Sequence
atgc intronic sequence ATGC exonic sequencegtgagtttgagttgttttgctggattgatgattgatgattgaatgtactggtattcgtgggctgatgaatacttttgaattttgtattgaagGTATTGCAAATGCGAGATGCCTTATAACCCAGATGATCTTATGGTCCAGTGCGAGGGGTGCAAGGACTG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv10s0116g00160.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os09g21770.1 (Oryza sativa), 3'ss of exon 2
----------------------------------gtgagtttgagttgttttgctggattgatgattgatgattgaatgtactggtattcgtgggctgatgaatacttttgaat-----tttgtat---tgaagGTATTGCAAATGCGAGATGCCTTATAACCCAGATGATCTTATGGTCCAGTGCGAGGGGTGCAAGGACTG
||| |||| | ||| || || || ||| ||||||| || | || || | | | |||| | | ||| | || ||||| ||||| ||||||||||| |||||||| |||||||| ||||| ||||||||||| |||||||||||
gtatttgctccaaccccccctccttttttgatcattgattttgcatctgcttgttgttatgcaatgtgggctttggttgtactgataatggttggtggtggttttggtttgggtgtgtgtgtgtgtgtgtgcagGTACTGCAAGTGCGAGATGCCGTATAACCCGGATGATCTAATGGTGCAGTGCGAGGGATGCAAGGACTG
upper sequence: Vv10s0116g00160.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os08g32620.1 (Oryza sativa), 3'ss of exon 2
----------------------------------gtgagtttga-gttgt-tttgctggattgatgattgatgattgaatgt--actggt-attcgtgggctgatgaatacttttgaattttgtattgaagGTATTGCAAATGCGAGATGCCTTATAACCCAGATGATCTTATGGTCCAGTGCGAGGGGTGCAAGGACTG
||| | |||| |||| | ||| |||| | |||||| | || | |||||| || | | || || | ||||| || ||||| || |||||||| || ||||| |||||||| ||||| |||||||| | |||||||||||
gtatgcttgaatgctgattgttcatttcccgttccccagtgcaatgttggatttgttcaatttccatgggatgttagaatgttgattgctgattcgtctctgcttgtgttttctttttcgtttttctgaagATACTGCAAGTGTGAGATGCCATACAACCCGGATGATCTCATGGTGCAGTGCGATGACTGCAAGGACTG
upper sequence: Vv10s0116g00160.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G119357_T01 (Zea mays), 3'ss of exon 2
-----gtgagtttgagttgttt---tgctggattgatgattgatgattgaatgtactg-gtattcgtgggctgatgaatacttttgaattttgtattgaagGTATTGCAAATGCGAGATGCCTTATAACCCAGATGATCTTATGGTCCAGTGCGAGGGGTGCAAGGACTG
| | | | | ||| || || || | | || || || | | | || | | || | || ||||| | ||||||||||||||| |||||||| || ||||| ||||| || ||||| |||||||| | |||||||||||
gtacggagctcctcaatcctttcattgttgactttttcttctctgtgcatgcgttttgagcctgcttgtgataatttgggtgtgtgtatttttctctaaagGTATTGCAAATGTGAGATGCCATACAACCCGGATGACCTCATGGTGCAGTGCGAAGCTTGCAAGGACTG
upper sequence: Vv10s0116g00160.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM5G871463_T02 (Zea mays), 3'ss of exon 2
--gtgagtttgagttgttttgctggattgatgattgatgattg-aatgtactggtattcgtgggctgatgaatacttttgaattttgtat------tgaagGTATTGCAAATGCGAGATGCCTTATAACCCAGATGATCTTATGGTCCAGTGCGAGGGGTGCAAGGACTG
||| | | | |||| || || || | ||| | | ||| | | || | | ||| || | ||| | ||||||||||||||| |||||||| || ||||| ||||| || ||||| |||||||| | |||||| ||||
gtatgaagctcctcaacccttcc--attgctggctgtcccttttactgtgcatgcatttttagcttgcttgtgatgattgggttgtctattttctctcaagGTATTGCAAATGTGAGATGCCGTACAACCCCGATGACCTCATGGTGCAGTGCGATGCTTGCAAGCACTG
upper sequence: Vv10s0116g00160.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G091265_T01 (Zea mays), 3'ss of exon 2
-----------------------gtgagtttgagttgttttgctggattgat--gattg-atgattgaatgtactggtatt-cgtgggctgatgaatacttttgaat----tttgtat-tgaagGTATTGCAAATGCGAGATGCCTTATAACCCAGATGATCTTATGGTCCAGTGCGAGGGGTGCAAGGACTG
|| | || || | | | | || || | ||| || ||| | ||| | | ||||| | | || | | | ||||||| ||||| |||||||| || |||||||| || ||||| ||||| || ||||| ||||| || || |||||||||||
gtgtacaaagctcttccttttctgtaaccttttgtcatgtggt--ggttaatcagtttgtattatttttgcttctgatgtaatgtgggatttttgatcttatgtgacattgtttgtatgtgaagatattgcaagTGTGAGATGCCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTG
upper sequence: Vv10s0116g00160.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G091265_T05 (Zea mays), 3'ss of exon 2
---------------------gtgagtttgagttgttttgctggattgatga--ttg-atgattgaatgtactggtatt-cgtgggctgatgaatacttttgaat----tttgtat-tgaagGTATTGCAAATGCGAGATGCCTTATAACCCAGATGATCTTATGGTCCAGTGCGAGGGGTGCAAGGACTG
|| | || || | | | | || || | ||| || ||| | ||| | | ||||| | | || | | | ||||||| ||||| |||||||| || |||||||| || ||||| ||||| || ||||| ||||| || || |||||||||||
gtacaaagctcttccttttctgtaaccttttgtcatgtggt--ggttaatcagtttgtattatttttgcttctgatgtaatgtgggatttttgatcttatgtgacattgtttgtatgtgaagATATTGCAAGTGTGAGATGCCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTG
upper sequence: Vv10s0116g00160.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA13G34740.1 (Glycine max), 3'ss of exon 2
gtgagtttgagt-----tgtttt-gctggattgatgat-----tgatgattgaatgtactggtattcgtgggct-------gatgaatacttttgaattt-tgtattgaagGTATTGCAAATGCGAGATGCCTTATAACCCAGATGATCTTATGGTCCAGTGCGAGGGGTGCAAGGACTG
|| ||||| | |||||| ||| | ||| | | || || || || | | | | ||||| | | ||| | |||| ||| ||| ||||||||||||||| |||||||||||||||||||||||||| || ||||| ||||| |||||||||||||| ||
gtaagtttttttatttctgtttttactgagataatggtgttgtttgtgttttaa-gtgtttgaaatggtgggttttgttttgttgatttagtttggttttgtgttttgaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTG
upper sequence: Vv10s0116g00160.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA13G34740.3 (Glycine max), 3'ss of exon 2
gtgagtttg---agtt---gttttgctggattgatgat-----tgatgattgaatgtactggtattcgtggg-------ctgatgaatacttttgaattt-tgtattgaagGTATTGCAAATGCGAGATGCCTTATAACCCAGATGATCTTATGGTCCAGTGCGAGGGGTGCAAGGACTG-------------------------------
|| ||||| | || |||| ||| | ||| | | || || || || | | | | ||||| || ||| | |||| ||| ||| ||||||||||||||| |||||||||||||||||||||||||| || ||||| ||||| |||||||||||||| ||
gtaagtttttttatttctgtttttactgagataatggtgttgtttgtgttttaa-gtgtttgaaatggtgggttttgttttgttgatttagtttggttttgtgttttgaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTGGTAAAACCAGTATATTCTGCTTTTTTTTGTT
upper sequence: Vv10s0116g00160.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA12G35680.2 (Glycine max), 3'ss of exon 2
gtgagtttgagt-tgttttgctggatt-gatgat-tgatgattgaatgtactggtattcgtgggctgatgaatacttttgaattttgta--ttgaagGTATTGCAAATGCGAGATGCCTTATAACCCAGATGATCTTATGGTCCAGTGCGAGGGGTGCAAGGACTG
|| ||||| | |||||| | | ||| || | | | || || | |||| | | | | || || |||||| ||||||||||||||| |||||||||||||||||||||||||| || ||||| ||||| |||||||||||||| ||
gtaagtttatttctgttttttttagtgagataatgttgtaagtgtttgaaatggtgggttttgttttgttgatttggttcggttttgtggtttgaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTG
upper sequence: Vv10s0116g00160.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA06G34850.1 (Glycine max), 3'ss of exon 1
------gtgagtttgagtt--gttttgctggattgatgattgatgattgaatgtactggtattcgtgggctgatgaatacttttgaattttgtattgaagGTATTGCAAATGCGAGATGCCTTATAACCCAGATGATCTTATGGTCCAGTGCGAGGGGTGCAAGGACTG
|| |||| || | | || | || | || | || | |||| | | ||||| || ||| |||||||||||||||||| ||||||||||||||||| |||||||| ||||| || || || ||||||||||| ||
ggaggggtttttttggtttcaggcccgagggggttccttttttttttttttttggggggggggggggggcgggggggcttttttggtttgtgttttgaagGTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTG
upper sequence: Vv10s0116g00160.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA12G20180.1 (Glycine max), 3'ss of exon 2
-------------gtgagtttgagttgttttgctggattgatgattgatgattgaatgtactggtattcgtgggctgatgaatacttttgaattttgtattgaagGTATTGCAAATGCGAGATGCCTTATAACCCAGATGATCTTATGGTCCAGTGCGAGGGGTGCAAGGACTG
||| | || | ||||| || || | ||||| | | | || | ||| | ||| | || || || ||| |||||||||||||||||| ||||||||||||||||| |||||||| ||||| || || || ||||||||||| ||
gaggttattgattgtggggatgggg-attttg--ggttttggaactgatgg--ggcttttctttttttcttttcttgaactttttttgtggtttgtgttttgaagGTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTG
upper sequence: Vv10s0116g00160.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S307_14V6.1 (Physcomitrella patens), 3'ss of exon 2
---------gtgagtttgagttgttttgctggattgatgattgatgattgaatgtactggtattcgtgggctgatgaatacttttgaattttgtattgaagGTATTGCAAATGCGAGATGCCTTATAACCCAGATGATCTTATGGTCCAGTGCGAGGGGTGCAAGGACTG
|||| | | || | | | | | | | || ||| | | || | | | | | | | | | |||||||| ||||| |||||||||||||| ||||||||| | ||||| || || ||| ||||| || ||
tatcctaagtcgagtgtaaaacattgagttaagt-aaggtgtattcctttcttgtgatataaaggctgacccatttggtgttctctgactgttctgtatagGTATTGTAAATGTGAGATGCCTTATAATCCAGATGATTTGATGGTTCAATGTGAGACTTGCAAAGATTG
upper sequence: Vv10s0116g00160.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ05369 (Selaginella moellendorffii), 3'ss of exon 2
gtgagtttgagttgttttgctggattgatgattgatgattgaatgtactggtattcgtgggctgatgaatacttttgaattttgtattgaagGTATTGCAAATGCGAGATGCCTTATAACCCAGATGATCTTATGGTCCAGTGCGAGGGGTGCAAGGACTG
| |||||| | | | | | | | | || | | ||||| ||| ||||| ||||| |||||||||||||| ||||| |||||||||||||| ||||| |||| |||||| |||||
------------------gtaagattgacaa----agctctcactttggattctctatcttatgctctctttttttgggtttgcggaaacagGTACTGCAAGTGCGAGATGCCTTACAACCCGGATGATCTTATGGTGCAGTGTGAGGAGTGCAAAGACTG
upper sequence: Vv10s0116g00160.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ26805 (Selaginella moellendorffii), 3'ss of exon 2
gtgagtttgagttgttttgctggattgatgattgatgattgaatgtactggtattcgtgggctgatgaatacttttgaattttgtattgaagGTATTGCAAATGCGAGATGCCTTATAACCCAGATGATCTTATGGTCCAGTGCGAGGGGTGCAAGGACTG
| |||||| | | | | |||| || ||| ||||| | | ||||| ||||| |||||||||||||| ||||| |||||||||||||| ||||| |||| |||||| |||||
-------------------------gtaagattgacaaagctctcactttggattctctatcttatgctctctttttttgggtttgaaacagGTACTGCAAGTGCGAGATGCCTTACAACCCGGATGATCTTATGGTGCAGTGTGAGGAGTGCAAAGACTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attgaatgtactggtattcgtgggctgatgaatacttttgaattttgtattgaagGTATTGCAAATGCGAGATGCCTTATAACCCAGATGATCTTATGGTCCAGTGCGAGGGGTGCAAGGACTG
ggctgat putative branch site (score: 4)
aatacttttgaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtttgagttgttttgctggattgatgattgatgattgaatgtactggtattcgtgggctgatgaatacttttgaattttgtattgaagGTATTGCAAATGCGAGATGCCTTATAACCCAGATGATCTTATGGTCCAGTGCGAGGGGTGCAAGGACTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG