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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGACAGACTGTGAAGTGGACTTTGCGCCTCCTCTTGATTATAAAGAACCTGAGAAACCACGACAACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAGgtttgtatttagcatcttggagaaatcatggcctatgaattctgttgatttgttacatgtgcttgttttacagttgatcttatcgttcctatttatatag...

Basic information

species Zea mays
transcript GRMZM2G114220_T02
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G114220_T02 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os04g48770.2 (Oryza sativa), 5'ss of exon 4
GAGACAGACTGTGAAGTGGACTTTGCGCCTCCTCTTGATTATAAAGAACCTGAGAAACCACGACAACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAGgtttgtatttagcatcttggagaaatcatggcctatgaattctgttgatttgttacatgtgcttgttttacagttgatcttatcgttcctatttatatag---
||||| |||||||||||||||||||| |||||||||||||| ||||||||||| || || |  |||||| |||||||||||||  ||||| ||||||||||||||| |||||    ||      |   | |  |    ||    |||  |||  |       || | |     |      || |  |  |     | |     
GAGACGGACTGTGAAGTGGACTTTGCACCTCCTCTTGATTACAAAGAACCTGAAAATCCGCAGCAACCATCAGTTCCTGCAAGTGAGGCAACTGCTGAAGgtttgtctttaga---ttaagtgcactttagttttcagatgaacttgtattgaaaggctgaattttatcctcctcttctatagcaatttttcaagtgtgctgc

upper sequence: GRMZM2G114220_T02 (Zea mays), 5'ss of exon 8
lower sequence: Vv03s0038g00750.t01 (Vitis vinifera), 5'ss of exon 8
---GAGACAGACTGTGAAGTGGACTTTGCGCCTCCTCTTGATTATAAAGAACCTGAGAAACCACGACAACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAGgtttgtatttagcatcttggagaaatcatggcctatgaattctgttgatttgttacatgtgcttgttttacagttg-atcttatcgttcctatttatatag-
   |||||||||||||| ||||| ||||| |||||||||||||  |||||||| || || ||  |     || | |||||     |||||||| | |||||||||    || |       |     |   |||    ||  |||      |||   |   | |  ||   | | ||||  |  ||  | |||| |       |  
ATTGAGACAGACTGTGAGGTGGATTTTGCACCTCCTCTTGATTTCAAAGAACCAGAAAAGCC-TGTTG--CACCTGTTCCCCTGGGCAAGGCAGCAGCTGAAGgtgaacatctcatcagcttatttagctatgtttcatttatttcac--attgtctttctttcattccatcatagttctaggtttccattccaacaagcccact
















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|211226982|gb|FL456596.1|FL456596
EST:     TGAGAAACCACGACAACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAG                         ATGGCAACACTGCAGTGGAGGATGAACCAAAATTCAAACCATTTACTGGTT
genomic: TGAGAAACCACGACAACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAGgtttgtattt ... caacctgcagATGGCAACACTGCAGTGGAGGATGAACCAAAATTCAAACCATTTACTGGTT
EST: gi|76909136|gb|DV163240.1|DV163240
EST:     GAGAAAC-ACCGACAACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAG                         ATGGCAACACTGCAGTGGAGGATGAACCAAAATTCAA-CCATTTACTGGGT
genomic: GAGAAACCAC-GACAACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAGgtttgtattt ... caacctgcagATGGCAACACTGCAGTGGAGGATGAACCAAAATTCAAACCATTTACTGGTT
EST: gi|5080966|gb|AI738228.1|AI738228
EST:     AACCAACAGTTCTTGCAAGCAAGACACCTGCTGAAG                         ATGGCAACACTGCAGCGGAGGATGAACCAAAATTCAAACCATTTACTGGTT
genomic: AACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAGgtttgtattt ... caacctgcagATGGCAACACTGCAGTGGAGGATGAACCAAAATTCAAACCATTTACTGGTT
EST: gi|89251784|gb|DY623570.1|DY623570
EST:     TGAGAAACCACGACAACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAG                         ATGGCAACACTGCAGTGGAGGATGAACCAAAATTCAAACCATTTACTGGTT
genomic: TGAGAAACCACGACAACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAGgtttgtattt ... caacctgcagATGGCAACACTGCAGTGGAGGATGAACCAAAATTCAAACCATTTACTGGTT
EST: gi|37384441|gb|CF629292.1|CF629292
EST:     TGAGAAACCACGACAACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAG                         ATGGCAACACTGCAGTGGAGGATGAACCAAAATTCAAACCATTTACTGGTT
genomic: TGAGAAACCACGACAACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAGgtttgtattt ... caacctgcagATGGCAACACTGCAGTGGAGGATGAACCAAAATTCAAACCATTTACTGGTT
EST: gi|93282993|gb|EB675257.1|EB675257
EST:     AACCAACAGTTCCTGCTAGCAAGGCACCTGCTGAGG                         ATGGCAACACTGCAGTGGAGGATGAACCAAAATTCAAACCATTTACTGGTT
genomic: AACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAGgtttgtattt ... caacctgcagATGGCAACACTGCAGTGGAGGATGAACCAAAATTCAAACCATTTACTGGTT
EST: gi|60355921|gb|DN222894.1|DN222894
EST:     TGAGAAACCACGACAACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAG                         ATGGCAACACTGCAGTGGAGGATGAACCAAAATTCAAACCATTTACTGGTT
genomic: TGAGAAACCACGACAACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAGgtttgtattt ... caacctgcagATGGCAACACTGCAGTGGAGGATGAACCAAAATTCAAACCATTTACTGGTT
EST: gi|211469293|gb|FL298426.1|FL298426
EST:     TGAGAAACCACGACAACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAG                         ATGGCAACACTGCAGTGGAGGATGAACCAAAATTCAAACCATTTACTGGTT
genomic: TGAGAAACCACGACAACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAGgtttgtattt ... caacctgcagATGGCAACACTGCAGTGGAGGATGAACCAAAATTCAAACCATTTACTGGTT
EST: gi|60342371|gb|DN209344.1|DN209344
EST:     TGAGAAACCACGACAACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAG                         ATGGCAACACTGCAGTGGAGGATGAACCAAAATTCAAACCATTTACTGGTT
genomic: TGAGAAACCACGACAACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAGgtttgtattt ... caacctgcagATGGCAACACTGCAGTGGAGGATGAACCAAAATTCAAACCATTTACTGGTT
EST: gi|18174639|gb|BM350027.1|BM350027
EST:     TGAGAAACCACGACAACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAG                         ATGGCAACACTGCAGTGGAGGATGAACCAAAATTCAAACCATTTACTGGTT
genomic: TGAGAAACCACGACAACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAGgtttgtattt ... caacctgcagATGGCAACACTGCAGTGGAGGATGAACCAAAATTCAAACCATTTACTGGTT
EST: gi|14242735|gb|BG840580.2|BG840580
EST:     TGAGAAACCACGACAACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAG                         ATGGCAACACTGCAGTGGAGGATGAACCAAA
genomic: TGAGAAACCACGACAACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAGgtttgtattt ... caacctgcagATGGCAACACTGCAGTGGAGGATGAACCAAA
EST: gi|76909134|gb|DV163239.1|DV163239
EST:     TGAGAAACCACGACAACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAG                         ATGGCAACACTGCAGTGGAGGATGAACCAAAATTCAAACCATTTACTGGTT
genomic: TGAGAAACCACGACAACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAGgtttgtattt ... caacctgcagATGGCAACACTGCAGTGGAGGATGAACCAAAATTCAAACCATTTACTGGTT
EST: gi|32850146|gb|CD989827.1|CD989827
EST:     TGAGAAACCACGACAACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAG                         ATGGCAACACTGCAGTGGAGGATGAACCAAAATTCAAACCATTTACTGGTT
genomic: TGAGAAACCACGACAACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAGgtttgtattt ... caacctgcagATGGCAACACTGCAGTGGAGGATGAACCAAAATTCAAACCATTTACTGGTT
EST: gi|71417924|gb|DR804257.1|DR804257
EST:     TGAGAAACCACGACAACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAG                         ATGGCAACACTGCAGTGGAGGATGACCCAAAAATTCAAACCATTTAC
genomic: TGAGAAACCACGACAACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAGgtttgtattt ... caacctgcagATGGCAACACTGCAGTGGAGGATGAACCAAAA-TTCAAACCATTTAC
EST: gi|60352454|gb|DN219427.1|DN219427
EST:     TGAGAAACCACGACAACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAG                         ATGGCAACACTGCAGTGGAGGATGAACCAAAATTCAAACCATTTACTGGTT
genomic: TGAGAAACCACGACAACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAGgtttgtattt ... caacctgcagATGGCAACACTGCAGTGGAGGATGAACCAAAATTCAAACCATTTACTGGTT
EST: gi|88746722|gb|DY530863.1|DY530863
EST:     TGAGAAACCACGACAACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAG                         ATGGCAACACTGCAGTGGAGGATGAACCAAAATTCAAACCATTTACTGGTT
genomic: TGAGAAACCACGACAACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAGgtttgtattt ... caacctgcagATGGCAACACTGCAGTGGAGGATGAACCAAAATTCAAACCATTTACTGGTT
EST: gi|60399898|gb|DN232708.1|DN232708
EST:     TGAGAAACCACGACAACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAG                         ATGGCAACACTGCAGTGGAGGATGAACCAAAATTCAAACCATTTACTGGTT
genomic: TGAGAAACCACGACAACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAGgtttgtattt ... caacctgcagATGGCAACACTGCAGTGGAGGATGAACCAAAATTCAAACCATTTACTGGTT
EST: gi|28986284|gb|CB351059.1|CB351059
EST:     GAGAAACCACGACANACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAG                         ATGGCAACACTGCAGTGGAGGATGAACCAAAATTCAAACCATTTACTGGTT
genomic: GAGAAACCACGACA-ACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAGgtttgtattt ... caacctgcagATGGCAACACTGCAGTGGAGGATGAACCAAAATTCAAACCATTTACTGGTT
EST: gi|60354663|gb|DN221636.1|DN221636
EST:     TGAGAAACCACGACAACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAG                         ATGGCAACACTGCAGTGGAGGATGAACCAAAATTCAAACCATTTACTGGTT
genomic: TGAGAAACCACGACAACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAGgtttgtattt ... caacctgcagATGGCAACACTGCAGTGGAGGATGAACCAAAATTCAAACCATTTACTGGTT
EST: gi|60350571|gb|DN217544.1|DN217544
EST:     TGAGAAACCACGACAACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAG                         ATGGCAACACTGCAGTGGAGGATGAACCAAAATTCAAACCATTTACTGGTT
genomic: TGAGAAACCACGACAACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAGgtttgtattt ... caacctgcagATGGCAACACTGCAGTGGAGGATGAACCAAAATTCAAACCATTTACTGGTT
EST: gi|60349374|gb|DN216347.1|DN216347
EST:     TGAGAAACCACGACAACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAG                         ATGGCAACACTGCAGTGGAGGATGAACCAAAATTCAAACCATTTACTGGTT
genomic: TGAGAAACCACGACAACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAGgtttgtattt ... caacctgcagATGGCAACACTGCAGTGGAGGATGAACCAAAATTCAAACCATTTACTGGTT
EST: gi|32859778|gb|CD999459.1|CD999459
EST:     ACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAG                         ATGGCAACACTGCAGTGGAGGATGAACCAAAATTCAAACCATTTACTGGTT
genomic: ACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAGgtttgtattt ... caacctgcagATGGCAACACTGCAGTGGAGGATGAACCAAAATTCAAACCATTTACTGGTT
EST: gi|14243258|gb|BG840910.2|BG840910
EST:     TGAGAAACCACGACAACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAG                         ATGGCAACCCTGCAGTGGAGGATGAACCAAAATTCAAACCATTTACTGGTT
genomic: TGAGAAACCACGACAACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAGgtttgtattt ... caacctgcagATGGCAACACTGCAGTGGAGGATGAACCAAAATTCAAACCATTTACTGGTT
EST: gi|60396597|gb|DN229466.1|DN229466
EST:     TGAGAAACCACGACAACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAG                         ATGGCAACACTGCAGTGGAGGATGAACCAAAATTCAAACCATTTACTGGTT
genomic: TGAGAAACCACGACAACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAGgtttgtattt ... caacctgcagATGGCAACACTGCAGTGGAGGATGAACCAAAATTCAAACCATTTACTGGTT
EST: gi|50338445|gb|CO533571.1|CO533571
EST:     TGAGAAACCACGACAACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAG                         ATGGCAACACTGCAGTGGAGGATGAACCAAAATTCAAACCATTTACTGGTT
genomic: TGAGAAACCACGACAACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAGgtttgtattt ... caacctgcagATGGCAACACTGCAGTGGAGGATGAACCAAAATTCAAACCATTTACTGGTT
EST: gi|84970179|gb|DW468529.1|DW468529
EST:     TGAGAAACCACGACAACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAG                         ATGGCAACACTGCAGTGGAGGATGAACCAAAATTCAAACCATTTACTGGTT
genomic: TGAGAAACCACGACAACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAGgtttgtattt ... caacctgcagATGGCAACACTGCAGTGGAGGATGAACCAAAATTCAAACCATTTACTGGTT
EST: gi|60353567|gb|DN220540.1|DN220540
EST:     TGAGAAACCACGACAACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAG                         ATGGCAACACTGCAGTGGAGGATGAACCAAAATTCAAACCATTTACTGGTT
genomic: TGAGAAACCACGACAACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAGgtttgtattt ... caacctgcagATGGCAACACTGCAGTGGAGGATGAACCAAAATTCAAACCATTTACTGGTT

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: 49 (upstream exon), 40 (downstream exon)
Score: 131

GAGACAGACTGTGAAGTGGACTTTGCGCCTCCTCTTGATTATAAAGAACCTGAGAAACCACGACAACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAGgtttgtattt ... caacctgcagATGGCAACACTGCAGTGGAGGATGAACCAAAATTCAAACCATTTACTGGTTTTGGAAAGCGGTTGGATGGAAAAGCCTCAAAACTGCAAGCATCAGAGGT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 133

GAGACAGACTGTGAAGTGGACTTTGCGCCTCCTCTTGATTATAAAGAACCTGAGAAACCACGACAACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAGgtttgtattt ... caacctgcagATGGCAACACTGCAGTGGAGGATGAACCAAAATTCAAACCATTTACTGGTTTTGGAAAGCGGTTGGATGGAAAAGCCTCAAAACTGCAAGCATCAGAGGT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 79

GAGACAGACTGTGAAGTGGACTTTGCGCCTCCTCTTGATTATAAAGAACCTGAGAAACCACGACAACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAGgtttgtattt ... caacctgcagATGGCAACACTGCAGTGGAGGATGAACCAAAATTCAAACCATTTACTGGTTTTGGAAAGCGGTTGGATGGAAAAGCCTCAAAACTGCAAGCATCAGAGGT


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 158

GAGACAGACTGTGAAGTGGACTTTGCGCCTCCTCTTGATTATAAAGAACCTGAGAAACCACGACAACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAGgtttgtattt ... caacctgcagATGGCAACACTGCAGTGGAGGATGAACCAAAATTCAAACCATTTACTGGTTTTGGAAAGCGGTTGGATGGAAAAGCCTCAAAACTGCAAGCATCAGAGGT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGACAGACTGTGAAGTGGACTTTGCGCCTCCTCTTGATTATAAAGAACCTGAGAAACCACGACAACCAACAGTTCCTGCAAGCAAGGCACCTGCTGAAGgtttgtatttagcatcttggagaaatcatggcctatgaattctgttgatttgttacatgtgcttgttttacagttgatcttatcgttcctatttatatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG