Sequence
atgc intronic sequence ATGC exonic sequence...ttactgtcattttgggttcaattgtgttgaccaaactcttgtgtgtgtgtgtgtgtgtgtgtatcatgttggaccatcttttaacatctcttatcaccagATTTTGGTATGATGGGTGAATTTGAACCAGAACTCCGAGATGGATTTATTGAAGCCTGTCTCCATCTTGTAAACCGTGATTATGATGCATTGGCTAAGGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv18s0001g01620.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: LOC_Os04g54790.1 (Oryza sativa), 3'ss of exon 10
-----------------------------------ttactgtcattttgggttcaat--tgtgttga---ccaaactcttgtgtgtgtgtgtgtgtgtgtgtatcatgttggacc---atcttttaacatctcttatcacc-----agATTTTGGTATGATGGGTGAATTTGAACCAGAACTCCGAGATGGATTTATTGAAGCCTGTCTCCATCTTGTAAACCGTGATTATGATGCATTGGCTAAGGA
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gtaataattgtgttattctgtttctgcctttaatgtttctgattttttagtcttggtaatgagttagttcctaaatttactcatttgctaccctttacatgaatcttgttccattttaactatctgaaacattttgttctctatgtagATTTCGGAATGATGGGAGAATTCCGACAAGAACTTCGTGATGGATTTATTGAAGCCTGTCTTCACCTTGTTAACCGTGATTTTGATGGTTTAGCAAAAGA
upper sequence: Vv18s0001g01620.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G305007_T01 (Zea mays), 3'ss of exon 10
-----ttactgtcattttgggttcaattgtgttgaccaaactcttgtgtgtgtgtgtgtgt-gtgtgtatcatgttggaccatcttttaacatctcttatcaccagATTTTGGTATGATGGGTGAATTTGAACCAGAACTCCGAGATGGATTTATTGAAGCCTGTCTCCATCTTGTAAACCGTGATTATGATGCATTGGCTAAGGA
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caactttcctgtgtgtttaggaaaaaaag----aagaaaaactttacaaccaattgaatgaagctcaaattattttgattaaa--tgtgacactatttgtcaatagATTTTGGGATGATGGGAGAATTCCGACAAGAACTTCGTGATGGATTTATTGAAGCTTGTCTTCATCTTGTTAACCGTGATTTTGATGCTTTAGCAAAAGA
upper sequence: Vv18s0001g01620.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA16G27500.1 (Glycine max), 3'ss of exon 10
-------------------------------------------------------------------ttactgtcattttgggttcaattgtg----ttgaccaaactcttgtgtgtgtgtgtgtgtgtgtgtatcatgttggaccatcttttaacatctcttat-caccagATTTTGGTATGATGGGTGAATTTGAACCAGAACTCCGAGATGGATTTATTGAAGCCTGTCTCCATCTTGTAAACCGTGATTATGATGCATTGGCTAAGGA
| ||| | || || ||| | | | |||| |||| ||| | | | | | ||| ||| ||| | |||| | || |||||||||||||| ||||| || ||| |||| | || || ||||| || ||||| ||||| ||||||||||||||||||| |||||||||||| |||||
gtaattgaagattgaatatttaatatttcaaattctttggtttcttggttgatgtttacatagatttgtcttgtttctgaggatttaatgatagaaataagcgaaacacttggaataacttgttcatttcttgaatttaatggtgcattctttttcccttcttttgcaatagATTTTGGTATGACTGGTGAGTTCAAACAAGAATTACGCGACGGATTCATCGAAGCTTGTCTACATCTTGTAAACCGTGATTTTGATGCATTGGCCAAGGA
upper sequence: Vv18s0001g01620.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT1G71810.1 (Arabidopsis thaliana), 3'ss of exon 9
ttactgtcattttgggttcaattgtgttgaccaaactcttgtgtgtgtgtgtgtgtgtgtgtatcatg--ttggaccatcttttaacatctctt--atcaccagATTTTGGTATGATGGGTGAATTTGAACCAGAACTCCGAGATGGATTTATTGAAGCCTGTCTCCATCTTGTAAACCGTGATTATGATGCATTGGCTAAGGA
||| ||| | | | | | | ||| || | | | | || || | |||||| | | || |||||||||||||||||||| || ||| |||||| | || |||||||| || ||||| ||||| ||||||||||| ||||| | | || ||||||| ||
---ttgt-gtttgatatctacaaactaaagagagattttactgtcccaagaagtatcttttgtttataacttaattgaacttttagttttttttttgctgccagATTTTGGTATGATGGGGGACTTTAGGCCAGAATTACGTGATGGATTCATGGAAGCATGTCTTCATCTTGTAAATCGTGACTTCAAAGCGCTGGCTAAAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtgtgtgtgtgtgtgtatcatgttggaccatcttttaacatctcttatcaccagATTTTGGTATGATGGGTGAATTTGAACCAGAACTCCGAGATGGATTTATTGAAGCCTGTCTCCATCTTGTAAACCGTGATTATGATGCATTGGCTAAGGA
ttttaac putative branch site (score: 2)
tctcttatc CT-rich tract
atcttttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttactgtcattttgggttcaattgtgttgaccaaactcttgtgtgtgtgtgtgtgtgtgtgtatcatgttggaccatcttttaacatctcttatcaccagATTTTGGTATGATGGGTGAATTTGAACCAGAACTCCGAGATGGATTTATTGAAGCCTGTCTCCATCTTGTAAACCGTGATTATGATGCATTGGCTAAGGA
- -ctgtcat
- - - - - - - - - - - - - - - ccaaact
- - - - - - - - - - - - - - - - - - - -tgtgtgt
- - - - - - - - - - - - - - - - - - - - gtgtgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcatgtt