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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATAGTTGGTTGGAGAACATCATCGCTTCGACGTCAACATGAATTACCAAAAgtaaagcagcacttcttcttactaaggggcaataaaaatctccatgtgctttaccactaatctgtctataatgtggcctttctttgtttcccag

Basic information

species Zea mays
transcript GRMZM2G008242_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G008242_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os02g54580.1 (Oryza sativa), 5'ss of exon 7
ATATAGTTGGTTGGAGAACATCATCGCTTCGACGTCAACATGAATTACCAAAAgtaaagcagcactt---cttctta--ctaaggggcaataaaaatctccatgtgctttaccact-aatctgtctataatgtggcctttctttgtttcccag
|||||||||| ||||||||||||||  |||| ||||| || |||||||| ||||||||  | || ||   ||| | |   || | |||| || ||   | | ||||||||    || | |   |  ||||| |||||| | | ||  || |||
ATATAGTTGGCTGGAGAACATCATCAATTCGGCGTCAGCACGAATTACCTAAAgtaaattaccatttaaccttttcaatttaggaggcagtacaatgttgc-tgtgcttttatgctcactacattaataatctggcctgtttatgcatctcag
















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|166682627|gb|EG116329.1|EG116329
EST:     TAGTTGGTTGGAGAACATCATCGCTTCGACGTCAACATGAATTACCAAAA                         CTCAAGCTAACAGCAAACGATGAAAAGTATCCTCATGTTATTAA
genomic: TAGTTGGTTGGAGAACATCATCGCTTCGACGTCAACATGAATTACCAAAAgtaaagcagc ... tgtttcccagCTCAAGCTAACAGCAAACGATGAAAAGTATCCTCATATTATTAA
EST: gi|32942178|gb|CF046997.1|CF046997
EST:     ATCATCGCTTCGACGTCAACATGAATTACCAAAA                         CTCAAGCTAACAGCAAACGATGAAAAGTATCCTCATGTTATTAATGTCGAT
genomic: ATCATCGCTTCGACGTCAACATGAATTACCAAAAgtaaagcagc ... tgtttcccagCTCAAGCTAACAGCAAACGATGAAAAGTATCCTCATATTATTAATGTCGAT
EST: gi|40335909|gb|CK369979.1|CK369979
EST:     TAGTTGGTTGGAGAACATCATCGCTTCGACGTCAACATGAATTACCAAAA                         CTCAAGCTAACAGCAAACGATGAAAAGTATCCTCATGTTATTAATGTCGAT
genomic: TAGTTGGTTGGAGAACATCATCGCTTCGACGTCAACATGAATTACCAAAAgtaaagcagc ... tgtttcccagCTCAAGCTAACAGCAAACGATGAAAAGTATCCTCATATTATTAATGTCGAT
EST: gi|37419005|gb|CF647176.1|CF647176
EST:     TAGTTGGTTGGAGAACATCATCGCTTCGACGTCAACATGAATTACCAAAA                         CTCAAGCTAACAGCAAACGATGAAAAGTATCCTCATATTATTAATGTCGAT
genomic: TAGTTGGTTGGAGAACATCATCGCTTCGACGTCAACATGAATTACCAAAAgtaaagcagc ... tgtttcccagCTCAAGCTAACAGCAAACGATGAAAAGTATCCTCATATTATTAATGTCGAT
EST: gi|71433734|gb|DR814784.1|DR814784
EST:     TAGTTGGTTGGAGAACATCATCGCTTCGACGTCAACATGAATTACCAAAA                         CTCAAGCTAACAGCAAACGATGAAAAGTATCCTCATATTATTAATGTCGAT
genomic: TAGTTGGTTGGAGAACATCATCGCTTCGACGTCAACATGAATTACCAAAAgtaaagcagc ... tgtttcccagCTCAAGCTAACAGCAAACGATGAAAAGTATCCTCATATTATTAATGTCGAT
EST: gi|78022444|gb|DV490831.1|DV490831
EST:     TAGTTGGTTGGAGAACATCATCGCTTCGACGTCAACATGAATTACCAAAT                         CTCAAGCTAACAGCAAACGATGAAAAGTATCCTCATGTTATTAATGTCGAT
genomic: TAGTTGGTTGGAGAACATCATCGCTTCGACGTCAACATGAATTACCAAAAgtaaagcagc ... tgtttcccagCTCAAGCTAACAGCAAACGATGAAAAGTATCCTCATATTATTAATGTCGAT
EST: gi|12968783|gb|BG265820.1|BG265820
EST:     TAGTTGGTTGGAGAACATCATCGCTTCGACGTCAACATGAATTACCAAAT                         CTCAAGCTAACAGCAAACGATGAAAAGTATCCTCATGTTATTAATGTCGAT
genomic: TAGTTGGTTGGAGAACATCATCGCTTCGACGTCAACATGAATTACCAAAAgtaaagcagc ... tgtttcccagCTCAAGCTAACAGCAAACGATGAAAAGTATCCTCATATTATTAATGTCGAT
EST: gi|6194474|gb|AW146578.1|AW146578
EST:     TAGTTGGTTGGAGAACATCATCGCTTCGACGTCAACATGAATTACCAAAT                         CTCAAGCTAACAGCAAACGATGAAAAGTATCCTCATGTTATTAATGTCGAT
genomic: TAGTTGGTTGGAGAACATCATCGCTTCGACGTCAACATGAATTACCAAAAgtaaagcagc ... tgtttcccagCTCAAGCTAACAGCAAACGATGAAAAGTATCCTCATATTATTAATGTCGAT
EST: gi|37387733|gb|CF631065.1|CF631065
EST:     TAGTTGGTTGGAGAACATCATCGCTTCGACGTCAACATGAATTACCAAAA                         CTCAAGCTAACAGCAAACGATGAAAAGTATCCTCATGTTATTAATGTCGAT
genomic: TAGTTGGTTGGAGAACATCATCGCTTCGACGTCAACATGAATTACCAAAAgtaaagcagc ... tgtttcccagCTCAAGCTAACAGCAAACGATGAAAAGTATCCTCATATTATTAATGTCGAT

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

ATATAGTTGGTTGGAGAACATCATCGCTTCGACGTCAACATGAATTACCAAAAgtaaagcagc ... tgtttcccagCTCAAGCTAACAGCAAACGATGAAAAGTATCCTCATATTATTAATGTCGATAAAGGAAATCTAGAGGATCATCGGCAAGAGGGATCTGTAGAAGATTCAC


Block sizes: 41 (upstream exon), 38 (downstream exon)
Score: 34

ATATAGTTGGTTGGAGAACATCATCGCTTCGACGTCAACATGAATTACCAAAAgtaaagcagc ... tgtttcccagCTCAAGCTAACAGCAAACGATGAAAAGTATCCTCATATTATTAATGTCGATAAAGGAAATCTAGAGGATCATCGGCAAGAGGGATCTGTAGAAGATTCAC


Block sizes: 44 (upstream exon), 46 (downstream exon)
Score: 34

ATATAGTTGGTTGGAGAACATCATCGCTTCGACGTCAACATGAATTACCAAAAgtaaagcagc ... tgtttcccagCTCAAGCTAACAGCAAACGATGAAAAGTATCCTCATATTATTAATGTCGATAAAGGAAATCTAGAGGATCATCGGCAAGAGGGATCTGTAGAAGATTCAC


Block sizes: 45 (upstream exon), 45 (downstream exon)
Score: 43

ATATAGTTGGTTGGAGAACATCATCGCTTCGACGTCAACATGAATTACCAAAAgtaaagcagc ... tgtttcccagCTCAAGCTAACAGCAAACGATGAAAAGTATCCTCATATTATTAATGTCGATAAAGGAAATCTAGAGGATCATCGGCAAGAGGGATCTGTAGAAGATTCAC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATATAGTTGGTTGGAGAACATCATCGCTTCGACGTCAACATGAATTACCAAAAgtaaagcagcacttcttcttactaaggggcaataaaaatctccatgtgctttaccactaatctgtctataatgtggcctttctttgtttcccag

- - - - - TTGGAG
- - - - -  TGGAGA
- - - - - - GGAGAA