Sequence
atgc intronic sequence ATGC exonic sequencegtaagcaaataacatctcattttcactaaagcctcacatgaaatatttgcatgagtaactgtgcgttctgtccttttggtgacccacctttttctccataaactttcaagtatgactgatgtgtgatcttattgagtccattacagTGACGGAATTATGTGAATATGCTGCAAATGTTGATATTCCCATTGCAAGAGAGTCAATCCGGGCTGTTGGGAAAATAGCACTGCAGCAGTATGATGTGAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv04s0008g03880.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os01g43630.1 (Oryza sativa), 3'ss of exon 7
gtaagcaaataacatctcattttcactaaagcctcacatgaaatatttgcatgagtaactgtgcgttctgtccttttggtgacccacctttttctccataaactttcaagtatgactgatgtgtgatcttattgagtccattacagTGACGGAATTATGTGAATATGCTGCAAATGTTGATATTCCCATTGCAAGAGAGTCAATCCGGGCTGTTGGGAAAATAGCACTGCAGCAGTATGATGTGAA
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--gtacagcagatatct-gtttccattgattatacat-cggcatatct-cacaa-----catatgtgatatatttttaac--tccatgattttcattatg---tttataaaat------tttgtggccttctt----tcgttccagTAACTGAGTTGTGTGAATATGCTGGAAATGTTGATGTACCAATCGCACGTGAGTCTATTCGAGCAGTTGGGAAAATAGCGCTGCAGCAGTATGATGTGAA
upper sequence: Vv04s0008g03880.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G029077_T01 (Zea mays), 3'ss of exon 5
gtaagcaaataacatctcattttcactaaagcctcacatgaaatatttgcatgagtaactgtgcgttctgtccttttggtgacccacctttttctccataaactttcaagtatgactgatgtgtgatcttattgagtccattacagTGACGGAATTATGTGAATATGCTGCAAATGTTGATATTCCCATTGCAAGAGAGTCAATCCGGGCTGTTGGGAAAATAGCACTGCAGCAGTATGATGTGAA
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------------------------gtatatgcctgatattc--tatttccaactataatt---tgatatgttttcttattaa----------ttactattatttttaaaatatcgattttgcatgtttcttt-----ccac--cagTCACTGAACTATGTGAATATGCTGGAAATGTTGATGTACCAATTGCAAGAGAGTCTATCCGGGCAGTTGGAAAAATAGCACTGCAGCAGTATGATGTTAA
upper sequence: Vv04s0008g03880.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AC198725.4_FGT007 (Zea mays), 3'ss of exon 7
gtaagcaaataacatctcattttcactaaagcctcacatgaaatatttgcatgagtaactgtgcgttctgtccttttggtgacccacctttttctccataaactttcaagtatgactgatgtgtgatcttattgagtccattacagTGACGGAATTATGTGAATATGCTGCAAATGTTGATATTCCCATTGCAAGAGAGTCAATCCGGGCTGTTGGGAAAATAGCACTGCAGCAGTATGATGTGAA
|||| || | | | | | | |||| ||| | | || | | ||| | | | || || ||| |||| || ||| | |||||||| |||| ||||||||| | || |||||||| ||||| ||||| || ||||| |||||||||||||||||||||||||| ||
------------------------------------------------------gtaaatgccagacttccaactgtaatttgatatgttttactcattca--ttaccattatt-ttaaaaagcatgtttctt---cccac--cagTCACCGAACTGTGTGAATACGCTGGGAATGTTGATGTACCGATTGCAAGGGAGTCTATCCGCGCAGTTGGAAAAATAGCACTGCAGCAGTATGATGTTAA
upper sequence: Vv04s0008g03880.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA06G08590.1 (Glycine max), 3'ss of exon 5
gtaagcaaataacatctcattttcactaaagcctcacatgaaatatttgcatgagtaactg-tgcgttctgtccttttggtgacccacctttttctccataaactttcaa--gtatgactgatgtgtgatcttattgagtc-cattacagTGACGGAATTATGTGAATATGCTGCAAATGTTGATATTCCCATTGCAAGAGAGTCAATCCGGGCTGTTGGGAAAATAGCACTGCAGCAGTATGATGTGAA
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----gtaagaaacttca-atttgctatagaga---gaaagggttaggggagggagcgattgatttaagatttgcatttgatgttctattccctggtctg-aggctgcctgtcttatgacatattcatgaacttcttggatctcatttcagTGACAGAATTATGTGAATATGCTGCAAATGTTGACATTCCCATTGCAAGGGAATCAATTCGAGCTGTTGGGAAGATAGCATTGCAGCAGTATGATGTCAA
upper sequence: Vv04s0008g03880.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA04G08480.1 (Glycine max), 3'ss of exon 5
gtaagcaaataacatctcattttcactaaagcctcacatgaaatatttgcatgagtaactg-tgcgttctgtccttttggtgacccacctttttctccataaactttcaagt-atgactgatgtgtgatcttattgagtc-cattacagTGACGGAATTATGTGAATATGCTGCAAATGTTGATATTCCCATTGCAAGAGAGTCAATCCGGGCTGTTGGGAAAATAGCACTGCAGCAGTATGATGTGAA
| || |||| ||| ||| ||| || | ||| || | | |||||| || || | | | ||||||| | | | || | | |||||| | ||| ||| ||| || |||| ||||||| ||||||||||||||||||||||||||||| |||||||||||||| || ||||| || ||||||||||| |||||| |||||||||||||||| ||
----gtaagtaac--ttcaattt-gctatagagagaaatggt-taggggaaggagtaattgatgtaagatttgcatttggtgttctattccctggtctgaggctgcccgtcttatgacttactcatgaacttcttggatctcatttcagTGACAGAATTATGTGAATATGCTGCAAATGTTGACATTCCCATTGCAAGGGAATCAATTCGAGCTGTTGGGAAGATAGCATTGCAGCAGTATGATGTCAA
upper sequence: Vv04s0008g03880.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT5G11490.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaagcaaataacatctcattttcactaaagcctcacatgaaatatttgca---tgagtaactgtgcgttctgtccttttggtgacccacctttttctccataaactttcaagtatgactgatgtgtgatcttattgagtccattacagTGACGGAATTATGTGAATATGCTGCAAATGTTGATATTCCCATTGCAAGAGAGTCAATCCGGGCTGTTGGGAAAATAGCACTGCAGCAGTATGATGTGAA
| ||| || || | || | | || |||| | | ||| ||||| | || | | |||| || || | || | | || ||||||||||| | ||||| ||||||||||| ||||||||| | ||||| ||||||||||| || || ||||| || || || |||| ||||||||||| ||
---------------------------------------gtaatgatttcaaactatgtcaatatggaatctgaagcta-gaaaacctttcttttcc------ggctctttgattggactaattcgtactttt------ttcttttcagTGACGGAACTGTGTGAGTATGCTGCAAACGTTGATATTGCAATTGCGAGAGAGTCAATTCGAGCAGTTGGAAAGATTGCTTTGCAACAGTATGATGTAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctccataaactttcaagtatgactgatgtgtgatcttattgagtccattacagTGACGGAATTATGTGAATATGCTGCAAATGTTGATATTCCCATTGCAAGAGAGTCAATCCGGGCTGTTGGGAAAATAGCACTGCAGCAGTATGATGTGAA
gactgat putative branch site (score: 3)
ataaacttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcaaataacatctcattttcactaaagcctcacatgaaatatttgcatgagtaactgtgcgttctgtccttttggtgacccacctttttctccataaactttcaagtatgactgatgtgtgatcttattgagtccattacagTGACGGAATTATGTGAATATGCTGCAAATGTTGATATTCCCATTGCAAGAGAGTCAATCCGGGCTGTTGGGAAAATAGCACTGCAGCAGTATGATGTGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG