Sequence
atgc intronic sequence ATGC exonic sequencegtctgttttttactagcgttttcttttctctaccatgttcttgttccttctcgtctgttaccacgagctgattgattctctgtttgagcagAGTTATACACAGTACATTCCCTTGCCAATCAGTGAACTTGATTCCTGGTTGAAGACACCCTCCATCTATGTTTTCGACTGCTCTGCTGCTAGGATGATTC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G08850.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G08850.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA09G41510.1 (Glycine max), 3'ss of exon 4
-gtctgttttttactagcgttttcttttctctaccatgttcttgttccttctcgtctgttaccacgagctgattgattctctgt--------ttgagcagAGTTATACACAGTACATTCCCTTGCCAATCAGTGAACTTGATTCCTGGTTGAAGACACCCTCCATCTATGTTTTCGACTGCTCTGCTGCTAGGATGATTC
| || || | | | || | || ||| | | || | | | | || || ||| |||| ||| ||||||||||||||||| |||||||| || |||| |||||||||||||||| ||||||| || || || |||||||| || |||||||| ||| ||||||||
gatatgggttccaattgagtataattccctcatttacaatattatgatgaaaagagcttcatgacattcttattctcattctgcatcacatcttgttcagAGTTATACACAGTATATTCCCTTACCTATCAATGAACTTGATTCCTGGCTGAAGACCCCATCAATTTATGTTTTTGATTGCTCTGCGGCTGGGATGATTG
upper sequence: AT3G08850.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA18G44210.1 (Glycine max), 3'ss of exon 4
-gtctgttttttactagcgttttcttttctctaccatgttcttgttccttctcgtctgttaccacgagctgattg--attctctgtt------tgagcagAGTTATACACAGTACATTCCCTTGCCAATCAGTGAACTTGATTCCTGGTTGAAGACACCCTCCATCTATGTTTTCGACTGCTCTGCTGCTAGGATGATTC
| || || | | | || | | ||| | | | | | | || || ||| ||||| | || ||||||||||||||||| |||||||| || ||||||||||||||||||||| ||||||| || || || || || | || |||||||| ||| ||||||||
gatatgggttccaattgagtataatgccctcatttacaatatcatgatgaaaatagcttcatgacattcttattctcattcttcatcatatcatgttcagAGTTATACACAGTATATTCCCTTACCTATCAGTGAACTTGATTCCTGGCTGAAGACCCCATCAATTTACGTCATTGATTGCTCTGCGGCTGGGATGATTG
upper sequence: AT3G08850.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv08s0058g00890.t01 (Vitis vinifera), 3'ss of exon 4
gtctgttttttactagcgttttcttttctctaccatgttcttgttccttctcgtctgttaccacgagctgattgattctctgtttgagcagAGTTATACACAGTACATTCCCTTGCCAATCAGTGAACTTGATTCCTGGTTGAAGACACCCTCCATCTATGTTTTCGACTGCTCTGCTGCTAGGATGATTC
|| | || || | | || ||| | || | | | | | | | || | |||| || | | || | | |||| ||||| ||||| || |||||||||||||| || || |||||||||||||||||||| || || |||||||| || |||||||||||| ||||||||
gtattttattactttgaagttctgccgtgctattttattgatatcgcctttagatttttctcctattctgactggtg---tattggtgaagAGCTATACTCAGTATATCCCCTTGCCAATCAGCGACCTGGATTCCTGGTTGAAGACACCGTCAATATATGTTTTTGATTGCTCTGCTGCTGGGATGATTGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|116411080|gb|EG453672.1|EG453672EST: ATGGTGTGCCAAAACCTACAGCTAATGGTGAAATTTGGGTATTTAACAAG AGTTATACACAGTACATTCCCTTGCCAATCAGTGAACTTGATTCCTGGTTG
genomic: ATGGTGTGCCAAAACCTACAGCTAATGGTGAAATTTGGGTATTTAACAAGgtctgttttt ... gtttgagcagAGTTATACACAGTACATTCCCTTGCCAATCAGTGAACTTGATTCCTGGTTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttcttgttccttctcgtctgttaccacgagctgattgattctctgtttgagcagAGTTATACACAGTACATTCCCTTGCCAATCAGTGAACTTGATTCCTGGTTGAAGACACCCTCCATCTATGTTTTCGACTGCTCTGCTGCTAGGATGATTC
gattgat putative branch site (score: 4)
ttctctgttt CT-rich tract
attgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctgttttttactagcgttttcttttctctaccatgttcttgttccttctcgtctgttaccacgagctgattgattctctgtttgagcagAGTTATACACAGTACATTCCCTTGCCAATCAGTGAACTTGATTCCTGGTTGAAGACACCCTCCATCTATGTTTTCGACTGCTCTGCTGCTAGGATGATTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG