Sequence
atgc intronic sequence ATGC exonic sequencegtaagaaaactatcctgaccagcttacttaattaatatctttggtgaatattttcattaactgcattaatgtttcttctagGTATGTTGAAAAAACTGGTCAAAGAGCTGTCTACACGACTGGAAAGGGAGCTTCTGCTGTTGGTCTAACCGCAGCAGTACACAAAGATCCAGTTACAAGG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G44900.2 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G44900.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os11g29380.1 (Oryza sativa), 3'ss of exon 10
------gtaagaaaactatcctgaccagcttactta--attaatatctttggtgaatattt--tcattaactgcattaatg---tttcttctagGTATGTTGAAAAAACTGGTCAAAGAGCTGTCTACACGACTGGAAAGGGAGCTTCTGCTGTTGGTCTAACCGCAGCAGTACACAAAGATCCAGTTACAAGG
|| || | | | || || ||| ||| | || | ||||||| | || | ||||| | | || |||||||||||| |||||||| || ||||| || ||||| |||||||| ||||||||||||||||| || ||||||||||| ||||| |||||||| ||| ||
gtaaggaataggcaatcagtttcatcatctctctttttattgctccattaactcaatatttcattatctaaaaaattaactcactgttttgtagGTATGTTGAGAAAACTGGACACAGAGCAGTGTACACAACTGGAAAAGGAGCTTCTGCTGTTGGACTCACCGCAGCAGTTCACAAGGATCCAGTAACACGG
upper sequence: AT1G44900.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G139894_T02 (Zea mays), 3'ss of exon 10
gtaagaaaactatcctgaccagcttacttaattaatatctttggtgaatattttcattaactgcattaatgtttcttctagGTATGTTGAAAAAACTGGTCAAAGAGCTGTCTACACGACTGGAAAGGGAGCTTCTGCTGTTGGTCTAACCGCAGCAGTACACAAAGATCCAGTTACAAGG
||||| | |||| | | | || || | || ||| | || | || | ||| |||| |||||||| || ||||| || || ||||| || || || |||||||| ||||| |||||||||||||| || || ||||| |||||||||||||| ||| |
gtaagga-------ctgattaa-tcattt--ttcagttccttga-ggatgtgccaataacttgc-------catcttgcagGTATGTGGAGAAAACAGGACACAGAGCAGTATATACAACTGGAAAAGGAGCCTCTGCTGTTGGTCTTACTGCTGCAGTTCACAAAGATCCAGTAACACGA
upper sequence: AT1G44900.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA07G36680.1 (Glycine max), 3'ss of exon 9
gtaagaaaactatcctgaccagcttacttaattaatatcttt--------ggtgaatattttcattaactgcattaa-tgtttcttctagGTATGTTGAAAAAACTGGTCAAAGAGCTGTCTACACGACTGGAAAGGGAGCTTCTGCTGTTGGTCTAACCGCAGCAGTACACAAAGATCCAGTTACAAGG
| || | || | ||| || || |||||||| | | |||| || | || | | || | | || | |||||||||||||||||||| || |||||||| ||||| ||||| || || |||||||| || ||||| || || || || || || |||||||| ||||||
---gtagaattttctcaatt---ttattttgttgatatctttatactagtgattaataaattaacaaaatatttcaaattctgctgcaagGTATGTTGAAAAAACTGGACAGAGAGCTGTATACACTACTGGTAAAGGGGCTTCTGCCGTGGGTCTTACTGCCGCGGTTCATAAGGATCCAGTCACAAGG
upper sequence: AT1G44900.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA17G03920.1 (Glycine max), 3'ss of exon 9
--------gtaagaaaactatcctg-----accagcttact--taattaatatctttggtgaatattttcattaac---tgcattaatgttt-cttctagGTATGTTGAAAAAACTGGTCAAAGAGCTGTCTACACGACTGGAAAGGGAGCTTCTGCTGTTGGTCTAACCGCAGCAGTACACAAAGATCCAGTTACAAGG
| | ||| || | | ||||| | || |||| || ||| | | |||||| | | || | | || | ||||||||||| |||||||| || |||||||| ||||| ||||| || || |||||||| || ||||| || || || || || || |||||||| ||||||
gtataattttctagattttattttgtagatatctttttactagtgatcaataaatt-aacaaatctataaattaacaaatatttcaaaatctactgcaagGTATGTTGAGAAAACTGGACAGAGAGCTGTATACACTACTGGTAAAGGGGCTTCTGCCGTGGGTCTTACAGCTGCCGTTCATAAGGATCCAGTCACAAGG
upper sequence: AT1G44900.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv01s0150g00390.t01 (Vitis vinifera), 3'ss of exon 9
gtaagaa-------aactatcctg--accagctt-acttaattaatatctttggt-gaatattttcattaactgcattaatgtttcttctagGTATGTTGAAAAAACTGGTCAAAGAGCTGTCTACACGACTGGAAAGGGAGCTTCTGCTGTTGGTCTAACCGCAGCAGTACACAAAGATCCAGTTACAAGG
|||||| || || ||| | |||| ||| || ||| | | | || | | | | | | |||| | |||||||||||||| ||||| || |||||||| || || ||||| || || ||||| ||||| ||||| || ||| |||||||||| ||||| || ||| |
gtaagaccgaccccaattaatctgtgagtggcttgactggtttgataatagcaatcggttgttaacttccaaaaaaacattttttccccaagGTATGTTGAAAAGACTGGGCAGAGAGCTGTGTATACCACTGGTAAAGGTGCTTCCGCTGTGGGTCTCACAGCATCAGTACACAAGGATCCTGTCACACGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttaattaatatctttggtgaatattttcattaactgcattaatgtttcttctagGTATGTTGAAAAAACTGGTCAAAGAGCTGTCTACACGACTGGAAAGGGAGCTTCTGCTGTTGGTCTAACCGCAGCAGTACACAAAGATCCAGTTACAAGG
tgtttcttct CT-rich tract
tgaatattttcattaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagaaaactatcctgaccagcttacttaattaatatctttggtgaatattttcattaactgcattaatgtttcttctagGTATGTTGAAAAAACTGGTCAAAGAGCTGTCTACACGACTGGAAAGGGAGCTTCTGCTGTTGGTCTAACCGCAGCAGTACACAAAGATCCAGTTACAAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT