAACTTATGCTTATT
genomic: CCATTGAGAAGTTAGTTCAGCAGCTTTACAAGCTTATTGATGTGCACGAAgtaagctgca ... attcctgcagGTTCATGACATTACCCACTCACCTTTTGCTGAAAGGGAACTTATGCTTATT
EST: gi|211033398|gb|FL443777.1|FL443777
EST:     CCATTGAGAAGTTAGTTCAGCAGCTTTACAAGCTTATTGATGTGCACGAA                         GTTCATGACATTACCCACTCACCTTTTGCTGAAAGGGAACTTATGCTTATT
genomic: CCATTGAGAAGTTAGTTCAGCAGCTTTACAAGCTTATTGATGTGCACGAAgtaagctgca ... attcctgcagGTTCATGACATTACCCACTCACCTTTTGCTGAAAGGGAACTTATGCTTATT
EST: gi|32940948|gb|CF045767.1|CF045767
EST:     CCATTGAGAAGTTAGTTCAGCAGCTTTACAAGCTTATTGATGTGCACGAA                         GTTCATGACATTACCCACTCACCTTTTGCTGAAAGGGAACTTATGCTTATT
genomic: CCATTGAGAAGTTAGTTCAGCAGCTTTACAAGCTTATTGATGTGCACGAAgtaagctgca ... attcctgcagGTTCATGACATTACCCACTCACCTTTTGCTGAAAGGGAACTTATGCTTATT
EST: gi|211350147|gb|FL469218.1|FL469218
EST:     TATTGATGTGCACGAA                         GTTCATGACATTACCCACTCACCTTTTGCTGAAAGGGAACTTATGCTTATT
genomic: TATTGATGTGCACGAAgtaagctgca ... attcctgcagGTTCATGACATTACCCACTCACCTTTTGCTGAAAGGGAACTTATGCTTATT
EST: gi|116818053|gb|EC860984.1|EC860984
EST:     AGCTTATTGATGTGCACGAA                         G-TCATGACATTACCTACTCACCTTTTGCTGAAAGGGAA-TTATGCTTATT
genomic: AGCTTATTGATGTGCACGAAgtaagctgca ... attcctgcagGTTCATGACATTACCCACTCACCTTTTGCTGAAAGGGAACTTATGCTTATT
EST: gi|78122763|gb|DV541147.1|DV541147
EST:     CCATTGAGAAGTTAGTTCAGCAGCTTTACAAGCTTATTGATGTGCACGAA                         GTTCATGACATTACCCACTCACCTTTTGCTGAAAGGGAACTTATGCTTATT
genomic: CCATTGAGAAGTTAGTTCAGCAGCTTTACAAGCTTATTGATGTGCACGAAgtaagctgca ... attcctgcagGTTCATGACATTACCCACTCACCTTTTGCTGAAAGGGAACTTATGCTTATT
EST: gi|60343820|gb|DN210793.1|DN210793
EST:     CCATTGAGAAGTTAGTTCAGCAGCTTTACAAGCTTATTGATGTGCACGAA                         GTTCATGACATTACCCACTCACCTTTTGCTGAAAGGGAACTTATGCTTATT
genomic: CCATTGAGAAGTTAGTTCAGCAGCTTTACAAGCTTATTGATGTGCACGAAgtaagctgca ... attcctgcagGTTCATGACATTACCCACTCACCTTTTGCTGAAAGGGAACTTATGCTTATT
EST: gi|60340849|gb|DN207822.1|DN207822
EST:     CCATTGAGAAGTTAGTTCAGCAGCTTTACAAGCTTATTGATGTGCACGAA                         GTTCATGACATTACCCACTCACCTTTTGCTGAAAGGGAACTTATGCTTATT
genomic: CCATTGAGAAGTTAGTTCAGCAGCTTTACAAGCTTATTGATGTGCACGAAgtaagctgca ... attcctgcagGTTCATGACATTACCCACTCACCTTTTGCTGAAAGGGAACTTATGCTTATT
EST: gi|211449937|gb|FL278245.1|FL278245
EST:     CCATTGAGAAGTTAGTTCAGCAGCTTTACAAGCTTATTGATGTGCACGAA                         GTTCATGACATTACCCACTCACCTTTTGCTGAAAGGGAACTTATGCTTATT
genomic: CCATTGAGAAGTTAGTTCAGCAGCTTTACAAGCTTATTGATGTGCACGAAgtaagctgca ... attcctgcagGTTCATGACATTACCCACTCACCTTTTGCTGAAAGGGAACTTATGCTTATT
EST: gi|24773364|gb|CA408618.1|CA408618
EST:     CCATTGAGAAGTTAGTTCAGCAGCTTTACAAGCTTATTGATGTGCACGAA                         GTTCATGACATTACCCACTCACCTTTTGCTGAAAGGGAACTTATGCTTATT
genomic: CCATTGAGAAGTTAGTTCAGCAGCTTTACAAGCTTATTGATGTGCACGAAgtaagctgca ... attcctgcagGTTCATGACATTACCCACTCACCTTTTGCTGAAAGGGAACTTATGCTTATT
EST: gi|211452064|gb|FL278249.1|FL278249
EST:     CCATTGAGAAGTTAGTTCAGCAGCTTTACAAGCTTATTGATGTGCACGAA                         GTTCATGACATTACCCACTCACCTTTTGCTGAAAGGGAACTTATGCTTATT
genomic: CCATTGAGAAGTTAGTTCAGCAGCTTTACAAGCTTATTGATGTGCACGAAgtaagctgca ... attcctgcagGTTCATGACATTACCCACTCACCTTTTGCTGAAAGGGAACTTATGCTTATT
EST: gi|211132731|gb|FL016679.1|FL016679
EST:     CCATTGAGAAGTTAGTTCAGCAGCTTTACAAGCTTATTGATGTGCACGAA                         GTTCATGACATTACCCACTCACCTTTTGCTGAAAGGGAACTTATGCTTATT
genomic: CCATTGAGAAGTTAGTTCAGCAGCTTTACAAGCTTATTGATGTGCACGAAgtaagctgca ... attcctgcagGTTCATGACATTACCCACTCACCTTTTGCTGAAAGGGAACTTATGCTTATT

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: 138

GAAGGAAGGCATTTCGCGGATTACAACAGTTGTTCCTGGTACTGTTGAATCCATTGAGAAGTTAGTTCAGCAGCTTTACAAGCTTATTGATGTGCACGAAgtaagctgca ... attcctgcagGTTCATGACATTACCCACTCACCTTTTGCTGAAAGGGAACTTATGCTTATTAAGGTTTCTGTCAACACTGCTGCTCGGAAGGAAATCCTAGATATTGCTG


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

GAAGGAAGGCATTTCGCGGATTACAACAGTTGTTCCTGGTACTGTTGAATCCATTGAGAAGTTAGTTCAGCAGCTTTACAAGCTTATTGATGTGCACGAAgtaagctgca ... attcctgcagGTTCATGACATTACCCACTCACCTTTTGCTGAAAGGGAACTTATGCTTATTAAGGTTTCTGTCAACACTGCTGCTCGGAAGGAAATCCTAGATATTGCTG


Block sizes: 45 (upstream exon), 46 (downstream exon)
Score: 25

GAAGGAAGGCATTTCGCGGATTACAACAGTTGTTCCTGGTACTGTTGAATCCATTGAGAAGTTAGTTCAGCAGCTTTACAAGCTTATTGATGTGCACGAAgtaagctgca ... attcctgcagGTTCATGACATTACCCACTCACCTTTTGCTGAAAGGGAACTTATGCTTATTAAGGTTTCTGTCAACACTGCTGCTCGGAAGGAAATCCTAGATATTGCTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 78

GAAGGAAGGCATTTCGCGGATTACAACAGTTGTTCCTGGTACTGTTGAATCCATTGAGAAGTTAGTTCAGCAGCTTTACAAGCTTATTGATGTGCACGAAgtaagctgca ... attcctgcagGTTCATGACATTACCCACTCACCTTTTGCTGAAAGGGAACTTATGCTTATTAAGGTTTCTGTCAACACTGCTGCTCGGAAGGAAATCCTAGATATTGCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgtttgtgattgcaattttattatgttagctaacaaaagcatgtgattcctgcagGTTCATGACATTACCCACTCACCTTTTGCTGAAAGGGAACTTATGCTTATTAAGGTTTCTGTCAACACTGCTGCTCGGAAGGAAATCCTAGATATTGCTG
                           agctaac  putative branch site (score: 78)
                                              ttcctgc  putative PPT
             aattttattatgtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagctgcaaaaacttctgtcaaaatcgtttgtgattgcaattttattatgttagctaacaaaagcatgtgattcctgcagGTTCATGACATTACCCACTCACCTTTTGCTGAAAGGGAACTTATGCTTATTAAGGTTTCTGTCAACACTGCTGCTCGGAAGGAAATCCTAGATATTGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA