Sequence
atgc intronic sequence ATGC exonic sequence...ccttttatttataagatcttctaaactatgcacaaaaagagaatatttttcttgtaaattgcttagtgatactaaaaggttctttgttttgatttatcagATGGGCCTAATGAGAAAACATCCTTCAATCATACCATTCATGATTTACATCTCAAATGAAGACAAACATTTGGAACGATTTGCAGTTCGTGCAAAATACA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv08s0040g01610.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os09g39870.2 (Oryza sativa), 3'ss of exon 1
------------------------------------------------------------ccttttatttataagatcttctaaactatgcaca----aaaagagaatatt----tttcttgtaaattgcttagtgatactaaaa-------ggttct------ttgttttgatttatcagATGGGCCTAATGAGAAAACATCCTTCAATCATACCATTCATGATTTACATCTCAAATGAAGACAAACATTTGGAACGATTTGCAGTTCGTGCAAAATACA
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gtacgtgcttcctaaactgttaccattatttagtttcccaaatttatattttactctatttattatgccaatagaaatagatacactatactcactgcaaagtgcaatgataggcttcttcatgcattcatctatcctaatttaaccttgttggttttatcgaatcattttgatatttcagATGGGGCTAATGAGGAAACATCCTTCTATAATACCTTTTATGATCTACATATCCGATGAGGGCAAGCACACCGAGAGGTTTGCCGTACGTGCAAAGTACA
upper sequence: Vv08s0040g01610.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G017334_T01 (Zea mays), 3'ss of exon 4
-----------------------------------------------------------cctttta---tttataagatcttctaaactatgc----------acaaaaagagaatatttttcttgtaa-attgcttagtgata---ctaaaaggttctttgttttgattta------tcagATGGGCCTAATGAGAAAACATCCTTCAATCATACCATTCATGATTTACATCTCAAATGAAGACAAACATTTGGAACGATTTGCAGTTCGTGCAAAATACA
|||||| ||| ||| | ||| | | | | ||| | | | || |||||| ||| || | | | ||| |||| ||| |||| |||||||| |||||||| ||||||||||| |||||||| |||||||| |||||||| ||||| | || || || | ||||| || |||||||| ||||
gtatgtgcttccagaaaactattcatttgcatttctttcctatcattccagctattgattcttttaggtcgtatcagacccactatattgcatttcttctgctaatagaagtggagttgttagttgtaacattcattgttaacttgcccaaattattctacatttccttttaattattccagATGGGTCTAATGAGGAAACATCCTTCGATCATACCTTTCATGATCTACATCTCTAATGAGGGTAAGCACACAGAGAGGTTTGCTGTACGTGCAAAGTACA
upper sequence: Vv08s0040g01610.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G342327_T01 (Zea mays), 3'ss of exon 4
---------------------------------ccttttatttataagatcttctaaactatgc--acaaaaagagaatatttttcttgtaaattgcttagtgat--actaaaaggttctt-tgttttgatttatcagATGGGCCTAATGAGAAAACATCCTTCAATCATACCATTCATGATTTACATCTCAAATGAAGACAAACATTTGGAACGATTTGCAGTTCGTGCAAAATACA
| || | || || | || |||| || || | | | | | ||| | | |||| ||||| || | | | | | |||||||| |||||| ||||||||||| || |||||||| ||| | ||||| ||||||| || ||||| ||||||||||||| || |||||||| ||||
gtacgtattagtcaagaaacagtgcaggggtgaggggtatttcaaaaaattgtttagtttatgttgttttccgttatttagttatatctcatttctcgtagccactgattaaagtcttcttctgctgttaatcaacagATGGGATTAATGAAGAAACATCCTTCCATAATACCATTTATGGTATACATTACAAATGAGGATAAACACATGGAACGATTTGCTGTACGTGCAAAGTACA
upper sequence: Vv08s0040g01610.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G048553_T02 (Zea mays), 3'ss of exon 4
-ccttttatttataagatcttctaaactatgcacaaaaagagaat-atttttcttgtaaattgcttagtgatactaaaaggttctttgttttgatt-tatcagATGGGCCTAATGAGAAAACATCCTTCAATCATACCATTCATGATTTACATCTCAAATGAAGACAAACATTTGGAACGATTTGCAGTTCGTGCAAAATACA
| ||| || | | ||| | ||| || | | | | | || | | | || || ||||| ||| | ||||||||| |||||||| ||||||||||| || ||||| |||||||| ||||| || ||||| || || || | ||||| || ||||| || ||||
agagccactatattgcatttgttttgcta---ataaaggtggagttgtaactttcattgtttacatgcccactttattccacatttcgttttaattatttcagATGGGTCTAATGAGGAAACATCCTTCGATAATACCTTTCATGATCTACATATCTAATGAGAGTAAGCACACAGAGAGGTTTGCTGTACGTGCGAAGTACA
upper sequence: Vv08s0040g01610.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G60760.1 (Arabidopsis thaliana), 3'ss of exon 5
ccttttatttataagatcttctaaactatgcacaaaaagagaatatttttcttgtaaattgcttagtgatactaaaaggttctttgttttgatttatcagATGGGCCTAATGAGAAAACATCCTTCAATCATACCATTCATGATTTACATCTCAAATGAAGACAAACATTTGGAACGATTTGCAGTTCGTGCAAAATACA
||||| || | | | | || | | | | | ||| || ||| | || |||| | | ||| ||| |||||||| || |||| ||| |||||||| || | || |||||| | |||||| |||| || || |||||||||||||||||||||||| | || || ||||
----------gtaagactc---aatttgttctctttaacacatt--tcattttgaaagttg-----taattctaa-----cttctaacttgtttt--cagATGGGACTGATGAAAAAGCATCCTTCTATAGTTCCTTTCATGGTATACATCGCAAACGAGGAGAAACATTTGGAACGATTTGCAGTTAGAGCTAAGTACA
upper sequence: Vv08s0040g01610.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S88_103V6.1 (Physcomitrella patens), 3'ss of exon 6
---------------------------------------------------------------------------------ccttttat--ttataagatcttctaaactat---gcacaaaaagagaatatttttcttgtaaattgctt-agtgatactaaaaggttctttgttttgatttatcagATGGGCCTAATGAGAAAACATCCTTCAATCATACCATTCATGATTTACATCTCAAATGAAGACAAACATTTGGAACGATTTGCAGTTCGTGCAAAATACA
|| | || || | | | | | | |||| | |||| | | || ||| || | | || | | ||| | |||| | ||||||||| || |||| ||| ||||| ||||||||||| |||||||| |||||| | || ||| |||||| |||| | ||||||||||||||||| ||||
gtaagcatttctgactctagcactgttatttattgacatgatcgttgctatgtcgtgcaatggtattcaaggttgtccaactctatcatggttgtcttacacacctgaatgtccagcactcgcaaagaaatactccatagtgaataaattcattcatgtttgatggt-----gaattgaatcttcagATGGGTCTCATGAAAAAGCATCCATCAATCATACCGTTCATGATGTACATCGCTAACGAAAGCAAACACATGGAGAGGTTTGCAGTTCGTGCAAAGTACA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttttcttgtaaattgcttagtgatactaaaaggttctttgttttgatttatcagATGGGCCTAATGAGAAAACATCCTTCAATCATACCATTCATGATTTACATCTCAAATGAAGACAAACATTTGGAACGATTTGCAGTTCGTGCAAAATACA
tttgttttgatttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccttttatttataagatcttctaaactatgcacaaaaagagaatatttttcttgtaaattgcttagtgatactaaaaggttctttgttttgatttatcagATGGGCCTAATGAGAAAACATCCTTCAATCATACCATTCATGATTTACATCTCAAATGAAGACAAACATTTGGAACGATTTGCAGTTCGTGCAAAATACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - -ctatgca
- - - - - - - - - - - - - - - - -aaaaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcttag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - actaaaa