Sequence
atgc intronic sequence ATGC exonic sequence...gcttgcatttgtatggttgaataaaagctatgattttagcttctagatgttctgtttcatgacaattgatgtttgggtaccttaatcctattcttttcagGTTCCTGTGGAGGAAAAATGCCAGTTTTGCAATCTCTAGACATTATAGACGCTTTGATGTGTTTGTAGAAGCTGAGGCAAATAAAGCTGCTGCGAAGTAT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv00s0265g00120.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os05g45490.1 (Oryza sativa), 3'ss of exon 6
gcttgcatttgtatggttgaataaaagctatgattttagcttctagatgttctgtttcatgacaattgatgtttgggtaccttaatcctattct---tttcagGTTCCTGTGGAGGAAAAATGCCAGTTTTGCAATCTCTAGACATTATAGACGCTTTGATGTGTTTGTAGAAGCTGAGGCAAATAAAGCTGCTGCGAAGTAT
| | ||||| | || || |||||| || || || | |||| | || | | | || || ||| | | | ||||| |||||||||| ||||| | |||||| |||||| | || || | |||||||||||| |||| |||||| || || ||||||||||||| ||||||
--tagaatttgga-acttaccagcttttcattattttaagatcgcaatattgcaatatttgactactgtgttgagtctgactgtgtcatatcatggctattagGTTTTTGTGGAGGAAGAATGCTACTTTTGCTATCTCTCGGCACTACAAACGCTTTGATGTATTTGAAGAAGCAGAAGCTAATAAAGCTGCTGGCAAGTAT
upper sequence: Vv00s0265g00120.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G044866_T01 (Zea mays), 3'ss of exon 6
gcttgcatttgtatggttgaataaaagctatgattttagcttctagatgtt---ctgtttca--tgacaattgatgtttgggtaccttaatcctattcttttcagGTTCCTGTGGAGGAAAAATGCCAGTTTTGCAATCTCTAGACATTATAGACGCTTTGATGTGTTTGTAGAAGCTGAGGCAAATAAAGCTGCTGCGAAGTAT
| || || | | | | ||| | | | ||| ||| | | ||| ||| | | | | || | || | | | | |||||||| |||||||| ||| ||| ||||||||||||| | ||||| | ||||||||||||||||| |||||| || || || |||||||||| |||||
--gtatcccatcattgtagtacgacatttatttgactgatccatgaaagttgggctgctgtaagtgataatgagtaatctgatttctcactc---tacctgttagGTTCCTTTGGAGGAAGAATACCACTTTTGCAATCTCTCGGCATTACAAACGCTTTGATGTGTTTGAAGAAGCAGAAGCGAACAAAGCTGCTGGAAAGTAC
upper sequence: Vv00s0265g00120.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G421791_T01 (Zea mays), 3'ss of exon 6
gcttgcatttgtatggttgaataaaagctatgattttagcttctagatgttctgtttcatgacaattgatgtttgggtaccttaatcct-attct---tttcagGTTCCTGTGGAGGAAAAATGCCAGTTTTGCAATCTCTAGACATTATAGACGCTTTGATGTGTTTGTAGAAGCTGAGGCAAATAAAGCTGCTGCGAAGTAT
| || | || |||| | | || | ||| | || || |||| | | || | | || | ||| | | ||||||||||||||||| ||| ||| ||||||||||||| | ||||| | ||||||||||||||| | |||||| || || || |||||||||| ||||||
----gtatcttatcatttcaatacggcatttatttgacggttccatgaaaattggactgctgtaactgataaggagcaatctgatttcttactctgcatattagGTTCCTGTGGAGGAAGAATACCACTTTTGCAATCTCTCGGCATTACAAACGCTTTGATGTGTTCGAAGAAGCAGAAGCTAACAAAGCTGCTGGAAAGTAT
upper sequence: Vv00s0265g00120.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AC233864.1_FGT014 (Zea mays), 3'ss of exon 6
----------------------------------------------------------------gcttgcatttgtatggttgaataaaagctatgattttagcttc--tagatgt-tctgtttcatgacaattgatgtttgggt-accttaatcctattct-tttcagGTTCCTGTGGAGGAAAAATGCCAGTTTTGCAATCTCTAGACATTATAGACGCTTTGATGTGTTTGTAGAAGCTGAGGCAAATAAAGCTGCTGCGAAGTAT
| | | | || | | | | | ||| | ||| | | | | | || ||| | | || | |||| | | || | | | || | || ||||||| |||||||||| |||| || |||||||| || || ||||| |||||||| ||||| || | ||||||||||| || || |||| || || |||
gtaaacagtcacttgttttgcattatgtactcttcacatagcttaaggaacatttatatatgctgttagaaattaagttctctagttgccagtgtgactgatgctccatttgctctatcaattttgtcccggtttgtttttgatttatctcactacacttatgttacagGTTCTTGTGGAGGAAGAATGTTAGCTTTGCAATTTCCAGGCATTACAGACGCTTCGATGTTTTCGAGGAAGCTGAGGCCAACAAGGCTGGTGGAAAATAT
upper sequence: Vv00s0265g00120.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM5G891056_T01 (Zea mays), 3'ss of exon 6
--------------------------------------------------------------------gcttgcatttgtatggttgaataaaagctatgattttagcttc--tagatgt-tctgtttcatgacaattgatgtttgggtaccttaatcctattct-tttcagGTTCCTGTGGAGGAAAAATGCCAGTTTTGCAATCTCTAGACATTATAGACGCTTTGATGTGTTTGTAGAAGCTGAGGCAAATAAAGCTGCTGCGAAGTAT
| | | | || | | | | | ||| | ||| | | | | | || ||| | | || | || || || | | | || | || ||||||| |||||||||| |||| || |||||||| || || ||||| |||||||| ||||| || | ||||||||||| || || |||| || || |||
gtaaacagtcacttgttttgcattatgtactcttcacatatatagcttaaggaacatttagatatgctgttagaaattaagttctctagttgccagtgtgactgatgctccatttgctctatcaattttgtcccggtttgttttgatttatctcactacacttatgttacagGTTCTTGTGGAGGAAGAATGTTAGCTTTGCAATTTCCAGGCATTACAGACGCTTCGATGTTTTCGAGGAAGCTGAGGCCAACAAGGCTGGTGGAAAATAT
upper sequence: Vv00s0265g00120.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G162884_T02 (Zea mays), 3'ss of exon 6
-------------------------------------------------------------------------------gcttgcatttgtatggttgaataaaagctatgattttagcttc--tagatgt-tctgtttcatgacaattgatgtttgggtaccttaatcctattct-tttcagGTTCCTGTGGAGGAAAAATGCCAGTTTTGCAATCTCTAGACATTATAGACGCTTTGATGTGTTTGTAGAAGCTGAGGCAAATAAAGCTGCTGCGAAGTAT
| | | | || | | | | | ||| | ||| | | | | | || ||| | | || | || || || | | | || | || ||||||| |||||||||| |||| || |||||||| || || ||||| |||||||| ||||| || | ||||||||||| || || |||| || || |||
gtattagaaaggtaaacagtcacttgttttgcattatgtactcttcacatatatagcttaaggaacatttagatatgctgttagaaattaagttctctagttgccagtgtgactgatgctccatttgctctatcaattttgtcccggtttgttttgatttatctcactacacttatgttacagGTTCTTGTGGAGGAAGAATGTTAGCTTTGCAATTTCCAGGCATTACAGACGCTTCGATGTTTTCGAGGAAGCTGAGGCCAACAAGGCTGGTGGAAAATAT
upper sequence: Vv00s0265g00120.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA13G31260.1 (Glycine max), 3'ss of exon 6
gcttgcatttgtatggttgaataaaagctatgattttagcttctagatgttctgtttcatgacaattgatgtttgggtaccttaat----cctattctt-ttcagGTTCCTGTGGAGGAAAAATGCCAGTTTTGCAATCTCTAGACATTATAGACGCTTTGATGTGTTTGTAGAAGCTGAGGCAAATAAAGCTGCTGCGAAGTAT
||| || | || || || | | || | | | | || || ||| |||| | || || ||||| | || ||| || ||||| |||||||||| ||||| | ||||||||| |||| ||||||||||||||||||||| ||||| || || || |||||||||||||||| ||||||
--acacataatcatacct--atgctgactttgtactaggtttatgtgagattttcttgatag-aatacatgtgttggcacattaattgttctcatccttatttagGTTTTTGTGGAGGAAGAATGCAACTTTTGCAATATCTAAACATTATAGACGCTTTGATGTATTTGTTGAGGCCGAAGCAAATAAAGCTGCTGGAAAGTAT
upper sequence: Vv00s0265g00120.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA15G08090.1 (Glycine max), 3'ss of exon 6
gcttgcatttgtatggttgaataaaagctatgattttagcttctagatgttctgtttcatgacaattgatgtttgggtaccttaat----cctattctt-ttcagGTTCCTGTGGAGGAAAAATGCCAGTTTTGCAATCTCTAGACATTATAGACGCTTTGATGTGTTTGTAGAAGCTGAGGCAAATAAAGCTGCTGCGAAGTAT
||| || | || || || | | || | | | | || || ||| |||||| || || ||||| | || ||| || ||||| |||||||||| ||||| | ||||||||| |||| ||||||||||||||||||||| ||||| || || || |||||||||||||||| ||||||
--acacataatcatacct--atgccgactttgtactaggtttatgttggattttcttgatag-aatacatgtttcggcacattaattgctctcatccttatttagGTTTTTGTGGAGGAAGAATGCAACTTTTGCAATATCTAAACATTATAGACGCTTTGATGTATTTGTTGAGGCCGAAGCAAATAAAGCTGCTGGAAAGTAT
upper sequence: Vv00s0265g00120.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA07G18630.1 (Glycine max), 3'ss of exon 5
gcttgcatttgtatggttgaataaaagctatgattttagcttctagatgttctgtttcatgacaattgatgtttgggtaccttaatcct----attctt-ttcagGTTCCTGTGGAGGAAAAATGCCAGTTTTGCAATCTCTAGACATTATAGACGCTTTGATGTGTTTGTAGAAGCTGAGGCAAATAAAGCTGCTGCGAAGTAT
| ||| || | || || || | | || | | | || || ||| |||| | || || ||||| | || ||| || || | |||||||||| ||||| | ||||||||| |||| |||||||||| |||||||||| ||||| || || || |||||||||||||||| ||
--tcacataatcatacct--atggtgactttgtactaggtttatgttaaattttcttgatag-aatacatgtgttggcacattaattgttgtcatccttatttagACTTTTGTGGAGGAAGAATGCAATTTTTGCAATATCTAAACATTATAGATGCTTTGATGTATTTGTTGAGGCCGAAGCAAATAAAGCTGCTGGAAA----
upper sequence: Vv00s0265g00120.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA13G24770.1 (Glycine max), 3'ss of exon 6
gcttgcatttgtatggttgaataaaagctatgattttagcttctagatgttctgtttcatgacaattgatgtttgggtaccttaatcctattc-----ttttcagGTTCCTGTGGAGGAAAAATGCCAGTTTTGCAATCTCTAGACATTATAGACGCTTTGATGTGTTTGTAGAAGCTGAGGCAAATAAAGCTGCTGCGAAGTAT
||| || | || | || ||||||| |||| || || ||| | | |||||| | |||| || | ||| | | ||||| ||||||| || ||||| | ||||||||| || | ||||||||||||||||||||| || | || |||||||||||||||||||||| ||||||
-tatgctctt-tctgactttttacaagctatatttttgctttgcctatccataaacccataatac---atgttttgacacctaaactcccttcacacttatctagGTTTTTGTGGAGAAAGAATGCTACTTTTGCAATATCAAAACATTATAGACGCTTTGATGTATTCATTGAGGCTGAGGCAAATAAAGCTGCTGGAAAGTAT
upper sequence: Vv00s0265g00120.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA07G31680.1 (Glycine max), 3'ss of exon 6
--------gcttgcatttgtatggttgaataaaagctatgattttagcttctagatgttctgtttcatgacaattgatgtttgggtaccttaatcctattcttttcagGTTCCTGTGGAGGAAAAATGCCAGTTTTGCAATCTCTAGACATTATAGACGCTTTGATGTGTTTGTAGAAGCTGAGGCAAATAAAGCTGCTGCGAAGTAT
| || |||| | || | || ||||||| ||||| || | || | | |||| |||| | || | || | | ||| ||||| ||||||| || ||||| | |||||| || || | ||||||||||||||||||||| || | || |||||||||||||||||||||| ||||||
tatttcatacatg-atttttctgactttttacaagctat-attttgctttatgtat-ccataatacatgtt--ttgacacctaaactccct--tcacacttgttt-agGTTTTTGTGGAGAAAGAATGCTACTTTTGCCATATCAAAACATTATAGACGCTTTGATGTATTCATTGAGGCTGAGGCAAATAAAGCTGCTGGAAAGTAT
upper sequence: Vv00s0265g00120.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT1G28240.1 (Arabidopsis thaliana), 3'ss of exon 6
gcttgcatttgtat-ggttgaataaaagctatgattttag-----ctt----ctagatgttctgtttcatgacaattgatgtttgggtaccttaatcctattcttttcagGTTCCTGTGGAGGAAAAATGCCAGTTTTGCAATCTCTAGACATTATAGACGCTTTGATGTGTTTGTAGAAGCTGAGGCAAATAAAGCTGCTGCGAAGTAT
| |||| | | | | | || | | ||| ||||| ||| | | ||| |||||| ||| | ||| | | | || |||| |||| ||| |||||||||||||||| | |||||| || ||||||||||| | ||| |||||||| || || ||||| || |||||||||||||||| || |||
------agttgtttcagataagttaacggtttgagtttagaaggccttaagcttggtggttatgtttctggactgcagcaatttaactgacat----ctcttctcatcagATTCTTGTGGAGGAAAAATGCTACTTTTGCTATTTCTAGACATTACAAACGATTTGATGTCTTAGTGGAAGCCGAAGCAAATAAAGCTGCTGGTAAATAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatgttctgtttcatgacaattgatgtttgggtaccttaatcctattcttttcagGTTCCTGTGGAGGAAAAATGCCAGTTTTGCAATCTCTAGACATTATAGACGCTTTGATGTGTTTGTAGAAGCTGAGGCAAATAAAGCTGCTGCGAAGTAT
ccttaat putative branch site (score: 4)
tcctattcttttc CT-rich tract
tattctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcttgcatttgtatggttgaataaaagctatgattttagcttctagatgttctgtttcatgacaattgatgtttgggtaccttaatcctattcttttcagGTTCCTGTGGAGGAAAAATGCCAGTTTTGCAATCTCTAGACATTATAGACGCTTTGATGTGTTTGTAGAAGCTGAGGCAAATAAAGCTGCTGCGAAGTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
gcttgca
- - - - -tgtatgg
- - - - - - - - - -aataaaa
- - - - - - - - - - - - - gctatga
- - - - - - - - - - - - - - - - - - - -cttctag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttgg