Sequence
atgc intronic sequence ATGC exonic sequencegttagtttctggtgacccgatgagtaaattggcattgtaatttcaccacaagaaatctgatgtttatgcacttgcctgtgttgattcttctcatttcatgaaacagATTGAAGTGGGTGATGTCATAGGTGAGATCGAGACTGACAAAGCCACTCTGGAATTTGAAAGCCTTGAAGAGGG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G52200.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G52200.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os06g30460.3 (Oryza sativa), 3'ss of exon 5
-------gttagtttctggtgacccgatgagtaaattgg--cattgtaatttcaccacaagaa-----atctgatgtttatgcacttgcctgtgttgattcttctcatttcatgaaacagATTGAAGTGGGTGATGTCATAGGTGAGATCGAGACTGACAAAGCCACTCTGGAATTTGAAAGCCTTGAAGAGGG
|| | | || | || | ||||| ||| | || || || || | | ||||| | | | | | | || || || | ||||| ||||| |||||||| || ||||||| || ||||||||||| || || || ||||| ||||||||||||||
gttaggattttgctctgggatatttcataatagaattgaaacatcttgtttccaattcagagttctttatttcttttttatatattagtttcgatcaaaagttatctgttgtttg--cagATAGAAGTTGGTGATGTGATCTGTGAGATAGAAACTGACAAAGCTACGCTTGAGTTTGAGAGCCTTGAAGAGGG
upper sequence: AT3G52200.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G082664_T01 (Zea mays), 3'ss of exon 7
------------------gttagtttctggtgacccgatgagtaaattggcattgtaatttcaccacaagaaatctgatgtttatgcacttgcctgtgttgattct-------------tctcatttcatgaa---acagATTGAAGTGGGTGATGTCATAGGTGAGATCGAGACTGACAAAGCCACTCTGGAATTTGAAAGCCTTGAAGAGGG
|||| ||| | | | || || ||| | || || || || | | | || || ||| | | ||| || |||| | | || ||| ||||| || || |||||||| ||| ||||||| || ||||| ||||||||||| || ||||||||||||||||||||
gttgtgcttttgctagctgttattttttta-aattcaataagaaaaat---atcctatttccagcttagggtttcccattttttttgtttaatgtgttttagttctgagaacactatcgttgaactttatgttgttgcagATAGAGGTTGGTGATGTGATATGTGAGATAGAAACTGATAAAGCCACTCTTGAGTTTGAAAGCCTTGAAGAGGG
upper sequence: AT3G52200.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA10G34480.1 (Glycine max), 3'ss of exon 6
--------------gttagtttctggt---gacccgatgagtaaattggcattgtaa--tttcaccacaagaa-atctgatgtttatgcacttgcctgtgttgattcttc--tcatttcatgaaacagATTGAAGTGGGTGATGTCATAGGTGAGATCGAGACTGACAAAGCCACTCTGGAATTTGAAAGCCTTGAAGAGGG
| || |||| | || | | | | | || ||| ||| | | || || | ||| ||| | | | | ||| | | | | || || ||||||||||||||||||||| | || ||||||| ||||| |||||||| || || |||||||| || |||||||||||
gttagtgttttaacctaaggttctaatagagattctacttttcatatatatttttaatattttaaaatgtgagcatgagtcgttaatgggcatatattttttgtctgaacatttaatttatcaaacagATTGAAGTGGGTGATATATTATGTGAGATAGAGACAGACAAAGCTACACTTGAATTTGAGAGTCTTGAAGAGGG
upper sequence: AT3G52200.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA20G33080.1 (Glycine max), 3'ss of exon 10
--------------gttagtttctggt---gacccgatgagtaaattggcattgtaatttcaccacaagaa-atctgatgtttatgcacttgcctgtgttgattctt-----------ctcatttcatgaaacagATTGAAGTGGGTGATGTCATAGGTGAGATCGAGACTGACAAAGCCACTCTGGAATTTGAAAGCCTTGAAGAGGG
| || |||| | || | | | | || |||| | | | ||| || | || |||| | | | || | | | | || || |||||||||||||||| ||| | || ||||||||||||| |||||||| || || |||||||||| |||||||||||
gttagtgttttaacctaaggttctaatagagattgtacttttcatatatttttaatattttaaaatatgaacatgagtcattaatgcccatattttctttatctgatatgcaataacatttaatttatctaacagATTGAAGTGGGCGATATATTATGTGAGATCGAGACAGACAAAGCTACACTTGAATTTGAAACTCTTGAAGAGGG
upper sequence: AT3G52200.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA10G34480.1 (Glycine max), 3'ss of exon 2
----------------gttagtttctggtgacccgatgagtaaattggcattg-taatttcaccacaagaaatctgatgttt-atgcacttgcctgtgttgattct--tctcatttcatgaaacagATTGAAGTGGGTGATGTCATAGGTGAGATCGAGACTGACAAAGCCACTCTGGAATTTGAAAGCCTTGAAGAGGG
| ||||| | | | || | ||| | ||||| | | | ||| | | || | |||| | || || ||||||| |||||||| ||||| || |||| || || ||||||||||| || || ||||||||||| |||||||||||
gtcagttagtatatagctctgtttcatacttctgtttagttctgtttgtgttgatgctttcattttggagattgacttctttgaattaattaatcattttgacatgggtactgattaatctaacagATAGAAGTGGGGGATGTACTATGTGAAATTGAAACTGACAAAGCTACACTAGAATTTGAAAGTCTTGAAGAGGG
upper sequence: AT3G52200.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA20G33080.1 (Glycine max), 3'ss of exon 6
----------------------------gttagtttctggtgac-ccgatgagtaaattggcattgtaatttcaccacaagaaatctgatgtttatgca--cttgcctgtgttgattcttctcatttcatgaaacagATTGAAGTGGGTGATGTCATAGGTGAGATCGAGACTGACAAAGCCACTCTGGAATTTGAAAGCCTTGAAGAGGG
| | ||| | | | | || | || | | |||| || ||| ||| | ||| | ||| | ||| | | | | |||||| |||||||| ||||| || |||| || || ||||||||||| || || ||||||||||| |||||||||||
gtcagttagtatatagttcttatattttgatggttatggatcatacttttgtttgtgctgatgctttcattttggagattgacttctttgaattaattaatcttttcgacattggtacttattaatcta----acagATAGAAGTGGGGGATGTACTATGTGAAATTGAAACTGACAAAGCTACACTAGAATTTGAAAGTCTTGAAGAGGG
upper sequence: AT3G52200.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv13s0074g00150.t01 (Vitis vinifera), 3'ss of exon 10
----------gttagtttctggtgacccgatgagtaaattggcattgtaatttcaccacaagaaatctgatgtttatgcactt-gcctgtgttgattcttc------tcatttcatgaaacagATTGAAGTGGGTGATGTCATAGGTGAGATCGAGACTGACAAAGCCACTCTGGAATTTGAAAGCCTTGAAGAGGG
||| || ||| | || | || | ||| | || | |||| ||||||| | | |||| | || | | | | || || ||||||| |||||||||||||| ||| ||||||| ||||| ||||||||||| || ||||||||||| |||||||||||
gtttgttatgcttaattaaaggttattgaatt--tcaagtaatattttttttcctgtttggaaaatact-tgtttatctattcagcctttcctgttctcttgatcatttacttgatctaacagATAGAAGTGGGTGATGTGATATGTGAGATAGAGACAGACAAAGCCACCCTTGAATTTGAAAGTCTTGAAGAGGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaaatctgatgtttatgcacttgcctgtgttgattcttctcatttcatgaaacagATTGAAGTGGGTGATGTCATAGGTGAGATCGAGACTGACAAAGCCACTCTGGAATTTGAAAGCCTTGAAGAGGG
tgttgat putative branch site (score: 4)
ttcttctcatttcat CT-rich tract
atgtttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtttctggtgacccgatgagtaaattggcattgtaatttcaccacaagaaatctgatgtttatgcacttgcctgtgttgattcttctcatttcatgaaacagATTGAAGTGGGTGATGTCATAGGTGAGATCGAGACTGACAAAGCCACTCTGGAATTTGAAAGCCTTGAAGAGGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG