Sequence
atgc intronic sequence ATGC exonic sequencegtaagatctcttattcattcattattttatttctatgtttatttgtgtggttttcaggaggacagataaagtggtttctctgtggtattcactgcgttcaggatttactaaatttatgtgattttgcagATGGGTATATTTTGTATGCCACCTTCTTCAGTTATCCCACTTCATAATCATCCTGGAATGACTGTACTTAGCAAGCTTCTTTATGGACGTCTGCATGCTG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G162175_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os04g06790.2 (Oryza sativa), 3'ss of exon 4
gtaagatctcttattcattcatt------------attttatttctatgtttatttgtgtggttttcaggaggacagataaagtggttt---ctctgtggtattcactgcgttcaggatttactaaatttatgtgattttgcagATGGGTATATTTTGTATGCCACCTTCTTCAGTTATCCCACTTCATAATCATCCTGGAATGACTGTACTTAGCAAGCTTCTTTATGGACGTCTGCATGCTG
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gtaagatatcatcatcatttttttaagatcgtgatgttttttatttgaactgttctgtaagtactttgaggctttaaaattagtagatagaacactcctgtgttt-cagcatctgatgaacactaaatttttcaatatatgtagATGGGTATATTTTGTATGCCGCCGTCATCAGTTATTCCACTTCACAATCACCCAGGAATGACAGTTCTGAGCAAGCTTCTCTATGGCACACTGCATGCTG
upper sequence: GRMZM2G162175_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA06G42920.2 (Glycine max), 3'ss of exon 3
gtaagatctcttattcattcattattttatttctatgtttatttgtgtggttttcaggaggacagataaagtggtttctctgtggtattcactgcgttcaggatttactaaatttatgtgattttgcagATGGGTATATTTTGTATGCCACCTTCTTCAGTTATCCCACTTCATAATCATCCTGGAATGACTGTACTTAGCAAGCTTCTTTATGGACGTCTGCATGCTG
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------------gtaagtaaagtctcaaacttcagatcacgtttattcag---tcagaaatttttataaatttgggcct-taaattggctatacctactgaagttgatttgctttatc---ttttgcagATAGGAATTTTTTGCATGCCCCCCTCGTCTATCATCCCCCTCCATAATCATCCTGGAATGACAGTATTGAGCAAGCTGTTATATGGCTCGATGTATGTTA
upper sequence: GRMZM2G162175_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA15G08980.4 (Glycine max), 3'ss of exon 3
gtaagatctcttattcattcattattttatttctatgtttatttgtgtggttttcaggaggacagataaagtggtttct---ctgtggtattca--ctgcgttcaggatttactaaat-ttatgtgattttgcagATGGGTATATTTTGTATGCCACCTTCTTCAGTTATCCCACTTCATAATCATCCTGGAATGACTGTACTTAGCAAGCTTCTTTATGGACGTCTGCATGCTG
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gtatgtttttttattccctttctctctacagcttgtgacagacagtcttcttgttaatctatttgtagtatttctttctgaattgagatgtggaatttggattcacaaggaaagagtccttttttttttttgcagATGGGAATCTTCTGTATGTCTCCTGGTTCCGTTATTCCGCTTCATAACCATCCCGGAATGACTGTTTTGAGCAAGCTTCTTTATGGTTCATTACTTGTGA
upper sequence: GRMZM2G162175_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA12G33920.1 (Glycine max), 3'ss of exon 3
gtaagatctcttattcattcattattttatttctatgtttatttgtgtggttttcaggaggacagataaagtggtttctctgtg-gtattcactgcgttcaggatttactaaatttatgtgattttgcagATGGGTATATTTTGTATGCCACCTTCTTCAGTTATCCCACTTCATAATCATCCTGGAATGACTGTACTTAGCAAGCTTCTTTATGGACGTCTGCATGCTG
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----------gtaagtattaataatcagaaatctacgctatttcattcagc------aattttatacaatattgctcttatgggtatagctactgaagtttg-actaataaattttatc---tttaccagATAGGAATTTTTTGTATGCCCCCTTCATCTGTTATTCCTCTCCATAATCATCCTGGAATGACAGTCTTAAGCAAGCTCTTATATGGTTCAGTGTATGTTA
upper sequence: GRMZM2G162175_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA13G36610.1 (Glycine max), 3'ss of exon 3
gtaagatctcttattcattcattattttatttctatgtttatttgtgtggttttcaggaggacagataaagtggtttctctgtggtattcactgcgttcaggatttactaaatttatgtgattttgc-agATGGGTATATTTTGTATGCCACCTTCTTCAGTTATCCCACTTCATAATCATCCTGGAATGACTGTACTTAGCAAGCTTCTTTATGGACGTCTGCATGCTG
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----------gtaagtattaattatcagaaatctacaca-atttcagt------cagcaatttttatacaatattgctcttatgggtatagctac--tgaagtttggttaataatttttatctttaccagATAGGAATTTTTTGTATGCCCCCTTCATCTATTATTCCTCTCCATAATCATCCTGGAATGACAGTCTTAAGCAAGCTCTTATATGGTTCAGTGTATGTTA
upper sequence: GRMZM2G162175_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA13G30140.1 (Glycine max), 3'ss of exon 4
gtaagatctcttattcattcattattttatttctatgtttatttgtgtggttttcaggaggacagataaagtggtttctctgtggtattcactgcgttcaggatttactaaatttatgtgattttgcagATGGGTATATTTTGTATGCCACCTTCTTCAGTTATCCCACTTCATAATCATCCTGGAATGACTGTACTTAGCAAGCTTCTTTATGGACGTCTG--CATGCTG
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-----------------------gtcttcttgtta-atctatttggagtatttctttctgaattga-gatgtgg-----caattggattcacaaggaagaagtctt-------ttttttctttttgcagATGGAAATCTTCTGTAGGTCTCCAGGTTCTGTTATCCCGCTTCATAATCACCCCGGAATGACTGTTTTGAGCAAGCTTCTTATTACTTGTAAGGTCATAT--
upper sequence: GRMZM2G162175_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA06G42920.5 (Glycine max), 3'ss of exon 3
gtaagatctcttattcattcattattttatttctatgtttatttgtgtggttttcaggaggacagataaagtggtttctctgtggtattcactgcgttcaggatttactaaatttatgtgattttgcagATGGGTATATTTTGTATGCCACCTTCTTCAGTTATCCCACTTCATAATCATCCTGGAATGACTGTACTTAGCAAGCTTCTTTATGGACGTCTGCATGCTG
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------------gtaagtaaagtctcaaacttcagatcacgtttattcag---tcagaaatttttataaatttgggcct-taaattggctatacctactgaagTTGATTTGCTTTATC---TTTTGCAGATAGGAATTTTTTGCATGCCCCCCTCGTCTATCATCCCCCTCCATAATCATCCTGGAATGACAGTATTGAGCAAGCT-----------------------
upper sequence: GRMZM2G162175_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT3G58670.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaagatctcttattcattcattattttatttctatgtttatttgtgtggttttcaggaggacagataaagtggtttctctgtggtattcactgcgttcaggatttactaaatttatgtgattttgcagATGGGTATATTTTGTATGCCACCTTCTTCAGTTATCCCACTTCATAATCATCCTGGAATGACTGTACTTAGCAAGCTTCTTTATGGACGTCTGCATGCTG
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---------------------caacacgctccacatgtttac---tgcagttaaacaaagttctga-aatgcaatattcttgctttacttg-tctgcttattatgctttga--tcat-tattttgtcagATTGGAATTTTCTGCATGCCACCTGGGTCTATCATACCACTTCATAATCATCCAGGCATGACAGTGCTAAGCAAGCTTGTTTATGGTTCAATGCACGTTA
upper sequence: GRMZM2G162175_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv10s0003g01390.t01 (Vitis vinifera), 3'ss of exon 4
gtaagatctcttattcattcattattt-tatttctatgtttatttgtgtggttttcaggaggacagataaagtggtttctctgtggtattcactgcgttcaggatttactaaatttatgtgattttgcagATGGGTATATTTTGTATGCCACCTTCTTCAGTTATCCCACTTCATAATCATCCTGGAATGACTGTACTTAGCAAGCTTCTTTATGGACGTCTGCATGCTG
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------------ttcgagtcacaattggttcctgcagagtgggttgcttgattcttcaaaaactgaat---ctggtttatcatgaattcttggtgatttttggattt---------------tgctgcagATAGGAATATTCTGCATGCCACCTTCCTCTATCATACCCCTCCATAATCATCCTGGAATGACAGTGTTGAGCAAGCTTCTGTATGGTACACTACATGTGA
upper sequence: GRMZM2G162175_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv12s0028g02070.t01 (Vitis vinifera), 3'ss of exon 2
gtaagatctcttattcattcattattttatttctatgtttatttgtgtggttttcaggaggacagataaagtggtttctctgtggtattcactgcgttcaggatttactaaattt-atgtgattttgcagATGGGTATATTTTGTATGCCACCTTCTTCAGTTATCCCACTTCATAATCATCCTGGAATGACTGTACTTAGCAAGCTTCTTTATGGACGTCTGCATGCTG
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-------------------------gacctttcccttgctgtttcctcg---tccagacaggcccttaatgttctgaaact-tgaaagctag-ataacagagactcactggtttttgaattttcttgcagATAGGAGTCTTTTGCATGCCACCTTCCTCTATTATACCCCTTCATAATCATCCTGGAATGACTGTGTTGAGCAAGCTTCTATATGGTTCATTATATGTAAMapped 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|211037838|gb|FL428696.1|FL428696EST: TCGCGGCTCCAATCAAATATTTGCACATTCATGAATGTGAAAGCTTCTCT ATGGGTATATTTTGTATGCCACCTTCTTCAGTTATCCCACTTCATAATCAT
genomic: TCGCGGCTCCAATCAAATATTTGCACATTCATGAATGTGAAAGCTTCTCTgtaagatctc ... gattttgcagATGGGTATATTTTGTATGCCACCTTCTTCAGTTATCCCACTTCATAATCAT
EST:
gi|71435494|gb|DR816544.1|DR816544EST: TCGCGGCTCCAATCAAATATTTGCACATTCATGAATGTGAAAGCTTCTCT ATGGGTATATTTTGTATGCCACCTTCTTCAGTTATCCCACTTCATAATCAT
genomic: TCGCGGCTCCAATCAAATATTTGCACATTCATGAATGTGAAAGCTTCTCTgtaagatctc ... gattttgcagATGGGTATATTTTGTATGCCACCTTCTTCAGTTATCCCACTTCATAATCAT
EST:
gi|76919420|gb|DV167706.1|DV167706EST: TCGCGGCTCCAATCAAATATTTGCACATTCATGAATGTGAAAGCTTCTCT ATGGGTATATTTTGTATGCCACCTTCTTCAGTTATCCCACTTCATAATCAT
genomic: TCGCGGCTCCAATCAAATATTTGCACATTCATGAATGTGAAAGCTTCTCTgtaagatctc ... gattttgcagATGGGTATATTTTGTATGCCACCTTCTTCAGTTATCCCACTTCATAATCAT
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),
45 (downstream exon)
Score:
161TTCTACGCGTCCATCAAATGGGAGACGAGGACGCAATGGGGCTAACCAGTTCGCGGCTCCAATCAAATATTTGCACATTCATGAATGTGAAAGCTTCTCTgtaagatctc ... gattttgcagATGGGTATATTTTGTATGCCACCTTCTTCAGTTATCCCACTTCATAATCATCCTGGAATGACTGTACTTAGCAAGCTTCTTTATGGACGTCTGCATGCTG
Block sizes:
49 (upstream exon),
48 (downstream exon)
Score:
96TTCTACGCGTCCATCAAATGGGAGACGAGGACGCAATGGGGCTAACCAGTTCGCGGCTCCAATCAAATATTTGCACATTCATGAATGTGAAAGCTTCTCTgtaagatctc ... gattttgcagATGGGTATATTTTGTATGCCACCTTCTTCAGTTATCCCACTTCATAATCATCCTGGAATGACTGTACTTAGCAAGCTTCTTTATGGACGTCTGCATGCTG
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
88TTCTACGCGTCCATCAAATGGGAGACGAGGACGCAATGGGGCTAACCAGTTCGCGGCTCCAATCAAATATTTGCACATTCATGAATGTGAAAGCTTCTCTgtaagatctc ... gattttgcagATGGGTATATTTTGTATGCCACCTTCTTCAGTTATCCCACTTCATAATCATCCTGGAATGACTGTACTTAGCAAGCTTCTTTATGGACGTCTGCATGCTG
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
118TTCTACGCGTCCATCAAATGGGAGACGAGGACGCAATGGGGCTAACCAGTTCGCGGCTCCAATCAAATATTTGCACATTCATGAATGTGAAAGCTTCTCTgtaagatctc ... gattttgcagATGGGTATATTTTGTATGCCACCTTCTTCAGTTATCCCACTTCATAATCATCCTGGAATGACTGTACTTAGCAAGCTTCTTTATGGACGTCTGCATGCTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttctctgtggtattcactgcgttcaggatttactaaatttatgtgattttgcagATGGGTATATTTTGTATGCCACCTTCTTCAGTTATCCCACTTCATAATCATCCTGGAATGACTGTACTTAGCAAGCTTCTTTATGGACGTCTGCATGCTG
tactaaa putative branch site (score: 118)
atttactaaatttatg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagatctcttattcattcattattttatttctatgtttatttgtgtggttttcaggaggacagataaagtggtttctctgtggtattcactgcgttcaggatttactaaatttatgtgattttgcagATGGGTATATTTTGTATGCCACCTTCTTCAGTTATCCCACTTCATAATCATCCTGGAATGACTGTACTTAGCAAGCTTCTTTATGGACGTCTGCATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG