Sequence
atgc intronic sequence ATGC exonic sequencegtaaggatatgaaaacctgtatttcccaaaatctacagttccatgtttgagtccatattgattacaattatacagGTAGTAGCCTCCCAAGACTGGCCAGAAGTCACCAAGTATGCTGGATTGGTATGTGCTCAGGCTCATCGGCAAGAACTTATTCAAGATTTGTATAAAACCT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv11s0016g04620.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 14
gtaaggatatgaaaacctgtatttcccaaaatctacagttccatgtttgagtccatattgattacaat------tatacagGTAGTAGCCTCCCAAGACTGGCCAGAAGTCACCAAGTATGCTGGATTGGTATGTGCTCAGGCTCATCGGCAAGAACTTATTCAAGATTTGTATAAAACCT
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gtaaggctgagcatttctatggttac--atggccatcattttttttttaacctcttaccctctctaataagctgcatgcagGTTGTTGCATCTCAAGACTGGCCAGAAGTTACAAAGTATGCTGGATTGGTGTGTGCTCAGGCTCATCGGCAAGAGCTCATTCAAGATCTTTACAAGACAT
upper sequence: Vv11s0016g04620.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GRMZM2G079080_T02 (Zea mays), 3'ss of exon 14
---------------------------------------gtaaggat-atgaaaacctgtatttcccaaaatctacagttccatgtttgagtccatattgattacaattatacagGTAGTAGCCTCCCAAGACTGGCCAGAAGTCACCAAGTATGCTGGATTGGTATGTGCTCAGGCTCATCGGCAAGAACTTATTCAAGATTTGTATAAAACCT
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gtaaggctcgttactactttgccatttcttcatcaatatgtcacattcatcaggatatgcacatccttattttt---gttccgaacttatctgtctgcctctttctgct-cacagGTTGTTGCTTCTCAAGATTGGCCAGAAGTTACAAAGTATGCTGGATTGGTTTGTGCTCAGGCACACCGGCAAGAGCTCATTCAAGACCTTTACAAAACAT
upper sequence: Vv11s0016g04620.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: AC189879.3_FGT003 (Zea mays), 3'ss of exon 13
----------------------gtaaggatatgaaaac-ctgtatttcccaaaatctacagttccatgt-ttgagtccatattgattacaattat---------acagGTAGTAGCCTCCCAAGACTGGCCAGAAGTCACCAAGTATGCTGGATTGGTATGTGCTCAGGCTCATCGGCAAGAACTTATTCAAGATTTGTATAAAACCT
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gtaaggctcattactactttccatttctgcatcaacatgtcatattcatcaagatatgcacatctttgtcttggttttggacttatctcactcatatgctgctgacagGTTGTTGCTTCTCAAGATTGGCCAGAAGTTACAAAGTATGCTGGATTGGTTTGTGCTCAGGCACACCGGCAAGAGCTCATTCAGGACCTTTACAAAACAT
upper sequence: Vv11s0016g04620.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA05G08170.1 (Glycine max), 3'ss of exon 13
gtaaggatatgaaaacctgtatttcccaaaatctacagttccatgtttgagtccatattgattacaattatacagGTAGTAGCCTCCCAAGACTGGCCAGAAGTCACCAAGTATGCTGGATTGGTATGTGCTCAGGCTCATCGGCAAGAACTTATTCAAGATTTGTATAAAACCT
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gtaagtatttccaaagtcctttaacttatagctggccat---atatttg-gtc--ttctgattactgttattcagGTTGTAGCCTCCCAGGACTGGCCAGAAGTGACAAAATATGCAGGATTGGTATGTGCTCAGCCTCATCGCGAGGAACTCATTCAAGACCTTTTTAAATGTT
upper sequence: Vv11s0016g04620.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA06G23920.1 (Glycine max), 3'ss of exon 14
gtaaggatatgaaaacctgtatttcccaaaatctacagttccatgtttgagtccatattgattacaattatacagGTAGTAGCCTCCCAAGACTGGCCAGAAGTCACCAAGTATGCTGGATTGGTATGTGCTCAGGCTCATCGGCAAGAACTTATTCAAGATTTGTATAAAACCT
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gtaagcatttccaaactcctatatacagctaagggatgtgctatgcttga-tatatactgaatacggtaatccagGTTGTAGCCTCCCAGGACTGGCCTGAAGTAACAAAGTATGCAGGGTTGGTTTGTGCTCAGCCTCATCGAGAAGAACTAATTCAAGATCTTTTCCGATGTT
upper sequence: Vv11s0016g04620.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA17G12850.1 (Glycine max), 3'ss of exon 14
gtaaggatatgaaaacctgtatttcccaaaatctacagttccatgtttgagtccatattgattacaattatacagGTAGTAGCCTCCCAAGACTGGCCAGAAGTCACCAAGTATGCTGGATTGGTATGTGCTCAGGCTCATCGGCAAGAACTTATTCAAGATTTGTATAAAACCT
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gtaagtatttccaaagtcctttaccttatagctggccat---acatttggttttcta---atcactgttattcagGTTGTAGCCTCCCAGGACTGGCCGGAAGTAACAAAGTACGCAGGATTGGTATGCGCTCAGCCTCATCGTGAGGAACTCATTCAAGATCTTTTTAAATGTTMapped 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|33407837|gb|CF213464.1|CF213464EST: ACTCTTGTCCATCAATTGCTGCT GTAGTAGCCTCCCAAGNCTTGACAGAAGTCACCAAGTATGCTGGATTGGTA
genomic: ACTCTTGTCCATCAATTGCTGCTgtaaggatat ... aattatacagGTAGTAGCCTCCCAAGACTGGCCAGAAGTCACCAAGTATGCTGGATTGGTA
EST:
gi|349828457|gb|FQ417199.1|FQ417199EST: ATGTAACTCATCCAGAGACTGGAGATGACTCTTGTCCATCAATTGCTGCT GTAGTAGCCTCCCAAGACTGGCCAGAAGTCACCAAGTATGCTGGATTGGTA
genomic: ATGTAACTCATCCAGAGACTGGAGATGACTCTTGTCCATCAATTGCTGCTgtaaggatat ... aattatacagGTAGTAGCCTCCCAAGACTGGCCAGAAGTCACCAAGTATGCTGGATTGGTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttcccaaaatctacagttccatgtttgagtccatattgattacaattatacagGTAGTAGCCTCCCAAGACTGGCCAGAAGTCACCAAGTATGCTGGATTGGTATGTGCTCAGGCTCATCGGCAAGAACTTATTCAAGATTTGTATAAAACCT
tattgat putative branch site (score: 3)
atattgattacaatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaggatatgaaaacctgtatttcccaaaatctacagttccatgtttgagtccatattgattacaattatacagGTAGTAGCCTCCCAAGACTGGCCAGAAGTCACCAAGTATGCTGGATTGGTATGTGCTCAGGCTCATCGGCAAGAACTTATTCAAGATTTGTATAAAACCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC