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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATCCCGTTTGTGGCAGTGCACATTGTGTTTTAGCACCTTACTGGGGTGGGAAGCTGGGGAAACACAAACTGATAGCGTTTCAAgtacgtttctgcaccactttaggccttgttcggttgcatctggatagttaagagggattaaatcctcttctattcagttttgactagaaagtgatttaat...

Basic information

species Zea mays
transcript GRMZM2G050325_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G050325_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g16146.1 (Oryza sativa), 5'ss of exon 5
GATCCCGTTTGTGGCAGTGCACATTGTGTTTTAGCACCTTACTGGGGTGGGAAGCTGGGGAAACACAAACTGATAGCGTTTCAAgtac-gtttctgcaccactttaggccttgttcggttgcatctggatagttaagagggattaaatcctcttctattcagttttgactaga---aagtgatttaat--------------
||||| || ||||| || |||||||||||| | ||||||||||||||||| |||||||||||||| ||||| |  |||||||| |||   |   |   | || ||      ||    || |    |  | | ||       |    || || ||||    |        ||     ||  |    |||              
GATCCTGTGTGTGGAAGCGCACATTGTGTTCTGGCACCTTACTGGGGTGGAAAGCTGGGGAAACAAAAACTTACGGCGTTTCAGgtattatccttttgctaccttc--ttgtgacaagtagggggtaaacaattgttgccaacattatacttttctgaaaaaaaaaagataagtacaaacggcacaataccatggtcgtcag
















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|50336611|gb|CO531737.1|CO531737
EST:     CACCTTACTGGGGTGGGAAGCTGGGGAAACACAAACTGATAGCGTTTCAA                         GCATCCCCTCGGAGTGGAATACTATACCTGGAGTTAGAAGCTACAGGCAGG
genomic: CACCTTACTGGGGTGGGAAGCTGGGGAAACACAAACTGATAGCGTTTCAAgtacgtttct ... atgtcaccagGCATCCCCTCGGAGTGGAATACTATACCTGGAGTTAGAAGCTACAGGCAGG
EST: gi|18171147|gb|BM340987.1|BM340987
EST:     CACCTTACTGGGGTGGGAAGCTGGGGAAACACAAACTGATAGCGTTTCAA                         GCATCCCCTCGGAGTGGAATACTATACCTGGAGTTAGAAGCTACAGGCAGG
genomic: CACCTTACTGGGGTGGGAAGCTGGGGAAACACAAACTGATAGCGTTTCAAgtacgtttct ... atgtcaccagGCATCCCCTCGGAGTGGAATACTATACCTGGAGTTAGAAGCTACAGGCAGG
EST: gi|33097551|gb|CF057511.1|CF057511
EST:     AAACACAAACTGATAGCGTTTCAA                         GCATCCCCTCGGAGTGGAATACTATACCTGGAGTTAGAAGCTACAGGCAGG
genomic: AAACACAAACTGATAGCGTTTCAAgtacgtttct ... atgtcaccagGCATCCCCTCGGAGTGGAATACTATACCTGGAGTTAGAAGCTACAGGCAGG
EST: gi|166674323|gb|EG063021.1|EG063021
EST:     CACCTTACTGGGGTGGGAAGCTGGGGAAACACAAACTGATAGCGTTTCAA                         GCATCCCCTCGGAGTGGAA
genomic: CACCTTACTGGGGTGGGAAGCTGGGGAAACACAAACTGATAGCGTTTCAAgtacgtttct ... atgtcaccagGCATCCCCTCGGAGTGGAA
EST: gi|50338931|gb|CO534057.1|CO534057
EST:     CACCTTACTGGGGTGGGAAGCTGGGGAAACACAAACTGATAGCGTTTCAA                         GCATCCCCTCGGAGTGGAATACTATACCTGGAGTTAGAAGCTACAGGCAGG
genomic: CACCTTACTGGGGTGGGAAGCTGGGGAAACACAAACTGATAGCGTTTCAAgtacgtttct ... atgtcaccagGCATCCCCTCGGAGTGGAATACTATACCTGGAGTTAGAAGCTACAGGCAGG
EST: gi|116816281|gb|EC859000.1|EC859000
EST:     ACCTTACCTGGGGTGGGAAGC-GGGGAAACACAAACTGATAGCGTTTCAA                         GCATCCCCTCGGAGTGGAATACTATACCTGGAGTTAGAAGCTACAGGCAGG
genomic: ACCTTA-CTGGGGTGGGAAGCTGGGGAAACACAAACTGATAGCGTTTCAAgtacgtttct ... atgtcaccagGCATCCCCTCGGAGTGGAATACTATACCTGGAGTTAGAAGCTACAGGCAGG
EST: gi|71775486|gb|DR973364.1|DR973364
EST:     CACCTTACTGGGGTGGGGAGCTGGGGAAACACAAACTGATAGCGTTTCAA                         GCATCCCCTCGGAGTGGAATACTATACCTG
genomic: CACCTTACTGGGGTGGGAAGCTGGGGAAACACAAACTGATAGCGTTTCAAgtacgtttct ... atgtcaccagGCATCCCCTCGGAGTGGAATACTATACCTG
EST: gi|60356851|gb|DN223824.1|DN223824
EST:     CACCTTACTGGGGTGGGAAGCTGGGGAAACACAAACTGATAGCGTTTCAA                         GCATCCCCTCGGAGTGGAATACTATACCTGGAGTTAGAAGCTACAGGCAGG
genomic: CACCTTACTGGGGTGGGAAGCTGGGGAAACACAAACTGATAGCGTTTCAAgtacgtttct ... atgtcaccagGCATCCCCTCGGAGTGGAATACTATACCTGGAGTTAGAAGCTACAGGCAGG
EST: gi|50331530|gb|CO526656.1|CO526656
EST:     CACCTTACTGGGGTGGGAAGCTGGGGAAACACAAACTGATAGCGTTTCAA                         GCATCCCCTCGGAGTGGAATACTATACCTGGAGTTAGAAGCTACAGGCAGG
genomic: CACCTTACTGGGGTGGGAAGCTGGGGAAACACAAACTGATAGCGTTTCAAgtacgtttct ... atgtcaccagGCATCCCCTCGGAGTGGAATACTATACCTGGAGTTAGAAGCTACAGGCAGG
EST: gi|148986829|gb|EE030628.2|EE030628
EST:     CACCTTACTGGGGTGGGAAGCTGGGGAAACACAAACTGATAGCGTTTCAA                         GCATCCCCTCGGAATGGATTACTA
genomic: CACCTTACTGGGGTGGGAAGCTGGGGAAACACAAACTGATAGCGTTTCAAgtacgtttct ... atgtcaccagGCATCCCCTCGGAGTGGAATACTA
EST: gi|37375249|gb|CF624050.1|CF624050
EST:     CACCTTACTGGGGTGGGAAGCTGGGGAAACACAAACTGATAGCGTTTCAA                         GCATCCCCTCGGAGTGGAATACTATACCTGGAGTTAGAAGCTACAGGCAGG
genomic: CACCTTACTGGGGTGGGAAGCTGGGGAAACACAAACTGATAGCGTTTCAAgtacgtttct ... atgtcaccagGCATCCCCTCGGAGTGGAATACTATACCTGGAGTTAGAAGCTACAGGCAGG
EST: gi|37384216|gb|CF629166.1|CF629166
EST:     CACCTTACTGGGGTGGGAAGCTGGGGAAACACAAACTGATAGCGTTTCAA                         GCATCCCCTCGGAGTGGAATACTATACCTGGAGTTAGAAGCTACAGGCAGG
genomic: CACCTTACTGGGGTGGGAAGCTGGGGAAACACAAACTGATAGCGTTTCAAgtacgtttct ... atgtcaccagGCATCCCCTCGGAGTGGAATACTATACCTGGAGTTAGAAGCTACAGGCAGG
EST: gi|211213647|gb|FL457806.1|FL457806
EST:     CACCTTACTGGGGTGGGAAGCTGGGGAAACACAAACTGATAGCGTTTCAA                         GCATCCCCTCGGAGTGGAATACTATACCTGGAGTTAGAAGCTACAGGCAGG
genomic: CACCTTACTGGGGTGGGAAGCTGGGGAAACACAAACTGATAGCGTTTCAAgtacgtttct ... atgtcaccagGCATCCCCTCGGAGTGGAATACTATACCTGGAGTTAGAAGCTACAGGCAGG
EST: gi|37376720|gb|CF624915.1|CF624915
EST:     CACCTTACTGGGGTGGGAAGCTGGGGAAACACAAACTGATAGCGTTTCAA                         GCATCCCCTCGGAGTGGAATACTATACCTGGAGTTAGAAGCTACAGGCAGG
genomic: CACCTTACTGGGGTGGGAAGCTGGGGAAACACAAACTGATAGCGTTTCAAgtacgtttct ... atgtcaccagGCATCCCCTCGGAGTGGAATACTATACCTGGAGTTAGAAGCTACAGGCAGG
EST: gi|33104525|gb|CF064485.1|CF064485
EST:     CACCTTACTGGGGTGGGAAGCTGGGGAAACACAAACTGATAGCGTTTCAA                         GCATCCCCTCGGAGTGGAATACTATACCTGGAGTTAGAAGCTACAGGCAGG
genomic: CACCTTACTGGGGTGGGAAGCTGGGGAAACACAAACTGATAGCGTTTCAAgtacgtttct ... atgtcaccagGCATCCCCTCGGAGTGGAATACTATACCTGGAGTTAGAAGCTACAGGCAGG
EST: gi|9254288|gb|BE344756.1|BE344756
EST:     CACCTTACTGGGGTGGGAAGCTGGGGAAACACAAACTGATAGCGTTTCAA                         GCATCCCCTCGGAGTGGAATACTATACCTGGAGTTAGAAGCTACATGCAGG
genomic: CACCTTACTGGGGTGGGAAGCTGGGGAAACACAAACTGATAGCGTTTCAAgtacgtttct ... atgtcaccagGCATCCCCTCGGAGTGGAATACTATACCTGGAGTTAGAAGCTACAGGCAGG
EST: gi|93015163|gb|EB640683.1|EB640683
EST:     CACCTTACTGGGGTGGGAAGCTGGGGGAACACAAACTGATAGCGTTTCAA                         GCATCCCCTCGGAGTGGAATACTATACCTGGAGTTAGAAGCT
genomic: CACCTTACTGGGGTGGGAAGCTGGGGAAACACAAACTGATAGCGTTTCAAgtacgtttct ... atgtcaccagGCATCCCCTCGGAGTGGAATACTATACCTGGAGTTAGAAGCT
EST: gi|33099705|gb|CF059665.1|CF059665
EST:     CACCTTACTGGGGTGGGAAGCTGGGGAAACACAAACTGATAGCGTTTCAA                         GCATCCCCTCGGAGTGGAATACTATACCTGGAGTTAGAAGCTACAGGCAGG
genomic: CACCTTACTGGGGTGGGAAGCTGGGGAAACACAAACTGATAGCGTTTCAAgtacgtttct ... atgtcaccagGCATCCCCTCGGAGTGGAATACTATACCTGGAGTTAGAAGCTACAGGCAGG
EST: gi|44901068|gb|CK827613.1|CK827613
EST:     CACCTTACTGGGGTGGGAAGCTGGGGAAACACAAACTGATAGCGTTTCAA                         GCATCCCCTCGGAGTGGAATACTATACCTGGAGTTAGAAGCTACAGGCAGG
genomic: CACCTTACTGGGGTGGGAAGCTGGGGAAACACAAACTGATAGCGTTTCAAgtacgtttct ... atgtcaccagGCATCCCCTCGGAGTGGAATACTATACCTGGAGTTAGAAGCTACAGGCAGG
EST: gi|78119655|gb|DV538039.1|DV538039
EST:     CACCTTACTGGGGTGGGAAGCTGGGGAAACACAAACTGATAGCGTTTCAA                         GCATCCCCTCGGAGTGGAATACTATACCTGGAGTTAGAAGCTACAGGCAGG
genomic: CACCTTACTGGGGTGGGAAGCTGGGGAAACACAAACTGATAGCGTTTCAAgtacgtttct ... atgtcaccagGCATCCCCTCGGAGTGGAATACTATACCTGGAGTTAGAAGCTACAGGCAGG
EST: gi|113701518|gb|EE679022.1|EE679022
EST:     CACCTTACTGGGGTGGGAAGCTGGGGAAACACAAACTGATAGCGTTTCAA                         GCATCCCCTCGGAGTGGAATATTATACCTGGAGTTAGAAGCTACAGGCAGG
genomic: CACCTTACTGGGGTGGGAAGCTGGGGAAACACAAACTGATAGCGTTTCAAgtacgtttct ... atgtcaccagGCATCCCCTCGGAGTGGAATACTATACCTGGAGTTAGAAGCTACAGGCAGG

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), 47 (downstream exon)
Score: 110

GATCCCGTTTGTGGCAGTGCACATTGTGTTTTAGCACCTTACTGGGGTGGGAAGCTGGGGAAACACAAACTGATAGCGTTTCAAgtacgtttct ... atgtcaccagGCATCCCCTCGGAGTGGAATACTATACCTGGAGTTAGAAGCTACAGGCAGGAGAGTGCGAATTCAGGGAGAAGCGGTCAGTGTGATGACTGGCACCCTCT


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 274

GATCCCGTTTGTGGCAGTGCACATTGTGTTTTAGCACCTTACTGGGGTGGGAAGCTGGGGAAACACAAACTGATAGCGTTTCAAgtacgtttct ... atgtcaccagGCATCCCCTCGGAGTGGAATACTATACCTGGAGTTAGAAGCTACAGGCAGGAGAGTGCGAATTCAGGGAGAAGCGGTCAGTGTGATGACTGGCACCCTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 586

GATCCCGTTTGTGGCAGTGCACATTGTGTTTTAGCACCTTACTGGGGTGGGAAGCTGGGGAAACACAAACTGATAGCGTTTCAAgtacgtttct ... atgtcaccagGCATCCCCTCGGAGTGGAATACTATACCTGGAGTTAGAAGCTACAGGCAGGAGAGTGCGAATTCAGGGAGAAGCGGTCAGTGTGATGACTGGCACCCTCT


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 60

GATCCCGTTTGTGGCAGTGCACATTGTGTTTTAGCACCTTACTGGGGTGGGAAGCTGGGGAAACACAAACTGATAGCGTTTCAAgtacgtttct ... atgtcaccagGCATCCCCTCGGAGTGGAATACTATACCTGGAGTTAGAAGCTACAGGCAGGAGAGTGCGAATTCAGGGAGAAGCGGTCAGTGTGATGACTGGCACCCTCT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATCCCGTTTGTGGCAGTGCACATTGTGTTTTAGCACCTTACTGGGGTGGGAAGCTGGGGAAACACAAACTGATAGCGTTTCAAgtacgtttctgcaccactttaggccttgttcggttgcatctggatagttaagagggattaaatcctcttctattcagttttgactagaaagtgatttaat

- - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG