Sequence
atgc intronic sequence ATGC exonic sequencegtctaaatctctatttcaagccttactaatatactcttctatgtatttacttaatccaattttggtctctaaacattttctgctttttaaactcgatgcttaaacagTTTATCGTGGTTTCGCTGAAAGAAGGAATGTTCAACAATGCCAATGTTCTTTTCCGGACAAAGTTCGTTGATGGAGTTTCAACAGTCCAAAGGACAGTAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G62410.1 |
intron # | 19 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G62410.1 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: GLYMA12G36520.1 (Glycine max), 3'ss of exon 20
----------------------------------------------------------gtctaaatct-ctat--ttcaagccttactaatatac--tcttctatgtatttacttaatccaattttggtctctaaacatt------ttctgctttttaaactcgatgcttaaacagTTTATCGTGGTTTCGCTGAAAGAAGGAATGTTCAACAATGCCAATGTTCTTTTCCGGACAAAGTTCGTTGATGGAGTTTCAACAGTCCAAAGGACAGTAA
| | ||| |||| || || | | || | || | ||| | || | || || || | | | | || || || || | | |||||||| |||||||| |||| ||||| |||||||| ||||| |||||||||||||||||||| || || ||||| |||||||| || || | || ||
gtagaggataattgttgatgttgtcgtgtgatttttttggtttcttgtatacttctccttttggttctgctattgttaaattcattctgacatgtcattttcaaagttcctgctagtgacagttcagcatccaataagttgaataacctcatttctttggttcttttgatttgcagTTTATTGTGGTTTCCTTGAAGGAAGGCATGTTCAATAATGCAAATGTTCTTTTCCGGACAAAATTTGTGGATGGTGTTTCAACTGTTCAGCGAACTGTTG
upper sequence: AT5G62410.1 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: GLYMA13G27210.1 (Glycine max), 3'ss of exon 20
gtctaaatctctatttcaagccttactaatatactcttctatgtatttacttaatccaattttggtctctaaacattttctgctttttaaactcgatgcttaaacagTTTATCGTGGTTTCGCTGAAAGAAGGAATGTTCAACAATGCCAATGTTCTTTTCCGGACAAAGTTCGTTGATGGAGTTTCAACAGTCCAAAGGACAGTAA
| | | | || | | | | ||| | | | || || || | | | | | || | | || || |||||||| |||||||| |||| ||||| |||||||| ||||| |||||||||||||||||||| || || ||||| |||||||| || || | || ||
-----tgtttggcgtatacttctctttgagtttattttcaaaattcctgctagcgacagttcagcacccaataagttgaataacctcatttcttttgatttg--cagTTTATTGTGGTTTCCTTGAAGGAAGGCATGTTCAATAATGCAAATGTTCTTTTCCGGACAAAATTTGTGGATGGTGTTTCAACTGTTCAGCGAACTGTTG
upper sequence: AT5G62410.1 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: Vv16s0022g00060.t01 (Vitis vinifera), 3'ss of exon 19
gtctaaatctctatttcaagccttactaatatactcttctatgtatttacttaatccaattttg--gtctctaaacattttctgctttttaaactcgatgcttaaacagTTTATCGTGGTTTCGCTGAAAGAAGGAATGTTCAACAATGCCAATGTTCTTTTCCGGACAAAGTTCGTTGATGGAGTTTCAACAGTCCAAAGGACAGTAA
||| | | ||||| | | | | || |||| || || ||| |||||| || || || |||| || | | | | ||||| || |||||||| || |||||||| |||||||| |||||||||||||||||||||||||| || || ||||| ||||| ||||| || || || ||
------atcaggaat-caagcagttggcagacaagatttcatgttctt--tttatcaaattttcatgtatccaatgggtttccttttcgtttgttttcttgtctttcagTTCATTGTGGTTTCTCTTAAAGAAGGCATGTTCAATAATGCCAATGTTCTTTTCCGGACAAAATTTGTGGATGGTGTTTCCACAGTTCAGAGAACTGTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatccaattttggtctctaaacattttctgctttttaaactcgatgcttaaacagTTTATCGTGGTTTCGCTGAAAGAAGGAATGTTCAACAATGCCAATGTTCTTTTCCGGACAAAGTTCGTTGATGGAGTTTCAACAGTCCAAAGGACAGTAA
ctctaaa putative branch site (score: 3)
taaacatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctaaatctctatttcaagccttactaatatactcttctatgtatttacttaatccaattttggtctctaaacattttctgctttttaaactcgatgcttaaacagTTTATCGTGGTTTCGCTGAAAGAAGGAATGTTCAACAATGCCAATGTTCTTTTCCGGACAAAGTTCGTTGATGGAGTTTCAACAGTCCAAAGGACAGTAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA