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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggcgctccctagctcggcccctcctcccccttacataatacaagttttttcgttcgattcgcggctgcaatgcagacggcgcgagcgagtgctaacgccgtgtggtctcctccgtctctccccgggccgggcgcagCGGCGAACCACAGCTACAACATCGACTGCGGCGGCGCGGCGGACTTCACCTCGGCCTTGGGGCGCCGGTGGCTCGCCGACCGGTTCTTCTCCGCGGGCGG

Basic information

species Zea mays
transcript GRMZM2G022897_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G022897_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g04720.1 (Oryza sativa), 3'ss of exon 1
gtaggcgctccctagctcggcccctcctcccccttacataatacaagttttttcgttcgattcgcggctgcaatgcagacggcgcgagcgagtgctaacgccgtgtggtctcctccgtctctccccgggccgggcgcagCGGCGAACCACAGCTACAACATCGACTGCGGCGGCGCGGCGGACTTCACCTCGGCCTTGGGGCGCCGGTGGCTCGCCGACCGGTTCTTCTCCGCGGGCGG
                        |   | | ||   || |       |  || | |  | | | |  ||  |||        |     | ||  |       | |||| |  |    |||  || | ||||||         |||||||||||||||||||||||||||||||||||||||||||  |||||  || || || |||||||||||||||| |||||||||||| ||   
-----------------------gtaagctcactcggatcagtgggaatggtttgctgaaattgagcttgagatggtagtaatggtgatgggt-ttggt----tttggttttgtgttcctcctccagCGCCGGG---------GAACCACAGCTACAACATCGACTGCGGCGGCGCGGCGGACTTCGTCTCGGTGTTCGGCCGACGGTGGCTCGCCGACCAGTTCTTCTCCGCCGG---
















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|211193272|gb|FL105061.1|FL105061
EST:     CCTCGCCGGCGCCGGCGCCCGCGCCTCCGACGACCCCTTCCTCTCCGGCG                         CGGCGAACCACAGCTACAACATCGACTGCGGCGGGGTGGCGGACTTCACCT
genomic: CCTCGCCGGCGCCGGCGCCCGCGCCTCCGACGACCCCTTCCTCTCCGGCGgtaggcgctc ... ccgggcgcagCGGCGAACCACAGCTACAACATCGACTGCGGCGGCGCGGCGGACTTCACCT
EST: gi|101399870|gb|EB821782.1|EB821782
EST:     CCTCGCCGGCGCCGGCGCCCGCGCCTCCGACGACCCCTTCCTCTCCGGCG                         CGGCGAACCACAGCTACAACATCGACTGCGGCGGGGTGGCGGACTTCACCT
genomic: CCTCGCCGGCGCCGGCGCCCGCGCCTCCGACGACCCCTTCCTCTCCGGCGgtaggcgctc ... ccgggcgcagCGGCGAACCACAGCTACAACATCGACTGCGGCGGCGCGGCGGACTTCACCT
EST: gi|211112994|gb|FL283014.1|FL283014
EST:     CCTCGCCGGCGCCGGCGCCCGCGCCTCCGACGACCCCTTCCTCTCCGGCG                         CGGCGAACCACAGCTACAACATCGACTGCGGCGGGGTGGCGGACTTCACCT
genomic: CCTCGCCGGCGCCGGCGCCCGCGCCTCCGACGACCCCTTCCTCTCCGGCGgtaggcgctc ... ccgggcgcagCGGCGAACCACAGCTACAACATCGACTGCGGCGGCGCGGCGGACTTCACCT
EST: gi|148975991|gb|EE025844.2|EE025844
EST:     CCTCGCCGGCGCCGGCGCCCGCGCCTCCGACGACCCCTTCCTCTCCGGCG                         CGGCGAACCACAGCTACAACATCGACTGCGGCGGCGCGGCGGACTTCACCT
genomic: CCTCGCCGGCGCCGGCGCCCGCGCCTCCGACGACCCCTTCCTCTCCGGCGgtaggcgctc ... ccgggcgcagCGGCGAACCACAGCTACAACATCGACTGCGGCGGCGCGGCGGACTTCACCT
EST: gi|78075156|gb|DV503590.1|DV503590
EST:     CCTCGCCGGCGCCGGCGCCCGCGCCTCCGACGACCCCTTCCTCTCCGGCG                         CGGCGAACCACAGCTACAACATCGACTGCGGCGGCGCGGCGGACTTCACCT
genomic: CCTCGCCGGCGCCGGCGCCCGCGCCTCCGACGACCCCTTCCTCTCCGGCGgtaggcgctc ... ccgggcgcagCGGCGAACCACAGCTACAACATCGACTGCGGCGGCGCGGCGGACTTCACCT
EST: gi|149073200|gb|EE161483.2|EE161483
EST:     CCTCGCCGGCGCCGGCGCCCGCGCCTCCGACGACCCCTTCCTCTCCGGCG                         CGGCGAACCACAGCTACAACATCGACTGCGGCGGCGCGGCGGACTTCACCT
genomic: CCTCGCCGGCGCCGGCGCCCGCGCCTCCGACGACCCCTTCCTCTCCGGCGgtaggcgctc ... ccgggcgcagCGGCGAACCACAGCTACAACATCGACTGCGGCGGCGCGGCGGACTTCACCT
EST: gi|149009248|gb|EE041346.2|EE041346
EST:     CCTCGCCGGCGCCGGCGCCCGCGCCTCCGACGACCCCTTCCTCTCCGGCG                         CGGCGAACCACAGCTACAACATCGACTGCGGCGGCGCGGCGGACTTCACCT
genomic: CCTCGCCGGCGCCGGCGCCCGCGCCTCCGACGACCCCTTCCTCTCCGGCGgtaggcgctc ... ccgggcgcagCGGCGAACCACAGCTACAACATCGACTGCGGCGGCGCGGCGGACTTCACCT
EST: gi|78110438|gb|DV528850.1|DV528850
EST:     CCTCGCCGGCGCCGGCGCCCGCGCCTCCGACGACCCCTTCCTCTCCGGCG                         CGGCGAACCACAGCTACAACATCGACTGCGGCGGCGCGGCGGACTTCACCT
genomic: CCTCGCCGGCGCCGGCGCCCGCGCCTCCGACGACCCCTTCCTCTCCGGCGgtaggcgctc ... ccgggcgcagCGGCGAACCACAGCTACAACATCGACTGCGGCGGCGCGGCGGACTTCACCT
EST: gi|78085794|gb|DV514187.1|DV514187
EST:     CCTCGCCGGCGCCGGCGCCCGCGCCTCCGACGACCCCTTCCTCTCCGGCG                         CGGCGAACCACAGCTACAACATCGACTGCGGCGGCGCGGCGGACTTCACCT
genomic: CCTCGCCGGCGCCGGCGCCCGCGCCTCCGACGACCCCTTCCTCTCCGGCGgtaggcgctc ... ccgggcgcagCGGCGAACCACAGCTACAACATCGACTGCGGCGGCGCGGCGGACTTCACCT
EST: gi|78078768|gb|DV507180.1|DV507180
EST:     CCTCGCCGGCGCCGGCGCCCGCGCCTCCGACGACCCCTTCCTCTCCGGCG                         CGGCGAACCACAGCTACAACATCGACTGCGGCGGCGCGGCGGACTTCACCT
genomic: CCTCGCCGGCGCCGGCGCCCGCGCCTCCGACGACCCCTTCCTCTCCGGCGgtaggcgctc ... ccgggcgcagCGGCGAACCACAGCTACAACATCGACTGCGGCGGCGCGGCGGACTTCACCT
EST: gi|149084614|gb|EE174090.2|EE174090
EST:     CCTCGCCGGCGCCGGCGCCCGCGCCTCCGACGACCCCTTCCTCTCCGGCG                         CGGCGAACCACAGCTACAACATCGACTGCGGCGGCGCGGCGGACTTCACCT
genomic: CCTCGCCGGCGCCGGCGCCCGCGCCTCCGACGACCCCTTCCTCTCCGGCGgtaggcgctc ... ccgggcgcagCGGCGAACCACAGCTACAACATCGACTGCGGCGGCGCGGCGGACTTCACCT

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 3 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 40

CGACAGGGGATCCCTCCCCCAATGCGGCTGCTCCCGCTCCTCCTGCTCCTCCTCGCCGGCGCCGGCGCCCGCGCCTCCGACGACCCCTTCCTCTCCGGCGgtaggcgctc ... ccgggcgcagCGGCGAACCACAGCTACAACATCGACTGCGGCGGCGCGGCGGACTTCACCTCGGCCTTGGGGCGCCGGTGGCTCGCCGACCGGTTCTTCTCCGCGGGCGG


Block sizes: 44 (upstream exon), 29 (downstream exon)
Score: 5

CGACAGGGGATCCCTCCCCCAATGCGGCTGCTCCCGCTCCTCCTGCTCCTCCTCGCCGGCGCCGGCGCCCGCGCCTCCGACGACCCCTTCCTCTCCGGCGgtaggcgctc ... ccgggcgcagCGGCGAACCACAGCTACAACATCGACTGCGGCGGCGCGGCGGACTTCACCTCGGCCTTGGGGCGCCGGTGGCTCGCCGACCGGTTCTTCTCCGCGGGCGG


Block sizes: 24 (upstream exon), 36 (downstream exon)
Score: 3

CGACAGGGGATCCCTCCCCCAATGCGGCTGCTCCCGCTCCTCCTGCTCCTCCTCGCCGGCGCCGGCGCCCGCGCCTCCGACGACCCCTTCCTCTCCGGCGgtaggcgctc ... ccgggcgcagCGGCGAACCACAGCTACAACATCGACTGCGGCGGCGCGGCGGACTTCACCTCGGCCTTGGGGCGCCGGTGGCTCGCCGACCGGTTCTTCTCCGCGGGCGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgagcgagtgctaacgccgtgtggtctcctccgtctctccccgggccgggcgcagCGGCGAACCACAGCTACAACATCGACTGCGGCGGCGCGGCGGACTTCACCTCGGCCTTGGGGCGCCGGTGGCTCGCCGACCGGTTCTTCTCCGCGGGCGG
        tgctaac  putative branch site (score: 3)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggcgctccctagctcggcccctcctcccccttacataatacaagttttttcgttcgattcgcggctgcaatgcagacggcgcgagcgagtgctaacgccgtgtggtctcctccgtctctccccgggccgggcgcagCGGCGAACCACAGCTACAACATCGACTGCGGCGGCGCGGCGGACTTCACCTCGGCCTTGGGGCGCCGGTGGCTCGCCGACCGGTTCTTCTCCGCGGGCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -CGGCGGCG