Sequence
atgc intronic sequence ATGC exonic sequenceGTACCCAATTTATATTGCATTGGAGATGCCAATGGCAAGCTCATGCTTGCCCATGCTGCCAGTGCACAAGGAATTTCAGgtacttgagagttcctttttcttgtggtttcttggagcatgcttattggtgtacttgtctgatgttgacttcctattcaaatgtag
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G152958_T02 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os05g06460.1 (Oryza sativa), 5'ss of exon 10
GTACCCAATTTATATTGCATTGGAGATGCCAATGGCAAGCTCATGCTTGCCCATGCTGCCAGTGCACAAGGAATTTCAGgtac-ttgagagttcctttttcttgtggtttcttggagcatgcttat--------tggtgtacttgtctgatgttgacttcctattcaaatgtag
|| || || |||||||||||||||||||||||||| || ||||||||||| ||||||||||||||||| ||||| || ||||| ||| | | ||| || ||||| | | | ||| | || || ||| ||||| | ||||||| ||||||||
GTTCCGAACTTATATTGCATTGGAGATGCCAATGGTAAACTCATGCTTGCTCATGCTGCCAGTGCACAGGGAATCTCTGgtacattgcaaatctgtttagatttcatcttcttctatcgctcctatgttgcttatcgtatagttgcctgataagtaattcctatgaaaatgtag
upper sequence: GRMZM2G152958_T02 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA17G03560.1 (Glycine max), 5'ss of exon 10
GTACCCAATTTATATTGCATTGGAGATGCCAATGGCAAGCTCATGCTTGCCCATGCTGCCAGTGCACAAGGAATTTCAGgtacttgagagttcctttttcttgtggtttcttggagcatgcttat-tggtgtacttgtctgatgttgacttcctattcaaatgtag
|| || |||||||||| ||||| ||||| ||||||||| | |||||||| ||||||||||||||||||||||||||||||| || | | | | ||| ||| | | |||| | | | ||||| | | | | || |
GTGCCTCATTTATATTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAGgtaagtggtaactgatgtaactt-----ttccaaaatttagtttatgcagcaatatcatttgatgaaaaaat--tgtctaacag---
upper sequence: GRMZM2G152958_T02 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA09G04270.1 (Glycine max), 5'ss of exon 5
GTACCCAATTTATATTGCATTGGAGATGCCAATGGCAAGCTCATGCTTGCCCATGCTGCCAGTGCACAAGGAATTTCAGgtacttga-gagttcctttttcttgtggtt--tcttggagcatgcttattggtgtacttgtctgatgttgac-ttcctattcaaatgtag
|| || |||| ||||||||||| ||| | ||||||||| | |||||||| ||||||||||||||||||||||||||||||| ||| | | ||| | | || ||| || | | | | | ||| | || | || || |
GTTCCTCATTTGTATTGCATTGGTGATACAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAGgtaagaagcaagtaatgtaattttgctactaatatttgagt-catttgct--tccattcacttaatgaaaatattgttgttggaaag---
upper sequence: GRMZM2G152958_T02 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA15G15310.1 (Glycine max), 5'ss of exon 10
GTACCCAATTTATATTGCATTGGAGATGCCAATGGCAAGCTCATGCTTGCCCATGCTGCCAGTGCACAAGGAATTTCAGgtacttgagagttcct----ttttcttgtggtttcttggagcatgcttattggtgtacttgtctgatgttgacttcctattcaaatgtag
|| || |||| ||||| ||||| ||||| ||||||||| | |||||||| ||||||||||| ||||||||||||||||||| || | | |||| | || ||| ||| || | | | || | ||| | | | || | |
GTTCCTCATTTGTATTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGCGCACAAGGAATTTCAGgtaagaagcaggtaatgtaattttgctactaatttttgagtcat--ttgct--tccatttacttaatgaaaagat--tgttggatag---
upper sequence: GRMZM2G152958_T02 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA07G37050.1 (Glycine max), 5'ss of exon 10
GTACCCAATTTATATTGCATTGGAGATGCCAATGGCAAGCTCATGCTTGCCCATGCTGCCAGTGCACAAGGAATTTCAGgtacttgagagttcctttttcttgtggtttcttggagcatgcttattggtgtact--tgtctgatgttgacttcctattcaaatgtag
|| || ||||||| || ||||| ||||| ||||||||| | |||||||| ||||||||||||||||||||||||||||||| || | || | | || | | | | || ||| || | | | ||||| | | | | || |
GTGCCTCATTTATACTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAGgtaagtggtaactcatgtaattt----tcccaaaaattttagtttttgctgcaatatcatttgatgaaaaaat--tgtctaacag---
upper sequence: GRMZM2G152958_T02 (Zea mays), 5'ss of exon 10
lower sequence: AT4G16155.1 (Arabidopsis thaliana), 5'ss of exon 10
GTACCCAATTTATATTGCATTGGAGATGCCAATGGCAAGCTCATGCTTGCCCATGCTGCCAGTGCACAAGGAATTTCAGgtacttg---------agagttcctttttcttgtggtttcttggagcatgcttattggtgtact---tgtctgatgttgacttcctattcaaatgtag---------------------
|| ||| | || || ||||| || ||||||||||| || || |||||||| ||||| || ||||| ||||||||||| |||| || | | ||| | || || | | | || | ||| | | | ||||| | |||| || | ||
GTTCCCCACTTGTACTGCATCGGTGATGCCAATGGTAAACTGATGCTTGCTCATGCAGCTAGTGCTCAAGGAATTTCTGgtaaatggttttatcaatatttcactccaaatgcatctttcttttgtttttccttttctacactgaatacgttagattgacctt-tattaaactctatgcatctacttgtgttggctag
upper sequence: GRMZM2G152958_T02 (Zea mays), 5'ss of exon 10
lower sequence: AT3G16950.2 (Arabidopsis thaliana), 5'ss of exon 10
GTACCCAATTTATATTGCATTGGAGATGCCAATGGCAAGCTCATGCTTGCCCATGCTGCCAGTGCACAAGGAATTTCAGgtacttgagagttcctttttcttgtggtttcttggagcatgcttattggtgtacttgtctgatgttga-cttcctattcaaatgtag-------------------
|| || || || || |||||||| ||||||||||| || | |||||||| ||||| |||||||| ||||||||||| |||| || | | || | || | | || | ||| | | | |||| | | |||| || | |
GTTCCGAACTTGTACTGCATTGGTGATGCCAATGGTAAATTGATGCTTGCACATGCAGCCAGTGCCCAAGGAATTTCTGgtaaatgg----cttatcagtaggaggctactaacaatgcaataatattttcccttttttcttcttgagccttgtattaaactctgagctcttactctgtggctag
upper sequence: GRMZM2G152958_T02 (Zea mays), 5'ss of exon 10
lower sequence: Vv05s0077g01210.t01 (Vitis vinifera), 5'ss of exon 10
GTACCCAATTTATATTGCATTGGAGATGCCAATGGCAAGCTCATGCTTGCCCATGCTGCCAGTGCACAAGGAATTTCAGgtacttgagagttcctt--tttcttgtggttt---cttggagcatgcttattggtgtacttgtctgatgttgacttcctattcaaatgtag
|| || | || |||||||| || ||||| ||||| || | |||||||| ||||| || ||||||||||||||||||||| || | | | | | | ||| |||| ||| | ||||| || | | || | ||| | || || ||| ||
GTTCCTCACTTGTATTGCATAGGTGATGCAAATGGTAAAATGATGCTTGCTCATGCAGCAAGTGCACAAGGAATTTCAGgttagtggtaactacctcatattttgctgttttacctttaaaaatgctacttaaaccatct-tcattttttgcttggctcttgtgatgcag
upper sequence: GRMZM2G152958_T02 (Zea mays), 5'ss of exon 10
lower sequence: Vv14s0060g01330.t01 (Vitis vinifera), 5'ss of exon 10
GTACCCAATTTATATTGCATTGGAGATGCCAATGGCAAGCTCATGCTTGCCCATGCTGCCAGTGCACAAGGAATTTCAGgtacttgagagttcctttttcttgtggtttcttggagcatgcttattggtgtacttgtctgatgttgacttcctattcaaatgtag--------------
|| || | || ||||||||||| ||||| ||||| || | |||||||| |||||||| ||||| |||||||| || |||| || | | | || | | | | |||| || ||| | | | | || | |||| | | | |
GTTCCTCACTTGTATTGCATTGGTGATGCAAATGGAAAAATGATGCTTGCTCATGCTGCAAGTGCCCAAGGAATCTCTGgtaatt-accttgtttgttgccactctctctctactacatggtttttgtcattcagttttaatatctacttgaaacctgacttttcttttgtcgacatag
upper sequence: GRMZM2G152958_T02 (Zea mays), 5'ss of exon 10
lower sequence: EFJ06739 (Selaginella moellendorffii), 5'ss of exon 10
GTACCCAATTTATATTGCATTGGAGATGCCAATGGCAAGCTCATGCTTGCCCATGCTGCCAGTGCACAAGGAATTTCAGgta--cttgagagttcctttttct-tgtggtttcttggagcatgcttattggtgtacttgtctgatgttgacttcctattcaaatgtag
||||| |||| || ||||| || ||||| |||||||| || |||||||| || ||||||||||| || || |||||||||| || ||||| | | || | |||| | | || | || | | || | || | |
GTACCTCATTTGTACTGCATCGGCGATGCAAATGGCAAACTGATGCTTGCTCACGCTGCCAGTGCTCAGGGCATTTCAGgtaatctcgagagagacatgttttgtgtgatgt----gaccgtgatcgt--gtctcttttgcag-------------------------
upper sequence: GRMZM2G152958_T02 (Zea mays), 5'ss of exon 10
lower sequence: EFJ16882 (Selaginella moellendorffii), 5'ss of exon 10
GTACCCAATTTATATTGCATTGGAGATGCCAATGGCAAGCTCATGCTTGCCCATGCTGCCAGTGCACAAGGAATTTCAGgta--cttgagagttcctttttct-tgtggtttcttggagcatgcttattggtgtacttgtctgatgttgacttcctattcaaatgtag
||||| |||| || ||||| || ||||| |||||||| || |||||||| || ||||||||||| || || |||||||||| || ||||| | | || | | || | | || | || | | || | || | |
GTACCTCATTTGTACTGCATCGGCGATGCAAATGGCAAACTGATGCTTGCTCACGCTGCCAGTGCTCAGGGCATTTCAGgtaatctcgagagaaacatgttttgtatgatgt----gaccgtgatcgt--gtctcttttgcag-------------------------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|32944152|gb|CF048971.1|CF048971EST: CAATGGCAAGCTCATGCTTGCCCATGCTGCCAGTGCACAAGGAATTTCAG TTGTTGAACAAATATCTGGAAAGGATCACATCCTAAATCATTTAAGCATCC
genomic: CAATGGCAAGCTCATGCTTGCCCATGCTGCCAGTGCACAAGGAATTTCAGgtacttgaga ... tcaaatgtagTTGTTGAACAAATCTCTGGAAAGGATCACATCCTAAATCATTTAAGCATCC
EST:
gi|67029833|gb|CO458582.1|CO458582EST: AATGGCAAGCTCATGTCTTGCCCATGCTGCCAGTGCACAAGGAATTTCAG TTGTTGAACAAATCTCTGGAAAGGATCACATCCTAAATCATTTAAGCATCC
genomic: AATGGCAAGCTCATG-CTTGCCCATGCTGCCAGTGCACAAGGAATTTCAGgtacttgaga ... tcaaatgtagTTGTTGAACAAATCTCTGGAAAGGATCACATCCTAAATCATTTAAGCATCC
EST:
gi|31354606|gb|CD438963.1|CD438963EST: CAATGGCAAGCTCATGCTTGCCCATGCTGCCAGTGCACAAGGAATTTCAG TTGTTGAACAAATCTCTGGAAAGGATCACATCCTAAATCATTTAAGCATCC
genomic: CAATGGCAAGCTCATGCTTGCCCATGCTGCCAGTGCACAAGGAATTTCAGgtacttgaga ... tcaaatgtagTTGTTGAACAAATCTCTGGAAAGGATCACATCCTAAATCATTTAAGCATCC
EST:
gi|78075765|gb|DV504199.1|DV504199EST: GGCAAGCTCATGCTTGCCCATGCTGCCAGTGCACAAGGAATTTCAG TTGTTGAACAAATCTCTGGAAAGGATCACATCCTAAATCATTTAAGCATCC
genomic: GGCAAGCTCATGCTTGCCCATGCTGCCAGTGCACAAGGAATTTCAGgtacttgaga ... tcaaatgtagTTGTTGAACAAATCTCTGGAAAGGATCACATCCTAAATCATTTAAGCATCC
EST:
gi|31353176|gb|CD437533.1|CD437533EST: CAATGGCAAGCTCATGCTTGCCCATGCTGCCAGTGCACAAGGAATTTCAG TTGTTGAACAAATCTCTGGAAAGGATCACATCCTAAATCATTTAAGCATCC
genomic: CAATGGCAAGCTCATGCTTGCCCATGCTGCCAGTGCACAAGGAATTTCAGgtacttgaga ... tcaaatgtagTTGTTGAACAAATCTCTGGAAAGGATCACATCCTAAATCATTTAAGCATCC
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:
129GTACCCAATTTATATTGCATTGGAGATGCCAATGGCAAGCTCATGCTTGCCCATGCTGCCAGTGCACAAGGAATTTCAGgtacttgaga ... tcaaatgtagTTGTTGAACAAATCTCTGGAAAGGATCACATCCTAAATCATTTAAGCATCCCAGCAGCATGTTTCACCCATCCAGAGATTAGTATGGTTGGATTGACAGA
Block sizes:
48 (upstream exon),
49 (downstream exon)
Score:
77GTACCCAATTTATATTGCATTGGAGATGCCAATGGCAAGCTCATGCTTGCCCATGCTGCCAGTGCACAAGGAATTTCAGgtacttgaga ... tcaaatgtagTTGTTGAACAAATCTCTGGAAAGGATCACATCCTAAATCATTTAAGCATCCCAGCAGCATGTTTCACCCATCCAGAGATTAGTATGGTTGGATTGACAGA
Block sizes:
48 (upstream exon),
49 (downstream exon)
Score:
105GTACCCAATTTATATTGCATTGGAGATGCCAATGGCAAGCTCATGCTTGCCCATGCTGCCAGTGCACAAGGAATTTCAGgtacttgaga ... tcaaatgtagTTGTTGAACAAATCTCTGGAAAGGATCACATCCTAAATCATTTAAGCATCCCAGCAGCATGTTTCACCCATCCAGAGATTAGTATGGTTGGATTGACAGA
Block sizes:
47 (upstream exon),
48 (downstream exon)
Score:
189GTACCCAATTTATATTGCATTGGAGATGCCAATGGCAAGCTCATGCTTGCCCATGCTGCCAGTGCACAAGGAATTTCAGgtacttgaga ... tcaaatgtagTTGTTGAACAAATCTCTGGAAAGGATCACATCCTAAATCATTTAAGCATCCCAGCAGCATGTTTCACCCATCCAGAGATTAGTATGGTTGGATTGACAGA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTACCCAATTTATATTGCATTGGAGATGCCAATGGCAAGCTCATGCTTGCCCATGCTGCCAGTGCACAAGGAATTTCAGgtacttgagagttcctttttcttgtggtttcttggagcatgcttattggtgtacttgtctgatgttgacttcctattcaaatgtag
- - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA