Sequence
atgc intronic sequence ATGC exonic sequence...ggagttctactaggctggcaattcatttaaatttctagttataagatacccttttgaaattttagcatatatactcattttctccttgtttcttgtgcagTTCTTCACAACGAAACCTTATGCTTGTGAACCATCTAGCCTTCCGCAATATCCTCCAAGCAAGGAGATGGATGCCAAGAGGCGAGATGATGAAGCTCGAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv14s0030g01260.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os03g22700.1 (Oryza sativa), 3'ss of exon 3
ggagttctactaggctgg-caattcatttaaatttct-----agttataagatacccttttgaaattttagcatatatactcattttctccttgtttcttgtgcagTTCTTCACAACGAAACCTTATGCTTGTGAACCATCTAGCCTTCCGCAATATCCTCCAAGCAAGGAGATGGATGCCAAGAGGCGAGATGATGAAGCTCGAA
| | | | | | | || ||| || | | | |||| | |||| | ||||| | | | || || || | |||||||||| ||||| |||||||||| ||||||||||| || || || ||||||||||||||| || |||||||| || | ||||||| ||||| ||
gataatgtgtgaagtagatctgtttattgtcatctttgttgaaattatgtagcattgttttacacttttactaaagaa------ttgcttattacaatctatgcagTTCTTTACAACTGAACCTTATGCATGTGAACCATCAAGTCTCCCAGCATATCCTCCAAGCAAAGAAATGGATGCAAAACGAAGAGATGAAGAAGCCAGAC
upper sequence: Vv14s0030g01260.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os01g27020.2 (Oryza sativa), 3'ss of exon 4
-ggagttctactaggctggcaattcatttaaatttctagttataagatacccttttgaaattttagcatatatactcattttctccttgtttcttgtgcagTTCTTCACAACGAAACCTTATGCTTGTGAACCATCTAGCCTTCCGCAATATCCTCCAAGCAAGGAGATGGATGCCAAGAGGCGAGATGATGAAGCTCGAA
| | | || | || || | | || | | | || || || | | | || || |||| | || || | |||||||||| |||| | |||||||| ||||| ||||| ||| | ||| |||||| ||||| |||||||||||||| |||| | ||||||| |||||| |||
taatatagctccacccttggtatacagtcctaatttttttattttgacgagctattaggctatcactatgtagtaaggttttatgct-gtgagtattgcagTTCTTTGCAACTGAGCCTTATGCATGTGATCCATCAAGCTTGCCGACATATCCACCAAGTAAGGAGATGGATGCTAAGATGAGAGATGAGGAAGCTAGAA
upper sequence: Vv14s0030g01260.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G052206_T02 (Zea mays), 3'ss of exon 4
ggagttctactaggctggcaattcatttaaatttctagtt---ataagatacccttttgaaattttagcatatatactcattttctccttgtttcttgtgcagTTCTTCACAACGAAACCTTATGCTTGTGAACCATCTAGCCTTCCGCAATATCCTCCAAGCAAGGAGATGGATGCCAAGAGGCGAGATGATGAAGCTCGAA
|| | | || | || | | | | | | ||| || ||| |||| || | || || | | | | ||| | |||||||||| ||||| |||||| ||| ||||||||||| || ||||| |||||||||||||||| || || |||| || || |||| || ||||| ||
-tagcac--ccagattcccatctttgtcacacatttggtttttgtagcatattttttttggtattgtgtattcatgccttctgtttactttctatggatgcagTTCTTTACAACTGAACCTTTTGCATGTGAACCATCGAGTCTTCCAAAATATCCTCCAAGCAAAGAAATAGATGTGAAAAGAAGAGACGAAGAAGCCAGAC
upper sequence: Vv14s0030g01260.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM5G873277_T01 (Zea mays), 3'ss of exon 4
ggagttctact-aggctggcaattc-atttaaatttctagttataagatacccttttgaaattttagcatatatactcattttctccttgtttcttgtgcagTTCTTCACAACGAAACCTTATGCTTGTGAACCATCTAGCCTTCCGCAATATCCTCCAAGCAAGGAGATGGATGCCAAGAGGCGAGATGATGAAGCTCGAA
| || | | | || |||| || || | ||| || | ||| | || | || || | | || | | | |||||||||| | ||| | |||||||| ||||||||||| || || || ||||| || |||||||| |||||||||||||| | |||| || |||||| ||
-tatttgaatttatgccaaaaattttatatagcgtgctatgcgta-gttactgtgaacaattcttttcaaaagcaagatccttattttcactgtacatgcagTTCTTTAAAACAGAGCCTTATGCGTGTGAACCATCAAGTCTGCCCCAATACCCGCCAAGCAAAGAGATGGATGCCAAACGAAGAGACGAAGAAGCTAGAC
upper sequence: Vv14s0030g01260.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G156251_T01 (Zea mays), 3'ss of exon 4
ggagttctactaggctggcaattcatttaaatttctagttataagatacccttttgaaatt-ttagcatatatac-tcattttctccttgtttctt-----------gtgcagTTCTTCACAACGAAACCTTATGCTTGTGAACCATCTAGCCTTCCGCAATATCCTCCAAGCAAGGAGATGGATGCCAAGAGGCGAGATGATGAAGCTCGAA
| | || || |||||| | || || || | || || | || || || || | |||| | ||| || ||| | |||| || |||| | |||||||||||| | || || || || || |||||| |||||||||||||||||||||||| |||| || || ||| |||
----------tggcctt---atgcatttatgctgcttgtaatgaactattattccgtcataactaccagttactcatcatgtgctcttttttttattaaaaaaatggacttagTTTTTTTCAACCGAGCCTTATGCTTGTAACCCTTCAAGTCTGCCAACATATCCACCAAGCAAGGAGATGGATGCCAAGTTAAGAGACGAGGAGGCTAGAA
upper sequence: Vv14s0030g01260.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G084347_T01 (Zea mays), 3'ss of exon 4
--ggagttctactaggctggcaattcatttaaatttctagttataagatacccttttgaaattttagcatatatactcattttctccttgtttcttgtgcagTTCTTCACAACGAAACCTTATGCTTGTGAACCATCTAGCCTTCCGCAATATCCTCCAAGCAAGGAGATGGATGCCAAGAGGCGAGATGATGAAGCTCGAA
||| | | || | || | | | | | ||| | | |||| ||| |||| || | | | ||| | |||||||||| ||||| |||||| ||| || ||||| || || ||||| |||||||||||||||| ||||| |||| || | |||| || ||||| ||
ttatagtac--ccagattcccatccttgtcacacattttgtttttgtagtttttttttggttttgtgcattaatgccttatgtgaactttctatgcatgcagTTCTTTACAACCGAACCTTTTGCATGCGAACCGTCAAGTCTTCCAAAATATCCTCCAAGCAAAGAGATAGATGTGAAACGAAGAGACGAAGAAGCCAGAC
upper sequence: Vv14s0030g01260.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA10G30030.1 (Glycine max), 3'ss of exon 4
ggagttctactaggctggcaattcatttaaatttctagttataagatacccttttgaaattttagcatatatactcattttctccttgtttcttgt------gcagTTCTTCACAACGAAACCTTATGCTTGTGAACCATCTAGCCTTCCGCAATATCCTCCAAGCAAGGAGATGGATGCCAAGAGGCGAGATGATGAAGCTCGAA
| | | | | | | || ||| || || | || |||| || || ||| | | | ||| | ||| | | ||||||||| || || |||||||||||||||| || ||||| ||||| ||||||| |||| |||||| |||||||| || | || ||||||||||| | |
--atctttgtcgaatt--tagatgctcta--tttttatttttcttttatttttttaaatcaaacccacatacatttactttgtttgaccttcctatcaatttgcagTTCTTTACCACAGAACCTTATGCTTGTGATCCTTCTAGTCTTCCAAAATATCCCCCAACCAAGGAAATGGATGCTAAACGACGGGATGATGAAGCAAGGA
upper sequence: Vv14s0030g01260.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA20G37360.1 (Glycine max), 3'ss of exon 4
ggagttctactaggctggcaattcatttaaatttctagttataagatacccttttgaaattttagcatatatactcattttctccttgtttcttgt------gcagTTCTTCACAACGAAACCTTATGCTTGTGAACCATCTAGCCTTCCGCAATATCCTCCAAGCAAGGAGATGGATGCCAAGAGGCGAGATGATGAAGCTCGAA
| || || ||| ||||| || || | | | ||| || || ||| | | | ||| | ||||| | ||||||||| || || |||||||||||||||| || ||||| ||||| ||||||| |||| |||||| |||||||| || | || ||||||||| | | |
-agatgttatct--ttgtcaa---atttagatgctctatttttcttttcttgtttaaatcaaacccacatacattgactttgtttgaccttcttatcattttgcagTTCTTTACCACAGAACCTTATGCTTGTGATCCTTCTAGTCTTCCAAAATATCCCCCAACCAAGGAAATGGATGCTAAACGACGGGATGATGAAACAAGGA
upper sequence: Vv14s0030g01260.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA03G40330.1 (Glycine max), 3'ss of exon 4
ggagttctactaggctggcaattcatttaaat-ttctagtta---taagatacccttttgaaattttag--catatatactcatttt---ctccttgtttcttgtgcagTTCTTCACAACGAAACCTTATGCTTGTGAACCATCTAGCCTTCCGCAATATCCTCCAAGCAAGGAGATGGATGCCAAGAGGCGAGATGATGAAGCTCGAA
|||| || | | ||||| | || | ||| | || | ||||| ||| | | |||||| | | | || ||| | || || ||||||| || || |||||||||||||||| || ||||| || || ||||||| ||||||||||| |||||||| || | || ||||||||| |||
--------actaccttga-atcttatttaggtgttattgttgagttttgacaatctttttaaaatcaaacccatatacatttaccttgcttctcttctacattttgtagTTCTTTACCACAGAACCTTATGCTTGTGATCCTTCTAGTCTCCCAAAATATCCCCCAAGCAAGGAAATGGATGCTAAACGACGGGATGATGAAATGAGAA
upper sequence: Vv14s0030g01260.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA19G42960.1 (Glycine max), 3'ss of exon 3
ggagttctactaggctggcaattcatttaaatttctagttataagatacccttttgaaattttag-catatatactcattttctccttgtttct----tgtgcagTTCTTCACAACGAAACCTTATGCTTGTGAACCATCTAGCCTTCCGCAATATCCTCCAAGCAAGGAGATGGATGCCAAGAGGCGAGATGATGAAGCTCGAA
|| || | | | | | | | |||| | | | | | |||| |||| | |||| || | || | | || | || |||||||||| || || ||||||||||||| || || || || ||||| ||||||| ||||||||||| |||||||| || || ||||||||| | |
----ttaccttaaatctgatttaggtgttattgttgagttttgata-atctttttaaaatcaaactcatacatttgccttgtttgtctgctcctacatcctgcagTTCTTTACCACAGAACCTTATGCTTGCGATCCTTCAAGTCTTCCAAAATATCCCCCAAGCAAGGAAATGGATGCTAAACAACGGGATGATGAAATGAGGA
upper sequence: Vv14s0030g01260.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: PP1S89_168V6.1 (Physcomitrella patens), 3'ss of exon 5
--------------------------------------------------------ggagttc-tactaggctggcaattcatttaaatttctagttataagatacccttttga-aattttagcatatatactcattttctc----------cttgtttct--tgtgcagTTCTTCACAACGAAACCTTATGCTTGTGAACCATCTAGCCTTCCGCAATATCCTCCAAGCAAGGAGATGGATGCCAAGAGGCGAGATGATGAAGCTCGAA
| ||| | | ||| ||| | | | | | | || | ||||| |||| | | | || | | || | |||| | | ||||||||||||||| ||||| ||| ||||||||| || || ||| | |||||||| ||||| ||||||||| | |||||||||| || || ||||| ||||| |
gtgagcaagtgctgtgattttgaaattgcggtgcatgcattgtaggggaagttggtgtggttgatgccagga-agcagtggaggcatgtgttagagggcatgaagcatttttgctaattatggtttgcgtaagcttactcacgaactgtgcgcttgctattggtgtgcagTTCTTCACGACGAAGCCTCTTGCTTGTGACCCTTCAAGCTTGCCGCAATACCCTCCGAGCAAGGAGTTCGATGCCAAGATTCGGGACGATGAGGCTCGCA
upper sequence: Vv14s0030g01260.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: EFJ30402 (Selaginella moellendorffii), 3'ss of exon 4
ggagttctactaggctggcaattcatttaaatttctagttataagatacccttttgaaattttagcatatatactcattttctccttgtttcttgtg-cagTTCTTCACAACGAAACCTTATGCTTGTGAACCATCTAGCCTTCCGCAATATCCTCCAAGCAAGGAGATGGATGCCAAGAGGCGAGATGATGAAGCTCGAA
|| || | | | || || || || | | | | |||||| || ||||||||||| | ||| || ||||| |||||||| || ||| | || || ||||||||||| || ||| |||||||||| || ||||| || ||||| |
---------------------------------gtacgtcttacagtggcatattaaatacttt---tagggagctaaagtgtttttgttttgcatggcagTTCTTCACGAAGAAGCCGTATGCATGTGAACCTTCAAGCTTACCACAGTATCCTCCAAGTAAAGAGCTGGATGCCAAATATCGCGATGAAGAGGCTCGCA
upper sequence: Vv14s0030g01260.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: EFJ28510 (Selaginella moellendorffii), 3'ss of exon 4
ggagttctactaggctggcaattcatttaaatttctagttataagatacccttttgaaattttagcatatatactcattttctccttgtttcttgtgcagTTCTTCACAACGAAACCTTATGCTTGTGAACCATCTAGCCTTCCGCAATATCCTCCAAGCAAGGAGATGGATGCCAAGAGGCGAGATGATGAAGCTCGAA
|| || | | | || |||| | || | | | | | | || | || |||||||||||||| ||| || ||||| |||||||| || ||| | || || ||||||||||| || ||| |||||||||| || ||||| || ||||| |
---------------------------------gtacgtcttacagtggcatatt-aaatactttcagggagctaaagtgtttttgttttgcatg-gcagTTCTTCACAAAGAAGCCGTATGCATGTGAACCTTCAAGCTTACCACAGTATCCTCCAAGTAAAGAGCTGGATGCCAAATATCGCGATGAAGAGGCTCGCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atacccttttgaaattttagcatatatactcattttctccttgtttcttgtgcagTTCTTCACAACGAAACCTTATGCTTGTGAACCATCTAGCCTTCCGCAATATCCTCCAAGCAAGGAGATGGATGCCAAGAGGCGAGATGATGAAGCTCGAA
tactcattttctcctt CT-rich tract
ttttgaaattttagca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggagttctactaggctggcaattcatttaaatttctagttataagatacccttttgaaattttagcatatatactcattttctccttgtttcttgtgcagTTCTTCACAACGAAACCTTATGCTTGTGAACCATCTAGCCTTCCGCAATATCCTCCAAGCAAGGAGATGGATGCCAAGAGGCGAGATGATGAAGCTCGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - -gctggca
- - - - - - - - - - - - - - - - - - - - - - - - ccctttt