Sequence
atgc intronic sequence ATGC exonic sequencegtaagcgttaaatctgtccatgatacaagttacatttagaggattgtgttaggatcatgttaagttgcatatccaataattgagagacagagtgtagagaagattaacctcagaactcactgacactctttatctgctctgtagGCTTCTTCAGGTTGCCATTGGAGGATTTTCATCATTTTTTCCTGATTATCAGGAGAGGATTGCTAGACATGAAGCAGCCCATTTTTTAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv07s0031g01560.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os04g54640.1 (Oryza sativa), 3'ss of exon 5
gtaagcgttaaatctgtccatgatacaagttacatttagaggattgtgttaggatcatgttaagttgcatatccaataattgagagac-agagtgtagagaagattaacctcagaactcactgacactctttatctgctc--tgtagGCTTCTTCAGGTTGCCATTGGAGGATTTTCATCATTTTTTCCTGATTATCAGGAGAGGATTGCTAGACATGAAGCAGCCCATTTTTTAG
|| | || || | | | | | || | | | | | | | | | || | | ||| | || | | | || || || ||||| || | || ||||| | ||||||| | |||||||||| ||||||||||| |||||||| |||||||| || |||||||| |
---------------------------------------------atggcatga-caaataacactatctgttttatgaatactcaatgaaaatatgttgcaactttatcat-gaatagattgtaattttccattccatcatcacagTCTTCTGCAAGCAGCAATTGGTGCATTTTCAACTGTTTTTCCTGACTATCAGGAGAGAATTGCTAGGCATGAAGCTGCTCATTTTTTGG
upper sequence: Vv07s0031g01560.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G004352_T01 (Zea mays), 3'ss of exon 5
gtaagcgttaaatctgtccatgatacaagttacatttagaggattgtgttaggatcatgttaagttgcatatccaataattgagagacagagtgtagagaagattaacc-tcagaactcactgacactctttatctgctctgtagGCTTCTTCAGGTTGCCATTGGAGGATTTTCATCATTTTTTCCTGATTATCAGGAGAGGATTGCTAGACATGAAGCAGCCCATTTTTTAG
| | ||| | || ||| || || ||||| | || | | | ||| | | ||||| ||| | | | | | || | | || || ||||| || | || || |||| || || || | |||||||| || ||||||||||||||||| |||||||| || ||||| |||
----------------------------------tgatgctcattcttttggga-cagagaaatttgcacgctccat--------gtaaaaatgttgc--atattaattgtcaaaccatgttaattatgcataccatcattgcagTCTTCTGCAAGCAGCAATCGGAGCGTTCTCTACAGTCTTTCCTGACTACCAGGAGAGGATTGCTAGGCATGAAGCTGCTCATTTCCTAG
upper sequence: Vv07s0031g01560.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA05G31720.1 (Glycine max), 3'ss of exon 5
gtaagcgttaaatctgtccatgatacaagttacatttagaggattgtgttaggatcatgttaagttgcatatccaataattgagagacagagtgtagagaagattaacctcagaactcactgacactctttatctgctctgtagGCTTCTTCAGGTTGCCATTGGAGGATTTTCATCATTTTTTCCTGATTATCAGGAGAGGATTGCTAGACATGAAGCAGCCCATTTTTTAG
| || || ||||| | ||||| || ||| || || || | | | || ||| | | | || | | ||| | || |||||||| || | ||| ||||| | |||||| || |||||||||||||||| || |||||||| || ||||||||||| || |||||
---------------------------------gtaagaagaatagtgtttg--ccatgtagcaatggataccccgc--ttcagtgttaaatgtta------attttcttta-----cattaatgctccaagttgctagtgcagGCTTCTCCAAGCTGCTATTGGCAGCTTTTCAACACTTTTTCCTGATTATCAAGAAAGGATTGCCAGGCATGAAGCAGCTCACTTTTTGA
upper sequence: Vv07s0031g01560.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA08G14970.1 (Glycine max), 3'ss of exon 5
gtaagcgttaaatctgtccatgatacaagttacatttagaggattgtgttaggatcatgttaagttgcatatccaataattgagagacagagtgtagagaagattaacctcagaactcactgacactctttatctgctctgtagGCTTCTTCAGGTTGCCATTGGAGGATTTTCATCATTTTTTCCTGATTATCAGGAGAGGATTGCTAGACATGAAGCAGCCCATTTTTTAG
| || |||||||| | ||||| ||| ||| || || || | | | || ||| | || | | ||| | ||||||||||| || | ||| ||||| | |||||| || |||||||||||||||| || |||||||| || |||||||| || || |||||
---------------------------------gtaagaagaattgtgtttg--ccatgtagcattggatacccctc--ttaagtgttaaatgtta------atttgttttg-----cattaatgctccaagttgctagtgtagGCTTCTCCAAGCTGCTATTGGCAGCTTTTCAACACTTTTTCCTGATTATCAAGAAAGGATTGCCAGGCATGAAGCTGCTCACTTTTTGAMapped 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|32270105|gb|CD719264.1|CD719264EST: ATTGGGAGCATCTCTTTAATAGTTTTGGCTATTGGCAGCATTTCCCCTGG GCTTCTTCAGGTTGCCATTGGAGGATTTTCATCATTTTTTCCTGATTATCA
genomic: ATTGGGAGCATCTCTTTAATAGTTTTGGCTATTGGCAGCATTTCCCCTGGgtaagcgtta ... tgctctgtagGCTTCTTCAGGTTGCCATTGGAGGATTTTCATCATTTTTTCCTGATTATCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gagtgtagagaagattaacctcagaactcactgacactctttatctgctctgtagGCTTCTTCAGGTTGCCATTGGAGGATTTTCATCATTTTTTCCTGATTATCAGGAGAGGATTGCTAGACATGAAGCAGCCCATTTTTTAG
cactgac putative branch site (score: 2)
ctctttatctgctct CT-rich tract
aagattaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcgttaaatctgtccatgatacaagttacatttagaggattgtgttaggatcatgttaagttgcatatccaataattgagagacagagtgtagagaagattaacctcagaactcactgacactctttatctgctctgtagGCTTCTTCAGGTTGCCATTGGAGGATTTTCATCATTTTTTCCTGATTATCAGGAGAGGATTGCTAGACATGAAGCAGCCCATTTTTTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC