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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacgctggataaccttccctttcacagaatggaaacccgggagattcaatttggttttgtttcaacgcagAGTTAATCCTATGACCCTTGGGTGCATAGCTGCCTCCCTTCTACTCCGGAAAGCTGCGTCACATGCTTTTGAGAAGAACAAGAGATCGACTGTCACCTCT

Basic information

species Zea mays
transcript GRMZM5G840928_T03
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G840928_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os11g17610.1 (Oryza sativa), 3'ss of exon 9
gtaacgctggataacc-ttccctttcac--------agaatggaaacccgggagattcaatttggttttgtttcaacgcagAGTTAATCCTATGACCCTTGGGTGCATAGCTGCCTCCCTTCTACTCCGGAAAGCTGCGTCACATGCTTTTGAGAAGAACAAGAGATCGACTGTCACCTCT
|| | | |  || ||  || ||   |||        |  |||  |       | |||    ||||  ||| | |    ||| || ||||| ||||  ||||||||||| |||| ||| || |||||  |||||||||| ||||||||||||||||||||||||||||| ||||||||| ||
gttatgatcaatcactgtttcccaccactcttgactaccatgatattaaataatatttgcgttggcattggtgcggtacagCGTGAATCCGATGATGCTTGGGTGCATTGCTGGCTCTCTACTACTTAGGAAAGCTGCATCACATGCTTTTGAGAAGAACAAGAGATCAACTGTCACCACT
















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|71763117|gb|DR961054.1|DR961054
EST:     TCATGGGCACGACACTTTGTCTTGACAAACGAAGAACCTACAGAGAAAAG                         AGTTAATCCTATGACCCTTGGGTGCATAGCTGCCTCCCTTCTACTCCGGAA
genomic: TCATGGGCACGACACTTTGTCTTGACAAACGAAGAACCTACAGAGAAAAGgtaacgctgg ... ttcaacgcagAGTTAATCCTATGACCCTTGGGTGCATAGCTGCCTCCCTTCTACTCCGGAA
EST: gi|76282803|gb|DV022371.1|DV022371
EST:     TCATGGGCACGACACTTTGTCTTGACAAACGAAGAACCTACAGAGAAAAG                         AGTTAATCCTATGACCCTTGGGTGCATAGCTGCCTCCCTTCTACTCCGGAA
genomic: TCATGGGCACGACACTTTGTCTTGACAAACGAAGAACCTACAGAGAAAAGgtaacgctgg ... ttcaacgcagAGTTAATCCTATGACCCTTGGGTGCATAGCTGCCTCCCTTCTACTCCGGAA
EST: gi|76018445|gb|DT945615.1|DT945615
EST:     TCATGGGCCCGACACTTTGTCTTGACAAACGAAGAACCTACAGAGAAAAG                         AGTTAATCCTATGACCCTTGGGTGCATAGCTGCCTCCCTTCTACTCCGGAA
genomic: TCATGGGCACGACACTTTGTCTTGACAAACGAAGAACCTACAGAGAAAAGgtaacgctgg ... ttcaacgcagAGTTAATCCTATGACCCTTGGGTGCATAGCTGCCTCCCTTCTACTCCGGAA
EST: gi|76016157|gb|DT943327.1|DT943327
EST:     TCATGGGCACGACACTTTGTCTTGACAAACGAAGAACCTACAGAGAAAAG                         AGTTAATCCTATGACCCTTGGGTGCATAGCTGCCTCCCTTCTACTCCGGAA
genomic: TCATGGGCACGACACTTTGTCTTGACAAACGAAGAACCTACAGAGAAAAGgtaacgctgg ... ttcaacgcagAGTTAATCCTATGACCCTTGGGTGCATAGCTGCCTCCCTTCTACTCCGGAA
EST: gi|60400995|gb|DN233802.1|DN233802
EST:     TCATGGGCACGACACTTTGTCTTGACAAACGAAGAACCTACAGAGAAAAG                         AGTTAATCCTATGACCCTTGGGTGCATAGCTGCCTCCCTTCTACTCCGGAA
genomic: TCATGGGCACGACACTTTGTCTTGACAAACGAAGAACCTACAGAGAAAAGgtaacgctgg ... ttcaacgcagAGTTAATCCTATGACCCTTGGGTGCATAGCTGCCTCCCTTCTACTCCGGAA
EST: gi|211044162|gb|FL460073.1|FL460073
EST:     TCATGGGCACGACACTTTGTCTTGACAAACGAAGAACCTACAGAGAAAAG                         AGTTAATCCTATGACCCTTGGGTGCATAGCTGCCTCCCTTCTACTCCGGAA
genomic: TCATGGGCACGACACTTTGTCTTGACAAACGAAGAACCTACAGAGAAAAGgtaacgctgg ... ttcaacgcagAGTTAATCCTATGACCCTTGGGTGCATAGCTGCCTCCCTTCTACTCCGGAA
EST: gi|94474415|gb|EB703373.1|EB703373
EST:     TCATGGGCACGACACTTTGTCTTGACAAACGAAGAACCTACAGAGAAAAG                         AGTTAATCCTATGACCCTTGGGTGCATAGCTGCCTCCCTTCTACTCCGGAA
genomic: TCATGGGCACGACACTTTGTCTTGACAAACGAAGAACCTACAGAGAAAAGgtaacgctgg ... ttcaacgcagAGTTAATCCTATGACCCTTGGGTGCATAGCTGCCTCCCTTCTACTCCGGAA
EST: gi|71766336|gb|DR964273.1|DR964273
EST:     TCATGGGCACGACACTTTGTCTTGACAAACGAAGAACCTACAGAGAAAAG                         AGTTAATCCTATGACCCTTGGGTGCATAGCTGCCTCCCTTTTACTCCGGAA
genomic: TCATGGGCACGACACTTTGTCTTGACAAACGAAGAACCTACAGAGAAAAGgtaacgctgg ... ttcaacgcagAGTTAATCCTATGACCCTTGGGTGCATAGCTGCCTCCCTTCTACTCCGGAA
EST: gi|211044163|gb|FL460074.1|FL460074
EST:     TCATGGGCACGACACTTTGTCTTGACAAACGAAGAACCTACAGAGAAAAG                         AGTTAATCCTATGACCCTTGGGTGCATAGCTGCCTCCCTTCTACTCCGGAA
genomic: TCATGGGCACGACACTTTGTCTTGACAAACGAAGAACCTACAGAGAAAAGgtaacgctgg ... ttcaacgcagAGTTAATCCTATGACCCTTGGGTGCATAGCTGCCTCCCTTCTACTCCGGAA
EST: gi|32933908|gb|CF038720.1|CF038720
EST:     TCATGGGCACGACACTTTGGCTCGACAAACGAAGAACCTTCAGAGAAAAG                         AGTTAATCCTATGACCCTTGGGTGCATAGCTGCCTCCCTTCTACTCCGGAA
genomic: TCATGGGCACGACACTTTGTCTTGACAAACGAAGAACCTACAGAGAAAAGgtaacgctgg ... ttcaacgcagAGTTAATCCTATGACCCTTGGGTGCATAGCTGCCTCCCTTCTACTCCGGAA
EST: gi|76011914|gb|DT939084.1|DT939084
EST:     TCATGGGCACGACACTTTGTCTTGACAAACGAAGAACCTACAGAGAAAAG                         AGTTAATCCTATGACCCTTGGGTGCATAGCTGCCTCCCTTCTACTCCGGAA
genomic: TCATGGGCACGACACTTTGTCTTGACAAACGAAGAACCTACAGAGAAAAGgtaacgctgg ... ttcaacgcagAGTTAATCCTATGACCCTTGGGTGCATAGCTGCCTCCCTTCTACTCCGGAA
EST: gi|76020591|gb|DT947761.1|DT947761
EST:     TCATGGGCACGACACTTTGTCTTGACAAACGAAGAACCTACAGAGAAAAG                         AGTTAATCCTATGACCCTTGGGTGCATAGCTGCCTCCCTTCTACTCCGGAA
genomic: TCATGGGCACGACACTTTGTCTTGACAAACGAAGAACCTACAGAGAAAAGgtaacgctgg ... ttcaacgcagAGTTAATCCTATGACCCTTGGGTGCATAGCTGCCTCCCTTCTACTCCGGAA
EST: gi|60345505|gb|DN212478.1|DN212478
EST:     TCATGGGCACGACACTTTGGCTTGACAAACGAAGAACCTTCAGAGAAAAG                         AGTTAATCCTATGACCCTTGGGTGCATAGCTGCCTCCCTTCTACTCCGGAA
genomic: TCATGGGCACGACACTTTGTCTTGACAAACGAAGAACCTACAGAGAAAAGgtaacgctgg ... ttcaacgcagAGTTAATCCTATGACCCTTGGGTGCATAGCTGCCTCCCTTCTACTCCGGAA
EST: gi|78122651|gb|DV541035.1|DV541035
EST:     TCATGGGCACGACACTTTGTCTTGACAAACGAAGAACCTACAGAGAAAAG                         AGTTAATCCTATGACCCTTGGGTGCATATCTGCCTCCCTTCTACTCCGGAG
genomic: TCATGGGCACGACACTTTGTCTTGACAAACGAAGAACCTACAGAGAAAAGgtaacgctgg ... ttcaacgcagAGTTAATCCTATGACCCTTGGGTGCATAGCTGCCTCCCTTCTACTCCGGAA
EST: gi|60400210|gb|DN233017.1|DN233017
EST:     TCATGGGCACGACACTTTGTCTTGACAAACGAAGAACCTACAGAGAAAAG                         AGTTAATCCTATGACCCTTGGGTGCATAGCTGCCTCCCTTCTACTCCGGAA
genomic: TCATGGGCACGACACTTTGTCTTGACAAACGAAGAACCTACAGAGAAAAGgtaacgctgg ... ttcaacgcagAGTTAATCCTATGACCCTTGGGTGCATAGCTGCCTCCCTTCTACTCCGGAA
EST: gi|78122650|gb|DV541034.1|DV541034
EST:     TCATGGGCACGACACTTTGTCTTGACAAACGAAGAACCTACAGAGAAAAG                         AGTTAATCCTATGACCCTTGGGTGCATAGCTGCCTCCCTTCTACTCCGGAA
genomic: TCATGGGCACGACACTTTGTCTTGACAAACGAAGAACCTACAGAGAAAAGgtaacgctgg ... ttcaacgcagAGTTAATCCTATGACCCTTGGGTGCATAGCTGCCTCCCTTCTACTCCGGAA
EST: gi|50323071|gb|CO518197.1|CO518197
EST:     TCATGGGCACGACACTTTGTCTTGACAAACGAAGAACCTTCAGAGAAAAG                         AGTTAATCCTATGACCCTTGGGTGCATAGCTGCCTCCCTTTTACTCCGGAA
genomic: TCATGGGCACGACACTTTGTCTTGACAAACGAAGAACCTACAGAGAAAAGgtaacgctgg ... ttcaacgcagAGTTAATCCTATGACCCTTGGGTGCATAGCTGCCTCCCTTCTACTCCGGAA

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: 45 (upstream exon), 48 (downstream exon)
Score: 72

TGTGGCAGTATTTGCATCATGGGCACGACACTTTGTCTTGACAAACGAAGAACCTACAGAGAAAAGgtaacgctgg ... ttcaacgcagAGTTAATCCTATGACCCTTGGGTGCATAGCTGCCTCCCTTCTACTCCGGAAAGCTGCGTCACATGCTTTTGAGAAGAACAAGAGATCGACTGTCACCTCT


Block sizes: 38 (upstream exon), 48 (downstream exon)
Score: 37

TGTGGCAGTATTTGCATCATGGGCACGACACTTTGTCTTGACAAACGAAGAACCTACAGAGAAAAGgtaacgctgg ... ttcaacgcagAGTTAATCCTATGACCCTTGGGTGCATAGCTGCCTCCCTTCTACTCCGGAAAGCTGCGTCACATGCTTTTGAGAAGAACAAGAGATCGACTGTCACCTCT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 40

TGTGGCAGTATTTGCATCATGGGCACGACACTTTGTCTTGACAAACGAAGAACCTACAGAGAAAAGgtaacgctgg ... ttcaacgcagAGTTAATCCTATGACCCTTGGGTGCATAGCTGCCTCCCTTCTACTCCGGAAAGCTGCGTCACATGCTTTTGAGAAGAACAAGAGATCGACTGTCACCTCT


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 48

TGTGGCAGTATTTGCATCATGGGCACGACACTTTGTCTTGACAAACGAAGAACCTACAGAGAAAAGgtaacgctgg ... ttcaacgcagAGTTAATCCTATGACCCTTGGGTGCATAGCTGCCTCCCTTCTACTCCGGAAAGCTGCGTCACATGCTTTTGAGAAGAACAAGAGATCGACTGTCACCTCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccctttcacagaatggaaacccgggagattcaatttggttttgtttcaacgcagAGTTAATCCTATGACCCTTGGGTGCATAGCTGCCTCCCTTCTACTCCGGAAAGCTGCGTCACATGCTTTTGAGAAGAACAAGAGATCGACTGTCACCTCT
                                       ttttgtttc  CT-rich tract
                            attcaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacgctggataaccttccctttcacagaatggaaacccgggagattcaatttggttttgtttcaacgcagAGTTAATCCTATGACCCTTGGGTGCATAGCTGCCTCCCTTCTACTCCGGAAAGCTGCGTCACATGCTTTTGAGAAGAACAAGAGATCGACTGTCACCTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC