Sequence
atgc intronic sequence ATGC exonic sequencegtttgtccgcttcatcattaacattcttaatagatatgtataaatccgagttctaatctctttgggatcgttctgtacagTCAATCACTATCCAGTGTCTCGAATCACTTCAATTTCTACATGGCCTTGGACTTATACACTGTGATTTGAAGCCTGAGAACATATTGGTTAAAAGTTATA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G73460.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G73460.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os03g51020.1 (Oryza sativa), 3'ss of exon 4
------------------------------------------gtttgtccgcttcatcatta-acattcttaatagatatgtataaatccgagttctaatctctttgggatcgttctgtacagTCAATCACTATCCAGTGTCTCGAATCACTTCAATTTCTACATGGCCTTGGACTTATACACTGTGATTTGAAGCCTGAGAACATATTGGTTAAAAGTTATA
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gtattactagctagctaataggatccagtaatggtgattaatgtttttactctcagtaaatggacacaatataccaatttttgtgacaataattgattttccttttgcgtaccctttctgcagTCAATAGCTATTCAGTGTTTGGAGGCACTGCAGTTTTTGCATGGACTTGGTCTTATACATTGTGATCTGAAGCCGGAGAACATATTGGTAAAGAGCTACA
upper sequence: AT1G73460.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G06160.1 (Glycine max), 3'ss of exon 6
gtttg---tccgct-tcatcattaacattcttaatagatatgt-ataaatccgagttctaatctctttgggatcgttctgtacagTCAATCACTATCCAGTGTCTCGAATCACTTCAATTTCTACATGGCCTTGGACTTATACACTGTGATTTGAAGCCTGAGAACATATTGGTTAAAAGTTATA
||||| | ||| | | | | || ||||| || | || || | || || ||||| | || | | ||| |||||||| || || |||||| | ||| | ||||| ||| | ||| |||||||||| |||||||| || ||||| || ||||| || ||||||||||| ||||
gtttgtggtgtgctatttacttcatgatgtttaattttcatcttatctattctcattgcaaactcttctgaattgatgtgtgcagTCAATTACCATTCAGTGTTTGGAAGCTCTTCAGTTTTTGCATAGCCTTGGACTAATACACTGCGACTTGAAACCAGAGAATATTTTGGTTAAAAGCTATA
upper sequence: AT1G73460.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA05G33560.1 (Glycine max), 3'ss of exon 4
gtttgtc-cgcttcat---cattaacattcttaat--agatatgtataaatccgagttctaatctctttgggatcgttctgtacagTCAATCACTATCCAGTGTCTCGAATCACTTCAATTTCTACATGGCCTTGGACTTATACACTGTGATTTGAAGCCTGAGAACATATTGGTTAAAAGTTATA
||| ||| | ||| | | | || ||||| || | | | || ||| | || ||||| | || | | ||| |||||||| || || |||||| | ||| | ||||| ||| | ||| |||||||||| |||||||| || ||||| || ||||| || ||||||||||| ||||
gttcgtcgtgtgccatttacttcatgatgtttaattttaatcttttctattctcagtgcaaa-ctcttctgaattgatgtgtgcagTCAATTACCATTCAGTGTTTGGAAGCTCTTCAGTTTTTGCATAGCCTTGGACTAATACACTGCGACTTGAAACCAGAGAATATTTTGGTTAAAAGCTATA
upper sequence: AT1G73460.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA16G34510.1 (Glycine max), 3'ss of exon 4
------------------------------------------------gtttgtcc---gcttcatcattaacattcttaatagatatgtataaatccgagttctaatctctttgggatcgttctgtacagTCAATCACTATCCAGTGTCTCGAATCACTTCAATTTCTACATGGCCTTGGACTTATACACTGTGATTTGAAGCCTGAGAACATATTGGTTAAAAGTTATA
|||||| | | | | || ||| ||| | || | | | | || ||| | |||| | | ||| |||||||| || || |||||| | ||| ||||||| ||| | || | |||||||| ||||| ||||| |||||||| ||||| || ||||||||||| ||||
gttagtgctgtgctgtgatatgttctttctatatttacttatcatgctgtttgtactgtgatctttagttttcatcctttctgctagtgcaatactgtca-ttataaacacttttcaacttatgtgtgcagTCAATTACCATTCAGTGTTTGGAAGCACTTCAGTTTTTGCACAGTCTTGGACTAATACATTGTGACTTGAAGCCAGAGAATATTTTGGTTAAAAGCTATA
upper sequence: AT1G73460.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv01s0011g01590.t01 (Vitis vinifera), 3'ss of exon 10
-----gtttgtccgcttcatcattaacattcttaatagatatgtataaatccgagttctaatctctttgggatcgttctgtacagTCAATCACTATCCAGTGTCTCGAATCACTTCAATTTCTACATGGCCTTGGACTTATACACTGTGATTTGAAGCCTGAGAACATATTGGTTAAAAGTTATA
| | | || | | | || || || | | | | | |||| || ||||||| ||||| || || || |||||| | || ||||||| || | |||||||| || |||||||| |||||| ||||||||||||| || ||||| || || ||||
gttatggagttacatttttaaactgatatctttctctcctactgacatgctggtatgtaacctgcttttaaattgttctgtgcagTCCATTACAATTCAGTGTTTGGAGGCACTTCAGTTCTTGCATGGCCTAGGCCTTATACATTGTGATCTGAAGCCTGAGAATATTTTGGTGAAGAGCTATA
upper sequence: AT1G73460.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ25132 (Selaginella moellendorffii), 3'ss of exon 2
gtttgtccgcttcatcattaacattcttaatagatatgtataaatccgagttctaatctctttgggatcgttctgtacagTCAATCACTATCCAGTGTCTCGAATCACTTCAATTTCTACATGGCCTTGGACTTATACACTGTGATTTGAAGCCTGAGAACATATTGGTTAAAAGTTATA
| | |||| | | | || | | ||| | | | || | ||||| || ||| ||||||| | || |||| | || | |||||||||||| | ||||| || ||||||||||| ||||||||| | || || || || |
-------------gtaggaagtgttctagct---cacaggtggattttattcttaacac--tcgaaa-----ctttgcagTCTATTACTCGCCAGTGTTTGGAGGCACTGGAGTTCTTGCATGGCCTTGGATTGATACATTGCGATTTGAAGCCGGAGAACATACTAGTAAAGAGCTACA
upper sequence: AT1G73460.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ29918 (Selaginella moellendorffii), 3'ss of exon 2
gtttgtccgcttcatcattaacattcttaatagatatgtataaatccgagttctaatctctttgggatcgtt----ctgtacagTCAATCACTATCCAGTGTCTCGAATCACTTCAATTTCTACATGGCCTTGGACTTATACACTGTGATTTGAAGCCTGAGAACATATTGGTTAAAAGTTATA
|| | | | | || || || | | | | || | | | || | ||||| || ||| ||||||| | || |||| | || | |||||||||||| | ||||| || ||||||||||| ||||||||| | || || || || |
--------------------------gtaggaagtgt-tctagctcacaggtggattttattcgtaactctcgaaactttgcagTCTATTACTCGCCAGTGTTTGGAGGCACTGGAGTTCTTGCATGGCCTTGGATTGATACATTGCGATTTGAAGCCGGAGAACATACTAGTAAAGAGCTACA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttaatagatatgtataaatccgagttctaatctctttgggatcgttctgtacagTCAATCACTATCCAGTGTCTCGAATCACTTCAATTTCTACATGGCCTTGGACTTATACACTGTGATTTGAAGCCTGAGAACATATTGGTTAAAAGTTATA
ttctaat putative branch site (score: 2)
tcgttct putative PPT
tagatatgtataaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtccgcttcatcattaacattcttaatagatatgtataaatccgagttctaatctctttgggatcgttctgtacagTCAATCACTATCCAGTGTCTCGAATCACTTCAATTTCTACATGGCCTTGGACTTATACACTGTGATTTGAAGCCTGAGAACATATTGGTTAAAAGTTATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC