Sequence
atgc intronic sequence ATGC exonic sequencegtatggagtttcaatgcttaacacccttatatgagtttatgataattgcacagttgaccctcatgttgattattaggatttggggttaaatcccaattctgcacttgaatgttgtactactcccttataacatttaaacatcaattctgcagACACTTTGCCAAATGTTTATCATTAATGCTGGTCCAGGTTTTAGGCTGCTCTGGAACACCGTGAAGACTTTTCTTGATCCAAAAACAACTTCCAAGATTC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv18s0001g12950.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os02g04020.1 (Oryza sativa), 3'ss of exon 6
gtatggagtttcaatgcttaacacccttatatgagtttatgataattgcacagttgaccctcatgttgattattaggatttggggttaaatcccaattctgcacttgaatgttgtactactcccttataacatttaaacatcaattctgcagACACTTTGCCAAATGTTTATCATTAATGCTGGTCCAGGTTTTAGGCTGCTCTGGAACACCGTGAAGACTTTTCTTGATCCAAAAACAACTTCCAAGATTC
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-----------------------------------------------------------gtactgtcttctactca-attcgctgataag-cacagtactgtg-ttaattttcttgctaacttttttt----tcgtggttttatgtgttcagACCCTATATCAAATGTTTATTGTCAATGCTGGTCCGGGGTTTCGGCTCTTATGGAACACTGTGAAGTCCTTTCTGGACCCAAAAACCACTTCCAAGATAC
upper sequence: Vv18s0001g12950.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G171354_T03 (Zea mays), 3'ss of exon 6
gtatggagtttcaatgcttaacacccttatatgagtttatgataattgcacagttgaccctcatgttgattattaggatttggggttaaatcccaattctgcacttgaatgttgtactactcccttataacatttaaacatcaattctgcagACACTTTGCCAAATGTTTATCATTAATGCTGGTCCAGGTTTTAGGCTGCTCTGGAACACCGTGAAGACTTTTCTTGATCCAAAAACAACTTCCAAGATTC
|| || || | || | | | || | || ||| || | | ||| ||||| || | |||||||||||| | ||||||||||| ||||| |||| || |||||||| |||||| | ||||||||||| ||||| || ||||||| |
------------------------------------------------------------------------gtatgagcctcattttttttacactctcttttgttgtttttttgcttggaatatattgggttaatttgttgcatctccagACTCTATACCAAATGTTTATTGTCAATGCTGGTCCGGGTTTCCGGCTACTATGGAACACTGTGAAGTCCTTTCTTGATCCCAAAACTACCGCCAAGATAC
upper sequence: Vv18s0001g12950.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA06G03300.1 (Glycine max), 3'ss of exon 5
gtatggagtttcaatgcttaacacccttatatgagtttatgataattgcacagtt--gaccctcatgttgattattaggatttggggttaaatcccaattctgcacttgaatgttgtactactcccttataacatttaaacatcaattctgcagACACTTTGCCAAATGTTTATCATTAATGCTGGTCCAGGTTTTAGGCTGCTCTGGAACACCGTGAAGACTTTTCTTGATCCAAAAACAACTTCCAAGATTC
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------------------------------------------caagtatattgttttaatcatcacttt--ttttctgacttcagaatt---ttcttattgttca------tgtagtgcttctaagttctaatatctaaatgata-ccgtgcagACACTCTGCCAAATGTTTATCATTAATGCTGGTCCTGGTTTTAAGATGCTCTGGAACACGGTGAAAACATTTCTTGATCCCAAAACTACTTCAAAGATTC
upper sequence: Vv18s0001g12950.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA04G03230.1 (Glycine max), 3'ss of exon 4
gtatggagtttcaatgcttaacacccttatatgagtttatgataattgcacagtt--gaccctcatgttgattattaggatttggggttaaatcccaattctgcacttgaatgttgtactactcccttataacatttaaacatcaattctgcagACACTTTGCCAAATGTTTATCATTAATGCTGGTCCAGGTTTTAGGCTGCTCTGGAACACCGTGAAGACTTTTCTTGATCCAAAAACAACTTCCAAGATTC
|| | |||| | | ||| || || | | || | | | | ||| | || ||| || || || || ||| | |||| | |||||||||| ||||||||||||||||||||||||||||| ||||||| | | ||||||||||| ||||| || ||||||||||| ||||| ||||| |||||||
------------------------------------------caagtatgtagttttaatcatcacttt--ttttctgacttcagaat---gttcttattgttca------tgtagtgcttcttgattctaatctctaaatgata-ccgtgcagACACTCTGCCAAATGTTTATCATTAATGCTGGTCCTGGTTTTAAGATACTCTGGAACACGGTGAAAACATTTCTTGATCCCAAAACTACTTCAAAGATTC
upper sequence: Vv18s0001g12950.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA17G37150.1 (Glycine max), 3'ss of exon 5
gtatggagtttcaatgcttaacacccttatatgagtttatgataattgcacagttgaccctcatgttgattattagg---atttggggttaaatcccaattctgcacttgaatgttgtactactcccttataacatttaaacatcaattctgcagACACTTTGCCAAATGTTTATCATTAATGCTGGTCCAGGTTTTAGGCTGCTCTGGAACACCGTGAAGACTTTTCTTGATCCAAAAACAACTTCCAAGATTC
| |||| | | | |||||| | ||| ||| ||||| |||| | |||| | || || || |||| | |||| | |||||||| | || | ||||||||| || ||||||||||| ||||||| |||||| |||||||| ||||| | ||||||||||| ||||| ||||| |||||
-------------------------------------------------gtatgtgactttagtcataattattgtggtagtttttagttcttctaggtttctggactt-attgttctggta-tctgttctaacctataaatgatt-ctgtgcagACATTATGTCGAATGTTTATAATCAATGCTGGTCCCGGTTTTAAGCTGCTTTGGAACACAGTGAAATCATTTCTTGATCCCAAAACTACTTCAAAGATAA
upper sequence: Vv18s0001g12950.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA14G07850.1 (Glycine max), 3'ss of exon 5
gtatggagtttcaatgcttaacacccttatatgagtttatgataattgcacagttgaccctcatgttgattattaggatttggggttaaatcccaa----ttctgcacttgaatgttgtactactcccttataacatttaaacatcaattctgcagACACTTTGCCAAATGTTTATCATTAATGCTGGTCCAGGTTTTAGGCTGCTCTGGAACACCGTGAAGACTTTTCTTGATCCAAAAACAACTTCCAAGATTC
| |||| | | | |||||| | | | |||| || | ||||| |||| | |||| | || || || |||| | |||| | | |||||||| | || | ||||||||| || ||||||||||| ||||||| |||||| |||||||| ||||| | ||||||||||| ||||| ||||| |||||
-------------------------------------------------gtatgtgactttagtcataattattgtggta-gtttttaattcttcatggcttctggactt-attgttctggta-tctgttctaacctataaatgttt-ctgtgcagACATTATGTCGAATGTTTATAATCAATGCTGGTCCCGGTTTTAAGCTGCTTTGGAACACGGTGAAATCATTTCTTGATCCCAAAACTACTTCAAAGATAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctgcacttgaatgttgtactactcccttataacatttaaacatcaattctgcagACACTTTGCCAAATGTTTATCATTAATGCTGGTCCAGGTTTTAGGCTGCTCTGGAACACCGTGAAGACTTTTCTTGATCCAAAAACAACTTCCAAGATTC
ttataac putative branch site (score: 2)
ttataacatttaaaca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatggagtttcaatgcttaacacccttatatgagtttatgataattgcacagttgaccctcatgttgattattaggatttggggttaaatcccaattctgcacttgaatgttgtactactcccttataacatttaaacatcaattctgcagACACTTTGCCAAATGTTTATCATTAATGCTGGTCCAGGTTTTAGGCTGCTCTGGAACACCGTGAAGACTTTTCTTGATCCAAAAACAACTTCCAAGATTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA