Sequence
atgc intronic sequence ATGC exonic sequencegttaacttttgtataattgagacatgatgttctgtttttagagaatcttgatttgatgctaatctttgctcatatttggaatgtgtatatggaattgggatgtttcagACATTTGTATATGGTGATCTTTATCGACATGATATTGAGAAGCAGGAGTGGAAATTGATATCTAGCCCTAATAGTCCACCTCCTCGTAGTTCTCATCAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv17s0000g10130.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os04g40740.1 (Oryza sativa), 3'ss of exon 3
----------------------gttaacttttgtataattgagacatgatgttct-gtttttagagaatcttgatt-tgatgctaatctttgctcatatttggaatg-------tgtatatggaattgggatgttt---cagACATTTGTATATGGTGATCTTTATCGACATGATATTGAGAAGCAGGAGTGGAAATTGATATCTAGCCCTAATAGTCCACCTCCTCGTAGTTCTCATCAAG
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gtgggagacatatccttcacgatttcactgctggttgaatgagatatgttcatctagtgttctttttgcctctattctgcttctagaggtttttgagtactgaaatagtatttcttttcctcgccacaatctatttctgcagACCTTTGTTTATGGTGATCTTTATCGCTACGATGTAGAGAAAAATGAGTGGAAGTTGGTATCTAGTCCTAACAGTCCTCCTCCACGAAGTGCTCACCAAA
upper sequence: Vv17s0000g10130.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os04g40740.2 (Oryza sativa), 3'ss of exon 3
----------------------gttaacttttgtataattgagacatgatgttct-gtttttagagaatcttgatt-tgatgctaatctttgctcatatttggaatg-------tgtatatggaattgggatgtttc---agACATTTGTATATGGTGATCTTTATCGACATGATATTGAGAAGCAGGAGTGGAAATTGATATCTAGCCCTAATAGTCCACCTCCTCGTAGTTCTCATCAAG---------------------------------
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gtgggagacatatccttcacgatttcactgctggttgaatgagatatgttcatctagtgttctttttgcctctattctgcttctagaggtttttgagtactgaaatagtatttcttttcctcgccacaatctatttctgcagacctttgtttatggtgatctttatcgctacgatgtagAGAAAAATGAGTGGAAGTTGGTATCTAGTCCTAACAGTCCTCCTCCACGAAGTGCTCACCAAACAGTTGCCTGGAAGAATAATATATACATGTTTG
upper sequence: Vv17s0000g10130.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA04G36770.1 (Glycine max), 3'ss of exon 3
gttaacttttgtataattgagacatgatgttctgtttttagagaatcttgatttgatgctaatctttgctcatatttggaatgtgtatatggaattgggatgtttcagACATTTGTATATGGTGATCTTTATCGACATGATATTGAGAAGCAGGAGTGGAAATTGATATCTAGCCCTAATAGTCCACCTCCTCGTAGTTCTCATCAAG
|| | |||| || | | |||| | ||| |||| || | | | | | | | |||||| || || | ||||||||||| || || ||||| || || ||||| | ||||||| ||| ||||||||| | || || || |||||||| |||||||| ||| |||||||||
-------gttacgtgtttgaattgtgtttatttgttgattgagtgatatgatatgtaccgagtgaattgttgttgccgcaatgtgaatttg------------tgcagACATTTGTGTACGGCGATCTCTACCGGTATGATGTGGAGAAGCTGGAATGGAAATTGGTTTCAAGTCCGAATAGTCCTCCTCCTCGCAGTGCTCATCAAG
upper sequence: Vv17s0000g10130.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT5G50310.1 (Arabidopsis thaliana), 3'ss of exon 3
gttaacttttgtataattgagacatgatgttctgtttttagagaatcttgatttgatgctaatctttgctcatatt-tggaatgtgtatatggaattgggatgt---ttcagACATTTGTATATGGTGATCTTTATCGACATGATATTGAGAAGCAGGAGTGGAAATTGATATCTAGCCCTAATAGTCCACCTCCTCGTAGTTCTCATCAAG
|||| |||| | | ||| | | ||| | ||| || |||| || | | |||| | |||| | ||| || || |||| | ||||||| ||||||||||||||| || ||| ||||| | ||||||||||||||||| || | || ||||| ||||||||||||||||| || ||||||||||
gttagcttt-gcacaatc----ttttttcttcagagttttgattttctttgttaagg---agtgtttgattatatagtcatatgataatgattggtttccatgtaaatgcagACATATGTATATGGTGATCTCTACCGATATGATGTAGAGAAGCAGGAGTGGAAGTTAGTTTCAAGCCCCAATAGTCCACCTCCTCGCAGCTCTCATCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgatgctaatctttgctcatatttggaatgtgtatatggaattgggatgtttcagACATTTGTATATGGTGATCTTTATCGACATGATATTGAGAAGCAGGAGTGGAAATTGATATCTAGCCCTAATAGTCCACCTCCTCGTAGTTCTCATCAAG
tgctaat putative branch site (score: 2)
taatcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttaacttttgtataattgagacatgatgttctgtttttagagaatcttgatttgatgctaatctttgctcatatttggaatgtgtatatggaattgggatgtttcagACATTTGTATATGGTGATCTTTATCGACATGATATTGAGAAGCAGGAGTGGAAATTGATATCTAGCCCTAATAGTCCACCTCCTCGTAGTTCTCATCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC