Sequence
atgc intronic sequence ATGC exonic sequencegtatcttcctttctcagatataacatgtctacctacctatcatttaatgaatacctgttaaaagccatttgttgattcttcagagtcgtaaaacctatttgtctccttgatgaatgagcatgtgactttgctatatgcaatgcagGTATCATGTGACAAATTTTTTCGCACCTAGCAGCCGCTTTGGAACACCTGATGACCTTAAATCTTTGATAGACAAAGCTCATGAGCTAGGTCTGGTTGTT
Basic information
species | Arabidopsis thaliana |
transcript | AT2G36390.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G36390.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA19G37750.2 (Glycine max), 3'ss of exon 10
---------------gtatcttccttt-ctcagatataacatgtctacctacctatcatttaatgaatacctg------ttaaaagccat-ttgttgattcttcagagtcgtaaaacctatttgtct-ccttgatgaa-tgagcatgtgact-ttgctatatgcaatgcagGTATCATGTGACAAATTTTTTCGCACCTAGCAGCCGCTTTGGAACACCTGATGACCTTAAATCTTTGATAGACAAAGCTCATGAGCTAGGTCTGGTTGTT
||| || || | ||| | || | || | | | ||| || |||| | | || | || || | || |||| | || | | | |||||| ||| | | | ||| | | ||||||||| ||||| |||||||| || |||||||||||||| |||||||| || || || ||||| ||| ||||||||| ||| ||||| || |||||| |||||
gtaactcttctgttattatttttctctgctcccaaattgc-tgatggtttcaatgtgattcaaacaataacaggcagttttgtgtcctatatttcttgtttctcagtgcattagtgttttcctcctaactttgatggcctgattgtaaaaatattgttctgcatgatgcagGTACCATGTTACAAATTTCTTTGCACCTAGCAGCCGATTTGGAACTCCAGAGGAACTTAAGTCTCTGATAGACAGAGCCCATGAACTGGGTCTGCTTGTT
upper sequence: AT2G36390.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA03G35020.1 (Glycine max), 3'ss of exon 10
---------------gtatcttccttt-ctcagatataacatgtctacctacctatcatttaatgaatacctg------ttaaaagccat-ttgttgattcttcagagtcgtaaaacctatttgtctccttgatgaa--tgagcatgtgact-ttgctatatgcaatgcagGTATCATGTGACAAATTTTTTCGCACCTAGCAGCCGCTTTGGAACACCTGATGACCTTAAATCTTTGATAGACAAAGCTCATGAGCTAGGTCTGGTTGTT
||| || || | ||| | || | | | | ||| ||| || |||| | || || || || | || | || | || | | || | ||| || | | ||| | | ||||||||| ||||| |||||||| ||||||||||||||| | |||||||| || || || ||||| ||| ||||||||| ||| ||||| || |||||| |||||
gtaagtctgttgccaatatttttctctgctcccaaattgctgatggttccaa-tatgattcaaacaataataggcagttttgtgtgctatatttcttgtttcttagtgcattagtgttttcctcctaattttgcgggcctgattataaaaatattgttctgcatgatgcagGTACCATGTTACAAATTTCTTCGCACCTAGCAGCAGATTTGGAACTCCAGAGGAACTTAAGTCTCTGATAGACAGAGCCCATGAACTGGGTCTGCTTGTT
upper sequence: AT2G36390.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv08s0007g03750.t01 (Vitis vinifera), 3'ss of exon 10
-----------------------------------gtatcttcctttctcagatat---aacatgtctacctacctatcatttaatgaatacctgttaaa--agccatttgttgattcttcagagtcgtaaaacctatttgtctccttgatgaatgagcatgtgactttgctatatgcaatgcagGTATCATGTGACAAATTTTTTCGCACCTAGCAGCCGCTTTGGAACACCTGATGACCTTAAATCTTTGATAGACAAAGCTCATGAGCTAGGTCTGGTTGTT
|| |||| | ||| | | || ||| | | | | | | | | || | || || || || | | | || | | || | | | | | ||| | |||||| ||||| ||||| ||||| ||||| || || |||| |||||| |||||||| ||||| ||||||||||| |||||||||||||||||| || |||||
gtaattctttttccagtataaactttgatttattggtgtcttatgtgttcatgtttgtcaaaatgcttgctttcatggtttcgcctcttcttttagtagatagatcaggcattattttttttttttaattgggttttttctttacttttaactgaagattccaaattctcatttattttacacagGTACCATGTCACAAACTTTTTTGCACCCAGTAGTCGCTGTGGAACTCCTGATGATCTTAAGTCTTTGATAGATAAAGCTCATGAGCTAGGTTTGCTTGTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaacctatttgtctccttgatgaatgagcatgtgactttgctatatgcaatgcagGTATCATGTGACAAATTTTTTCGCACCTAGCAGCCGCTTTGGAACACCTGATGACCTTAAATCTTTGATAGACAAAGCTCATGAGCTAGGTCTGGTTGTT
ccttgat putative branch site (score: 5)
tatttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatcttcctttctcagatataacatgtctacctacctatcatttaatgaatacctgttaaaagccatttgttgattcttcagagtcgtaaaacctatttgtctccttgatgaatgagcatgtgactttgctatatgcaatgcagGTATCATGTGACAAATTTTTTCGCACCTAGCAGCCGCTTTGGAACACCTGATGACCTTAAATCTTTGATAGACAAAGCTCATGAGCTAGGTCTGGTTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA