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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcttacaaccgaaaaggaaaatctagcaatacattagtatgtttgccctgtatgatgtaattcatggtcgctagtcatttaaatgcgcatcttttatagGATCGGGAAATGTGCGAATGGGGTTTGCTAGTCAGGATGTGCCATTCAATATACCACATTGCATTGCCCGACACATCAATCCACAAGAGGGCGAAGAACC

Basic information

species Zea mays
transcript GRMZM2G101250_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G101250_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os04g09860.1 (Oryza sativa), 3'ss of exon 2
tgcttacaaccgaaaaggaaaatctagcaatacattagtatgtttgccctgtatgatgtaattcatggtcgctagtcatttaaatgcgcatcttttatagGATCGGGAAATGTGCGAATGGGGTTTGCTAGTCAGGATGTGCCATTCAATATACCACATTGCATTGCCCGACACATCAATCCACAAGAGGGCGAAGAACC
| |  |  | | |   |       || | | |      | || |  |  |  |    ||| ||  |    |||   || | || |   | | || | |||||||   ||||||||| || ||||| || ||||||||||| |||||||||||||| || |||||||| ||||| |||| ||  ||  |||  ||   |||
ttcgcagcagctaggtgcctgccttatctagatgcagttttgctgccagttcaattcgtagttgctttcagctgaccaatcaattatccgtgttctctagGATCTTCAAATGTGCGCATTGGGTTCGCAAGTCAGGATGTTCCATTCAATATACCGCACTGCATTGCTCGACATATCACTCAGCAGAAGGATGATACACC
















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|211065118|gb|FL021085.1|FL021085
EST:     GTCACAACTCTTGGCAGAGCGCGGCTCCAATCTTGTCGTCATCAACCCAG                         GATCGGGAAATGTGCGAATGGGGTTTGCTAGTCAGGATGTGCCATTCAATA
genomic: GTCACAACTCTTGGCAGAGCGCGGCTCCAATCTTGTCGTCATCAACCCAGgttcggccct ... tcttttatagGATCGGGAAATGTGCGAATGGGGTTTGCTAGTCAGGATGTGCCATTCAATA
EST: gi|211065127|gb|FL021094.1|FL021094
EST:     GTCACAACTCTTGGCAGAGCGCGGCTCCAATCTTGTCGTCATCAACCCAG                         GATCGGGAAATGTGCGAATGGGGTTTGCTAGTCAGGATGTGCCATTCAATA
genomic: GTCACAACTCTTGGCAGAGCGCGGCTCCAATCTTGTCGTCATCAACCCAGgttcggccct ... tcttttatagGATCGGGAAATGTGCGAATGGGGTTTGCTAGTCAGGATGTGCCATTCAATA
EST: gi|211065129|gb|FL021096.1|FL021096
EST:     GTCACAACTCTTGGCAGAGCGCGGCTCCNATCTTGTCGTCATCAACCCAG                         GATCGGGAAATGTGCGAATGGGGTTTGCTAGTCAGGATGTGCCATTCAATA
genomic: GTCACAACTCTTGGCAGAGCGCGGCTCCAATCTTGTCGTCATCAACCCAGgttcggccct ... tcttttatagGATCGGGAAATGTGCGAATGGGGTTTGCTAGTCAGGATGTGCCATTCAATA
EST: gi|211065122|gb|FL021089.1|FL021089
EST:     GTCACAACTCTTGGCAGAGCGCGGCTCCAATCTTGTCGTCATCAACCCAG                         GATCGGGAAATGTGCGAATGGGGTTTGCTAGTCAGGATGTGCCATTCAATA
genomic: GTCACAACTCTTGGCAGAGCGCGGCTCCAATCTTGTCGTCATCAACCCAGgttcggccct ... tcttttatagGATCGGGAAATGTGCGAATGGGGTTTGCTAGTCAGGATGTGCCATTCAATA
EST: gi|211067851|gb|FL021097.1|FL021097
EST:     GTCACAACTCTTGGCAGAGCGCGGCTCCAATCTTGTCGTCATCAACCCAG                         GATCGGGAAATGTGCGAATGGGGTTTGCTAGTCAGGATGTGCCATTCAATA
genomic: GTCACAACTCTTGGCAGAGCGCGGCTCCAATCTTGTCGTCATCAACCCAGgttcggccct ... tcttttatagGATCGGGAAATGTGCGAATGGGGTTTGCTAGTCAGGATGTGCCATTCAATA
EST: gi|211065128|gb|FL021095.1|FL021095
EST:     GTCACAACTCTTGGCAGAGCGCGGCTCCAATCTTGTCGTCATCAACCCAG                         GATCGGGAAATGTGCGAATGGGGTTTGCTAGTCAGGATGTGCCATTCAATA
genomic: GTCACAACTCTTGGCAGAGCGCGGCTCCAATCTTGTCGTCATCAACCCAGgttcggccct ... tcttttatagGATCGGGAAATGTGCGAATGGGGTTTGCTAGTCAGGATGTGCCATTCAATA
EST: gi|211065119|gb|FL021086.1|FL021086
EST:     GTCACAACTCTTGGCAGAGCGCGGCTCCAATCTTGTCGTCATCAACCCAG                         GATCGGGAAATGTGCGAATGGGGTTTGCTAGTCAGGATGTGCCATTCAATA
genomic: GTCACAACTCTTGGCAGAGCGCGGCTCCAATCTTGTCGTCATCAACCCAGgttcggccct ... tcttttatagGATCGGGAAATGTGCGAATGGGGTTTGCTAGTCAGGATGTGCCATTCAATA
EST: gi|91056341|gb|EB166759.1|EB166759
EST:     GTCACAACTCTTGGCAGAGCGCGGCTCCAATCTTGTCGTCATCAACCCAG                         GATCGGGAAATGTGCGAATGGGGTTTGCTAGTCAGGATGTGCCATTCAATA
genomic: GTCACAACTCTTGGCAGAGCGCGGCTCCAATCTTGTCGTCATCAACCCAGgttcggccct ... tcttttatagGATCGGGAAATGTGCGAATGGGGTTTGCTAGTCAGGATGTGCCATTCAATA
EST: gi|211065125|gb|FL021092.1|FL021092
EST:     GTCACAACTCTTGGCAGAGCGCGGCTCCAATCTTGTCGTCATCAACCCAG                         GATCGGGAAATGTGCGAATGGGGTTTGCTAGTCAGGATGTGCCATTCAATA
genomic: GTCACAACTCTTGGCAGAGCGCGGCTCCAATCTTGTCGTCATCAACCCAGgttcggccct ... tcttttatagGATCGGGAAATGTGCGAATGGGGTTTGCTAGTCAGGATGTGCCATTCAATA
EST: gi|148934269|gb|EC878292.2|EC878292
EST:     GTCACAACTCTTGGCAGAGCGCGGCTCCAATCTTGTCGTCATCAACCCAG                         GATCGGGAAATGTGCGAATGGGGTTTGCTAGTCAGGATGTGCCATTCAATA
genomic: GTCACAACTCTTGGCAGAGCGCGGCTCCAATCTTGTCGTCATCAACCCAGgttcggccct ... tcttttatagGATCGGGAAATGTGCGAATGGGGTTTGCTAGTCAGGATGTGCCATTCAATA

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 1 RNA-Seqlibrary.


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 2

GACTACCTCAGGACGGTGGTTCCGTCACAACTCTTGGCAGAGCGCGGCTCCAATCTTGTCGTCATCAACCCAGgttcggccct ... tcttttatagGATCGGGAAATGTGCGAATGGGGTTTGCTAGTCAGGATGTGCCATTCAATATACCACATTGCATTGCCCGACACATCAATCCACAAGAGGGCGAAGAACC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccctgtatgatgtaattcatggtcgctagtcatttaaatgcgcatcttttatagGATCGGGAAATGTGCGAATGGGGTTTGCTAGTCAGGATGTGCCATTCAATATACCACATTGCATTGCCCGACACATCAATCCACAAGAGGGCGAAGAACC
                                           catctttt  CT-rich tract
                              tcatttaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcttacaaccgaaaaggaaaatctagcaatacattagtatgtttgccctgtatgatgtaattcatggtcgctagtcatttaaatgcgcatcttttatagGATCGGGAAATGTGCGAATGGGGTTTGCTAGTCAGGATGTGCCATTCAATATACCACATTGCATTGCCCGACACATCAATCCACAAGAGGGCGAAGAACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC