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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACTATGTTCCAACTGTGTTCGACAACTTCAGTGCCAATGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAGgtctcttcccttggcattaaaatccttctttgtatctgcattccttcctgctccaaagtacagtaactgatattctatgatttttttag

Basic information

species Zea mays
transcript GRMZM2G375002_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G375002_T03 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g58730.2 (Oryza sativa), 5'ss of exon 2
GACTATGTTCCAACTGTGTTCGACAACTTCAGTGCCAATGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAGgtc---tcttcccttggcattaa--aatccttctttgtatct----gcattccttcctgctccaaagt----acagtaactgata-ttctatgatttttttag------
||||||||||||||||| || || ||||||||||| ||||||||||| || ||||||||||| ||||||||  |||||||||||||||||      ||||| |    ||||   || | |   |  | ||      || | | |    | ||  ||    | | ||| | | | ||  |  | |||   ||      
GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAGgttctactttcccctccttttaatggatgcatgcgtaaacctccttatatacatccacctttcacggtcatcaaaataaataaaaatttgacaaatttaacaggacaag

upper sequence: GRMZM2G375002_T03 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g58730.1 (Oryza sativa), 5'ss of exon 2
GACTATGTTCCAACTGTGTTCGACAACTTCAGTGCCAATGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAGgtct---cttcccttggcattaa--aatccttctttgtatctgc----attccttcctgctccaaagt----acagtaactgata-ttctatgatttttttag
||||||||||||||||| || || ||||||||||| ||||||||||| || ||||||||||| ||||||||  |||||||||||||||||      ||||| |    ||||   || | |   |  | || |    || | | |    | ||  ||    | | ||| | | | ||  |  | |||   ||
GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAGgttctactttcccctccttttaatggatgcatgcgtaaacctccttatatacatccacctttcacggtcatcaaaataaataaaaatttgacaaatttaacag

upper sequence: GRMZM2G375002_T03 (Zea mays), 5'ss of exon 2
lower sequence: AT4G35020.3 (Arabidopsis thaliana), 5'ss of exon 4
GACTATGTTCCAACTGTGTTCGACAACTTCAGTGCCAATGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAGgtctcttcccttggcattaaaatccttctttgtatctgcattccttcctgctccaaagtacagtaactgatattctatgatttttttag----
|| ||||| |||||||||||||| || ||||||||||||||  | ||||| || | |||| ||||||||||  |||||||||| |||||    ||          |   ||  || | | | | || ||| | ||||  |||| ||   ||| | |  | || | ||| ||  | |     
GATTATGTGCCAACTGTGTTCGATAATTTCAGTGCCAATGTGATTGTTGATGGCAACACTATCAACTTGGGATTGTGGGATACTGCAGgcaagttgttac----cttggatttttttgtct-tttgaatttcctcctcttccagag---agtcatttgtgtttt-tgacttggtgaaacag

upper sequence: GRMZM2G375002_T03 (Zea mays), 5'ss of exon 2
lower sequence: PP1S257_74V6.1 (Physcomitrella patens), 5'ss of exon 2
GACTATGTTCCAACTGTGTTCGACAACTTCAGTGCCAATGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAGgtctcttccc--------ttggcattaaaatccttctttgt-atctgcattccttcctgctccaaagtacagtaactgatattctatgatttttttag--
|| || || || ||||| |||||||||||||| || ||||| ||||| || ||||  || |||||| |||| || |||||||||||||||  |   |         | | | | | | | |    |||| |  |||| |  |   || |    |   | ||   |  |   || ||||||  | |   
GATTACGTCCCTACTGTATTCGACAACTTCAGCGCGAATGTCGTGGTCGATGGGAATACCGTCAACCTGGGACTATGGGATACAGCAGgtaacacacgcaataggatagacttcacagttcgcggttgtcagttgcactggtagttggtgaggaagtcggtgtttattcacctgtgatttagtgaaag

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|211163176|gb|FK955403.1|FK955403
EST:     TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAG                         GACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATG
genomic: TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAGgtctcttccc ... atttttttagGACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATG
EST: gi|211163177|gb|FK955404.1|FK955404
EST:     TGTTGTGGTTGACGGGAGCACTGTCAACTTNGGTCTGTGGGATACAGCAG                         GACAAGAAGATTACRATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATG
genomic: TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAGgtctcttccc ... atttttttagGACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATG
EST: gi|32909548|gb|CF014360.1|CF014360
EST:     TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAG                         GACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCG
genomic: TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAGgtctcttccc ... atttttttagGACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCG
EST: gi|211236584|gb|FK955431.1|FK955431
EST:     TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAG                         GACAAGAAGATTACAATATGACTGCGTCCGTTGAGCTATCGTGGTGCTGAT
genomic: TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAGgtctcttccc ... atttttttagGACAAGAAGATTACAATA-GACTGCGTCCGTTGAGCTATCGTGGTGCTGAT
EST: gi|211520026|gb|FL347002.1|FL347002
EST:     TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAG                         GACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATG
genomic: TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAGgtctcttccc ... atttttttagGACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATG
EST: gi|67018898|gb|CO447647.1|CO447647
EST:     TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAG                         GACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATG
genomic: TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAGgtctcttccc ... atttttttagGACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATG
EST: gi|32936373|gb|CF041192.1|CF041192
EST:     TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAG                         GACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATG
genomic: TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAGgtctcttccc ... atttttttagGACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATG
EST: gi|32827834|gb|CD967512.1|CD967512
EST:     TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAG                         GACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATG
genomic: TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAGgtctcttccc ... atttttttagGACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATG
EST: gi|211356949|gb|FL222513.1|FL222513
EST:     TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAG                         GACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATG
genomic: TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAGgtctcttccc ... atttttttagGACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATG
EST: gi|78107806|gb|DV526224.1|DV526224
EST:     TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAG                         GACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATG
genomic: TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAGgtctcttccc ... atttttttagGACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATG
EST: gi|16918068|gb|BM073562.1|BM073562
EST:     TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAG                         GACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATG
genomic: TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAGgtctcttccc ... atttttttagGACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATG
EST: gi|12047201|gb|BF729340.1|BF729340
EST:     TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAG                         GACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATG
genomic: TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAGgtctcttccc ... atttttttagGACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATG
EST: gi|32858427|gb|CD998108.1|CD998108
EST:     TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAG                         GACAAGAAGATTACAATAGACTTGCGTCCGTTG
genomic: TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAGgtctcttccc ... atttttttagGACAAGAAGATTACAATAGACT-GCGTCCGTTG
EST: gi|33467050|gb|CF244099.1|CF244099
EST:     TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACCGCAG                         GACAAGAAGATTACAATAGACTGCGTCC
genomic: TGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAGgtctcttccc ... atttttttagGACAAGAAGATTACAATAGACTGCGTCC

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: 156

GACTATGTTCCAACTGTGTTCGACAACTTCAGTGCCAATGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAGgtctcttccc ... atttttttagGACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATGTTTTTCTGCTCGCCTTTTCTCTTATCAGCAAAGCAAGCTATGAGAATGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 298

GACTATGTTCCAACTGTGTTCGACAACTTCAGTGCCAATGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAGgtctcttccc ... atttttttagGACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATGTTTTTCTGCTCGCCTTTTCTCTTATCAGCAAAGCAAGCTATGAGAATGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 382

GACTATGTTCCAACTGTGTTCGACAACTTCAGTGCCAATGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAGgtctcttccc ... atttttttagGACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATGTTTTTCTGCTCGCCTTTTCTCTTATCAGCAAAGCAAGCTATGAGAATGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 237

GACTATGTTCCAACTGTGTTCGACAACTTCAGTGCCAATGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAGgtctcttccc ... atttttttagGACAAGAAGATTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATGTTTTTCTGCTCGCCTTTTCTCTTATCAGCAAAGCAAGCTATGAGAATGT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACTATGTTCCAACTGTGTTCGACAACTTCAGTGCCAATGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAGgtctcttcccttggcattaaaatccttctttgtatctgcattccttcctgctccaaagtacagtaactgatattctatgatttttttag

- - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA