Sequence
atgc intronic sequence ATGC exonic sequencegtatcttaatgcactacaaattattctgcatttcctaatgaaatattgggttttcatgtgcttttatttgtcttgcagAGTGAAGAGGCAAGGATAGCAAAGGAAGTTGAAGCTCATGAAAAAAGAATTCGAAAAGAGCTTGAGAAACAAGATATTTTGAGGCGAAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv12s0028g03090.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os01g48180.1 (Oryza sativa), 3'ss of exon 1
--------------------gtatcttaatgcactacaaattattctgcatttcctaat--gaaatattgggttttc--atgtgctt-ttatttgtc-ttgcagAGTGAAGAGGCAAGGATAGCAAAGGAAGTTGAAGCTCATGAAAAAAGAATTCGAAAAGAGCTTGAGAAACAAGATATTTTGAGGCGAAAG
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gtatgttttcctctgaccccatatagtcatat-ttgcatctttcttcatatccttaaatcttagttatagacatattgaatttgtttaccatctgccatagCACAATGAGGAAGCAAAAATTGCAAAGGAAGTTGAAGCTCATGAAAGACGAATTAGGAAGGAGCTTGAAAAACAAGACATGATGAAGAGAAAG
upper sequence: Vv12s0028g03090.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os05g48820.1 (Oryza sativa), 3'ss of exon 4
-----gtatcttaatg-cactacaaattattctgcatt-tcctaatgaaatattgggttttcatgtgcttttatttgtctt-----gcagAGTGAAGAGGCAAGGATAGCAAAGGAAGTTGAAGCTCATGAAAAAAGAATTCGAAAAGAGCTTGAGAAACAAGATATTTTGAGGCGAAAG
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gtatggtttttcactgactttatgtaaacttgctcattattccggatatgcactagttgctgatgtgtgatcattttcttaaaacagCATAGCGAGGAAGTGAAGATTGCAAAGGAAGTTGAGGCTCATGAAAAACGAATCAGAAAGGAGCTCGAGAAGCAAGATATGTTGAACAGAAAG
upper sequence: Vv12s0028g03090.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G159357_T01 (Zea mays), 3'ss of exon 4
---------gtatcttaatgcactacaaattattctgcatttcctaatgaaatattgggttttcatgtgcttttatttgtctt--gcagAGTGAAGAGGCAAGGATAGCAAAGGAAGTTGAAGCTCATGAAAAAAGAATTCGAAAAGAGCTTGAGAAACAAGATATTTTGAGGCGAAAG
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gtatgatttctgagttcatatact-catgttgcccttcagctt-tatagtcgtatacattttaaatttgtctgggattttcttcagCATAGTGAAGAAGCAAAGATTGCAAAGGAAGTTGAAGCTCACGAAAGACGAATTAGGAAGGAGCTTGAGAAACAAGATATGTTGAATAAAAAG
upper sequence: Vv12s0028g03090.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G359237_T01 (Zea mays), 3'ss of exon 4
----------------------------gta-tcttaatgcactacaaattattctgcatttcctaatg-aaatattgggttttcatgtgcttttatttgtcttgcagAGTGAAGAGGCAAGGATAGCAAAGGAAGTTGAAGCTCATGAAAAAAGAATTCGAAAAGAGCTTGAGAAACAAGATATTTTGAGGCGAAAG
|| || || ||| || ||| || | | | | || | | ||||| ||| || | |||| || ||| | |||||| |||| ||| ||||| |||||||||||||| |||| | ||||| | || |||||||||||||||||| |||||| |||||
gtatgattcttaattagtttgagtttatatactcatattgcccttcaactttatagtcgtatacttgtatacatattaaatttgtctgggattttcttca----gCATAATGAAGAAGCAAAGATTGCAAAAGAAGTTGAAGCTCACGAAAGACGAATTAGGAAGGAGCTTGAGAAACAAGATTTTTTGAATAGAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctgcatttcctaatgaaatattgggttttcatgtgcttttatttgtcttgcagAGTGAAGAGGCAAGGATAGCAAAGGAAGTTGAAGCTCATGAAAAAAGAATTCGAAAAGAGCTTGAGAAACAAGATATTTTGAGGCGAAAG
tcctaat putative branch site (score: 2)
cttttatttgtctt putative PPT
taatgaaatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatcttaatgcactacaaattattctgcatttcctaatgaaatattgggttttcatgtgcttttatttgtcttgcagAGTGAAGAGGCAAGGATAGCAAAGGAAGTTGAAGCTCATGAAAAAAGAATTCGAAAAGAGCTTGAGAAACAAGATATTTTGAGGCGAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT