Sequence
atgc intronic sequence ATGC exonic sequence...tgtttcaactccttagacaatcacctctctctctctctctcgtgtttgcactgattcatcttaagtttgaatgtaacagtcagctcttttatgcttgtagATCAACGTCTCAATGATATTGTTGGAAGTGCATACTATGTTGCACCCGAAGTACTCCACAGATCCTACAATCTTGAAGCTGATGTTTGGAGCATTGGCGT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv16s0098g01140.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os10g36710.1 (Oryza sativa), 3'ss of exon 5
--------------------------------------------------------------------------------tgtttcaactccttagacaatcacctctctctctctctctcgtgtttgcactgattcatcttaagtttgaatgta---acagtcagctcttttatgcttgt--agATCAACGTCTCAATGATATTGTTGGAAGTGCATACTATGTTGCACCCGAAGTACTCCACAGATCCTACAATCTTGAAGCTGATGTTTGGAGCATTGGCGT
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gtatttccccccaaaagaattatgcccttccaaagaacttgtgtttcatcttatgttttttttttactctattatgaatttgtcctgacatggtgaaaatactgttttttgaaaccaaatagtgaaaatactcaagtgttttgatgacacacatatttatgattggtcaatgccttcttttacagATGAAAGATTAAATGATATTGTTGGTAGTGCATACTATGTTGCTCCAGAAGTCCTACATAGGTCATATAGCACGGAAGCAGACATGTGGAGTATTGGTGT
upper sequence: Vv16s0098g01140.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os06g50030.1 (Oryza sativa), 3'ss of exon 5
tgtttcaactccttagacaatcacctctctct---ctctctctcgtgtttgcactgattcatcttaagtttgaatgtaacagtcagctcttttatgcttgtagATCAACGTCTCAATGATATTGTTGGAAGTGCATACTATGTTGCACCCGAAGTACTCCACAGATCCTACAATCTTGAAGCTGATGTTTGGAGCATTGGCGT
|| | || | || | | ||||| || | || | || || | | | | | | | | | | | ||| | | |||| || | || ||||||||||||||||||||||| |||||||| || || || | |||||||| || | | | ||||| || ||||||| || || ||
--ttaatgaactttggctaactatttttctcttcactgttgcttggtatttcattagctgaccagacaccttgttctttgtattttgtgctatataat-gcagATGAAAGGCTTAATGATATTGTTGGAAGTGCATATTATGTTGCCCCAGAGGTTTTACACAGATCATATAGTATGGAAGCAGACATTTGGAGTATAGGTGT
upper sequence: Vv16s0098g01140.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G031893_T01 (Zea mays), 3'ss of exon 5
--------------------------------------------------------tgtttcaactccttagacaatcacctctctctctctctctcgtgtttgcactgattcatcttaagtttgaatgtaacagtcagctcttttatgcttgtagATCAACGTCTCAATGATATTGTTGGAAGTGCATACTATGTTGCACCCGAAGTACTCCACAGATCCTACAATCTTGAAGCTGATGTTTGGAGCATTGGCGT
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gtattacatacctccgcacaagggccatccaattgtaaagttctgttttacaaatatgttagaagtccattgaca-taaaatgaaacatgatatgaccttcctccaaaaaatgttctaacgcctga-tgctcctgatgccttttccccctttacagATGAAAGGCTTAATGACATTGTTGGAAGTGCATACTATGTTGCTCCAGAAGTCTTGCATAGGTCATATAGCACAGAAGCAGACATGTGGAGCATTGGTGT
upper sequence: Vv16s0098g01140.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G100560_T01 (Zea mays), 3'ss of exon 5
--------------------------------------------------------tgtttcaactccttagacaatcacctctctctctctctctcgtgtttgcactgattcatcttaagtttgaatgtaacagtcagctcttttatgcttgtagATCAACGTCTCAATGATATTGTTGGAAGTGCATACTATGTTGCACCCGAAGTACTCCACAGATCCTACAATCTTGAAGCTGATGTTTGGAGCATTGGCGT
|||| || ||| | | || | | | | | | | | | || | | ||| | | ||| || | | | || || |||| || | || ||||| |||||||||||||||||||||||||| || ||||| | || || || || | ||||| || | ||||| ||||| ||
gtattacatacctccacacaagggccatccaattgtaaagttctgttttacaaatatgttagaagtccattgcca-taaaatgaaacatgatatgaccttcctccaaaaaatgttctaatgcctga-tgctcctgatgctttttccccctttacagATGAAAGGCTTAATGACATTGTTGGAAGTGCATACTATGTTGCTCCAGAAGTCTTGCATAGGTCATATAGCACAGAAGCAGACATGTGGAGAATTGGTGT
upper sequence: Vv16s0098g01140.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G115518_T01 (Zea mays), 3'ss of exon 5
tgtttcaactccttagacaatcacc-tctctctctctctctcgtgtttgcactgattca-tcttaagtttgaatgtaacagtcagctcttttatgct-tgtagATCAACGTCTCAATGATATTGTTGGAAGTGCATACTATGTTGCACCCGAAGTACTCCACAGATCCTACAATCTTGAAGCTGATGTTTGGAGCATTGGCGT
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tggaata-cactatcaacatttacagttaatattttttttcagttcactcattaactaaatcttatacttaattttgtgtgtt--ctgcactatgcaatgcagATGAAAGGCTCAATGATATTGTTGGAAGTGCTTATTATGTTGCTCCAGAGGTTCTACACAGATCATACAGTATGGAAGCAGACATTTGGAGTATAGGTGT
upper sequence: Vv16s0098g01140.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G138245_T01 (Zea mays), 3'ss of exon 5
-----------------------------------------------------------tgtttcaactccttagacaatcacctctctctctctctctcgtgtttgcactgattcatcttaagtttgaatgtaacagtcagctcttttatgcttgtagATCAACGTCTCAATGATATTGTTGGAAGTGCATACTATGTTGCACCCGAAGTACTCCACAGATCCTACAATCTTGAAGCTGATGTTTGGAGCATTGGCGT
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gtattacatacctccacacaaggatcatccattcctaatggagttctattttacaaatatgttagaagtccattgacataaaacgaaacatgatatgagcttcctctaaaagat--gttttaaagcctgatgctcctgatgcctcctcccc-ctcacagATGAAAGGCTTAATGACATTGTTGGAAGTGCATACTACGTTGCTCCAGAAGTCTTGCATAGGTCATATAGCACAGAAGCAGACATGTGGAGTATTGGTGT
upper sequence: Vv16s0098g01140.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G173928_T01 (Zea mays), 3'ss of exon 5
tgtttcaactccttagacaatcacctctctctctctctctcgtgtttgcactgattca-tcttaagtttgaatgtaacagtcagctcttttatgcttgtagATCAACGTCTCAATGATATTGTTGGAAGTGCATACTATGTTGCACCCGAAGTACTCCACAGATCCTACAATCTTGAAGCTGATGTTTGGAGCATTGGCGT
| || | | | | || | | | ||| | | | || | | ||| ||||| || | || || | | || ||| |||| || | |||||||||||||||||||| ||||| ||||| || || || || || |||||||| |||| | | ||||| || ||||||| || || ||
ttggaagacactatcattatttacagttaaccatttcttttgctcattcattaactcaatcttatacttaatcttatatgttctgtgctacata-ttgcagATGAAAGGCTCAATGATATTGTTGGAAGCGCATATTATGTCGCTCCAGAGGTTCTACACAGATCGTACAGTATGGAAGCAGACATTTGGAGTATAGGTGT
upper sequence: Vv16s0098g01140.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA06G13920.1 (Glycine max), 3'ss of exon 5
-tgtttcaactccttagacaatcacctctctctctctctctcgtgtttgcactgattcatcttaagtttgaatgt-aacagtcagctcttttatgcttgtagATCAACGTCTCAATGATATTGTTGGAAGTGCATACTATGTTGCACCCGAAGTACTCCACAGATCCTACAATCTTGAAGCTGATGTTTGGAGCATTGGCGT
|| | || || | | | | | ||||| | | | | | ||| | | | | | | ||| || | || ||||||||| ||||||||||||||||| ||||| |||||||||||||| ||||| ||||| ||||| || | | |||||| || | ||||| ||||| ||
cagtgtttgcta--taaattgttatcatttattctcttgtaatcggtgatatcctcttgttggttttttcactaccagctctgacttctaataaacatgcagATCAACGCCTCAATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAGTGCTCCATAGATCTTATAGTGTTGAAGGAGACTTATGGAGTATTGGGGT
upper sequence: Vv16s0098g01140.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT5G24430.1 (Arabidopsis thaliana), 3'ss of exon 5
-----tgtttcaactccttagacaatcacctctctctctctctctcgtgtttgcactgattcatcttaagtttgaatgtaacagtcagctcttttatgcttgtagATCAACGTCTCAATGATATTGTTGGAAGTGCATACTATGTTGCACCCGAAGTACTCCACAGATCCTACAATCTTGAAGCTGATGTTTGGAGCATTGGCGT
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gtaaccatatatgttcccttggca-ttattagtcttgccaaatctcatttgtacaagttttccgctcacattt---cttatttgttaa-tcttttatatatgcagATCAGCGTCTCAATGATGTTGTAGGAAGTGCATACTATGTTGCACCTGAAGTACTCCATAGGTCTTACAGCACTGAAGCAGATATGTGGAGCATCGGTGT
upper sequence: Vv16s0098g01140.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT3G49370.1 (Arabidopsis thaliana), 3'ss of exon 5
-tgtttcaactccttagacaatcacctctctctctctctctcgtgtttgcactgattcatcttaagtttgaatgtaacagtcagctcttttat---gcttg---tagATCAACGTCTCAATGATATTGTTGGAAGTGCATACTATGTTGCACCCGAAGTACTCCACAGATCCTACAATCTTGAAGCTGATGTTTGGAGCATTGGCGT
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gtaattctttgttcctctttcttatacatgactctgcttgtagtattt-tacttagaagactaaggatggaatgtttttttttttttttatgttgggctttaactagATCAGCGTCTCAACGATGTGGTAGGAAGTGCATACTATGTTGCACCTGAAGTACTTCACAGATCCTATAGCACCGAAGCAGATATATGGAGCATTGGTGTMapped 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|110720801|gb|EE097051.1|EE097051EST: TGCTCCGATGAAGGTTATTGATTTTGGTCTTTCTGATTTTATTAGAACAG ATCAACGTCTCAATGATGTTGTTGGAAGTGCATACTATGTTGCACCCGAAG
genomic: TGCTCCGATGAAGGTTATTGATTTTGGTCTTTCTGATTTTATTAGAACAGgtaatggttg ... atgcttgtagATCAACGTCTCAATGATATTGTTGGAAGTGCATACTATGTTGCACCCGAAG
EST:
gi|30126117|gb|CB911456.1|CB911456EST: TGCTCCGATGAAGGTTATTGATTTTGGTCTTTCTGATTTTATTAGAACAG ATCAACGTCTCAATGATATTGTTGGAAGTGCATACTATGTTGCACCCGAAG
genomic: TGCTCCGATGAAGGTTATTGATTTTGGTCTTTCTGATTTTATTAGAACAGgtaatggttg ... atgcttgtagATCAACGTCTCAATGATATTGTTGGAAGTGCATACTATGTTGCACCCGAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgcactgattcatcttaagtttgaatgtaacagtcagctcttttatgcttgtagATCAACGTCTCAATGATATTGTTGGAAGTGCATACTATGTTGCACCCGAAGTACTCCACAGATCCTACAATCTTGAAGCTGATGTTTGGAGCATTGGCGT
atgtaac putative branch site (score: 3)
ctcttttat putative PPT
ttaagttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtttcaactccttagacaatcacctctctctctctctctcgtgtttgcactgattcatcttaagtttgaatgtaacagtcagctcttttatgcttgtagATCAACGTCTCAATGATATTGTTGGAAGTGCATACTATGTTGCACCCGAAGTACTCCACAGATCCTACAATCTTGAAGCTGATGTTTGGAGCATTGGCGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - -caactcc
- - - - - - - - -caatcac
- - - - - - - - - - - - ctctctc
- - - - - - - - - - - - - - - - - - - - - tgtttgc
- - - - - - - - - - - - - - - - - - - - - - - - - ctgattc