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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgtcgcgtatcctgaccgcggactgcgctcttgcgccttaacggcggtatgtgatcccaagggtccttatccagtgagggaccgtggagattcagaattccagatgctttgtttctgatgattcatgacgtctctttgcagGAGATACTCGACAAGGGGAAGAAGGTGAAGGATGGAGGAGGGGGAGACGGGGAAACCGATCTCAACGAGGCTCTTACCTCGCAG

Basic information

species Zea mays
transcript GRMZM2G104133_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G104133_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g08980.4 (Oryza sativa), 3'ss of exon 1
gtgcgtcgcgtatcc-tgaccgcgga----------ctgcgctcttgcgccttaacggcggtatgtgatcccaagggtccttatccag-tgagggaccgt-ggagattcagaattccagatgctttgtttctgatga---ttcatg--------acgtctct------ttgcagGAGATACTCGACAAGGGGAAGAAGGTGAAGGATGGAGGAGGGGGAGACGGGGAAACCGATCTCAACGAGGCTCTTACCTCGCAG
||||||||||| |||    ||  ||           |  ||||||| | ||| | | |   |  |||||||    ||||||     || ||  ||  ||     |  |  || ||  |  || |||| |||||||||   | | ||        || |||||      |||||||||||||| ||||||||| |||||| ||| || |||| ||||||   |||||   ||||  | |  || || || ||    |||
gtgcgtcgcgtctccaccgccttggggggaagaatcccccgctcttcctcctcacctg-aatcggtgatcct---ggtcctgggagaggtggcggcgcgccaccggattggattttgatttggtttggttctgatgatgatccgtgccttgcggacctctctcactcgttgcagGAGATACTGGACAAGGGGGAGAAGGGGAAAGACGGAGAAGGGGG---CGGGGGCGCCGACATGACGGACGCGCTCACTAGACAG
















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|60352799|gb|DN219772.1|DN219772
EST:     CCGTCGTCCTCCGCAACGGCCGCCTCGCCGAGATCCTCGGCGAGCTCCAG                         GAGATACTCGACAAGGGGAAGAAGGTGAAGGATGGAGGAGGGGGAGACGGG
genomic: CCGTCGTCCTCCGCAACGGCCGCCTCGCCGAGATCCTCGGCGAGCTCCAGgtgcgtcgcg ... ctctttgcagGAGATACTCGACAAGGGGAAGAAGGTGAAGGATGGAGGAGGGGGAGACGGG
EST: gi|211416489|gb|FL082392.1|FL082392
EST:     CCGTCGTCCTCCGCAACGGCCGCCTCGCCGAGATCCTCGGCGAGCTCCAG                         GAGATACTCGACAAGGGGAAGAAGGTGAAGGATGGAGGAGGGGGAGACGGG
genomic: CCGTCGTCCTCCGCAACGGCCGCCTCGCCGAGATCCTCGGCGAGCTCCAGgtgcgtcgcg ... ctctttgcagGAGATACTCGACAAGGGGAAGAAGGTGAAGGATGGAGGAGGGGGAGACGGG
EST: gi|211170332|gb|FK988414.1|FK988414
EST:     CCGTCGTCCTCCGCAACGGCCGCCTCGCCGAGATCCTCGGCGAGCTCCAG                         GAGATACTCGACAAGGGGAAGAAGGTGAAGGATGGAGGAGGGGGAGACGGG
genomic: CCGTCGTCCTCCGCAACGGCCGCCTCGCCGAGATCCTCGGCGAGCTCCAGgtgcgtcgcg ... ctctttgcagGAGATACTCGACAAGGGGAAGAAGGTGAAGGATGGAGGAGGGGGAGACGGG
EST: gi|211170335|gb|FK988417.1|FK988417
EST:     CCGTCGTCCTCCGCAACGGCCGCCTCGCCGAGATCCTCGGCGAGCTCCAG                         GAGATACTCGACAAGGGGAAGAAGGTGAAGGATGGAGGAGGGGGAGACGGG
genomic: CCGTCGTCCTCCGCAACGGCCGCCTCGCCGAGATCCTCGGCGAGCTCCAGgtgcgtcgcg ... ctctttgcagGAGATACTCGACAAGGGGAAGAAGGTGAAGGATGGAGGAGGGGGAGACGGG
EST: gi|211170328|gb|FK988410.1|FK988410
EST:     CCGTCGTCCTCCGCAACGGCCGCCTCGCCGAGATCCTCGGCGAGCTCCAG                         GACATACTCGACAAGGGGAAGAAGGTGAAGGATGGAGGAGGGGGAGACGGG
genomic: CCGTCGTCCTCCGCAACGGCCGCCTCGCCGAGATCCTCGGCGAGCTCCAGgtgcgtcgcg ... ctctttgcagGAGATACTCGACAAGGGGAAGAAGGTGAAGGATGGAGGAGGGGGAGACGGG
EST: gi|211170338|gb|FK988420.1|FK988420
EST:     CCGTCGTCCTCCGCAACGGCCCCCTCGCCGAGATCCTCGGCGAGCTCCAG                         GAGATACTCGACAAGGGGAAGAAGGTGAAGGATGGAGGAGGGGGAGACGGG
genomic: CCGTCGTCCTCCGCAACGGCCGCCTCGCCGAGATCCTCGGCGAGCTCCAGgtgcgtcgcg ... ctctttgcagGAGATACTCGACAAGGGGAAGAAGGTGAAGGATGGAGGAGGGGGAGACGGG
EST: gi|211170331|gb|FK988413.1|FK988413
EST:     CCGTCGTCCTCCGCAACGGCCGCCTCGCCGAGATCCTCGGCGAGCTCCAG                         GAGATACTCGACAAGGGGAAGAAGGTGAAGGATGGAGGAGGGGGAGACGGG
genomic: CCGTCGTCCTCCGCAACGGCCGCCTCGCCGAGATCCTCGGCGAGCTCCAGgtgcgtcgcg ... ctctttgcagGAGATACTCGACAAGGGGAAGAAGGTGAAGGATGGAGGAGGGGGAGACGGG
EST: gi|211170336|gb|FK988418.1|FK988418
EST:     CCGTCGTCCTCCGCAACGGCCGCCTCGCCGAGATCCTCGGCGAGCTCCAG                         GAGATACTCGACAAGGGGAAGAAGGTGAAGGATGGAGGAGGGGGAGACGGG
genomic: CCGTCGTCCTCCGCAACGGCCGCCTCGCCGAGATCCTCGGCGAGCTCCAGgtgcgtcgcg ... ctctttgcagGAGATACTCGACAAGGGGAAGAAGGTGAAGGATGGAGGAGGGGGAGACGGG
EST: gi|37420028|gb|CF647700.1|CF647700
EST:     CCGTCGTCCTCCGCAACGGCCGCCTCGCCGAGATCCTCGGCGAGCTCCAG                         GAGATACTCGACAAGGGGAAGAAGGTGAAGGATGGAGGAGGGGGAGAC
genomic: CCGTCGTCCTCCGCAACGGCCGCCTCGCCGAGATCCTCGGCGAGCTCCAGgtgcgtcgcg ... ctctttgcagGAGATACTCGACAAGGGGAAGAAGGTGAAGGATGGAGGAGGGGGAGAC
EST: gi|211170337|gb|FK988419.1|FK988419
EST:     CCGTCGTCCTCCGCAACGGCCGCCTCGCCGAGATCCTCGGCGAGCTCCAG                         GAGATACTCGACAAGGGGAAGAAGGTGAAGGATGGAGGAGGGGGAGACGGG
genomic: CCGTCGTCCTCCGCAACGGCCGCCTCGCCGAGATCCTCGGCGAGCTCCAGgtgcgtcgcg ... ctctttgcagGAGATACTCGACAAGGGGAAGAAGGTGAAGGATGGAGGAGGGGGAGACGGG
EST: gi|211170340|gb|FK988422.1|FK988422
EST:     CCGTCGTCCTCCGCAACGGCCGCCTCGCCGAGATCCTCGGCGAGCTCCAG                         GAGATACTCGACAAGGGGAAGAAGGTGAAGGATGGAGGAGGGGGAGACGGG
genomic: CCGTCGTCCTCCGCAACGGCCGCCTCGCCGAGATCCTCGGCGAGCTCCAGgtgcgtcgcg ... ctctttgcagGAGATACTCGACAAGGGGAAGAAGGTGAAGGATGGAGGAGGGGGAGACGGG
EST: gi|60338640|gb|DN205613.1|DN205613
EST:     CCGTCGTCCTCCGCAACGGCCGCCTCGCCGAGATCCTCGGCGAGCTCCAG                         GAGATACTCGACAAGGGGAAGAAGGTGAAGGATGGAGGAGGGGGAGACGGG
genomic: CCGTCGTCCTCCGCAACGGCCGCCTCGCCGAGATCCTCGGCGAGCTCCAGgtgcgtcgcg ... ctctttgcagGAGATACTCGACAAGGGGAAGAAGGTGAAGGATGGAGGAGGGGGAGACGGG
EST: gi|211170339|gb|FK988421.1|FK988421
EST:     CCGTCGTCCTCCGCAACGGCCGCCTCGCCGAGATCCTCGGCGAGCTCCAG                         GAGATACTCGACAAGGGGAAGAAGGTGAAGGATGGAGGAGGGGGAGACGGG
genomic: CCGTCGTCCTCCGCAACGGCCGCCTCGCCGAGATCCTCGGCGAGCTCCAGgtgcgtcgcg ... ctctttgcagGAGATACTCGACAAGGGGAAGAAGGTGAAGGATGGAGGAGGGGGAGACGGG
EST: gi|211170333|gb|FK988415.1|FK988415
EST:     CCGTCGTCCTCCGCAACGGCCGCCTCGCCGAGATCCTCGGCGAGCTCCAG                         GAGATACTCGACAAGGGGAAGAAGGTGAAGGATGGAGGAGGGGGAGACGGG
genomic: CCGTCGTCCTCCGCAACGGCCGCCTCGCCGAGATCCTCGGCGAGCTCCAGgtgcgtcgcg ... ctctttgcagGAGATACTCGACAAGGGGAAGAAGGTGAAGGATGGAGGAGGGGGAGACGGG

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: 240

CATGGGCCTTACCCGGGTCGTTATCCTCGTCGGCGCCGGCGTTGCCGGCTCCGTCGTCCTCCGCAACGGCCGCCTCGCCGAGATCCTCGGCGAGCTCCAGgtgcgtcgcg ... ctctttgcagGAGATACTCGACAAGGGGAAGAAGGTGAAGGATGGAGGAGGGGGAGACGGGGAAACCGATCTCAACGAGGCTCTTACCTCGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 593

CATGGGCCTTACCCGGGTCGTTATCCTCGTCGGCGCCGGCGTTGCCGGCTCCGTCGTCCTCCGCAACGGCCGCCTCGCCGAGATCCTCGGCGAGCTCCAGgtgcgtcgcg ... ctctttgcagGAGATACTCGACAAGGGGAAGAAGGTGAAGGATGGAGGAGGGGGAGACGGGGAAACCGATCTCAACGAGGCTCTTACCTCGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 389

CATGGGCCTTACCCGGGTCGTTATCCTCGTCGGCGCCGGCGTTGCCGGCTCCGTCGTCCTCCGCAACGGCCGCCTCGCCGAGATCCTCGGCGAGCTCCAGgtgcgtcgcg ... ctctttgcagGAGATACTCGACAAGGGGAAGAAGGTGAAGGATGGAGGAGGGGGAGACGGGGAAACCGATCTCAACGAGGCTCTTACCTCGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 470

CATGGGCCTTACCCGGGTCGTTATCCTCGTCGGCGCCGGCGTTGCCGGCTCCGTCGTCCTCCGCAACGGCCGCCTCGCCGAGATCCTCGGCGAGCTCCAGgtgcgtcgcg ... ctctttgcagGAGATACTCGACAAGGGGAAGAAGGTGAAGGATGGAGGAGGGGGAGACGGGGAAACCGATCTCAACGAGGCTCTTACCTCGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagattcagaattccagatgctttgtttctgatgattcatgacgtctctttgcagGAGATACTCGACAAGGGGAAGAAGGTGAAGGATGGAGGAGGGGGAGACGGGGAAACCGATCTCAACGAGGCTCTTACCTCGCAG
                          ttctgat  putative branch site (score: 470)
                                          cgtctcttt  putative PPT
                     tttgttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgtcgcgtatcctgaccgcggactgcgctcttgcgccttaacggcggtatgtgatcccaagggtccttatccagtgagggaccgtggagattcagaattccagatgctttgtttctgatgattcatgacgtctctttgcagGAGATACTCGACAAGGGGAAGAAGGTGAAGGATGGAGGAGGGGGAGACGGGGAAACCGATCTCAACGAGGCTCTTACCTCGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG