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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttagtttctttttcttgtcacttctcattgcaacttgatcatcatgccaagtacgtgacttttgtttactcaaaatttcacatgtcagGGCCATGGACTTCCTTGTTGAGTTGTTTCGTAACCTGCTTGAGCATCCAGACTGGACCATGGGTCAATCTTGCACTGATTCATACACCAAGACTTTGAAG

Basic information

species Zea mays
transcript GRMZM2G125556_T03
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G125556_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g40890.1 (Oryza sativa), 3'ss of exon 4
gtacttagtttctttttcttgtcacttctcattgcaacttgatcatcatgccaagtacgtgacttttgtttactcaaaatttcacatgtcagGGCCATGGACTTCCTTGTTGAGTTGTTTCGTAACCTGCTTGAGCATCCAGACTGGACCATGGGTCAATCTTGCACTGATTCATACACCAAGACTTTGAAG
|| |||     ||| ||    | | || |||       || |    ||    ||| |        || || ||||||||||| || | ||||||| ||||||||||||||||| || || ||||||||||||||||||| ||||||||| ||| ||||| |||| ||||||||||| ||||| ||| |||||
gtgcttcaaaccttcttgg-ataatttatcacc----tttcagttgcagcttaagcag-----ccttattaactcaaaattttactt-tcagGGCTATGGACTTCCTTGTTGAATTATTCCGTAACCTGCTTGAGCATCAAGACTGGACTATGAGTCAAGCTTGTACTGATTCATATACCAAAACTCTGAAG
















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|76285485|gb|DV025053.1|DV025053
EST:     ACCGCAAAAGGTTCCTCAAGCTGCACAAATGGGCTTCTGTGGCTGACGAG                         GGCCATGGACTTCCTTGTTGAGTTGTTTCGTAACCTGCTTGAGCATCCAGA
genomic: ACCGCAAAAGGTTCCTCAAGCTGCACAAATGGGCTTCTGTGGCTGACGAGgtacttagtt ... cacatgtcagGGCCATGGACTTCCTTGTTGAGTTGTTTCGTAACCTGCTTGAGCATCCAGA
EST: gi|93282355|gb|EB674619.1|EB674619
EST:     ACCGCAAAAGGTTCCTCAAGCTGCACAAATGGGCTTTTGTGGCTGACGAG                         GGCCATGGACTTCCTTGTTGAGTTGTTTTGTAACCTGCTTGAGCATCCAGA
genomic: ACCGCAAAAGGTTCCTCAAGCTGCACAAATGGGCTTCTGTGGCTGACGAGgtacttagtt ... cacatgtcagGGCCATGGACTTCCTTGTTGAGTTGTTTCGTAACCTGCTTGAGCATCCAGA
EST: gi|211041272|gb|FL124819.1|FL124819
EST:     ACCGCAAAAGGTTCCTCAAGCTGCACAAATGGGCTTCTGTGGCTGACGAG                         GGCCATGGACTTCCTTGTTGAGTTGTTTCGTAACCTGCTTGAGCATCCAGA
genomic: ACCGCAAAAGGTTCCTCAAGCTGCACAAATGGGCTTCTGTGGCTGACGAGgtacttagtt ... cacatgtcagGGCCATGGACTTCCTTGTTGAGTTGTTTCGTAACCTGCTTGAGCATCCAGA
EST: gi|211464236|gb|FL298400.1|FL298400
EST:     ACCGCAAAAGGTTCCTCAAGCTGCACAAATGGGCTTCTGTGGCTGACGAG                         GGCCATGGACTTCCTTGTTGAGTTGTTTCGTAACCTGCTTGAGCATCCAGA
genomic: ACCGCAAAAGGTTCCTCAAGCTGCACAAATGGGCTTCTGTGGCTGACGAGgtacttagtt ... cacatgtcagGGCCATGGACTTCCTTGTTGAGTTGTTTCGTAACCTGCTTGAGCATCCAGA
EST: gi|211377924|gb|FL095474.1|FL095474
EST:     ACCGCAAAAGGTTCCTCAAGCTGCACAAATGGGCTTCTGTGGCTGACGAG                         GGCCATGGACTTCCTTGTTGAGTTGTTTCGTAACCTGCTTGAGCATCCAGA
genomic: ACCGCAAAAGGTTCCTCAAGCTGCACAAATGGGCTTCTGTGGCTGACGAGgtacttagtt ... cacatgtcagGGCCATGGACTTCCTTGTTGAGTTGTTTCGTAACCTGCTTGAGCATCCAGA
EST: gi|211041270|gb|FL124817.1|FL124817
EST:     ACCGCAAAAGGTTCCTCAAGCTGCACAAATGGGCTTCTGTGGCTGACGAG                         GGCCATGGACTTCCTTGTTGAGTTGTTTCGTAACCTGCTTGAGCATCCAGA
genomic: ACCGCAAAAGGTTCCTCAAGCTGCACAAATGGGCTTCTGTGGCTGACGAGgtacttagtt ... cacatgtcagGGCCATGGACTTCCTTGTTGAGTTGTTTCGTAACCTGCTTGAGCATCCAGA
EST: gi|211041278|gb|FL124825.1|FL124825
EST:     ACCGCAAAAGGTTCCTCAAGCTGCACAAATGGGCTTCTGTGGCTGACGAG                         GGCCATGGACTTCCTTGTTGAGTTGTTTCGTAACCTGCTTGAGCATCCAGA
genomic: ACCGCAAAAGGTTCCTCAAGCTGCACAAATGGGCTTCTGTGGCTGACGAGgtacttagtt ... cacatgtcagGGCCATGGACTTCCTTGTTGAGTTGTTTCGTAACCTGCTTGAGCATCCAGA
EST: gi|71771167|gb|DR969104.1|DR969104
EST:     ACCGCAAAAGGTTCCTCAAGCTGCACAAATGGGCTTCTGTGGCTGACGAG                         GGCCATGGACTTCCTTGTTGAGTTGTTTCGTAACCTGCTTGAGCATCCAGA
genomic: ACCGCAAAAGGTTCCTCAAGCTGCACAAATGGGCTTCTGTGGCTGACGAGgtacttagtt ... cacatgtcagGGCCATGGACTTCCTTGTTGAGTTGTTTCGTAACCTGCTTGAGCATCCAGA
EST: gi|211464240|gb|FL298404.1|FL298404
EST:     ACCGCAAAAGGTTCCTCAAGCTGCACAAATGGGCTTCTGTGGCTGACGAG                         GGCCCATGGACTTCCTTGTTGAGTTGGTTTCGTAACCTGCTTGAGCATCC
genomic: ACCGCAAAAGGTTCCTCAAGCTGCACAAATGGGCTTCTGTGGCTGACGAGgtacttagtt ... cacatgtcagGGCC-ATGGACTTCCTTGTTGAGTTG-TTTCGTAACCTGCTTGAGCATCC
EST: gi|211041276|gb|FL124823.1|FL124823
EST:     ACCGCAAAAGGTTCCTCAAGCTGCACAAATGGGCTTCTGTGGCTGACGAG                         GGCCATGGACTTCCTTGTTGAGTTGTTTCGTAACCTGCTTGAGCATCCAGA
genomic: ACCGCAAAAGGTTCCTCAAGCTGCACAAATGGGCTTCTGTGGCTGACGAGgtacttagtt ... cacatgtcagGGCCATGGACTTCCTTGTTGAGTTGTTTCGTAACCTGCTTGAGCATCCAGA
EST: gi|60400894|gb|DN233701.1|DN233701
EST:     ACCGCAAAAGGTTCCTCAAGCTGCACAAATGGGCTTCTGTGGCTGACGAG                         GGCCATGGACTTCCTTGTTGAGTTGTTTCGTAACCTGCTTGAGCATCCAGA
genomic: ACCGCAAAAGGTTCCTCAAGCTGCACAAATGGGCTTCTGTGGCTGACGAGgtacttagtt ... cacatgtcagGGCCATGGACTTCCTTGTTGAGTTGTTTCGTAACCTGCTTGAGCATCCAGA
EST: gi|211464238|gb|FL298402.1|FL298402
EST:     ACCGCAAAAGGTTCCTCAAGCTGCACAAATGGGCTTCTGTGGCTGACGAG                         GGCCATGGACTTCCTTGTTGAGTTGTTTCGTAACCTGCTTGAGCATCCAGA
genomic: ACCGCAAAAGGTTCCTCAAGCTGCACAAATGGGCTTCTGTGGCTGACGAGgtacttagtt ... cacatgtcagGGCCATGGACTTCCTTGTTGAGTTGTTTCGTAACCTGCTTGAGCATCCAGA
EST: gi|211466770|gb|FL298415.1|FL298415
EST:     ACCGCAAAAGGTTCCTCAAGCTGCACAAATGGGCTTCTGTGGCTGACGAG                         GGCCATGGACTTCCTTGTTGAGTTGTTTCGTAACCTKCTTGAGCATCCAGA
genomic: ACCGCAAAAGGTTCCTCAAGCTGCACAAATGGGCTTCTGTGGCTGACGAGgtacttagtt ... cacatgtcagGGCCATGGACTTCCTTGTTGAGTTGTTTCGTAACCTGCTTGAGCATCCAGA
EST: gi|211041277|gb|FL124824.1|FL124824
EST:     ACCGCAAAAGGTTCCTCAAGCTGCACAAATGGGCTTCTGTGGCTGACGAG                         GGCCATGGACTTCCTTG
genomic: ACCGCAAAAGGTTCCTCAAGCTGCACAAATGGGCTTCTGTGGCTGACGAGgtacttagtt ... cacatgtcagGGCCATGGACTTCCTTG
EST: gi|211041274|gb|FL124821.1|FL124821
EST:     ACCGCAAAAGGTTCCTCAAGCTGCACAAATGGGCTTCTGTGGCTGACGAG                         GGCCATGGACTTCCTTGTTGAGTTGTTTCGTAACCTGCTTGAGCATCCAGA
genomic: ACCGCAAAAGGTTCCTCAAGCTGCACAAATGGGCTTCTGTGGCTGACGAGgtacttagtt ... cacatgtcagGGCCATGGACTTCCTTGTTGAGTTGTTTCGTAACCTGCTTGAGCATCCAGA
EST: gi|211475759|gb|FL124816.1|FL124816
EST:     ACCGCAAAAGGTTCCTCAAGCTGCACAAATGGGCTTCTGTGGCTGACGAG                         GGCCATGGACTTCCTTGTTGAGTTGTTTCGTAACCTGCTTGAGCATCCAGA
genomic: ACCGCAAAAGGTTCCTCAAGCTGCACAAATGGGCTTCTGTGGCTGACGAGgtacttagtt ... cacatgtcagGGCCATGGACTTCCTTGTTGAGTTGTTTCGTAACCTGCTTGAGCATCCAGA
EST: gi|211041273|gb|FL124820.1|FL124820
EST:     ACCGCAAAAGGTTCCTCAAGCTGCACAAATGGGCTTCTGTGGCTGACGAG                         GGCCATGGACTTCCTTGTTGAGTTGTTTCGTAACCTGCTTGAGCATCCAGA
genomic: ACCGCAAAAGGTTCCTCAAGCTGCACAAATGGGCTTCTGTGGCTGACGAGgtacttagtt ... cacatgtcagGGCCATGGACTTCCTTGTTGAGTTGTTTCGTAACCTGCTTGAGCATCCAGA
EST: gi|211041271|gb|FL124818.1|FL124818
EST:     ACCGCAAAAGGTTCCTCAAGCTGCACAAATGGGCTTCTGTGGCTGACGAG                         GGCCATGGACTTCCTTGTTGAGTTGTTTCGTAACCTGCTTGAGCATCCAGA
genomic: ACCGCAAAAGGTTCCTCAAGCTGCACAAATGGGCTTCTGTGGCTGACGAGgtacttagtt ... cacatgtcagGGCCATGGACTTCCTTGTTGAGTTGTTTCGTAACCTGCTTGAGCATCCAGA
EST: gi|211475757|gb|FL124814.1|FL124814
EST:     ACCGCAAAAGGTTCCTCAAGCTGCACAAATGGGCTTCTGTGGCTGACGAG                         GGCCATGGACTTCCTTGTTGAGTTGTTTCGTAACCTGCTTGAGCATCCAGA
genomic: ACCGCAAAAGGTTCCTCAAGCTGCACAAATGGGCTTCTGTGGCTGACGAGgtacttagtt ... cacatgtcagGGCCATGGACTTCCTTGTTGAGTTGTTTCGTAACCTGCTTGAGCATCCAGA
EST: gi|93282356|gb|EB674620.1|EB674620
EST:     ACCGCAAAAGGTTCCTCAAGCTGCACAAATGGGCTTCTGTGGCTGACGAG                         GGCCATGGACTTCCTTGTTGAGTTGTTTCGTAACCTGCTTGAGCATCCAGA
genomic: ACCGCAAAAGGTTCCTCAAGCTGCACAAATGGGCTTCTGTGGCTGACGAGgtacttagtt ... cacatgtcagGGCCATGGACTTCCTTGTTGAGTTGTTTCGTAACCTGCTTGAGCATCCAGA
EST: gi|211466771|gb|FL298416.1|FL298416
EST:     ACCGCAAAAGGTTCCTCAAGCTGCACAAATGGGCTTCTGTGGCTGACGAG                         GGCCATGGACTTCCTTGTTGAGTTGTTTCGTAACCTGCTTGAGCATCCAGA
genomic: ACCGCAAAAGGTTCCTCAAGCTGCACAAATGGGCTTCTGTGGCTGACGAGgtacttagtt ... cacatgtcagGGCCATGGACTTCCTTGTTGAGTTGTTTCGTAACCTGCTTGAGCATCCAGA

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: 80

CAAAGTATGAACACTTGTACAGCATGGTTCAGGAAGAAGTTCAAAACAAGACCGCAAAAGGTTCCTCAAGCTGCACAAATGGGCTTCTGTGGCTGACGAGgtacttagtt ... cacatgtcagGGCCATGGACTTCCTTGTTGAGTTGTTTCGTAACCTGCTTGAGCATCCAGACTGGACCATGGGTCAATCTTGCACTGATTCATACACCAAGACTTTGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 164

CAAAGTATGAACACTTGTACAGCATGGTTCAGGAAGAAGTTCAAAACAAGACCGCAAAAGGTTCCTCAAGCTGCACAAATGGGCTTCTGTGGCTGACGAGgtacttagtt ... cacatgtcagGGCCATGGACTTCCTTGTTGAGTTGTTTCGTAACCTGCTTGAGCATCCAGACTGGACCATGGGTCAATCTTGCACTGATTCATACACCAAGACTTTGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 300

CAAAGTATGAACACTTGTACAGCATGGTTCAGGAAGAAGTTCAAAACAAGACCGCAAAAGGTTCCTCAAGCTGCACAAATGGGCTTCTGTGGCTGACGAGgtacttagtt ... cacatgtcagGGCCATGGACTTCCTTGTTGAGTTGTTTCGTAACCTGCTTGAGCATCCAGACTGGACCATGGGTCAATCTTGCACTGATTCATACACCAAGACTTTGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 94

CAAAGTATGAACACTTGTACAGCATGGTTCAGGAAGAAGTTCAAAACAAGACCGCAAAAGGTTCCTCAAGCTGCACAAATGGGCTTCTGTGGCTGACGAGgtacttagtt ... cacatgtcagGGCCATGGACTTCCTTGTTGAGTTGTTTCGTAACCTGCTTGAGCATCCAGACTGGACCATGGGTCAATCTTGCACTGATTCATACACCAAGACTTTGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgatcatcatgccaagtacgtgacttttgtttactcaaaatttcacatgtcagGGCCATGGACTTCCTTGTTGAGTTGTTTCGTAACCTGCTTGAGCATCCAGACTGGACCATGGGTCAATCTTGCACTGATTCATACACCAAGACTTTGAAG
 acttgat  putative branch site (score: 94)
                               tttactcaaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacttagtttctttttcttgtcacttctcattgcaacttgatcatcatgccaagtacgtgacttttgtttactcaaaatttcacatgtcagGGCCATGGACTTCCTTGTTGAGTTGTTTCGTAACCTGCTTGAGCATCCAGACTGGACCATGGGTCAATCTTGCACTGATTCATACACCAAGACTTTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG