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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCAATGTGCAGGGACAGTAGGATAATTCCTGGTGCTGCTGCAACAGAAATAGAGCTGGCAAAGAGATTGAAGGAGTTCTCTTTGAAGGAAACAGGgtaagtttgtttctaccatgatagttaataacttatcatgtacaaggtatgagtacatctgctttcaatatgagcagggttaaccctttgaaagaaaaaatagtttagtggccgacaccatgaagtgttgggttctatattatgttcccctcaatcattcactggttgctcttaacaattgtgcag

Basic information

species Zea mays
transcript GRMZM2G083095_T02
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G083095_T02 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os03g59020.1 (Oryza sativa), 5'ss of exon 10
TCAATGTGCAGGGACAGTAGGATAATTCCTGGTGCTGCTGCAACAGAAATAGAGCTGGCAAAGAGATTGAAGGAGTTCTCTTTGAAGGAAACAGGgtaagtttgtttctaccatgatagttaataacttatcatgtacaaggtatgagtacatctgctttcaatatgagcagggttaaccctttgaaagaaaaaatagtttagtggccgacaccatgaagtgttgggttctatattatgttcccctcaatcattcactggttgctcttaacaattgtgcag
|||||||||||||| ||| |||| |||||||| ||||||||||||||||||||  |||||| |||||||||||| || ||| ||||||||||||||||||| | ||| |       |||  || |  ||    |||  ||  |     || |  |   ||| || |        |||   ||||       | ||   |||  ||                                                                            
TCAATGTGCAGGGATAGTCGGATTATTCCTGGAGCTGCTGCAACAGAAATAGAATTGGCAAGGAGATTGAAGGAATTTTCTCTGAAGGAAACAGGgtaagtatatttgt-------tagacaaaattttcatgtgtggaacatgatgataaaaatatgttccatttt-------ttactacttttggtctgacaaacttttgttgtttc------------------------------------------------------------------------

upper sequence: GRMZM2G083095_T02 (Zea mays), 5'ss of exon 10
lower sequence: Vv08s0007g07460.t01 (Vitis vinifera), 5'ss of exon 10
TCAATGTGCAGGGACAGTAGGATAATTCCTGGTGCTGCTGCAACAGAAATAGAGCTGGCAAAGAGATTGAAGGAGTTCTCTTTGAAGGAAACAGGgtaagtttgtttctaccatgatagttaataacttatcatgtacaaggtatgagtacatctgctttcaatatgagcagggttaaccctttgaaagaaaaaatagtttagtggccgacaccatgaagtgttgggttctatattatgttcccctcaatcattcactggttgctcttaacaattgtgcag
 ||||||||||||||||  ||||  | ||||| ||||| || |||||||| ||||| || |  | ||||||||| |||||||| || || ||||||||  | | | | |    |    | |  | |  |||  || |     | ||  |  |||| || ||| | |  | |   ||     | |     | |||    |                                                                                  
GCAATGTGCAGGGACAGCCGGATTGTGCCTGGAGCTGCAGCTACAGAAATTGAGCTTGCTAGAAAATTGAAGGAATTCTCTTTTAAAGAGACAGGgtatttctttgtttcttcttcctgctg-tgatctatt-tgca-gttctgtggctttatct-ctatcagtctaggaaattttcgatttctcctccacaaagatct----------------------------------------------------------------------------------
















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|148978583|gb|EE026232.2|EE026232
EST:     GAAATAGAGCTGGCAAAGAGATGGAAGGAGTTCTCTTTGAAGGAAACAGG                         GTGGGACCAGTATGCTGTTGCGAAATTTGCTGAAAGCTTTGAAATGGTTCC
genomic: GAAATAGAGCTGGCAAAGAGATTGAAGGAGTTCTCTTTGAAGGAAACAGGgtaagtttgt ... aattgtgcagGTTGGACCAGTATGCTGTTGCGAAATTTGCTGAAAGCTTTGAAATGGTTCC
EST: gi|33092559|gb|CF052553.1|CF052553
EST:     GAAATAGAGCTGGCAAAGAGATTGAAGGAGTTCTCTTTGAAGGAAACAGG                         GTTGGACCAGTATGCTGTTGCGAAATTTGCTGAAAGCTTTGAAATGGTTCC
genomic: GAAATAGAGCTGGCAAAGAGATTGAAGGAGTTCTCTTTGAAGGAAACAGGgtaagtttgt ... aattgtgcagGTTGGACCAGTATGCTGTTGCGAAATTTGCTGAAAGCTTTGAAATGGTTCC
EST: gi|113703848|gb|EE681352.1|EE681352
EST:     GAAATAGAGCTGGCAAAGAGATTGAAGGAGTTCTCTTTGAAGGAAACAGG                         GTTGGACCAGTATGCTGTTGCGAAATTTGCTGAAAGCTTTGAAATGGTTCC
genomic: GAAATAGAGCTGGCAAAGAGATTGAAGGAGTTCTCTTTGAAGGAAACAGGgtaagtttgt ... aattgtgcagGTTGGACCAGTATGCTGTTGCGAAATTTGCTGAAAGCTTTGAAATGGTTCC
EST: gi|60357186|gb|DN224159.1|DN224159
EST:     GTTCTCTTTGAAGGAAACAGG                         GTTGGACCAGTATGCTGTTGCGAAATTTGCTGAAAGCTTTGAAATGGTTCC
genomic: GTTCTCTTTGAAGGAAACAGGgtaagtttgt ... aattgtgcagGTTGGACCAGTATGCTGTTGCGAAATTTGCTGAAAGCTTTGAAATGGTTCC
EST: gi|6626281|gb|AW257813.1|AW257813
EST:     GAAATAGAGCTGGCAAAGAGATTGAAGGAGTTCTCTTTGAAGGAAACAGG                         GTTGGACCAGTATGCTGATGCGAAATTTGCTGAAAGCTTTGAAATGGTTCC
genomic: GAAATAGAGCTGGCAAAGAGATTGAAGGAGTTCTCTTTGAAGGAAACAGGgtaagtttgt ... aattgtgcagGTTGGACCAGTATGCTGTTGCGAAATTTGCTGAAAGCTTTGAAATGGTTCC
EST: gi|60396537|gb|DN229406.1|DN229406
EST:     GAAATAGAGCTGGCAAAGAGATTGAAGGAGTTCTCTTTGAAGGAAACAGG                         GTTGGACCAGTATGCTGTTGCGAAATTTGCTGAAAGCTTTGAAATGGTTCC
genomic: GAAATAGAGCTGGCAAAGAGATTGAAGGAGTTCTCTTTGAAGGAAACAGGgtaagtttgt ... aattgtgcagGTTGGACCAGTATGCTGTTGCGAAATTTGCTGAAAGCTTTGAAATGGTTCC
EST: gi|60358886|gb|DN225859.1|DN225859
EST:     GAAATAGAGCTGGCAAAGAGATTGAAGGAGTTCTCTTTGAAGGAAACAGG                         GTTGGACCAGTATGCTGTTGCGAAATTTGCTGAAAGCTTTGAAATGGTTCC
genomic: GAAATAGAGCTGGCAAAGAGATTGAAGGAGTTCTCTTTGAAGGAAACAGGgtaagtttgt ... aattgtgcagGTTGGACCAGTATGCTGTTGCGAAATTTGCTGAAAGCTTTGAAATGGTTCC
EST: gi|24773918|gb|CA409172.1|CA409172
EST:     GAAATAGAGCTGGCAAAGAGATTGAAGGAGTTCTCTTTGAAGGAAACAGG                         GTTGGACCAGTATGCTGTTGCGAAATTTGCTGAAAGCTTTGAAATGGTTCC
genomic: GAAATAGAGCTGGCAAAGAGATTGAAGGAGTTCTCTTTGAAGGAAACAGGgtaagtttgt ... aattgtgcagGTTGGACCAGTATGCTGTTGCGAAATTTGCTGAAAGCTTTGAAATGGTTCC
EST: gi|211337113|gb|FK966354.1|FK966354
EST:     GAAATAGAGCTGGCAAAGAGATTGAAGGAGTTCTCTTTGAAGGAAACAGG                         GTTGGACCAGTATGCTGTTGCGAAATTTGCTGAAA-STTTGAAATGGTTCC
genomic: GAAATAGAGCTGGCAAAGAGATTGAAGGAGTTCTCTTTGAAGGAAACAGGgtaagtttgt ... aattgtgcagGTTGGACCAGTATGCTGTTGCGAAATTTGCTGAAAGCTTTGAAATGGTTCC
EST: gi|211337111|gb|FK966352.1|FK966352
EST:     AGGAGTTCTCTTTGAAGGAAACAGG                         GTTGGACCAGTATGCTGTTGCGAAATTTGCTGAAA-STTTGAAATGGTTCC
genomic: AGGAGTTCTCTTTGAAGGAAACAGGgtaagtttgt ... aattgtgcagGTTGGACCAGTATGCTGTTGCGAAATTTGCTGAAAGCTTTGAAATGGTTCC
EST: gi|33094754|gb|CF054748.1|CF054748
EST:     GAAATAGAGCTGGCAAAGAGATTGAAGGAGTTCTCTTTGAAGGAAACAGG                         GTTGGACCAGTATGCTGTTGCGAAATTTGCTGAAAGCTTTGAAATGGTTCC
genomic: GAAATAGAGCTGGCAAAGAGATTGAAGGAGTTCTCTTTGAAGGAAACAGGgtaagtttgt ... aattgtgcagGTTGGACCAGTATGCTGTTGCGAAATTTGCTGAAAGCTTTGAAATGGTTCC
EST: gi|13178118|gb|BG349376.1|BG349376
EST:     GAAATAGAGCTGGCAAAGAGATTGAAGGAGTTCTCTTTGAAGGAAACAGG                         GTTGGACCAGTATGCTGTTGCGAAATTTGCTGAAAGCTTTGAAATGGTTCC
genomic: GAAATAGAGCTGGCAAAGAGATTGAAGGAGTTCTCTTTGAAGGAAACAGGgtaagtttgt ... aattgtgcagGTTGGACCAGTATGCTGTTGCGAAATTTGCTGAAAGCTTTGAAATGGTTCC
EST: gi|71431586|gb|DR812636.1|DR812636
EST:     GAAATAGAGCTGGCAAAGAGATTGAAGGAGTTCTCTTTGAAGGAAACAGG                         GTTGGACCAGTATGCTGTTGCGAAATTTGCTGAAAGCTTTGAAATGGTTCC
genomic: GAAATAGAGCTGGCAAAGAGATTGAAGGAGTTCTCTTTGAAGGAAACAGGgtaagtttgt ... aattgtgcagGTTGGACCAGTATGCTGTTGCGAAATTTGCTGAAAGCTTTGAAATGGTTCC
EST: gi|148972050|gb|EE022890.2|EE022890
EST:     GAAATAGAGCTGGCAAAGAGATTGAAGGAGTTCTCTTTGAAGGAAACAGG                         GTTGGACCAGTATGCTGTTGCGAAATTTGCTGAAAGCTTTGAAATGGTTCC
genomic: GAAATAGAGCTGGCAAAGAGATTGAAGGAGTTCTCTTTGAAGGAAACAGGgtaagtttgt ... aattgtgcagGTTGGACCAGTATGCTGTTGCGAAATTTGCTGAAAGCTTTGAAATGGTTCC
EST: gi|211337115|gb|FK966356.1|FK966356
EST:     GAAATAGAGCTGGCAAAGAGATTGAAGGAGTTCTCTTTGAAGGAAACAGG                         GTTGGACCATTATGCTGTTGCGAAATTTGCTGAAAGCTTTGAAATGGTTCC
genomic: GAAATAGAGCTGGCAAAGAGATTGAAGGAGTTCTCTTTGAAGGAAACAGGgtaagtttgt ... aattgtgcagGTTGGACCAGTATGCTGTTGCGAAATTTGCTGAAAGCTTTGAAATGGTTCC
EST: gi|78024594|gb|DV492981.1|DV492981
EST:     GAAATAGAGCTGGCAAAGAGATTGAAGGAGTTCTCTTTGAAGGAAACAGG                         GTTGGACCAGTATGCTGTTGCGAAATTTGCTGAAAGCTTTGAAATGGTTCC
genomic: GAAATAGAGCTGGCAAAGAGATTGAAGGAGTTCTCTTTGAAGGAAACAGGgtaagtttgt ... aattgtgcagGTTGGACCAGTATGCTGTTGCGAAATTTGCTGAAAGCTTTGAAATGGTTCC
EST: gi|91053532|gb|EB163950.1|EB163950
EST:     GAAATAGAGCTGGCAAAGAGATTGAAGGAGTTCTCTTTGAAGGAAACAGG                         GTTGGACCAGTATGCTGTTGCGAAATTTGCTGAAAGCTTTGAAATGGTTCC
genomic: GAAATAGAGCTGGCAAAGAGATTGAAGGAGTTCTCTTTGAAGGAAACAGGgtaagtttgt ... aattgtgcagGTTGGACCAGTATGCTGTTGCGAAATTTGCTGAAAGCTTTGAAATGGTTCC
EST: gi|110194417|gb|EC876315.1|EC876315
EST:     GAAATAGAGCTGGCAAAGAGATTGAAGGAGTTCTCTTTGAAGGAAACAGG                         GTTGGACCAGTATGCTGTTGCGAAATTTGCTGAAAGCTTTGAAATGGTTCC
genomic: GAAATAGAGCTGGCAAAGAGATTGAAGGAGTTCTCTTTGAAGGAAACAGGgtaagtttgt ... aattgtgcagGTTGGACCAGTATGCTGTTGCGAAATTTGCTGAAAGCTTTGAAATGGTTCC
EST: gi|5919524|gb|AW054621.1|AW054621
EST:     AGGAGTTCTCTTTGAAGGAAACAGG                         GTTGGACCAGTATGCTGTTGCGAAATTTGCTGAAAGCTTTGAAATGGTTCC
genomic: AGGAGTTCTCTTTGAAGGAAACAGGgtaagtttgt ... aattgtgcagGTTGGACCAGTATGCTGTTGCGAAATTTGCTGAAAGCTTTGAAATGGTTCC
EST: gi|60337628|gb|DN204601.1|DN204601
EST:     GAAATAGAGCTGGCAAAGAGATTGAAGGAGTTCTCTTTGAAGGAAACAGG                         GTTGGACCAGTATGCTGTTGCGAAATTTGCTGAAAGCTTTGAAATGGTTCC
genomic: GAAATAGAGCTGGCAAAGAGATTGAAGGAGTTCTCTTTGAAGGAAACAGGgtaagtttgt ... aattgtgcagGTTGGACCAGTATGCTGTTGCGAAATTTGCTGAAAGCTTTGAAATGGTTCC
EST: gi|149105114|gb|EE290597.2|EE290597
EST:     GCAAAGAGATTGAAGGAGTTCTCTTTGAAGGAAACAGG                         GTTGGACCAGTATGCTGTTGCGAAATTTGCTGAAAGCTTTGAAATGGTTCC
genomic: GCAAAGAGATTGAAGGAGTTCTCTTTGAAGGAAACAGGgtaagtttgt ... aattgtgcagGTTGGACCAGTATGCTGTTGCGAAATTTGCTGAAAGCTTTGAAATGGTTCC
EST: gi|4885786|gb|AI676906.1|AI676906
EST:     GAAATAGAGCTGGCAAAGAGATTGAAGGAGTTCTCTTTGAAGGAAACAGG                         GTTGGANNCCAGTATGCTNGTTGCGAAATTTGCTGAAAGCTTTGAAATGGT
genomic: GAAATAGAGCTGGCAAAGAGATTGAAGGAGTTCTCTTTGAAGGAAACAGGgtaagtttgt ... aattgtgcagGTTGGA--CCAGTATGCT-GTTGCGAAATTTGCTGAAAGCTTTGAAATGGT

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), 46 (downstream exon)
Score: 212

TCAATGTGCAGGGACAGTAGGATAATTCCTGGTGCTGCTGCAACAGAAATAGAGCTGGCAAAGAGATTGAAGGAGTTCTCTTTGAAGGAAACAGGgtaagtttgt ... aattgtgcagGTTGGACCAGTATGCTGTTGCGAAATTTGCTGAAAGCTTTGAAATGGTTCCAAGAACCCTGGCAGAAAATGCCGGACTTAGCGCAATGGATGTAATATCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 132

TCAATGTGCAGGGACAGTAGGATAATTCCTGGTGCTGCTGCAACAGAAATAGAGCTGGCAAAGAGATTGAAGGAGTTCTCTTTGAAGGAAACAGGgtaagtttgt ... aattgtgcagGTTGGACCAGTATGCTGTTGCGAAATTTGCTGAAAGCTTTGAAATGGTTCCAAGAACCCTGGCAGAAAATGCCGGACTTAGCGCAATGGATGTAATATCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 136

TCAATGTGCAGGGACAGTAGGATAATTCCTGGTGCTGCTGCAACAGAAATAGAGCTGGCAAAGAGATTGAAGGAGTTCTCTTTGAAGGAAACAGGgtaagtttgt ... aattgtgcagGTTGGACCAGTATGCTGTTGCGAAATTTGCTGAAAGCTTTGAAATGGTTCCAAGAACCCTGGCAGAAAATGCCGGACTTAGCGCAATGGATGTAATATCC


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 73

TCAATGTGCAGGGACAGTAGGATAATTCCTGGTGCTGCTGCAACAGAAATAGAGCTGGCAAAGAGATTGAAGGAGTTCTCTTTGAAGGAAACAGGgtaagtttgt ... aattgtgcagGTTGGACCAGTATGCTGTTGCGAAATTTGCTGAAAGCTTTGAAATGGTTCCAAGAACCCTGGCAGAAAATGCCGGACTTAGCGCAATGGATGTAATATCC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCAATGTGCAGGGACAGTAGGATAATTCCTGGTGCTGCTGCAACAGAAATAGAGCTGGCAAAGAGATTGAAGGAGTTCTCTTTGAAGGAAACAGGgtaagtttgtttctaccatgatagttaataacttatcatgtacaaggtatgagtacatctgctttcaatatgagcagggttaaccctttgaaagaaaaaatagtttagtggccgacaccatgaagtgttgggttctatattatgttcccctcaatcattcactggttgctcttaacaattgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA