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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgtttacagagtagcatgctcatggtcatgtgatgaccattgaggattatgcattgtacctgtgctccgggcattacctagttactcacatacgattacaatagctagattatgaatttggaaacataaatgatttgttttgtgtaatttcgcaaaaggtcttatgttttggtgtcttatttttttttctgcagAATGTTCACCATGCTGGTCAGCCTATGCCTGGTGAGGAACAGGAGGACATTGTCATGACTAGCACTCAGATGAGCATCTTAAATGTCACATGCCCATTAA

Basic information

species Zea mays
transcript GRMZM2G022065_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G022065_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g48880.1 (Oryza sativa), 3'ss of exon 4
gtatgtgtttacagagtagcatgctcatggtcatgtgatgaccattgaggattatgcattgtacctgtgctccgggcattacctagttactcacatacgattacaatagctagattatgaatttggaaacataaatgatttgttttgtgtaatttcgcaaaaggtcttatgttttggtgtcttatttttttttctgcagAATGTTCACCATGCTGGTCAGCCTATGCCTGGTGAGGAACAGGAGGACATTGTCATGACTAGCACTCAGATGAGCATCTTAAATGTCACATGCCCATTAA
                                                                                          | |  || | |  |   |  ||| | |||  || |  ||  |||| | |||||   |  | | |||   ||   | || | | |  ||   || | || | |||| |||||||||||||||||||| || || ||||||||||| |||||||||||  || | ||||| || || || |  ||||||||||||||||| ||||||||||
------------------------------------------------------------------------------------------tta-gtatggtatctccaa-taggtcatgt-ttggagaaagtaaaaggtttgt---gcattacttct--aattattttctctctctgtaa-ttgtgttgtcttctacagAATGTTCACCATGCTGGCCAACCAATGCCTGGTGATGAACAGGAGGATGTTCTTATGACCAGTACCCAAACTAGCATCTTAAATGTCACGTGCCCATTAA

upper sequence: GRMZM2G022065_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT3G15150.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatgtgtttacagagtagcatgctcatggtcatgtgatgaccattgaggattatgcattgtacctgtgctccgggcattacctagttactcacatacgattacaatagctagattatgaatttggaaacataaatgatttgttttgtgtaatttcgcaaaaggtcttatgttttggtgtcttatt--tttttttctgcagAATGTTCACCATGCTGGTCAGCCTATGCCTGGTGAGGAACAGGAGGACATTGTCATGACTAGCACTCAGATGAGCATCTTAAATGTCACATGCCCATTAA
                                                                                                              ||  || | || ||  |    |   ||  |||| |    ||  |    |    |  ||   ||||    | || |   | |||| |||||||||||||| ||||| ||| | || ||||||||||| ||  | ||||||||||| ||||| || ||||||       |  ||||  | ||||| || || |
-------------------------------------------------------------------------------------------------------------gtatgtttttaacttaaagttct---tggcttgtatctaataggtctatagtccgatttcctttttaagttattgtcaatgttttgctgcagAATGTTCATCATGCAGGTGAACCAATGCCTGGTGACGATGATGAGGACATTGTTATGACCAGTACTCAGTGCCCTCTTCTAAACATGACATGTCCCTTGA

upper sequence: GRMZM2G022065_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv19s0014g02100.t01 (Vitis vinifera), 3'ss of exon 4
gtatgtgtttacagagtagcatgctcatggtcatgtgatgaccattgaggattatgcattgtacctgtgctccgggcattacctagttactcacatacgattacaatagctagattatgaatttggaaacataaatgatttgttttgtgtaatttcgcaaaaggtcttatgttttggtgtcttatttttttttctgcagAATGTTCACCATGCTGGTCAGCCTATGCCTGGTGAGGAACAGGAGGACATTGTCATGACTAGCACTCAGATGAGCATCTTAAATGTCACATGCCCATTAA
                                                                                                   |||| |||    | |  ||   | ||    ||  | | |||| |    | || |||  | |||  |||||| |  || |||  |   | || | |||||||||||||||||||| || ||||| ||||| ||||| || |||||||||||||| ||||| || || ||    | | |||| ||| | || ||||||||||
------------------------------------------------------------------------------------------------ttcattataatgtgaatagaatttctctgttgtcaagagtaatttctcgaatttattttttctaaa--tcttatataatg-tgttctcactattctcctgcagAATGTTCACCATGCAGGACAGCCAATGCCAGGTGATGAGCAGGAGGACATTGTAATGACCAGTACACAATGCAACCTCTTGAATATTACTTGCCCATTAA

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|5439456|gb|AI820377.1|AI820377
EST:     CATCACAACAGAACCACCCACTCTTTCGGCAGTTCAGGGAGTCTGTCTGG                         AATGTTCACCATGCTGGTCAGCCTATGCCTGGTGAGGAACAGGAGGACATT
genomic: CATCACAACAGAACCACCCACTCTTTCGGCAGTTCAGGGAGTCTGTCTGGgtatgtgttt ... ttttctgcagAATGTTCACCATGCTGGTCAGCCTATGCCTGGTGAGGAACAGGAGGACATT
EST: gi|71758566|gb|DR956503.1|DR956503
EST:     CATCACAACAGAACCACCCACTCTTTCGGCAGTTCAGGGAGTCTGTCTGG                         AATGTTCACCATGCTGGTCAGCCTATGCCTGGTGAGGAACAGGAGGACATT
genomic: CATCACAACAGAACCACCCACTCTTTCGGCAGTTCAGGGAGTCTGTCTGGgtatgtgttt ... ttttctgcagAATGTTCACCATGCTGGTCAGCCTATGCCTGGTGAGGAACAGGAGGACATT
EST: gi|67023801|gb|CO452550.1|CO452550
EST:     CATCACAACAGAACCACCCACTCTTTCGGCAGTTCAGGGAGTCTGTCTGG                         AATGTTCACCATGCTGGTCAGCCTATGCCTGGTGAGGAACAGGAGGACATT
genomic: CATCACAACAGAACCACCCACTCTTTCGGCAGTTCAGGGAGTCTGTCTGGgtatgtgttt ... ttttctgcagAATGTTCACCATGCTGGTCAGCCTATGCCTGGTGAGGAACAGGAGGACATT
EST: gi|71437320|gb|DR818370.1|DR818370
EST:     CATCACAACAGAACCACCCACTCTTTCGGCAGTTCAGGGAGTCTGTCTGG                         AATGTTCACCATGCTGGTCAGCCTATGCCTGGTGAGGAACAGGAGGACATT
genomic: CATCACAACAGAACCACCCACTCTTTCGGCAGTTCAGGGAGTCTGTCTGGgtatgtgttt ... ttttctgcagAATGTTCACCATGCTGGTCAGCCTATGCCTGGTGAGGAACAGGAGGACATT
EST: gi|33285491|gb|CF075286.1|CF075286
EST:     CATCACAACAGAACCACCCACTCTTTCGGCAGTTCAGGGAGTCTGTCTGG                         AATGTTCACCATGCTGGTCAGCCTATGCCTGGTGAGGAACAGGAGGACATT
genomic: CATCACAACAGAACCACCCACTCTTTCGGCAGTTCAGGGAGTCTGTCTGGgtatgtgttt ... ttttctgcagAATGTTCACCATGCTGGTCAGCCTATGCCTGGTGAGGAACAGGAGGACATT
EST: gi|76918178|gb|DV167176.1|DV167176
EST:     CATCACAACAGAACCACCCACTCTTTCGGCAGTTCAGGGAGTCTGTCTGG                         AATGTTCACCATGCTGGTCAGCCTATGCCTGGTGAGGAACAGGAGGACATT
genomic: CATCACAACAGAACCACCCACTCTTTCGGCAGTTCAGGGAGTCTGTCTGGgtatgtgttt ... ttttctgcagAATGTTCACCATGCTGGTCAGCCTATGCCTGGTGAGGAACAGGAGGACATT
EST: gi|211006591|gb|FL191428.1|FL191428
EST:     CATCACAACAGAACCACCCACTCTTTCGGCAGTTCAGGGAGTCTGTCTGG                         AATGTTCACCATGCTGGTCAGCCTATGCCTGGTGAGGAACAGGAGGACATT
genomic: CATCACAACAGAACCACCCACTCTTTCGGCAGTTCAGGGAGTCTGTCTGGgtatgtgttt ... ttttctgcagAATGTTCACCATGCTGGTCAGCCTATGCCTGGTGAGGAACAGGAGGACATT
EST: gi|78025758|gb|DV494145.1|DV494145
EST:     CATCACAACAGAACCACCCACTCTTTCGGCAGTTCAGGGAGTCTGTCTGG                         AATGTTCACCATGCTGGTCAGCCTATGCCTGGTGAGGAACAGGAGGACATT
genomic: CATCACAACAGAACCACCCACTCTTTCGGCAGTTCAGGGAGTCTGTCTGGgtatgtgttt ... ttttctgcagAATGTTCACCATGCTGGTCAGCCTATGCCTGGTGAGGAACAGGAGGACATT
EST: gi|37391616|gb|CF633052.1|CF633052
EST:     CATCACAACAGAACCACCCACTCTTTCGGCAGTTCAGGGAGTCTGTCTGG                         AATGTTCACCATGCTGGTCAGCCTATGCCTGGTGAGGAACAGGAGGACATT
genomic: CATCACAACAGAACCACCCACTCTTTCGGCAGTTCAGGGAGTCTGTCTGGgtatgtgttt ... ttttctgcagAATGTTCACCATGCTGGTCAGCCTATGCCTGGTGAGGAACAGGAGGACATT
EST: gi|5455912|gb|AI833602.1|AI833602
EST:     TCGGCAGTTCAGGGAGTCTGTCTGG                         AATGTTCACCATGCTGGTCAGCCTATGCCTGGTGAGGAACAGGAGGACATT
genomic: TCGGCAGTTCAGGGAGTCTGTCTGGgtatgtgttt ... ttttctgcagAATGTTCACCATGCTGGTCAGCCTATGCCTGGTGAGGAACAGGAGGACATT
EST: gi|76918177|gb|DV167175.1|DV167175
EST:     AGTTCAGGGAGTCTGTCTGG                         AATGTTCACCATGCTGGTCAGCCTATGCCTGGTGAGGAACAGGAGGACATT
genomic: AGTTCAGGGAGTCTGTCTGGgtatgtgttt ... ttttctgcagAATGTTCACCATGCTGGTCAGCCTATGCCTGGTGAGGAACAGGAGGACATT
EST: gi|71428156|gb|DR809206.1|DR809206
EST:     CATCACAACAGAACCACCCACTCTTTCGGCAGTTCAGGGAGTCTGTCTGG                         AATGTTCACCATGCTGGTCA
genomic: CATCACAACAGAACCACCCACTCTTTCGGCAGTTCAGGGAGTCTGTCTGGgtatgtgttt ... ttttctgcagAATGTTCACCATGCTGGTCA
EST: gi|60348363|gb|DN215336.1|DN215336
EST:     CATCACAACAGAACCACCCACTCTTTCGGCAGTTCAGGGAGTCTGTCTGG                         AATGTTCACCATGCTGGTCAGCCTATGCCTGGTGAGGAACAGGAGGACATT
genomic: CATCACAACAGAACCACCCACTCTTTCGGCAGTTCAGGGAGTCTGTCTGGgtatgtgttt ... ttttctgcagAATGTTCACCATGCTGGTCAGCCTATGCCTGGTGAGGAACAGGAGGACATT
EST: gi|71436348|gb|DR817398.1|DR817398
EST:     CATCACAACAGAACCACCCACTCTTTCGGCAGTTCAGGGAGTCTGTCTGG                         AATGTTCACCATGCTGGTCAGCCTATGCCTGGTGAGGAACAGGAGGACATT
genomic: CATCACAACAGAACCACCCACTCTTTCGGCAGTTCAGGGAGTCTGTCTGGgtatgtgttt ... ttttctgcagAATGTTCACCATGCTGGTCAGCCTATGCCTGGTGAGGAACAGGAGGACATT

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: 169

CAAAACATTGATCGGGGTGGAGGCTAGCAAGATTAGGGAAGCGTCATCGGCATCACAACAGAACCACCCACTCTTTCGGCAGTTCAGGGAGTCTGTCTGGgtatgtgttt ... ttttctgcagAATGTTCACCATGCTGGTCAGCCTATGCCTGGTGAGGAACAGGAGGACATTGTCATGACTAGCACTCAGATGAGCATCTTAAATGTCACATGCCCATTAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 67

CAAAACATTGATCGGGGTGGAGGCTAGCAAGATTAGGGAAGCGTCATCGGCATCACAACAGAACCACCCACTCTTTCGGCAGTTCAGGGAGTCTGTCTGGgtatgtgttt ... ttttctgcagAATGTTCACCATGCTGGTCAGCCTATGCCTGGTGAGGAACAGGAGGACATTGTCATGACTAGCACTCAGATGAGCATCTTAAATGTCACATGCCCATTAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 124

CAAAACATTGATCGGGGTGGAGGCTAGCAAGATTAGGGAAGCGTCATCGGCATCACAACAGAACCACCCACTCTTTCGGCAGTTCAGGGAGTCTGTCTGGgtatgtgttt ... ttttctgcagAATGTTCACCATGCTGGTCAGCCTATGCCTGGTGAGGAACAGGAGGACATTGTCATGACTAGCACTCAGATGAGCATCTTAAATGTCACATGCCCATTAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 142

CAAAACATTGATCGGGGTGGAGGCTAGCAAGATTAGGGAAGCGTCATCGGCATCACAACAGAACCACCCACTCTTTCGGCAGTTCAGGGAGTCTGTCTGGgtatgtgttt ... ttttctgcagAATGTTCACCATGCTGGTCAGCCTATGCCTGGTGAGGAACAGGAGGACATTGTCATGACTAGCACTCAGATGAGCATCTTAAATGTCACATGCCCATTAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtgtaatttcgcaaaaggtcttatgttttggtgtcttatttttttttctgcagAATGTTCACCATGCTGGTCAGCCTATGCCTGGTGAGGAACAGGAGGACATTGTCATGACTAGCACTCAGATGAGCATCTTAAATGTCACATGCCCATTAA
                                 tgtcttattttttttt  CT-rich tract
                                 tgtcttattttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgtttacagagtagcatgctcatggtcatgtgatgaccattgaggattatgcattgtacctgtgctccgggcattacctagttactcacatacgattacaatagctagattatgaatttggaaacataaatgatttgttttgtgtaatttcgcaaaaggtcttatgttttggtgtcttatttttttttctgcagAATGTTCACCATGCTGGTCAGCCTATGCCTGGTGAGGAACAGGAGGACATTGTCATGACTAGCACTCAGATGAGCATCTTAAATGTCACATGCCCATTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG