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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtatatattccccctgctggtatcggtatcggttgcggcagtctggcgagaacgaactagcagcactacccagtcgggtcccgttggtccattgccgatggatatggatttcctgacccgtttccccctgctggtgctggggcaacttcgttgttggtttcagGTTGGCGGTGAAGGAGATTGAACTGCACGGCAGGAATGCCAGGCTG

Basic information

species Zea mays
transcript GRMZM2G057283_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G057283_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g50440.1 (Oryza sativa), 3'ss of exon 2
gtatgtatatattccccctgctggtatcggtatcggttgcggcagtctggcgagaacgaactagcagcactacccagtcgggtcccgttggtccattgccgatggatatggatttcctgacccgtttccccctgctggtgctggggcaacttcgttgttggtttcagGTTGGCGGTGAAGGAGATTGAACTGCACGGCAGGAATGCCAGGCTG
                                                          || || |   ||||   | || |  || ||    ||  |||  ||| ||| || | | || |  |  || ||     |  |            | |||   | |||||| ||||| || ||||||||||| |||||||||||||| |||||  ||
-------------------------------------------------------gtaaattaacgcaacta---aatctgaccctgt----cccatgc--atgcatacgggtatactaaatcaatttccttgattcat------------ttgttac-gttttcagATTGGCCGTCAAGGAGATTGACCTGCACGGCAGGAACGCCAGATTG
















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|91871799|gb|EB401756.1|EB401756
EST:     GCGGCCTCCGCCGGGTTCATTGCCTGGACGCTCACCCTGCTCGCCATGGG                         GTTGGCGGTGAAGGAGATTGAACTGCACGGCAGGAATGCCAGGCTG
genomic: GCGGCCTCCGCCGGGTTCATTGCCTGGACGCTCACCCTGCTCGCCATGGGgtatgtatat ... ttggtttcagGTTGGCGGTGAAGGAGATTGAACTGCACGGCAGGAATGCCAGGCTG
EST: gi|78089270|gb|DV517644.1|DV517644
EST:     GCGGCCTCCGCCGGGTTCATTGCCTGGACGCTCACCCTGCTCGCCATGGG                         GTTGGCGGTGAAGGAGATTGAACTGCACGGCAGGAATGCCAGGCTG
genomic: GCGGCCTCCGCCGGGTTCATTGCCTGGACGCTCACCCTGCTCGCCATGGGgtatgtatat ... ttggtttcagGTTGGCGGTGAAGGAGATTGAACTGCACGGCAGGAATGCCAGGCTG
EST: gi|211368356|gb|FL375187.1|FL375187
EST:     GCGGCCTCCGCCGGGTTCATTGCCTGGACGCTCACCCTGCTCGCCATGGG                         GTTGGCGGTGAAAGAGATTGAACTGCACGGCAGGAATGCCAGGCTG
genomic: GCGGCCTCCGCCGGGTTCATTGCCTGGACGCTCACCCTGCTCGCCATGGGgtatgtatat ... ttggtttcagGTTGGCGGTGAAGGAGATTGAACTGCACGGCAGGAATGCCAGGCTG
EST: gi|91871798|gb|EB401755.1|EB401755
EST:     GCGGCCTCCGCCGGGTTCATTGCCTGGACGCTCACCCTGCTCGCCATGGG                         GTTGGCGGTGAAGGAGATTGAACTGCACGGCAGGAATGCCAGGCTG
genomic: GCGGCCTCCGCCGGGTTCATTGCCTGGACGCTCACCCTGCTCGCCATGGGgtatgtatat ... ttggtttcagGTTGGCGGTGAAGGAGATTGAACTGCACGGCAGGAATGCCAGGCTG
EST: gi|78089269|gb|DV517643.1|DV517643
EST:     GCGGCCTCCGCCGGGTTCATTGCCTGGACGCTCACCCTGCTCGCCATGGG                         GTTGGCGGTGAAGGAGATTGAACTGCACGGCAGGAATGCCAGGCTG
genomic: GCGGCCTCCGCCGGGTTCATTGCCTGGACGCTCACCCTGCTCGCCATGGGgtatgtatat ... ttggtttcagGTTGGCGGTGAAGGAGATTGAACTGCACGGCAGGAATGCCAGGCTG
EST: gi|4314713|gb|AI438625.2|AI438625
EST:     GCGGCCTCCGCCGGGTTCATTGCCTGGACGCTCACCCTGCTCGCCATGGG                         GTTGGCGGTGAAGGAGATTGAACTGCACGGCAGGAATGCCAGGCTG
genomic: GCGGCCTCCGCCGGGTTCATTGCCTGGACGCTCACCCTGCTCGCCATGGGgtatgtatat ... ttggtttcagGTTGGCGGTGAAGGAGATTGAACTGCACGGCAGGAATGCCAGGCTG
EST: gi|16925336|gb|BM078404.1|BM078404
EST:     GCGGCCTCCGCCGGGTTCATTGCCTGGACGCTCACCCTGCTCGCCATGGG                         GTTGGCGGTGAAGGAGATTGAACTGCACGGCAGGAATGCCAGGCTG
genomic: GCGGCCTCCGCCGGGTTCATTGCCTGGACGCTCACCCTGCTCGCCATGGGgtatgtatat ... ttggtttcagGTTGGCGGTGAAGGAGATTGAACTGCACGGCAGGAATGCCAGGCTG
EST: gi|14244256|gb|BG842235.2|BG842235
EST:     GCGGCCTCCGCCGGGTTCATTGCCTGGACGCTCACCCTGCTCGCCATGGG                         GTTGGCGGTGAAGGAGATTGAACTGCACGGCAGGAATGCCAGGCTG
genomic: GCGGCCTCCGCCGGGTTCATTGCCTGGACGCTCACCCTGCTCGCCATGGGgtatgtatat ... ttggtttcagGTTGGCGGTGAAGGAGATTGAACTGCACGGCAGGAATGCCAGGCTG

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: 46 (upstream exon), 17 (downstream exon)
Score: 8

TCGCGGGGTTCCACCACGTCCGCGCCTGGAACGCCGAGAGCCTGCCGGCGGCGGCCTCCGCCGGGTTCATTGCCTGGACGCTCACCCTGCTCGCCATGGGgtatgtatat ... ttggtttcagGTTGGCGGTGAAGGAGATTGAACTGCACGGCAGGAATGCCAGGCTG


Block sizes: 46 (upstream exon), 42 (downstream exon)
Score: 18

TCGCGGGGTTCCACCACGTCCGCGCCTGGAACGCCGAGAGCCTGCCGGCGGCGGCCTCCGCCGGGTTCATTGCCTGGACGCTCACCCTGCTCGCCATGGGgtatgtatat ... ttggtttcagGTTGGCGGTGAAGGAGATTGAACTGCACGGCAGGAATGCCAGGCTG


Block sizes: 42 (upstream exon), 46 (downstream exon)
Score: 51

TCGCGGGGTTCCACCACGTCCGCGCCTGGAACGCCGAGAGCCTGCCGGCGGCGGCCTCCGCCGGGTTCATTGCCTGGACGCTCACCCTGCTCGCCATGGGgtatgtatat ... ttggtttcagGTTGGCGGTGAAGGAGATTGAACTGCACGGCAGGAATGCCAGGCTG


Block sizes: 24 (upstream exon), 28 (downstream exon)
Score: 3

TCGCGGGGTTCCACCACGTCCGCGCCTGGAACGCCGAGAGCCTGCCGGCGGCGGCCTCCGCCGGGTTCATTGCCTGGACGCTCACCCTGCTCGCCATGGGgtatgtatat ... ttggtttcagGTTGGCGGTGAAGGAGATTGAACTGCACGGCAGGAATGCCAGGCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcctgacccgtttccccctgctggtgctggggcaacttcgttgttggtttcagGTTGGCGGTGAAGGAGATTGAACTGCACGGCAGGAATGCCAGGCTG
  tcctgac  putative branch site (score: 3)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtatatattccccctgctggtatcggtatcggttgcggcagtctggcgagaacgaactagcagcactacccagtcgggtcccgttggtccattgccgatggatatggatttcctgacccgtttccccctgctggtgctggggcaacttcgttgttggtttcagGTTGGCGGTGAAGGAGATTGAACTGCACGGCAGGAATGCCAGGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT