Sequence
atgc intronic sequence ATGC exonic sequencegttagttttatgcgggtttttttatgtctgttgaactctcatgtcctctgaactacgtttaactcggtttttccaaaatatacagGAGATACGGGGCTTGTTTCCTCCCGAACACAACCCATTCTATGCTGGTTTTGGAAACAGAGACACAGATGAGATAAGCTACCTTAAAGTCGGAATCCCCC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G42870.2 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G42870.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os11g40080.1 (Oryza sativa), 3'ss of exon 7
---------------------gttagttttatgcgggt-ttttttatgtctgttgaactctcat-gtcctc-tgaacta---cgtttaa---ctcggtttttccaaaatatacagGAGATACGGGGCTTGTTTCCTCCCGAACACAACCCATTCTATGCTGGTTTTGGAAACAGAGACACAGATGAGATAAGCTACCTTAAAGTCGGAATCCCCC
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gtcagtactcagcaacacaaagataaatatatgaacatacattgaataattgcttgctcttcattgcgctcatgaaataattcgtaccaagtcttgattcacctgtttcacacagGCTATCAAAGCACTATTTCCTCCTGACTCAAATCCATTCTATGCTGGATTTGGAAATAGAGATACAGATGAGCTTAGTTACCTCAAGGTTGGGATTCCTA
upper sequence: AT5G42870.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA04G04060.1 (Glycine max), 3'ss of exon 13
gttagttttatgcgggt-ttttttatgtctgttgaact-ctcatgtcctctgaactacgtttaactcggtttttccaaaatatacagGAGATACGGGGCTTGTTTCCTCCCGAACACAACCCATTCTATGCTGGTTTTGGAAACAGAGACACAGATGAGATAAGCTACCTTAAAGTCGGAATCCCCC
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gttagtttcccgctgctacatattacaatgatcatattacattcataatgttattaaagtctatttgaatttttatgtcat---cagGACATCAAGGCACTTTTTCCTTCTGATAGCAGTCCATTCTATGCTGGTTTTGGTAATAGGGATACGGATGAAATCAGCTACCTTAAGGTTGGAATTCCCC
upper sequence: AT5G42870.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA06G04230.1 (Glycine max), 3'ss of exon 14
gttagttttatgcgggt-ttttttatgtctgttgaactctcatgtcctctgaactacgtttaactcggtttttccaaaatatacagGAGATACGGGGCTTGTTTCCTCCCGAACACAACCCATTCTATGCTGGTTTTGGAAACAGAGACACAGATGAGATAAGCTACCTTAAAGTCGGAATCCCCC
|||||||| || | | | |||| | | | | || | || | | |||| | | ||||| || || | |||||| | || || |||||||||||||||||||| || || || || ||||| || ||||||||||| || ||||| ||||
gttagtttcccgctgctacatattataatgagcatattacagtcataatgttattaaagtcaatttgaattttt--atgtcatcagGACATCAAGGCACTTTTTCCTTCTGATAGCAGTCCATTCTATGCTGGTTTTGGTAATAGGGATACTGATGAAATCAGCTACCTTAAGGTTGGAATTCCCC
upper sequence: AT5G42870.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv18s0001g10680.t01 (Vitis vinifera), 3'ss of exon 10
----------gttagttttatgcgggtttttttatgtctgt-tgaactctcatgtcctctgaactacgtttaactcggttttt----ccaaaatatacagGAGATACGGGGCTTGTTTCCTCCCGAACACAACCCATTCTATGCTGGTTTTGGAAACAGAGACACAGATGAGATAAGCTACCTTAAAGTCGGAATCCCCC
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gtgtatggtctttgtgcatgcccggatcatttgttggatgagtggaaggttaaggatgaaaaaaggtagctaataatgcttttagttccccaattttcagGATATCAAGGCATTATTTCCTTCTGATTGCAATCCATTCTATGCTGGTTTTGGAAACCGGGACACTGATGAGTTTAGCTACCTTAAGGTTGGAATTCCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgaactctcatgtcctctgaactacgtttaactcggtttttccaaaatatacagGAGATACGGGGCTTGTTTCCTCCCGAACACAACCCATTCTATGCTGGTTTTGGAAACAGAGACACAGATGAGATAAGCTACCTTAAAGTCGGAATCCCCC
gtttaac putative branch site (score: 3)
tttttccaaaatata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagttttatgcgggtttttttatgtctgttgaactctcatgtcctctgaactacgtttaactcggtttttccaaaatatacagGAGATACGGGGCTTGTTTCCTCCCGAACACAACCCATTCTATGCTGGTTTTGGAAACAGAGACACAGATGAGATAAGCTACCTTAAAGTCGGAATCCCCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG