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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTGTGCGGGCCAGCCTCGATGCCGACGAGTTCATGGCGCTGATGCACGGCTCGGATCCCGTCAGGGTCGAGCTCACCCGCCTGGAGAACGAGCTCAGGGgtcggtttattgatctgtctgttcatttcgtgctttgattttcttcattgcagtggtatctagtgttttgttttggagcgaggatttatttgtgtgcggtttttgctggtgtcag

Basic information

species Zea mays
transcript GRMZM2G039325_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G039325_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os06g14080.1 (Oryza sativa), 5'ss of exon 1
CCTGTGCGGGCCAGCCTCGATGCCGACGAGTTCATGGCGCTGATGCACGGCTCGGATCCCGTCAGGGTCGAGCTCACCCGCCTGGAGAACGAGCTCAGGGgtcggtttat-tgatctgtctgttcatttcg-tgctttgattttcttcattgca-gtggtatctagtgttttgttttggagcgaggatttattt-gtgtgcggtttttgctggtgtcag
 | ||||||||||||||||| |||||||||||||| |||||||||||||||||||||||||||||||| |||||||||||||| ||||||||||| ||||||  | | || || ||   |||||| ||||| || |||  |        |||   |||| |      | ||  ||||     ||   ||| ||| | ||  || ||    |||||| ||
ACCGTGCGGGCCAGCCTCGACGCCGACGAGTTCATCGCGCTGATGCACGGCTCGGATCCCGTCAGGGTGGAGCTCACCCGCCTCGAGAACGAGCTGAGGGgtgagctgatctgctcctgctgttcgtttcggtgattttgtccagggatttgtttgtggaagaggaggcttgattttcttttgatttttttttttgggtatggcttcg--tggtgttag
















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|211233997|gb|FL170990.1|FL170990
EST:     CTCGGATCCCGTCAGGGTCGAGCTCACCCGCCTGGAGAACGAGCTCAGGG                         ACAAGGAGAGGGAGCYTGGGGAGGC-CAGACGGAGATACGCGCACTG-GCT
genomic: CTCGGATCCCGTCAGGGTCGAGCTCACCCGCCTGGAGAACGAGCTCAGGGgtcggtttat ... ctggtgtcagACAAGGAGAGGGAGCTTGGGGAGGCACAGACGGAGATACGCGCACTGCGCT
EST: gi|211234001|gb|FL170994.1|FL170994
EST:     CTCGGATCCCGTCAGGGTCGAGCTCACCCGCCTGGAGAACGAGCTCAGGG                         ACAAGGAGAGGGAGCTTGGGGAGGCACAGACGGAGATACGCGCACTGCGCT
genomic: CTCGGATCCCGTCAGGGTCGAGCTCACCCGCCTGGAGAACGAGCTCAGGGgtcggtttat ... ctggtgtcagACAAGGAGAGGGAGCTTGGGGAGGCACAGACGGAGATACGCGCACTGCGCT
EST: gi|211233996|gb|FL170989.1|FL170989
EST:     CTCGGATCCCGTCAGGGTCGAGCTCACCCGCCTGGAGAACGAGCTCAGGG                         ACAAGGAGAGGGAGCTTGGGGAGGCACAGACGGAGATACGCGCACTGCGCT
genomic: CTCGGATCCCGTCAGGGTCGAGCTCACCCGCCTGGAGAACGAGCTCAGGGgtcggtttat ... ctggtgtcagACAAGGAGAGGGAGCTTGGGGAGGCACAGACGGAGATACGCGCACTGCGCT
EST: gi|149084677|gb|EE174161.2|EE174161
EST:     CTCGGATCCCGTCAGGGTCGAGCTCACCCGCCTGGAGAACGAGCTCAGGG                         ACAAGGAGAGGGAGCTTGGGGAGGCACAGACGGAGATACGCGCACTGCGCT
genomic: CTCGGATCCCGTCAGGGTCGAGCTCACCCGCCTGGAGAACGAGCTCAGGGgtcggtttat ... ctggtgtcagACAAGGAGAGGGAGCTTGGGGAGGCACAGACGGAGATACGCGCACTGCGCT
EST: gi|211234006|gb|FL170999.1|FL170999
EST:     CTCGGATCCCGTCAGGGTCGAGCTCACCCGCCTGGAGAACGAGCTCAGGG                         ACAAGGAGAGGGAGCCTGGGGAGGC
genomic: CTCGGATCCCGTCAGGGTCGAGCTCACCCGCCTGGAGAACGAGCTCAGGGgtcggtttat ... ctggtgtcagACAAGGAGAGGGAGCTTGGGGAGGC
EST: gi|211233998|gb|FL170991.1|FL170991
EST:     CTCGGATCCCGTCAGGGTCGAGCTCACCCGCCTGGAGAACGAGCTCAGGG                         ACAAGGAGAGGGAGCTTGGGGAGGCACAGACGGAGATACGCGCACTGCGCT
genomic: CTCGGATCCCGTCAGGGTCGAGCTCACCCGCCTGGAGAACGAGCTCAGGGgtcggtttat ... ctggtgtcagACAAGGAGAGGGAGCTTGGGGAGGCACAGACGGAGATACGCGCACTGCGCT
EST: gi|211231947|gb|FL170987.1|FL170987
EST:     TCGGATCCCGTCAGGGTCGAGCTCACCCGCCTGGAGAACGAGCTCCAGGG                         ACAAGGAGAGGGAGCTTGGGGAGGCACAGACGGAGATACGCGCACTGCGC
genomic: TCGGATCCCGTCAGGGTCGAGCTCACCCGCCTGGAGAACGAGCTC-AGGGgtcggtttat ... ctggtgtcagACAAGGAGAGGGAGCTTGGGGAGGCACAGACGGAGATACGCGCACTGCGC
EST: gi|71444483|gb|DR825533.1|DR825533
EST:     CTCGGATCCCGTCAGGGTCGAGCTCACCCGCCTGGAGAACGAGCTCAGGG                         ACAAGGAGAGGGAGCTTGGGGAGGCACAGACGGAGATACGCGCACTGCGCT
genomic: CTCGGATCCCGTCAGGGTCGAGCTCACCCGCCTGGAGAACGAGCTCAGGGgtcggtttat ... ctggtgtcagACAAGGAGAGGGAGCTTGGGGAGGCACAGACGGAGATACGCGCACTGCGCT
EST: gi|211453386|gb|FL460028.1|FL460028
EST:     CTCGGATCCCGTCAGGGTCGAGCTCACCCGCCTGGAGAACGAGCTCAGGG                         ACAAGGAGAGGGAGCTTGGGGAGGCACAGACGGAGATACGCGCACTGCGCT
genomic: CTCGGATCCCGTCAGGGTCGAGCTCACCCGCCTGGAGAACGAGCTCAGGGgtcggtttat ... ctggtgtcagACAAGGAGAGGGAGCTTGGGGAGGCACAGACGGAGATACGCGCACTGCGCT
EST: gi|211234007|gb|FL171000.1|FL171000
EST:     CTCGGATCCCGTCAGGGTCGAGCTCACCCGCCTGGAGAACGAGCTCAGGG                         ACAAGGAGAGGGAGCTTGGNGAGGCACAGACGGAGATACGCGCACTGCGCT
genomic: CTCGGATCCCGTCAGGGTCGAGCTCACCCGCCTGGAGAACGAGCTCAGGGgtcggtttat ... ctggtgtcagACAAGGAGAGGGAGCTTGGGGAGGCACAGACGGAGATACGCGCACTGCGCT
EST: gi|211234003|gb|FL170996.1|FL170996
EST:     CTCGGATCCCGTCAGGGTCGAGCTCACCCGCCTGGAGAACGAGCTCAGGG                         ACAAGGAGAGGGAGCTTGGGGAGGCACAGACGGAGATACGCGCACTGCGCT
genomic: CTCGGATCCCGTCAGGGTCGAGCTCACCCGCCTGGAGAACGAGCTCAGGGgtcggtttat ... ctggtgtcagACAAGGAGAGGGAGCTTGGGGAGGCACAGACGGAGATACGCGCACTGCGCT
EST: gi|149113193|gb|EE295942.2|EE295942
EST:     CTCGGATCCCGTCAGGGTCGAGCTCACCCGCCTGGAGAACGAGCTCAGGG                         ACAAGGAGAGGGAGCTTGGGGAGGCACAGACGGAGATACGCGCACTGCGCT
genomic: CTCGGATCCCGTCAGGGTCGAGCTCACCCGCCTGGAGAACGAGCTCAGGGgtcggtttat ... ctggtgtcagACAAGGAGAGGGAGCTTGGGGAGGCACAGACGGAGATACGCGCACTGCGCT
EST: gi|211231946|gb|FL170986.1|FL170986
EST:     CTCGGATCCCGTCAGGGTCGAGCTCACCCGCCTGGAGAACGAGCTCAGGG                         ACAAGGAGAGGGAGCTTGGGGAGGCACAGACGGAGATACGCGCACTGCGCT
genomic: CTCGGATCCCGTCAGGGTCGAGCTCACCCGCCTGGAGAACGAGCTCAGGGgtcggtttat ... ctggtgtcagACAAGGAGAGGGAGCTTGGGGAGGCACAGACGGAGATACGCGCACTGCGCT
EST: gi|211234004|gb|FL170997.1|FL170997
EST:     CTCGGATCCCGTCAGGGTCGAGCTCACCCGCCTGGAGAACGAGCTCAGGG                         ACAAGGAGAGGGAGCTTGGGGAGGCACAGACGGAGATACGCGCACTGCGCT
genomic: CTCGGATCCCGTCAGGGTCGAGCTCACCCGCCTGGAGAACGAGCTCAGGGgtcggtttat ... ctggtgtcagACAAGGAGAGGGAGCTTGGGGAGGCACAGACGGAGATACGCGCACTGCGCT
EST: gi|211415054|gb|FL462009.1|FL462009
EST:     CTCGGATCCCGTCAGGGTCGAGCTCACCCGCCTGGAGAACGAGCTCAGGK                         WCAAGGAGAGGGAGCTTGGGGAGGCACAGACGGAGATACGCGCACTGCGCT
genomic: CTCGGATCCCGTCAGGGTCGAGCTCACCCGCCTGGAGAACGAGCTCAGGGgtcggtttat ... ctggtgtcagACAAGGAGAGGGAGCTTGGGGAGGCACAGACGGAGATACGCGCACTGCGCT
EST: gi|211233999|gb|FL170992.1|FL170992
EST:     CTCGGATCCCGTCAGGGTCGAGCTCACCCGCCTGGAGAACGAGCTCAGGG                         ACAAGGAGAGGGAGCTTGGGGAGGCACAGACGGAGATACGCGCACT
genomic: CTCGGATCCCGTCAGGGTCGAGCTCACCCGCCTGGAGAACGAGCTCAGGGgtcggtttat ... ctggtgtcagACAAGGAGAGGGAGCTTGGGGAGGCACAGACGGAGATACGCGCACT
EST: gi|211234009|gb|FL171002.1|FL171002
EST:     CTCGGATCCCGTCAGGGTCGAGCTCACCCGCCTGGAGAACGAGCTCAGGN                         ACAAGGAGAGGGAGCTTGGGGAGGCAC
genomic: CTCGGATCCCGTCAGGGTCGAGCTCACCCGCCTGGAGAACGAGCTCAGGGgtcggtttat ... ctggtgtcagACAAGGAGAGGGAGCTTGGGGAGGCAC
EST: gi|211234008|gb|FL171001.1|FL171001
EST:     CTCGGATCCCGTCAGGGTCGAGCTCACCCGCCTGGAGAACGAGCTCAGGG                         ACAAGGAGAGGGAGCTTGGGGAGGCACAGACGGA
genomic: CTCGGATCCCGTCAGGGTCGAGCTCACCCGCCTGGAGAACGAGCTCAGGGgtcggtttat ... ctggtgtcagACAAGGAGAGGGAGCTTGGGGAGGCACAGACGGA
EST: gi|148943243|gb|EC888304.2|EC888304
EST:     CTCGGATCCCGTCAGGGTCGAGCTCACCCGCCTGGAGAACGAGCTCAGGG                         ACAAGGAGAGGGAGCTTGGGGAGGCACAGACGGAGATACGCGCACTGCGCT
genomic: CTCGGATCCCGTCAGGGTCGAGCTCACCCGCCTGGAGAACGAGCTCAGGGgtcggtttat ... ctggtgtcagACAAGGAGAGGGAGCTTGGGGAGGCACAGACGGAGATACGCGCACTGCGCT
EST: gi|148967769|gb|EE019046.2|EE019046
EST:     CTCGGATCCCGTCAGGGTCGAGCTCACCCGCCTGGAGAACGAGCTCAGGG                         ACAAGGAGAGGGAGCTTGGGGAGGCACAGACGGAGATACGCGCACTGCGCT
genomic: CTCGGATCCCGTCAGGGTCGAGCTCACCCGCCTGGAGAACGAGCTCAGGGgtcggtttat ... ctggtgtcagACAAGGAGAGGGAGCTTGGGGAGGCACAGACGGAGATACGCGCACTGCGCT
EST: gi|211231948|gb|FL170988.1|FL170988
EST:     CTCGGATCCCGTCAGGGTCGAGCTCACCCGCCTGGAGAACGAGCTCAGGG                         ACAAGGAGAGGGAGCTTGGGGAGGCAC
genomic: CTCGGATCCCGTCAGGGTCGAGCTCACCCGCCTGGAGAACGAGCTCAGGGgtcggtttat ... ctggtgtcagACAAGGAGAGGGAGCTTGGGGAGGCAC
EST: gi|76930993|gb|DV172583.1|DV172583
EST:     CTCGGATCCCGTCAGGGTCGAGCTCACCCGCCTGGAGAACGAGCTCAGGG                         ACAAGGAGAGGGAGCTTGGGGAGGCACAGACGGAGATACGCGCACTGCGCT
genomic: CTCGGATCCCGTCAGGGTCGAGCTCACCCGCCTGGAGAACGAGCTCAGGGgtcggtttat ... ctggtgtcagACAAGGAGAGGGAGCTTGGGGAGGCACAGACGGAGATACGCGCACTGCGCT
EST: gi|71444482|gb|DR825532.1|DR825532
EST:     CTCGGATCCCGTCAGGGTCGAGCTCACCCGCCTGGAGAACGAGCTCAGGG                         ACAAGGAGAGGGAGCTTGGGGAGGCACAGACGGAGATACGCGCACTGCGCT
genomic: CTCGGATCCCGTCAGGGTCGAGCTCACCCGCCTGGAGAACGAGCTCAGGGgtcggtttat ... ctggtgtcagACAAGGAGAGGGAGCTTGGGGAGGCACAGACGGAGATACGCGCACTGCGCT
EST: gi|71439208|gb|DR820258.1|DR820258
EST:     CTCGGATCCCGTCAGGGTCGAGCTCACCCGCCTGGAGAACGAGCTCAGGG                         ACAAGGAGAGGGAGCTTGGGGAGGCACAGACGGAGATACGCGCACTGCGCT
genomic: CTCGGATCCCGTCAGGGTCGAGCTCACCCGCCTGGAGAACGAGCTCAGGGgtcggtttat ... ctggtgtcagACAAGGAGAGGGAGCTTGGGGAGGCACAGACGGAGATACGCGCACTGCGCT

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: 85

CCTGTGCGGGCCAGCCTCGATGCCGACGAGTTCATGGCGCTGATGCACGGCTCGGATCCCGTCAGGGTCGAGCTCACCCGCCTGGAGAACGAGCTCAGGGgtcggtttat ... ctggtgtcagACAAGGAGAGGGAGCTTGGGGAGGCACAGACGGAGATACGCGCACTGCGCTTGTCGGAGAGGGCGCGGGAGAAAGCCGTCGAGGAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 39

CCTGTGCGGGCCAGCCTCGATGCCGACGAGTTCATGGCGCTGATGCACGGCTCGGATCCCGTCAGGGTCGAGCTCACCCGCCTGGAGAACGAGCTCAGGGgtcggtttat ... ctggtgtcagACAAGGAGAGGGAGCTTGGGGAGGCACAGACGGAGATACGCGCACTGCGCTTGTCGGAGAGGGCGCGGGAGAAAGCCGTCGAGGAG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 53

CCTGTGCGGGCCAGCCTCGATGCCGACGAGTTCATGGCGCTGATGCACGGCTCGGATCCCGTCAGGGTCGAGCTCACCCGCCTGGAGAACGAGCTCAGGGgtcggtttat ... ctggtgtcagACAAGGAGAGGGAGCTTGGGGAGGCACAGACGGAGATACGCGCACTGCGCTTGTCGGAGAGGGCGCGGGAGAAAGCCGTCGAGGAG


Block sizes: 43 (upstream exon), 47 (downstream exon)
Score: 39

CCTGTGCGGGCCAGCCTCGATGCCGACGAGTTCATGGCGCTGATGCACGGCTCGGATCCCGTCAGGGTCGAGCTCACCCGCCTGGAGAACGAGCTCAGGGgtcggtttat ... ctggtgtcagACAAGGAGAGGGAGCTTGGGGAGGCACAGACGGAGATACGCGCACTGCGCTTGTCGGAGAGGGCGCGGGAGAAAGCCGTCGAGGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTGTGCGGGCCAGCCTCGATGCCGACGAGTTCATGGCGCTGATGCACGGCTCGGATCCCGTCAGGGTCGAGCTCACCCGCCTGGAGAACGAGCTCAGGGgtcggtttattgatctgtctgttcatttcgtgctttgattttcttcattgcagtggtatctagtgttttgttttggagcgaggatttatttgtgtgcggtttttgctggtgtcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA