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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGTCCATGTTGATACTGTTGTCATGAATCCTCCCTTTGGTACACGAAGGAATGGAGCAGACATGGAGTTCCTCTCTATGGCCTTGCAGgtcagaaccggtgcttgtttgcgactagcagtttcctttggaagatgatatttgacattttaagtgcccatttgctactgacag

Basic information

species Zea mays
transcript GRMZM2G113640_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G113640_T03 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os06g06730.1 (Oryza sativa), 5'ss of exon 6
GCGTCCATGTTGATACTGTTGTCATGAATCCTCCCTTTGGTACACGAAGGAATGGAGCAGACATGGAGTTCCTCTCTATGGCCTTGCAGgtcaga--accggtgcttgtttgcgacta-gcagtttcct----ttggaagatgatatttgacattttaagtgcccatttgctactgacag
|| | | |||||| |||||||||||||||||||||||||| ||| | || || ||||| |||||||| ||| | ||||||| | || |||| ||   || ||       |||| |  |  ||  |  ||    ||     ||||| ||| | ||||| | |  | ||| |||| |  |||
GCCTTCTTGTTGACACTGTTGTCATGAATCCTCCCTTTGGGACAAGCAGAAAAGGAGCTGACATGGAATTCATTTCTATGGGCATGAAGgtgagggcactgggcagcagttgccatcatacacatgactgagattattgcatgatgtttaaaatttttaatatctatt-gctatttgcag

upper sequence: GRMZM2G113640_T03 (Zea mays), 5'ss of exon 5
lower sequence: AT4G28830.1 (Arabidopsis thaliana), 5'ss of exon 6
GCGTCCATGTTGATACTGTTGTCATGAATCCTCCCTTTGGTACACGAAGGAATGGAGCAGACATGGAGTTCCTCTCTATGGCCTTGCAGgt------cagaaccggtgcttgtttgcgactagcagtttcctttggaagatgatatttgacattttaagtgcccatttg-ctactgacag
|| |   ||| ||||| ||||| ||||| ||||| ||||||||||| | ||| ||||| ||||||||||| ||||||  |||  || ||||      |||||  |    |   ||   |||      |   || | |  |     ||  |  |||  | |     |||| ||||   |||
GCCTGATTGTGGATACGGTTGTAATGAACCCTCCATTTGGTACACGGAAGAAAGGAGCTGACATGGAGTTTCTCTCTGCGGCAATGAAGgtaaacaacagaaaagaatatctctttttactgttttctaatttcgtatcactcggttacatgtttacattcgatgtttggctac--gcag

upper sequence: GRMZM2G113640_T03 (Zea mays), 5'ss of exon 5
lower sequence: Vv11s0016g03520.t01 (Vitis vinifera), 5'ss of exon 6
GCGTCCA--TGTTGATACTGTTGTCATGAATCCTCCCTTTGGTACACGAAGGAATGGAGCAGACATGGAGTTCCTCTCTATGGCCTTGCAGgtcagaaccggtgcttgtttgcgactagcagtttcct-ttggaagatgatatttgacattttaagtgcccatttgctactgacag----------
  ||| |  ||||||||||||||| ||||||||||| ||||| ||||| | ||| || || |||||||| || ||| || |||| ||| |||| |  |  |   | | ||  |   |  ||| | | |  | |    | |||||||   || ||| |   |  ||   | | |  |          
--GTCAAATTGTTGATACTGTTGTAATGAATCCTCCATTTGGAACACGGAAGAAGGGGGCTGACATGGATTTTCTCGCTGTGGCTTTGAAGgtaaagatggtaccattttctcatttttcagatacatgcttgtgatttatatttg---ttctaattaatctattttcattaattggttgtgtcag

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|32928356|gb|CF033168.1|CF033168
EST:     ACACGAAGGAATGGAGCAGACATGGAGTTCCTCTCTATGGCCTTGCAG                         GTTGCTTCTCAAGCTGTCTATTCTCTACACAAGACTTCCACTAGAGAA
genomic: ACACGAAGGAATGGAGCAGACATGGAGTTCCTCTCTATGGCCTTGCAGgtcagaaccg ... ctactgacagGTTGCTTCTCAAGCTGTCTATTCTCTACACAAGACTTCCACTAGAGAA
EST: gi|211270654|gb|FL248444.1|FL248444
EST:     TCCATGTTGATACTGTTGTCATGAATCCTCCCTTTGGTACACGAAGGAATGGAGCAGACATGGAGTTCCTCTCTATGGCCTTGMAG
genomic: GTACACGAAGGAATGGAGCAGACATGGAGTTCCTCTCTATGGCCTTGCAGgtcagaaccg ... ctactgacagGTTGCTTCTCA
EST: gi|71438832|gb|DR819882.1|DR819882
EST:     TCCATGTTGATACTGTTGTCATGAATCCTCCCTTTGGTACACGAAGGAATGGAGCAGACATGGAGTTCCTCTCTATGGCCTTGCAG
genomic: GTACACGAAGGAATGGAGCAGACATGGAGTTCCTCTCTATGGCCTTGCAGgtcagaaccg ... ctactgacagGTTGCTTCTCA
EST: gi|213171204|gb|FM188301.1|FM188301
EST:     GTACACGAAGGAATGGAGCAGACATGGAGTTCCTCTCTATGGCCTTGCAG                         GTTGCTTCTCAAGCTGTCTATTCTCTACACAAGACTTCCACTAGAGAA
genomic: GTACACGAAGGAATGGAGCAGACATGGAGTTCCTCTCTATGGCCTTGCAGgtcagaaccg ... ctactgacagGTTGCTTCTCAAGCTGTCTATTCTCTACACAAGACTTCCACTAGAGAA
EST: gi|76012002|gb|DT939172.1|DT939172
EST:     TCCATGTTGATACTGTTGTCATGAATCCTCCCTTTGGTACACGAAGGAATGGAGCAGACATGGAGTTCCTCTCTATGGCCTTGCAG
genomic: GTACACGAAGGAATGGAGCAGACATGGAGTTCCTCTCTATGGCCTTGCAGgtcagaaccg ... ctactgacagGTTGCTTCTCA
EST: gi|6227108|gb|AW155812.1|AW155812
EST:     TCATGAATCCTCCCTTTGGTACACGAAGGAATGGAGCAGACATGGAGTTCCTCTCTATGGCCTTGCAG        
genomic: GTACACGAAGGAATGGAGCAGACATGGAGTTCCTCTCTATGGCCTTGCAGgtcagaaccg ... ctactgacagG
EST: gi|50327796|gb|CO522922.1|CO522922
EST:     TCCATGTTGATACTGTTGTCATGAATCCTCCCTTTGGTACACGAAGGAATGGAGCAGACATGGAGTTCCTCTCTATGGCCTTGCAG
genomic: GTACACGAAGGAATGGAGCAGACATGGAGTTCCTCTCTATGGCCTTGCAGgtcagaaccg ... ctactgacagGTTGCTTCTCA

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: 30 (upstream exon), 49 (downstream exon)
Score: 115

GCGTCCATGTTGATACTGTTGTCATGAATCCTCCCTTTGGTACACGAAGGAATGGAGCAGACATGGAGTTCCTCTCTATGGCCTTGCAGgtcagaaccg ... ctactgacagGTTGCTTCTCAAGCTGTCTATTCTCTACACAAGACTTCCACTAGAGAA


Block sizes: 34 (upstream exon), 48 (downstream exon)
Score: 145

GCGTCCATGTTGATACTGTTGTCATGAATCCTCCCTTTGGTACACGAAGGAATGGAGCAGACATGGAGTTCCTCTCTATGGCCTTGCAGgtcagaaccg ... ctactgacagGTTGCTTCTCAAGCTGTCTATTCTCTACACAAGACTTCCACTAGAGAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 146

GCGTCCATGTTGATACTGTTGTCATGAATCCTCCCTTTGGTACACGAAGGAATGGAGCAGACATGGAGTTCCTCTCTATGGCCTTGCAGgtcagaaccg ... ctactgacagGTTGCTTCTCAAGCTGTCTATTCTCTACACAAGACTTCCACTAGAGAA


Block sizes: 25 (upstream exon), 49 (downstream exon)
Score: 69

GCGTCCATGTTGATACTGTTGTCATGAATCCTCCCTTTGGTACACGAAGGAATGGAGCAGACATGGAGTTCCTCTCTATGGCCTTGCAGgtcagaaccg ... ctactgacagGTTGCTTCTCAAGCTGTCTATTCTCTACACAAGACTTCCACTAGAGAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGTCCATGTTGATACTGTTGTCATGAATCCTCCCTTTGGTACACGAAGGAATGGAGCAGACATGGAGTTCCTCTCTATGGCCTTGCAGgtcagaaccggtgcttgtttgcgactagcagtttcctttggaagatgatatttgacattttaagtgcccatttgctactgacag

- - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA