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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCTGCCTCTAGCTCGATCGGTTAGTTTGTCGTGTTGCTTACGTACGTCAGCAGAGGCCATCGTCGAGTGTATCCCGTGGTCGAGAAGAGGGAAGAAATGgttagtgcgtatacagtttatcttacttaattttctcgatcatcgttcttgtgtgctccttcctcgcgtcagcactcgtactacaggcagttccagcagt...

Basic information

species Zea mays
transcript GRMZM2G044851_T01
intron # 1
splice site 5'
intron type U2

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|76927974|gb|DV171443.1|DV171443
EST:     GCAGAGGCCATCGTCGAGTGTATCCCGTGGTCGAGAAGAGGGAAGAAATG                         TCTGCGAACGACGGCGCCGGCGACACGAAGATGAGGGCGATCGTCGTCGTA
genomic: GCAGAGGCCATCGTCGAGTGTATCCCGTGGTCGAGAAGAGGGAAGAAATGgttagtgcgt ... gctgctgcagTCTGCGAACGACGGCGCCGGCGACACGAAGATGAGGGCGATCGTCGTCGTA
EST: gi|148987145|gb|EE030973.2|EE030973
EST:     GCAGAGGCCATCGTCGAGTGTATCCCGTGGTCGAGAAGAGGGAAGAAATG                         TCTGCGAACGACGGCGCCGGCGACACGAAGATGAGGGCGATCGTCGTCGTA
genomic: GCAGAGGCCATCGTCGAGTGTATCCCGTGGTCGAGAAGAGGGAAGAAATGgttagtgcgt ... gctgctgcagTCTGCGAACGACGGCGCCGGCGACACGAAGATGAGGGCGATCGTCGTCGTA
EST: gi|211540626|gb|FL330694.1|FL330694
EST:     GCAGAGGCCATCGTCGAGTGTATCCAGTGGTCGAGAAGAGGGAAGAAATG                         TCTGCGAACGACGGCGCCGGCGACACGAAGATGAGGGCGATCGTCGTCGTA
genomic: GCAGAGGCCATCGTCGAGTGTATCCCGTGGTCGAGAAGAGGGAAGAAATGgttagtgcgt ... gctgctgcagTCTGCGAACGACGGCGCCGGCGACACGAAGATGAGGGCGATCGTCGTCGTA
EST: gi|50328864|gb|CO523990.1|CO523990
EST:     GCAGAGGCCATCGTCGAGTGTATCCCGTGGTCGAGAAGAGGGAAGAAATG                         TCTGCGAACGACGGCGCCGGCGACACGAAGATGAGGGCGATCGTCGTCGTA
genomic: GCAGAGGCCATCGTCGAGTGTATCCCGTGGTCGAGAAGAGGGAAGAAATGgttagtgcgt ... gctgctgcagTCTGCGAACGACGGCGCCGGCGACACGAAGATGAGGGCGATCGTCGTCGTA
EST: gi|211020704|gb|FL318028.1|FL318028
EST:     GCAGAGGCCATCGTCGAGTGTATCCAGTGGTCGAGAAGAGGGAAGAAATG                         TCTGCGAACGACGGCGCCGGCGACACGAAGATGAGGGCGATCGTCGTCGTA
genomic: GCAGAGGCCATCGTCGAGTGTATCCCGTGGTCGAGAAGAGGGAAGAAATGgttagtgcgt ... gctgctgcagTCTGCGAACGACGGCGCCGGCGACACGAAGATGAGGGCGATCGTCGTCGTA
EST: gi|86474663|gb|DY241033.1|DY241033
EST:     GCAGAGGCCATCGTCGAGTGTATCCCGTGGTCGAGAAGAGGGAAGAAATG                         TCTGCAAACGACGGCGCCGGCGACACAAAGATGAGGGCGATCGTCGTCGTA
genomic: GCAGAGGCCATCGTCGAGTGTATCCCGTGGTCGAGAAGAGGGAAGAAATGgttagtgcgt ... gctgctgcagTCTGCGAACGACGGCGCCGGCGACACGAAGATGAGGGCGATCGTCGTCGTA
EST: gi|71417415|gb|DR804042.1|DR804042
EST:     GCAGAGGCCATCGTCGAGTGTATCCCGTGGTCGAGAAGAGGGAAGAAATG                         TCTGCGAACGACGGCGCCGGCGACACGAAGATGAGGGCGATCGTCGTCGTA
genomic: GCAGAGGCCATCGTCGAGTGTATCCCGTGGTCGAGAAGAGGGAAGAAATGgttagtgcgt ... gctgctgcagTCTGCGAACGACGGCGCCGGCGACACGAAGATGAGGGCGATCGTCGTCGTA
EST: gi|74245993|gb|DT653907.1|DT653907
EST:     GCAGAGGCCATCGTCGAGTGTATCCCGTGGTCGAGAAGAGGGAAGAAATG                         TCTGCGAACGACGGCGCCGGCGACACGAAGATGAGGGCGATCGTCGTCGTA
genomic: GCAGAGGCCATCGTCGAGTGTATCCCGTGGTCGAGAAGAGGGAAGAAATGgttagtgcgt ... gctgctgcagTCTGCGAACGACGGCGCCGGCGACACGAAGATGAGGGCGATCGTCGTCGTA
EST: gi|74237215|gb|DT645129.1|DT645129
EST:     GCAGAGGCCATCGTCGAGTGTATCCCGTGGTCGAGAAGAGGGAAGAAATG                         TCTGCGAACGACGGCGCCGGCGACACGAAGATGAGGGCGATCGTCGTCGTA
genomic: GCAGAGGCCATCGTCGAGTGTATCCCGTGGTCGAGAAGAGGGAAGAAATGgttagtgcgt ... gctgctgcagTCTGCGAACGACGGCGCCGGCGACACGAAGATGAGGGCGATCGTCGTCGTA
EST: gi|71314199|gb|DR793714.1|DR793714
EST:     GCAGAGGCCATCGTCGAGTGTATCCCGTGGTCGAGAAGAGGGAAGAAATG                         TCTGCGAACGACGGCGCCGGCGACACGAAGATGAGGGCGATCGTCGTCGTA
genomic: GCAGAGGCCATCGTCGAGTGTATCCCGTGGTCGAGAAGAGGGAAGAAATGgttagtgcgt ... gctgctgcagTCTGCGAACGACGGCGCCGGCGACACGAAGATGAGGGCGATCGTCGTCGTA
EST: gi|71424538|gb|DR806351.1|DR806351
EST:     GCAGAGGCCATCGTCGAGTGTATCCCGTGGTCGAGAAGAGGGAAGAAATG                         TCTGCGAACGACGGCGCCGGCGACACGAAGATGAGGGCGATCGTCGTCGTA
genomic: GCAGAGGCCATCGTCGAGTGTATCCCGTGGTCGAGAAGAGGGAAGAAATGgttagtgcgt ... gctgctgcagTCTGCGAACGACGGCGCCGGCGACACGAAGATGAGGGCGATCGTCGTCGTA
EST: gi|211010835|gb|FL363372.1|FL363372
EST:     GCAGAGGCCATCGTCGAGTGTATCCAGTGGTCGAGAAGAGGGAAGAAATG                         TCTGCGAACGACGGCGCCGGCGACACGAAGATGAGGGCGATCGTCGTCGTA
genomic: GCAGAGGCCATCGTCGAGTGTATCCCGTGGTCGAGAAGAGGGAAGAAATGgttagtgcgt ... gctgctgcagTCTGCGAACGACGGCGCCGGCGACACGAAGATGAGGGCGATCGTCGTCGTA
EST: gi|74240219|gb|DT648133.1|DT648133
EST:     GCAGAGGCCATCGTCGAGTGTATCCCGTGGTCGAGAAGAGGGAAGAAATG                         TCTGCGAACGACGGCGCCGGCGACACGAAGATGAGGGCGATCGTCGTCGTA
genomic: GCAGAGGCCATCGTCGAGTGTATCCCGTGGTCGAGAAGAGGGAAGAAATGgttagtgcgt ... gctgctgcagTCTGCGAACGACGGCGCCGGCGACACGAAGATGAGGGCGATCGTCGTCGTA

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: 39 (upstream exon), 38 (downstream exon)
Score: 5

AGCTGCCTCTAGCTCGATCGGTTAGTTTGTCGTGTTGCTTACGTACGTCAGCAGAGGCCATCGTCGAGTGTATCCCGTGGTCGAGAAGAGGGAAGAAATGgttagtgcgt ... gctgctgcagTCTGCGAACGACGGCGCCGGCGACACGAAGATGAGGGCGATCGTCGTCGTAGAGGAAGGGGAGATGAGCGCGCCGGCGGCGACGCCGAAGCAGGGCAAGT


Block sizes: 22 (upstream exon), 45 (downstream exon)
Score: 5

AGCTGCCTCTAGCTCGATCGGTTAGTTTGTCGTGTTGCTTACGTACGTCAGCAGAGGCCATCGTCGAGTGTATCCCGTGGTCGAGAAGAGGGAAGAAATGgttagtgcgt ... gctgctgcagTCTGCGAACGACGGCGCCGGCGACACGAAGATGAGGGCGATCGTCGTCGTAGAGGAAGGGGAGATGAGCGCGCCGGCGGCGACGCCGAAGCAGGGCAAGT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 86

AGCTGCCTCTAGCTCGATCGGTTAGTTTGTCGTGTTGCTTACGTACGTCAGCAGAGGCCATCGTCGAGTGTATCCCGTGGTCGAGAAGAGGGAAGAAATGgttagtgcgt ... gctgctgcagTCTGCGAACGACGGCGCCGGCGACACGAAGATGAGGGCGATCGTCGTCGTAGAGGAAGGGGAGATGAGCGCGCCGGCGGCGACGCCGAAGCAGGGCAAGT


Block sizes: 39 (upstream exon), 45 (downstream exon)
Score: 11

AGCTGCCTCTAGCTCGATCGGTTAGTTTGTCGTGTTGCTTACGTACGTCAGCAGAGGCCATCGTCGAGTGTATCCCGTGGTCGAGAAGAGGGAAGAAATGgttagtgcgt ... gctgctgcagTCTGCGAACGACGGCGCCGGCGACACGAAGATGAGGGCGATCGTCGTCGTAGAGGAAGGGGAGATGAGCGCGCCGGCGGCGACGCCGAAGCAGGGCAAGT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCTGCCTCTAGCTCGATCGGTTAGTTTGTCGTGTTGCTTACGTACGTCAGCAGAGGCCATCGTCGAGTGTATCCCGTGGTCGAGAAGAGGGAAGAAATGgttagtgcgtatacagtttatcttacttaattttctcgatcatcgttcttgtgtgctccttcctcgcgtcagcactcgtactacaggcagttccagcagt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA