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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGGATGGAGGCATACTCTGGCCCTCTCCGAGAAGAAAAATGTCTTCTCCTGGGGGAGGGGCACTAGCGGACAGCTCGGCAACGGTGAAATAGTCGACAGgtggttcttaccccgcgcgcgagctctcagtgtctatgtcttcccccgccccttgtaggaacacgcctgtgctgatctgatctgatctgacaactaacgtctcatcatcctgaag

Basic information

species Zea mays
transcript GRMZM2G003565_T02
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G003565_T03 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os04g35570.3 (Oryza sativa), 5'ss of exon 8
GCGGATGGAGGCATACTCTGGCCCTCTCCGAGAAGAAAAATGTCTTCTCCTGGGGGAGGGGCACTAGCGGACAGCTCGGCAACGGTGAAATAGTCGACAGgtggttcttaccccgcgcgcgagctctcagtgtctatgtcttcccccgccccttgtaggaacacgcctgtgctgatctgatctgatctgacaactaacgtctcatcatcctgaag
|||| |||||||||||||| ||  |  | || ||||||||||| ||||| ||||||||||| ||||||||||| || ||  | ||||||||||| |||||||| ||| || |         |  | || ||  | ||    ||   | |||        ||     |  |  || |||  | | |  | ||||   ||   || | |  ||||||
GCGGGTGGAGGCATACTCTTGCATTTACAGAAAAGAAAAATGTTTTCTCATGGGGGAGGGGTACTAGCGGACAACTTGGTCATGGTGAAATAGTTGACAGgtgtttcctatc--------aatatttctgtacccataatatcttgctccc------aaaatgaatcatttttggtcttctgtaaattaacaatctaccattc-tgaatctgaag
















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|29130842|gb|CB381546.1|CB381546
EST:     TGGGGGAGGGGCACTAGCGGACAGCTCGGCAACGGTGAAATAGTCGACAG                         GAACACGCCTGTGCTGATTCGATGCCCTGAGCTCAGACGGCTCTGCCTGCA
genomic: TGGGGGAGGGGCACTAGCGGACAGCTCGGCAACGGTGAAATAGTCGACAGgtggttctta ... catcctgaagGAACACGCCTGTGCTGAT-CGATGCCCTGAGCTCAGACGGTTCTGCCTGCA
EST: gi|211087172|gb|FL255715.1|FL255715
EST:     TGGGGGAGGGGCACTAGCGGACAGCTCGGCAACGGTGAAATAGTCGACAG                         GAACACGCCTGTGCTGATCGATGCCCTGAGCTCAGACGGTTCTGCCTGCAA
genomic: TGGGGGAGGGGCACTAGCGGACAGCTCGGCAACGGTGAAATAGTCGACAGgtggttctta ... catcctgaagGAACACGCCTGTGCTGATCGATGCCCTGAGCTCAGACGGTTCTGCCTGCAA
EST: gi|194716840|gb|FK933999.1|FK933999
EST:     TGGGGGAGGGGCACTAGCGGACAGCTCGGCAACGGTGAAATAGTCGACAG                         GAACACACCTGTGCTGATCGATGCCCTGAGCTCAGATGGTTCTGCCTGCAA
genomic: TGGGGGAGGGGCACTAGCGGACAGCTCGGCAACGGTGAAATAGTCGACAGgtggttctta ... catcctgaagGAACACGCCTGTGCTGATCGATGCCCTGAGCTCAGACGGTTCTGCCTGCAA
EST: gi|60342864|gb|DN209837.1|DN209837
EST:     TGGGGGAGGGGCACTAGCGGACAGCTCGGCAACGGTGAAATAGTCGACAG                         GAACACGCCTGTGCTGATCGATGCCCTGAGCTCAGACGGTTCTGCCTGCAA
genomic: TGGGGGAGGGGCACTAGCGGACAGCTCGGCAACGGTGAAATAGTCGACAGgtggttctta ... catcctgaagGAACACGCCTGTGCTGATCGATGCCCTGAGCTCAGACGGTTCTGCCTGCAA
EST: gi|211471127|gb|FL255671.1|FL255671
EST:     TGGGGGAGGGGCACTAGCGGACAGCTCGGCAACGGTGAAATAGTCGACAG                         GAACACGCCTGTGCTGATCGATGCCCTGAGCTCAGACGGTTCTGCCTGCAA
genomic: TGGGGGAGGGGCACTAGCGGACAGCTCGGCAACGGTGAAATAGTCGACAGgtggttctta ... catcctgaagGAACACGCCTGTGCTGATCGATGCCCTGAGCTCAGACGGTTCTGCCTGCAA
EST: gi|211476174|gb|FL255694.1|FL255694
EST:     TGGGGGAGGGGCACTAGCGGACAGCTCGGCAACGGTGAAATAGTCGACAG                         GAACACACCTGTGCTGATCGATGCCCTGAGCTCARATGGTTCTGCCTGCAA
genomic: TGGGGGAGGGGCACTAGCGGACAGCTCGGCAACGGTGAAATAGTCGACAGgtggttctta ... catcctgaagGAACACGCCTGTGCTGATCGATGCCCTGAGCTCAGACGGTTCTGCCTGCAA
EST: gi|60339276|gb|DN206249.1|DN206249
EST:     TGGGGGAGGGGCACTAGCGGACAGCTCGGCAACGGTGAAATAGTCGACAG                         GAACACGCCTGTGCTGATCGATGCCCTGAGCTCAGACGGTTCTGCCTGCAA
genomic: TGGGGGAGGGGCACTAGCGGACAGCTCGGCAACGGTGAAATAGTCGACAGgtggttctta ... catcctgaagGAACACGCCTGTGCTGATCGATGCCCTGAGCTCAGACGGTTCTGCCTGCAA

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 3 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 45

GCGGATGGAGGCATACTCTGGCCCTCTCCGAGAAGAAAAATGTCTTCTCCTGGGGGAGGGGCACTAGCGGACAGCTCGGCAACGGTGAAATAGTCGACAGgtggttctta ... catcctgaagGAACACGCCTGTGCTGATCGATGCCCTGAGCTCAGACGGTTCTGCCTGCAAGAAGCTGGAGTCATCCACGGCAGCCCCATTCGCAG


Block sizes: 49 (upstream exon), 34 (downstream exon)
Score: 23

GCGGATGGAGGCATACTCTGGCCCTCTCCGAGAAGAAAAATGTCTTCTCCTGGGGGAGGGGCACTAGCGGACAGCTCGGCAACGGTGAAATAGTCGACAGgtggttctta ... catcctgaagGAACACGCCTGTGCTGATCGATGCCCTGAGCTCAGACGGTTCTGCCTGCAAGAAGCTGGAGTCATCCACGGCAGCCCCATTCGCAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 27

GCGGATGGAGGCATACTCTGGCCCTCTCCGAGAAGAAAAATGTCTTCTCCTGGGGGAGGGGCACTAGCGGACAGCTCGGCAACGGTGAAATAGTCGACAGgtggttctta ... catcctgaagGAACACGCCTGTGCTGATCGATGCCCTGAGCTCAGACGGTTCTGCCTGCAAGAAGCTGGAGTCATCCACGGCAGCCCCATTCGCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGGATGGAGGCATACTCTGGCCCTCTCCGAGAAGAAAAATGTCTTCTCCTGGGGGAGGGGCACTAGCGGACAGCTCGGCAACGGTGAAATAGTCGACAGgtggttcttaccccgcgcgcgagctctcagtgtctatgtcttcccccgccccttgtaggaacacgcctgtgctgatctgatctgatctgacaactaacgtctcatcatcctgaag

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