Sequence
atgc intronic sequence ATGC exonic sequencegttggccttatctttaatcttattttgaaaaactatttagattacatataatattctcattcattctacaattaatgttgcagTGCTTCTTAAAAAGTTTGCTGGTGAGGAAGGAGAAAGGGTTGATGTGCAAAAGTTGTTTGGATATATTGGATTATTTACACTGGTAGCACTGTGGTGGCT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv04s0008g06500.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os04g55260.1 (Oryza sativa), 3'ss of exon 4
gttggccttatctttaatcttattttgaaaaactatttagattacatataatattctcattcattctacaattaatgttgcagTGCTTCTTAAAAAGTTTGCTGGTGAGGAAGGAGAAAGGGTTGATGTGCAAAAGTTGTTTGGATATATTGGATTATTTACACTGGTAGCACTGTGGTGGCT
| | || | ||| | | || | | |||| | | || ||| ||| ||| | || ||||||||| |||||||||||||| ||||||||||||| ||||||||| ||||| ||||||| || | ||| | || | || || || ||||||||
-----gttagttctttgcttcctttagttgatctgtcttgattcaac------tgctaattgtttcaacatt----attttagTGCTTCTAAAAAAGTTTGCTGGAGAGGAAGGAGAAAAGGTTGATGTCCAAAAACTGTTTGGCTACCTCGGACTTTTCAGTCTTGTTCTTCTCTGGTGGCT
upper sequence: Vv04s0008g06500.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G064831_T02 (Zea mays), 3'ss of exon 4
gttggccttatctttaatcttattttgaaaaactatttagattacatataatattctcattcattctacaattaatgttgcagTGCTTCTTAAAAAGTTTGCTGGTGAGGAAGGAGAAAGGGTTGATGTGCAAAAGTTGTTTGGATATATTGGATTATTTACACTGGTAGCACTGTGGTGGCT
|| || | | ||| |||| | | | || ||| | | ||| | || |||| ||||||| |||||||| ||| ||| ||||||||||||| ||||||||| ||||| ||||||| ||| ||||| | ||||| || || || || |||||| |
gtaggttggtttgctttgctttatttgcag------tggagctctatg-aattcggcccctaattgtttcgatattgtttcagTGCTGCTTAAAAAATTTTGTGGGGAGGAAGGAGAAAAGGTTGATGTCCAAAAACTGTTTGGTTATCTTGGACTTTTTACCCTTGTTGCTCTCTGGTGGAT
upper sequence: Vv04s0008g06500.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM5G882708_T03 (Zea mays), 3'ss of exon 5
gttggccttatctttaatcttattttgaaaaactatttagattacatataatattctcattcattctacaattaatgttgcagTGCTTCTTAAAAAGTTTGCTGGTGAGGAAGGAGAAAGGGTTGATGTGCAAAAGTTGTTTGGATATATTGGATTATTTACACTGGTAGCACTGTGGTGGCT
|| || | | | ||| |||| | | ||| | ||| | | ||| | || | || ||||||| |||||||| ||| ||| ||||||||||||| ||||||||| ||||| ||||||| ||| |||| | ||||| || || || || |||||| |
gtaggttgttttactttgctttatttgcag-------ttgatctctctgaattcagcccctaattgtttcgatattatttcagTGCTGCTTAAAAAATTTTGTGGAGAGGAAGGAGAAAAGGTTGATGTCCAAAAACTGTTTGGTTATCTTGGGCTTTTTACCCTTGTTGCTCTATGGTGGAT
upper sequence: Vv04s0008g06500.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA04G06930.1 (Glycine max), 3'ss of exon 5
----gttggccttatctttaatcttattttgaaaaactatttagattacatataatattctcattcattctacaattaatgttgcagTGCTTCTTAAAAAGTTTGCTGGTGAGGAAGGAGAAAGGGTTGATGTGCAAAAGTTGTTTGGATATATTGGATTATTTACACTGGTAGCACTGTGGTGGCT
| | | || ||| |||| | | |||||||| || | || | | || |||| | |||||| |||||||| |||||| ||||||| ||||||||||||||||||||||||||| ||||||| ||||||||||| |||||||| |||||| ||||||||||
gttaagcaatgtcctgtctattctgtttttatcagataatttagatagatcatgaccacttcttcaactc----attactactgcagTTCTTCTTAAGAAGTTTTCTGGTGAAGAAGGAGAAAGGGTTGATGTGCAAAAGCTGTTTGGGTATATTGGATTGTTTACACTTGTAGCATTGTGGTGGCT
upper sequence: Vv04s0008g06500.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA06G07010.1 (Glycine max), 3'ss of exon 4
gttg-gccttatctt---taatcttattttgaaaaactatttagattacatataatattctcattcattctacaattaatgttgcagTGCTTCTTAAAAAGTTTGCTGGTGAGGAAGGAGAAAGGGTTGATGTGCAAAAGTTGTTTGGATATATTGGATTATTTACACTGGTAGCACTGTGGTGGCT
||| || | || | | ||| |||| | | |||||||| | || || | | | | || |||| | |||||| |||||||| |||||| ||||||| ||||||||||||||||||||||||||| ||||||| ||||||||||| |||||||| |||||||| ||||||||
gttaagcaatgtcctggctgttctgtttttatcagataatttagat---agatcatgaccacttcaactc----attactactgcagTTCTTCTTAAGAAGTTTTCTGGTGAAGAAGGAGAAAGGGTTGATGTGCAAAAGCTGTTTGGGTATATTGGATTGTTTACACTTGTAGCACTCTGGTGGCT
upper sequence: Vv04s0008g06500.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA17G32170.1 (Glycine max), 3'ss of exon 4
------------gttggccttatctttaatctta--ttttgaaaaactatttagattacatataatattctcattcattctacaattaatg--ttgcagTGCTTCTTAAAAAGTTTGCTGGTGAGGAAGGAGAAAGGGTTGATGTGCAAAAGTTGTTTGGATATATTGGATTATTTACACTGGTAGCACTGTGGTGGCT
|| || || | ||| | || |||| | | ||||||| | |||| | || | || |||||| | |||||||||| ||||| || ||||||| ||||||||| | ||||||||||||||||||||||||||| ||||||| |||||||| |||||||| ||||||||
gttagacaatgtcttagctttttgtttgttttttgtctttgtcagataatttaga------agaataatgacagcttctttaacgttaatgcctcacagTGCTTCTCAAAAAAATTTCTGGTGAAGAAGGAGAACGAGTTGATGTGCAAAAGTTGTTTGGATATGTTGGATTGTTTACACTTGTAGCACTATGGTGGCT
upper sequence: Vv04s0008g06500.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA14G14010.1 (Glycine max), 3'ss of exon 4
------------gttggccttatctttaat----cttattttgaaaaactatttagattacatataatattc-tcattcattctacaa--ttaatgttgcagTGCTTCTTAAAAAGTTTGCTGGTGAGGAAGGAGAAAGGGTTGATGTGCAAAAGTTGTTTGGATATATTGGATTATTTACACTGGTAGCACTGTGGTGGCT--
|| || || | ||| || ||| |||| | | | | || | || || | | | | ||||| || |||||| |||||||||||||||| || ||||||| | ||||||| ||||||||||||||||| ||||||||||| ||||||| |||||||| |||||||| ||||||||
gttagataatgtcttagctttttgtttgatttctcttgttttttgtcattgtc-aaataatgtagaagaataatgacggattctttaacgttaatgcctcagtgcttcttaaaaaaatttctggtgaagGAGGAGAACGGGTTGATGTGCAAAAGCTGTTTGGATATGTTGGATTGTTTACACTTGTAGCACTATGGTGGCTTA
upper sequence: Vv04s0008g06500.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA14G14010.2 (Glycine max), 3'ss of exon 3
------------gttggccttatctttaat----cttattttgaaaaactatttagattacatataatattc-tcattcattctacaa--ttaatgttgcagTGCTTCTTAAAAAGTTTGCTGGTGAGGAAGGAGAAAGGGTTGATGTGCAAAAGTTGTTTGGATATATTGGATTATTTACACTGGTAGCACTGTGGTGGCT
|| || || | ||| || ||| |||| | | | | || | || || | | | | ||||| || |||||| |||||||||||||||| || ||||||| | ||||||| ||||||||||||||||| ||||||||||| ||||||| |||||||| |||||||| ||||||||
gttagataatgtcttagctttttgtttgatttctcttgttttttgtcattgtc-aaataatgtagaagaataatgacggattctttaacgttaatgcctcagTGCTTCTTAAAAAAATTTCTGGTGAAGGAGGAGAACGGGTTGATGTGCAAAAGCTGTTTGGATATGTTGGATTGTTTACACTTGTAGCACTATGGTGGCT
upper sequence: Vv04s0008g06500.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT4G32140.1 (Arabidopsis thaliana), 3'ss of exon 4
gttggccttatctttaatctt----attttgaaaaactatttagattacatataatattctcattcat------------tctacaattaatgttgcagTGCTTCTTAAAAAGTTTGCTGGTGAGGAAGGAGAAAGGGTTGATGTGCAAAAGTTGTTTGGATATATTGGATTATTTACACTGGTAGCACTGTGGTGGCT
||| | || |||||||| ||| | | || | | || | ||| |||||| || ||| ||| | ||||||||||||| |||||||| ||||| ||||||||| |||||||||| |||||| |||||||||| || |||||||||||||| || || || ||||||||
gttagaa--atgattaatctttaaaggtttagagtattagtgtg-ttggggaggataacctcattgatggcttgtacccttctgatattgacaacacagTGCTTCTTAAGAAGTTTGCCGGTGAAGAAGGAGAAGGGGTTGATGTCCAAAAGCTGTTTGGATACATAGGATTATTTACACTTGTTGCTCTCTGGTGGCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaactatttagattacatataatattctcattcattctacaattaatgttgcagTGCTTCTTAAAAAGTTTGCTGGTGAGGAAGGAGAAAGGGTTGATGTGCAAAAGTTGTTTGGATATATTGGATTATTTACACTGGTAGCACTGTGGTGGCT
aattaat putative branch site (score: 3)
tatttagattacatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttggccttatctttaatcttattttgaaaaactatttagattacatataatattctcattcattctacaattaatgttgcagTGCTTCTTAAAAAGTTTGCTGGTGAGGAAGGAGAAAGGGTTGATGTGCAAAAGTTGTTTGGATATATTGGATTATTTACACTGGTAGCACTGTGGTGGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG