Sequence
atgc intronic sequence ATGC exonic sequencegtacgatactcttgtgtttaaagatgaatgcttgcatgtcacaacggaaaaggttaaatcatattgaaaatttctgcagGTACCGAAATTATCCACCTGAGCAGCTTGTGGATATAGTTGCAAGGATTCTCTCCATGGTACCTCCATGGACACGTGTATATAGAGTTCAGCGTGATATT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G50320.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G50320.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os04g40840.1 (Oryza sativa), 3'ss of exon 5
-------------------------------gtacgatactcttgtgtttaaagatgaatgcttgcatgtcacaac------ggaaaaggttaaatcatattgaaaatttctg-----cagGTACCGAAATTATCCACCTGAGCAGCTTGTGGATATAGTTGCAAGGATTCTCTCCATGGTACCTCCATGGACACGTGTATATAGAGTTCAGCGTGATATT
| | || ||||||||| | | || || ||| | ||| | | | ||| | | | || || ||| |||||||| ||||||||||| | || |||||||| |||||||| ||||| ||||||||||| || |||||||| || || | || || | |||||
gtacttattttatctagcacttgatattctagattgctagtcttgtgttcactgttg--tgtttgttctctagaactttttagtgagaacttaggccctgccaatgtttgttgtgtttcagATACCGAAACTATCCACCTGAACTTCTGGTGGATATTGTTGCAAGAATTCTATCCATGGTACCACCTTGGACACGAGTTTACCGTGTACAAAGAGATATC
upper sequence: AT5G50320.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G100872_T01 (Zea mays), 3'ss of exon 5
-------------------------------------------------------------------------gtacgatactcttgtgtttaaagatgaatgcttgcatgtcacaacggaaaaggttaaatcatattgaaaatttctgcagGTACCGAAATTATCCACCTGAGCAGCTTGTGGATATAGTTGCAAGGATTCTCTCCATGGTACCTCCATGGACACGTGTATATAGAGTTCAGCGTGATATT
||| || ||| ||| ||| || | ||| | || || | ||| | | || | |||||| || |||||||||||||||||| | |||||||| || ||||| ||||| || ||||| || ||||||||||| || ||| | || ||| | ||||||
gtacttctctaatctagtatcattcagtgtcttgaatcttataaacattcctgtggttatttctaattttacagtaaga-acttctgtacttat-gacaagggctcataaatccagggttaacccggtaacttttgctg-----tgctgcagATATAGAAATTATCCACCTGAGCTCTTGGTGGATATCGTGGCAAGAATTCTGTCTATGGTTCCACCATGGACACGAGTGTATCGGGTCCAGAGAGATATT
upper sequence: AT5G50320.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G359735_T01 (Zea mays), 3'ss of exon 5
-----------gtacgat--actcttgtgtttaaagatgaatgcttgcatgtcacaacgg---aaaaggttaaatcatattg---aaaatttct---gcagGTACCGAAATTATCCACCTGAGCAGCTTGTGGATATAGTTGCAAGGATTCTCTCCATGGTACCTCCATGGACACGTGTATATAGAGTTCAGCGTGATATT
|| | | | | ||| ||| ||| | | | |||| || | ||| | || || |||||| |||| || |||||||||||||||||| | | |||||||| || ||||| ||||| || ||||||| || |||||||| || ||| | || ||| | ||||||
ataaaccaacagttcagtttggtttccggttaaaaaatgttcaaccgta-atgacaagggctcacaagtccaggatttacccagtaagatttctgctgcagATATAGAAATTATCCACCTGAGCTGTTGGTGGATATTGTGGCAAGAATTCTGTCTTTGGTACCACCTTGGACACGAGTGTATCGGGTCCAGAGAGATATT
upper sequence: AT5G50320.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA04G36790.1 (Glycine max), 3'ss of exon 5
----------------------------------------------------gtacgatactcttgtgtttaaagatgaatgcttgcatgtcacaacggaaaaggttaaatcatattgaaaatttctgcagGTACCGAAATTATCCACCTGAGCAGCTTGTGGATATAGTTGCAAGGATTCTCTCCATGGTACCTCCATGGACACGTGTATATAGAGTTCAGCGTGATATT
| | || |||| | | | | | || ||| | | || | || ||||| |||| |||||||||||||| |||||||| || | |||||||| || | |||||||| |||||||||||||| |||||||||||||| ||||||
gtatatatcaaatgttttcttattattggactgctttttcctcaaacatctcaattttcatcttagtatttattagttttttttaatgtcctgtagaaattaaaaaaaaaaattcattaatgtaattgtagGTATAGAAACTATCCACCTGAGCAACTTGTGGACATTATAGCAAGGATCCTTGCAATGGTACCCCCATGGACACGTGTTTATAGAGTTCAGCGGGATATT
upper sequence: AT5G50320.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA06G18150.1 (Glycine max), 3'ss of exon 5
----------------------------------------------gtacgatactcttgtgtttaaagatgaatgcttgcatgtcacaacggaaaaggttaaatcatattgaaaatttctgcagGTACCGAAATTATCCACCTGAGCAGCTTGTGGATATAGTTGCAAGGATTCTCTCCATGGTACCTCCATGGACACGTGTATATAGAGTTCAGCGTGATATT
| || || | | || || | | || | | | | || || ||| | ||| || || || ||||| |||| |||||||| ||||| |||||||| || | |||||||| || | |||||||| |||||||||||||| |||||||||||||| ||||||
gtatatatcaattttttttaatattggactgctttttcctcaaacttctcaattttcatcttagtatttattagtttttttaaatggtc-tgtagaaagtaaaaaaacatt-aatataattgtagGTATAGAAACTATCCACCAGAGCAACTTGTGGACATTATAGCAAGGATCCTTGCAATGGTACCCCCATGGACACGTGTTTATAGAGTTCAGCGGGATATT
upper sequence: AT5G50320.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv17s0000g10190.t01 (Vitis vinifera), 3'ss of exon 5
gtacgatactcttg-tgtttaa-agatgaatgcttgcatgtcacaacggaaaaggttaaatcatattgaaaattt--ctgcagGTACCGAAATTATCCACCTGAGCAGCTTGTGGATATAGTTGCAAGGATTCTCTCCATGGTACCTCCATGGACACGTGTATATAGAGTTCAGCGTGATATT
||| || || |||| || | |||||| | ||| | |||| ||| | || | | |||||||| | ||||| ||||||||||| ||||| || || || ||||| ||||| |||||||||| || ||||| ||||| |||||||||||| | ||||||
gtaaaatgtcattcctgttcaataagctggcaactgcatggctcaatgagaaagcaataattacatccatgtcctgtttgcagGTATAGGAATTACCCACCTGAGCAACTTGTAGACATTGTAGCAAGAATTCTAGCCATGGTACCCCCTTGGACTCGTGTTTATAGAGTTCAGAGGGATATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgaatgcttgcatgtcacaacggaaaaggttaaatcatattgaaaatttctgcagGTACCGAAATTATCCACCTGAGCAGCTTGTGGATATAGTTGCAAGGATTCTCTCCATGGTACCTCCATGGACACGTGTATATAGAGTTCAGCGTGATATT
tttctgc CT-rich tract
ttaaatcatattgaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgatactcttgtgtttaaagatgaatgcttgcatgtcacaacggaaaaggttaaatcatattgaaaatttctgcagGTACCGAAATTATCCACCTGAGCAGCTTGTGGATATAGTTGCAAGGATTCTCTCCATGGTACCTCCATGGACACGTGTATATAGAGTTCAGCGTGATATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA