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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtccttaattatcattttcttatcctagatatctctattaattatataagtgaatcctttgttcttatgtaattag

Basic information

species Zea mays
transcript GRMZM2G088974_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G088974_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os12g08270.1 (Oryza sativa), 5'ss of exon 6
ATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtccttaattatcattttcttatcctagatat--ctctattaattatataagtgaatcctttgttcttatg-taattag
|| ||||| || || | ||  |||||||| || ||||||||||||||||| | ||||  |  ||||| || ||||||||  |||  |||||||||||||||||||||  ||   |    | | ||   |   | |      | |||| | | |||| ||||   |  | ||||| |    ||
ATCAGTGTCTGTTCTATCAGCAATCCAGTGGATGCCTCATTCTTTGAATCTTATGAAAGAAAACACTGCATGCGTGATTGCACTTCCTCCATTGCAGAGgttggtccccaaaagttgcatacctaatttgtttctgatatgaataatcacacaagtaaatctgattatattatgcttggcag

upper sequence: GRMZM2G088974_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA08G09180.1 (Glycine max), 5'ss of exon 6
ATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtcctt----------aattatcat-tttcttatcctagatatctctattaattatataagtgaatcctttgttcttatgtaattag-------------------------------
 |   ||| ||    |   |||| ||||  || || ||||| |||||||| ||||||||| ||||||||   | ||| ||| |||||||||||||||| ||    |  |          | ||| ||| ||| |  |  |  |||| | | ||| || |     |   || |||    ||||                                       
GTGCATGTCTGTGATATTGATAACCCAGAGGAAGCATCATTTTTTGAATCTTTTGAAGCAGCACACTCCTCACATGACTTATCTAGCTCCATTGCAGAAgtaatactgttagaactagaagttaacatatttgtcctttttcatattttttttagtttttcttttagctcttttagatttattctgcagacatttcttgaccattattacttcatgaacag

upper sequence: GRMZM2G088974_T01 (Zea mays), 5'ss of exon 6
lower sequence: Vv04s0044g01480.t01 (Vitis vinifera), 5'ss of exon 6
ATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtccttaattatcattttcttatcctagatatctctattaattatataagtgaatcctttgttcttatgtaattag
 |   |||  || |||   | || || |  || || |||||||||||||| ||||||||| ||||||| |||| ||| ||  |||||||||| ||| ||||   |   |  |  |      | | |  | | | ||||| |   ||||||   | | |  ||| |    |         
GTGCATGTCAGCGCCATTGAAAACCCCGAGGAAGCATCATTCTTTGAATCATTTGAAGCAGCACACTCAAAGCATGACTTGTCTAGCTCCATAGCAAAGgt-actgtattgtctttgcagacgtcttattgttctctctgtc--ttatatgcctaattattttctgaacag--------

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|37375807|gb|CF624370.1|CF624370
EST:     CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG                         AAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
genomic: CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
EST: gi|76013309|gb|DT940479.1|DT940479
EST:     CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG                         AAACTTGGTGTCCGAGCTCCTC
genomic: CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTC
EST: gi|32933227|gb|CF038039.1|CF038039
EST:     CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG                         AAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
genomic: CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
EST: gi|60672399|gb|DN475149.1|DN475149
EST:     CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG                         AAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
genomic: CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
EST: gi|32928793|gb|CF033605.1|CF033605
EST:     CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG                         AAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
genomic: CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
EST: gi|113702970|gb|EE680474.1|EE680474
EST:     CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG                         AAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
genomic: CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
EST: gi|101401650|gb|EB822490.1|EB822490
EST:     CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG                         AAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
genomic: CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
EST: gi|5006217|gb|AI712279.1|AI712279
EST:     CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG                         AAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
genomic: CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
EST: gi|71762698|gb|DR960635.1|DR960635
EST:     CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG                         AAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
genomic: CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
EST: gi|88753523|gb|DY537664.1|DY537664
EST:     CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG                         AAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
genomic: CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
EST: gi|50334940|gb|CO530066.1|CO530066
EST:     CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG                         AAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
genomic: CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
EST: gi|9952566|gb|BE639254.1|BE639254
EST:     CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG                         AAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
genomic: CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
EST: gi|32929425|gb|CF034237.1|CF034237
EST:     CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG                         AAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
genomic: CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
EST: gi|89754586|gb|DY685314.1|DY685314
EST:     CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG                         AAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
genomic: CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
EST: gi|86467594|gb|DY233964.1|DY233964
EST:     CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG                         AAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
genomic: CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
EST: gi|50334941|gb|CO530067.1|CO530067
EST:     CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG                         AAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
genomic: CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
EST: gi|6465587|gb|AW191182.1|AW191182
EST:     CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG                         AAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
genomic: CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
EST: gi|211320348|gb|FL456168.1|FL456168
EST:     CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG                         AAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
genomic: CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
EST: gi|93011705|gb|EB637225.1|EB637225
EST:     CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG                         AAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
genomic: CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
EST: gi|9731309|gb|BE510061.1|BE510061
EST:     CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG                         AAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
genomic: CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
EST: gi|71766942|gb|DR964879.1|DR964879
EST:     CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG                         AAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
genomic: CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
EST: gi|40333919|gb|CK367989.1|CK367989
EST:     CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG                         AAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
genomic: CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
EST: gi|44901269|gb|CK827814.1|CK827814
EST:     AAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG                         AAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
genomic: AAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
EST: gi|149080860|gb|EE169940.2|EE169940
EST:     CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG                         AAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
genomic: CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
EST: gi|76013308|gb|DT940478.1|DT940478
EST:     CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG                         AAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
genomic: CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
EST: gi|60338966|gb|DN205939.1|DN205939
EST:     CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG                         AAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
genomic: CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
EST: gi|32929156|gb|CF033968.1|CF033968
EST:     AGCTCCATTGCAGAG                         AAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
genomic: AGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
EST: gi|78075089|gb|DV503523.1|DV503523
EST:     CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG                         AAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT
genomic: CCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATAT

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), 49 (downstream exon)
Score: 143

ATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATATGGTGCCCTAGCACGTGGTGATGGTGCCATTTTTCTGCGCATCCCGCACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 103

ATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATATGGTGCCCTAGCACGTGGTGATGGTGCCATTTTTCTGCGCATCCCGCACA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 60

ATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATATGGTGCCCTAGCACGTGGTGATGGTGCCATTTTTCTGCGCATCCCGCACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 98

ATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtcctt ... atgtaattagAAACTTGGTGTCCGAGCTCCTCCTGTTAGAATGGATAGCCAAGCAAAATATGGTGCCCTAGCACGTGGTGATGGTGCCATTTTTCTGCGCATCCCGCACA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAGgttggtccttaattatcattttcttatcctagatatctctattaattatataagtgaatcctttgttcttatgtaattag

- - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC