Sequence
atgc intronic sequence ATGC exonic sequence...gtgcatgcgtaagcatgtgtatgtgtgccttatgaaatttaatgatttgattctactaatttatcttctttttgctaaccaaactttttctcctttgcagCCCACATACCCTTGTACCTGTACCCTTTCCTCAATACCAATAGCAAATCTAGGCCTTTTGAGTACTTGAGACTAACTAGCCTAGGTGTTATTGGTGCTTT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv19s0090g00930.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os03g57130.1 (Oryza sativa), 3'ss of exon 4
gtgcatgcgtaagcatgtgtatgtgtgccttatgaaatttaatgatttgattctactaatttatct-tctttttgctaaccaaactttttctcctttgcagCCCACATACCCTTGTACCTGTACCCTTTCCTCAATACCAATAGCAAATCTAGGCCTTTTGAGTACTTGAGACTAACTAGCCTAGGTGTTATTGGTGCTTT
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-tttgcgcataggaatgttcatctgtatgtggctttatgcttccagttggctattgtgagtgacctgtttcctctcttgatttttcccttcttcttttcagCTCACATCCCACTGTATCTGTACCCTTTCTTGAATACTACTAGCAAGACAAGGCCTTTTGAGTACTTGAGGCTTACCAGCTTGGGTGTCATTGGCGCACT
upper sequence: Vv19s0090g00930.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G045331_T01 (Zea mays), 3'ss of exon 5
----------------------gtgcatgcgtaa--gcatgtgta-tgtgtgccttatgaa---atttaatgatttgattctactaattt--atcttctttttgctaac---------caaactttttctcctttgcagCCCACATACCCTTGTACCTGTACCCTTTCCTCAATACCAATAGCAAATCTAGGCCTTTTGAGTACTTGAGACTAACTAGCCTAGGTGTTATTGGTGCTTT
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gtaacaagccatgccttgcataatatttgtttaaatgcacatataataaatgtattattaacctgtcctccgtctccttcctaatagtctcgatcatgtatgtcacaactattattgacagaatttaaattcttttcagCTCATATTCCATTGTACCTGTACCCTTTCCTCAACACTACCAGCAAAACGAGACCTTTTGAGTACCTAAGGCTTACTAGCTTGGGGGTCATTGGTGCTCT
upper sequence: Vv19s0090g00930.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA18G10400.1 (Glycine max), 3'ss of exon 4
gtgcatg-cgtaagcatgtgtatgtgtgccttatgaaatttaatgatttgattctactaatttatcttcttt-ttgctaaccaaactttttctcctttgcagCCCACATACCCTTGTACCTGTACCCTTTCCTCAATACCAATAGCAAATCTAGGCCTTTTGAGTACTTGAGACTAACTAGCCTAGGTGTTATTGGTGCTTT
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tcacaagatccattccagtttttgcttgttaaaggatagtacatgaagtg--tttgatatttcatacaataaattgttgcacttgctttttctcctttgcagCTCATATACCTCTATATCTGTATCCCTTCCTTAATACAACAAGCAAGTCAAGACCATTTGAGTACTTGAGGCTTACCAGCCTTGGTGTCATTGGTGCATT
upper sequence: Vv19s0090g00930.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA08G43220.1 (Glycine max), 3'ss of exon 4
gtgcatgcgtaagcatgtgtatgtgtgccttatgaa-atttaatgatttgattctactaatttatcttcttt-ttgctaaccaaactttttctcctttgcagCCCACATACCCTTGTACCTGTACCCTTTCCTCAATACCAATAGCAAATCTAGGCCTTTTGAGTACTTGAGACTAACTAGCCTAGGTGTTATTGGTGCTTT
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-cacaatatccgttatg-gtttttgctcgttaaaaggaccttacacgaagtgtttgatatttcatacaatgaattgttgcacatgctttttctcctctgcagCTCATATACCTTTATATCTGTATCCCTTCCTTAATACAACAAGCAAGTCAAGACCATTTGAGTACTTGAGGCTTACCAGTCTTGGTGTAATTGGTGCATTMapped 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|161707254|gb|FC056419.1|FC056419EST: TGTGTAGCTTCTCATTCAGAAACAAGGATGCTGTTCCTAAATG CCCACATACCCTTGTACCTGTACCCTTTCCTCAATACCAATAGCAAATCTA
genomic: TGTGTAGCTTCTCATTCAGAAACAAGGATGCTGTTCCTAAATGgtaattttct ... tcctttgcagCCCACATACCCTTGTACCTGTACCCTTTCCTCAATACCAATAGCAAATCTA
EST:
gi|110384705|gb|EC949163.1|EC949163EST: TCTCCAGTGTGTAGCTTCTCATTCAGAAACAAGGATGCTGTTCCTAAATG CCCACATACCCTTGTACCTGTACCCTTTCCTCAATACCAATAGCAAATCTA
genomic: TCTCCAGTGTGTAGCTTCTCATTCAGAAACAAGGATGCTGTTCCTAAATGgtaattttct ... tcctttgcagCCCACATACCCTTGTACCTGTACCCTTTCCTCAATACCAATAGCAAATCTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgattctactaatttatcttctttttgctaaccaaactttttctcctttgcagCCCACATACCCTTGTACCTGTACCCTTTCCTCAATACCAATAGCAAATCTAGGCCTTTTGAGTACTTGAGACTAACTAGCCTAGGTGTTATTGGTGCTTT
tgctaac putative branch site (score: 1)
ctttttctcctttgc putative PPT
taatttatcttctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgcatgcgtaagcatgtgtatgtgtgccttatgaaatttaatgatttgattctactaatttatcttctttttgctaaccaaactttttctcctttgcagCCCACATACCCTTGTACCTGTACCCTTTCCTCAATACCAATAGCAAATCTAGGCCTTTTGAGTACTTGAGACTAACTAGCCTAGGTGTTATTGGTGCTTT
- -catgcgt
- - - - - - -catgtgt
- - - - - - - - - - - - -tgcctta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccaaact