Sequence
atgc intronic sequence ATGC exonic sequence...gtcttcaatgagtctatcccccccccataggtgatgtagcatgtagtaaattgtgtatcttaagattgtaactgagtatgttggctggtttatccaacagTGCTGGTGTATCAATAGGCAGTGAAATGTCTGGTGGTGTCTCAAATGTCACAGTGGAAAACCTTCTTGTTTGGAACTCAAGGCGTGCTGTTCGGATCAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv11s0016g00720.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os09g26800.1 (Oryza sativa), 3'ss of exon 4
gtcttcaatgagtctatcccccccccataggtgatgtagcatgtagtaaa-ttgtgt-atcttaagattgtaactga--gtatgttggctggtttatccaacagTGCTGGTGTATCAATAGGCAGTGAAATGTCTGGTGGTGTCTCAAATGTCACAGTGGAAAACCTTCTTGTTTGGAACTCAAGGCGTGCTGTTCGGATCAAG
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----tcgcttaatttatttgttaagtgccagtagtcgagacttttctaaagccatgtgattgtgccattgtgtgtgacctttttttttctattttattggacagTGCTGGTGTATCTATAGGAAGTGAGATGTCTGGCGGTGTTTCAAATGTCTTGGTAGAGAATGTCCATATCTGGGATTCACGGCGAGGTGTGAGGATAAAG
upper sequence: Vv11s0016g00720.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA15G19820.1 (Glycine max), 3'ss of exon 4
gtcttcaatgagtctatcccccccccataggtgatgtagcatgtagtaaa--ttgtgtatcttaagattgtaactgagtatgttggctggttt---atccaacagTGCTGGTGTATCAATAGGCAGTGAAATGTCTGGTGGTGTCTCAAATGTCACAGTGGAAAACCTTCTTGTTTGGAACTCAAGGCGTGCTGTTCGGATCAAG
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----ctagttaa-caacttgatattcattagtgtcttcccatgtgctaaagtcttcacattgtaataatttaacttgggacttttgtttgtatgagatgcaacagTGCTGGCATCTCAATAGGCAGTGAGATGTCTGGTGGGGTATCCAATGTCCTGGTGGAGAACATTCTTGTATGGGAATCAAGGCGTGCCATGAGAATCAAG
upper sequence: Vv11s0016g00720.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA17G05550.1 (Glycine max), 3'ss of exon 4
----gtcttcaatgagtctatcccccccccataggtgatgtagcatgtagtaaattgtgtatcttaagattgtaactgagtatgttggctggtttatccaacagTGCTGGTGTATCAATAGGCAGTGAAATGTCTGGTGGTGTCTCAAATGTCACAGTGGAAAACCTTCTTGTTTGGAACTCAAGGCGTGCTGTTCGGATCAAG
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gttaaattttgacagcttcatatcagttt-gtgtctg-tctatctcatcatgtattggg-gtcttcatatcttaa-tgattttattttttatcaaatggaacagTGCTGGCATCTCAATAGGCAGTGAAATGTCTGGCGGGGTATCCAATGTCACGGTGGAGAATCTTCTTATATGGGATTCTAGGCGCGGTGTGAGGATCAAG
upper sequence: Vv11s0016g00720.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA09G08270.1 (Glycine max), 3'ss of exon 4
gtcttcaatgagtctatcccccccccataggtgatgtagcatgtagtaaa--ttgtgtatcttaagattgtaactgagtatgttggctggttt---atccaacagTGCTGGTGTATCAATAGGCAGTGAAATGTCTGGTGGTGTCTCAAATGTCACAGTGGAAAACCTTCTTGTTTGGAACTCAAGGCGTGCTGTTCGGATCAAG
| | | | || | | | ||||| | | | || |||| | | ||||| || | || | || | || |||||||||||| | |||||||||||||| ||||||||||| || || || ||| ||||| ||| ||||||| ||| | ||||||||||| | | ||||||
----attgcatattcgttactcattagtac-taacttcccatgtgctgaggtcttcacattttaataatttaacttaggacttttctttgtgtgaaatgcaacagTGCTGGCATCTCAATAGGCAGTGAGATGTCTGGTGGGGTATCCAACGTCCTGGTGGAGAACATTCTTGTATGGGAATCAAGGCGTGCCATGAGAATCAAG
upper sequence: Vv11s0016g00720.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT3G42950.1 (Arabidopsis thaliana), 3'ss of exon 4
gtcttcaatgagtctatcccccccccataggtgatgtagcatgtagtaaattgtgtatcttaagattgtaactgagtatgttggctggtttatccaacagTGCTGGTGTATCAATAGGCAGTGAAATGTCTGGTGGTGTCTCAAATGTCACAGTGGAAAACCTTCTTGTTTGGAACTCAAGGCGTGCTGTTCGGATCAAG
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---gtaagagagaattgctttccctaatcaatgttg-atctaataatcaac-gtgtacctaaagcct----ctgtgcaaa---------------aacagCGCTGGTATATCAATAGGAAGTGAGATGTCTGGTGGTGTCTCGAATATCACAGTCGAGAATATTCTGATTTGGAGCTCCCGGCGTGGAGTTAGGATTAAAMapped 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|30251734|gb|CB969467.1|CB969467EST: CCTTCAGTAAACATTCTCATCAGAAACCTTGTCATTCGCTCTATGGTCAG TGCTGGTGTATCAATAGGCAGTGAAATGTCTGGTGGTGTCTCAAATGTCAC
genomic: CCTTCAGTAAACATTCTCATCAGAAACCTTGTCATTCGCTCTATGGTCAGgtgagagctt ... tatccaacagTGCTGGTGTATCAATAGGCAGTGAAATGTCTGGTGGTGTCTCAAATGTCAC
EST:
gi|30251941|gb|CB969674.1|CB969674EST: CCTTCAGTAAACATTCTCATCAGAAACCTTGTCATTCGCTCTATGGTCAG TGCTGGTGTATCAATAGGCAGTGAAATGTCTGGTGGTGTCTCAAATGTCAC
genomic: CCTTCAGTAAACATTCTCATCAGAAACCTTGTCATTCGCTCTATGGTCAGgtgagagctt ... tatccaacagTGCTGGTGTATCAATAGGCAGTGAAATGTCTGGTGGTGTCTCAAATGTCAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtaaattgtgtatcttaagattgtaactgagtatgttggctggtttatccaacagTGCTGGTGTATCAATAGGCAGTGAAATGTCTGGTGGTGTCTCAAATGTCACAGTGGAAAACCTTCTTGTTTGGAACTCAAGGCGTGCTGTTCGGATCAAG
ttgtaac putative branch site (score: 2)
tttatcc putative PPT
tatcttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcttcaatgagtctatcccccccccataggtgatgtagcatgtagtaaattgtgtatcttaagattgtaactgagtatgttggctggtttatccaacagTGCTGGTGTATCAATAGGCAGTGAAATGTCTGGTGGTGTCTCAAATGTCACAGTGGAAAACCTTCTTGTTTGGAACTCAAGGCGTGCTGTTCGGATCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - -caatgag
- - - - - - tctatcc
- - - - - - - - -ccccccc
- - - - - - - - - - - - - - -ggtgatg
- - - - - - - - - - - - - - - - - - - gcatgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggctgg