Sequence
atgc intronic sequence ATGC exonic sequencegtaaacataactttactttgctctagctactccaatcttcctgaggctagcttgtttaaccattaactctctctggttattgtatatatattttaagGTGGTATGCTAAAAGGTTTCTGCATCCTGACATTGTGGCACCTTATGACTATGTATTCATCTGGGATGAAGACCTCGGCCTTGAAAACTTCGATGTAGAA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G13000.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G13000.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA11G37770.1 (Glycine max), 3'ss of exon 7
------------------------------gtaaacataactttacttt-gctctagctactccaatcttcctgaggctagcttgttt-aaccattaactctctctggttattgta--tatatattttaagGTGGTATGCTAAAAGGTTTCTGCATCCTGACATTGTGGCACCTTATGACTATGTATTCATCTGGGATGAAGACCTCGGCCTTGAAAACTTCGATGTAGAA
| | | | || | | | | | | || | | | | | | || || ||| || || | || ||| || | | | | ||||||||||| || |||||||||||||||||||||||||||| ||||||||| ||||||| |||||||||||||| || |||| | || ||| ||||
gtaaggagctaagatgttcattattttttagaggataaattttcattgtagtttttgcaattaatagtgtttagtgcttacctaatttcaattatgtcaatacattgacaattttagtttttccctcttagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATATTCATATGGGATGAAGACCTGGGTGTTGAGCATTTTAATGCAGAA
upper sequence: AT1G13000.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA18G01710.1 (Glycine max), 3'ss of exon 7
------------------------------gtaaacataactttacttt-gctctagctactccaatcttcctgaggctagcttgttt-aaccattaactctctctggttattgta--tatatattttaagGTGGTATGCTAAAAGGTTTCTGCATCCTGACATTGTGGCACCTTATGACTATGTATTCATCTGGGATGAAGACCTCGGCCTTGAAAACTTCGATGTAGAA
| || | | | | | | | | || | | | | | | || || ||| || || | || ||| | | | | | ||||||||||| || |||||||||||||||||||||||||||| ||||||||| ||||||| |||||||||||||| || |||| | || ||| |||
gttaggagctaagcggttaattattttttagataataaattatcgttgtagtttttgcaagtattagtgttcaatgcttacctaatttcaattatgttattatattgacaattttggtttttccctcttagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATATTCATATGGGATGAAGACCTGGGTGTTGAGCATTTTAATGCGGAA
upper sequence: AT1G13000.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA08G14050.1 (Glycine max), 3'ss of exon 5
gtaaacataa-ctttactttg-ctctagctactccaatcttcctgaggctagcttgtttaaccattaactctctctggttattgtatatatattttaagGTGGTATGCTAAAAGGTTTCTGCATCCTGACATTGTGGCACCTTATGACTATGTATTCATCTGGGATGAAGACCTCGGCCTTGAAAACTTCGATGTAGAA
||||| | || | ||| ||| | || | | | | | ||| ||| || | | |||||| | | | | | | ||||||||||| || |||||||| ||||| |||||||||||||| ||||||||| | ||||| |||||||||||||| || |||| || ||| ||| ||||
gtaaaaaagttctctgcttaaattctcattgtgtcatttccagttaatattgtttgccaaacttaaaatggttt---gttatt-tctttttcctctcagGTGGTATGCCAAGAGGTTTCTACATCCAGACATTGTGGCACCATATGACTATATTTTCATGTGGGATGAAGACCTGGGGGTTGAGAATTTCAATGCAGAA
upper sequence: AT1G13000.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA08G14040.1 (Glycine max), 3'ss of exon 7
--------------------------------------------------gtaaacataact-ttactttgctctagctactccaatcttcctgaggctagcttgtttaaccattaactctctctggttattgtatatatat---tttaagGTGGTATGCTAAAAGGTTTCTGCATCCTGACATTGTGGCACCTTATGACTATGTATTCATCTGGGATGAAGACCTCGGCCTTGAAAACTTCGATGTAGAA
| || | || | | | | | | ||| || | | ||| || || ||| | | ||| || | | | | ||||||||||| || |||||||||||||||||||||||||||| ||||||||| | || || |||||||||||||| || ||||| | || ||| |||
gtaagaatccattgcgctcgatcataaatattggatgacatattttccttgcaactcttaccatcattattgtttgcctaactaaagtcaaaagtgttctgctaattcaatcatgttatgatattaagcatttaatttttttccctcctagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATTTTTATATGGGATGAAGACCTGGGTGTTGAACATTTTAATGCAGAG
upper sequence: AT1G13000.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA05G30830.1 (Glycine max), 3'ss of exon 7
--------------------------------------------------gtaaacataact-ttactttgctctagctactccaatcttcctgaggctagcttgtttaaccat-taactctctctggttattg--tatatatattttaagGTGGTATGCTAAAAGGTTTCTGCATCCTGACATTGTGGCACCTTATGACTATGTATTCATCTGGGATGAAGACCTCGGCCTTGAAAACTTCGATGTAGAA
| || | || ||| | | | | ||| || | | |||| || | | || | | | | | || ||| | | ||||||||||| || |||||||||||||||||||||||||||| ||||||||| | || || |||||||||||||| || ||||| | || ||| ||||
gtaagaatccattgcgctcgatcgtaaatattggatgacaaattttccttgcaacttttaccattattattgtttgcctaactaaaatcaaaagtgttctgcttattcatctatgttatgatattaagcatttaattattttccctcctagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATTTTTATATGGGATGAAGACCTGGGTGTTGAACATTTTAATGCAGAA
upper sequence: AT1G13000.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA05G30850.1 (Glycine max), 3'ss of exon 5
gtaaacataactttactttgctctagctactccaatcttcctgaggctagc-ttgtttaacca-ttaactctctctggttattgtatatatattttaagGTGGTATGCTAAAAGGTTTCTGCATCCTGACATTGTGGCACCTTATGACTATGTATTCATCTGGGATGAAGACCTCGGCCTTGAAAACTTCGATGTAGAA
||||| || || | ||| | | | | | | | || ||||||| | | | | | | |||||| | | ||| |||||||||| || |||||||| ||||| |||||||||| ||| ||||||||| | ||||| |||||||||||||| || |||| || ||| ||| |||
gtaaaaatt-ctatgcttaaattt--tcattgtggcatattttcagttaatattgtttaccaaacttaaaatggtttgttatttctttcgcctctta-gGTGGTATGCCAAGAGGTTTCTACATCCAGACATTGTGGTACCATATGACTATATTTTCATGTGGGATGAAGACCTGGGGGTTGAGAATTTCAATGCTGAA
upper sequence: AT1G13000.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv00s0187g00030.t01 (Vitis vinifera), 3'ss of exon 3
---------------------------gtaaacataactttactttgctctagctactccaatcttcctgaggctagcttgtttaaccattaactctctctggttattgtatatatattttaagGTGGTATGCTAAAAGGTTTCTGCATCCTGACATTGTGGCACCTTATGACTATGTATTCATCTGGGATGAAGACCTCGGCCTTGAAAACTTCGATGTAGAA
| |||| || ||| || ||| | | | || || | || || | |||||| | | ||| | | | | || |||||||||| ||||| ||||||||||||||||||||||| || ||||||||| |||| |||||||||||||| || || |||| | || ||| ||||
gtaaggagcttctgcaaaggattatttttgaacagaagtttcactttttctggtaggtttcaataagctatggtctgttttatt--cttttaacttcat----tctttgcaattttgtccta-gGTGGTATGCCAAAAGATTTCTGCATCCTGACATTGTGGCGCCATATGACTATATATTTATCTGGGATGAAGATCTAGGAGTTGAGCATTTTAATGCAGAA
upper sequence: AT1G13000.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv01s0137g00770.t01 (Vitis vinifera), 3'ss of exon 7
---------------------------gtaaacataactttactttgctctagctactccaatcttcctgaggctagcttgtttaaccattaactctctctggttattgtatatatattttaagGTGGTATGCTAAAAGGTTTCTGCATCCTGACATTGTGGCACCTTATGACTATGTATTCATCTGGGATGAAGACCTCGGCCTTGAAAACTTCGATGTAGAA
| |||| || ||| || ||| | | | || || | || || | |||||| | | ||| | | | | || |||||||||| ||||||||||||||||||||||||||||| || ||||||||| |||| |||||||||||||| || || |||| | || ||| ||||
gtaaggagcttctgcaaaggattatttttgaacagaagtttcactttttctggtaggtttcaataagctatggtctgttttatt--cttttaacttcat----tctttgcaattttgtccta-gGTGGTATGCCAAAAGGTTTCTGCATCCTGACATTGTGGCGCCATATGACTATATATTTATCTGGGATGAAGATCTAGGAGTTGAGCATTTTAATGCAGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaggctagcttgtttaaccattaactctctctggttattgtatatatattttaagGTGGTATGCTAAAAGGTTTCTGCATCCTGACATTGTGGCACCTTATGACTATGTATTCATCTGGGATGAAGACCTCGGCCTTGAAAACTTCGATGTAGAA
cattaac putative branch site (score: 2)
tggttattgtatatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaacataactttactttgctctagctactccaatcttcctgaggctagcttgtttaaccattaactctctctggttattgtatatatattttaagGTGGTATGCTAAAAGGTTTCTGCATCCTGACATTGTGGCACCTTATGACTATGTATTCATCTGGGATGAAGACCTCGGCCTTGAAAACTTCGATGTAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA