Sequence
atgc intronic sequence ATGC exonic sequencegttctgttgttactcatctgatctctcatataacaaagagtaagcttatatgtttctcataaattttgtctttctttttccttccagATTGGTGATTTGGGGTTATCGAAGGTGAAACAGAAGACTCTAGTATCAGGAGGTGTTCGTGGGACTTTGCCATGGATGGCACCTGAGCTCTTGAGTGGGA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G57610.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G57610.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA13G01190.2 (Glycine max), 3'ss of exon 8
---gttctgttgttactcatctgatctctcatata-acaaagagtaagcttatatgtttctcataaatt----ttgtctttctttttccttccagATTGGTGATTTGGGGTTATCGAAGGTGAAACAGAAGACTCTAGTATCAGGAGGTGTTCGTGGGACTTTGCCATGGATGGCACCTGAGCTCTTGAGTGGGA
| ||| | | || || | ||||| || | | | | ||| | ||| | | || ||||||||||||||||| ||||| ||||| |||||| | |||||||| || || || || || |||||||||||||||||||| |||||||| | |||||||
gtacacataagaatacatacacatacactgatgcagacaaaagccaaaagcaacctgctagcggagattgaaatgagatttgtgtaatttttcagATTGGTGATTTGGGTTTATCAAAGGTTAAACAGCACACTCTAGTGTCTGGTGGAGTACGGGGGACTTTGCCATGGATGGCTCCTGAGCTACTTAGTGGGA
upper sequence: AT5G57610.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA17G07320.1 (Glycine max), 3'ss of exon 11
gttc-tgttgttactcatctg-atct-ctcatataacaaagagtaagcttatatgtttctcataaatt----ttgtctttctttttccttccagATTGGTGATTTGGGGTTATCGAAGGTGAAACAGAAGACTCTAGTATCAGGAGGTGTTCGTGGGACTTTGCCATGGATGGCACCTGAGCTCTTGAGTGGGA
|| | | | ||| || | || | |||||| || | | | | | ||| | ||| | | || ||||||||||||||||| ||||| ||||| |||||| | |||||||| || || || || || ||||| ||||| |||||||| ||||| || | |||||||
gtacacataagaatacattcacatatactgaggcaacaaaagccaaacgcaacctgctagcggagattgaaatgagatttgtgtaatttttcagATTGGTGATTTGGGTTTATCAAAGGTTAAACAGCACACTCTAGTGTCTGGTGGAGTACGGGGGACCTTGCCTTGGATGGCTCCTGAACTTCTTAGTGGGA
upper sequence: AT5G57610.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv11s0052g01480.t01 (Vitis vinifera), 3'ss of exon 5
--------gttctgttgt-tactcatctgatctctcatataacaaagagtaagcttatatg----tttctcataaattttgtctttctttttccttccagATTGGTGATTTGGGGTTATCGAAGGTGAAACAGAAGACTCTAGTATCAGGAGGTGTTCGTGGGACTTTGCCATGGATGGCACCTGAGCTCTTGAGTGGGA
|| ||||| || | | || | | | ||| || | | ||| ||| | | | || || | | | ||| |||||||||| ||||| ||||| ||||| |||||| | || |||||||||||||||||||||| || | || ||||||||||| ||||| | |||||||
tttagcagattatgttgcatatttacttgctgtacctaatagtaatcatatatattaaatgggattggatttgggagcttatccatttcatatcttgtagATTGGTGACTTGGGTTTATCAAAGGTTAAACAGCATACGTTAGTATCAGGAGGTGTTCGTGGAACACTTCCTTGGATGGCACCAGAGCTTCTTAGTGGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acaaagagtaagcttatatgtttctcataaattttgtctttctttttccttccagATTGGTGATTTGGGGTTATCGAAGGTGAAACAGAAGACTCTAGTATCAGGAGGTGTTCGTGGGACTTTGCCATGGATGGCACCTGAGCTCTTGAGTGGGA
atataac putative branch site (score: 3)
ttttgtctttcttttt putative PPT
ttatatgtttctcata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttctgttgttactcatctgatctctcatataacaaagagtaagcttatatgtttctcataaattttgtctttctttttccttccagATTGGTGATTTGGGGTTATCGAAGGTGAAACAGAAGACTCTAGTATCAGGAGGTGTTCGTGGGACTTTGCCATGGATGGCACCTGAGCTCTTGAGTGGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA