Sequence
atgc intronic sequence ATGC exonic sequencegtgagtgtctttatccattctaaggactaatcatactggtcttaaaaatcgttctcaaagaaacagtaacaaccatacctttctattttttcagGTGATTGCAGCTACTAACCGTGCAGATATTCTGGACCCAGCACTCATGCGTTCTGGTCGATTAGACAGAAAGATTGAGTTCCCACACCCAACCGAAGAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G05530.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G05530.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA03G39500.1 (Glycine max), 3'ss of exon 7
gtgagtgtctttatccattctaaggact---aatcatactggtcttaaaaatcgttctcaaagaaacagtaacaaccatacctttctattt---tttcagGTGATTGCAGCTACTAACCGTGCAGATATTCTGGACCCAGCACTCATGCGTTCTGGTCGATTAGACAGAAAGATTGAGTTCCCACACCCAACCGAAGAAG
| | || ||| | ||| || | | | || | ||| || | | || | || | | || |||||||||||||| || |||||||| || ||||| || || || || ||||||||||||||||| || |||| |||||||||||||||||||| |||||||
ctcaaaacaaacatacatgatgttgacacaaaaatgtgttagatttttattcagttagaaattaggtgattgaaatgccattttcacttgtaaattacagGTGATTGCAGCAACAAACCGTGCTGACATTCTTGATCCTGCCCTTATGCGTTCTGGTCGATTGGATCGAAAAATTGAGTTCCCACACCCAACTGAAGAAG
upper sequence: AT3G05530.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA20G38030.1 (Glycine max), 3'ss of exon 7
gtgagtgtctttatccattctaaggactaatcatactggtcttaaaaatcgttctcaaagaaacagt--aacaaccatacctttctatttttt-------cagGTGATTGCAGCTACTAACCGTGCAGATATTCTGGACCCAGCACTCATGCGTTCTGGTCGATTAGACAGAAAGATTGAGTTCCCACACCCAACCGAAGAAG
||| | |||| || | || || ||||| || ||| | | || || |||| | |||| || |||||||| ||||| || ||||||||||||||||| ||||| || || |||||||||||||||||||| | || |||||||| |||||||||| |||||||
gtggctagatttagaagtt---ggcaccaaattaactggatttttgttcagttaggctataggttgttgaagtgccattttcatttattcttgtaaattgcagGTGATAGCAGCAACAAACCGTGCAGATATTCTTGACCCTGCCCTTATGCGTTCTGGTCGATTAGATCGTAAAATTGAGTTTCCACACCCAAGTGAAGAAG
upper sequence: AT3G05530.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA10G29250.1 (Glycine max), 3'ss of exon 7
-----gtgagtgtctttatccattctaaggactaatcatactggtcttaaaaatcgttctcaaagaaacagtaacaaccatacctttctatt--ttttcagGTGATTGCAGCTACTAACCGTGCAGATATTCTGGACCCAGCACTCATGCGTTCTGGTCGATTAGACAGAAAGATTGAGTTCCCACACCCAACCGAAGAAG
|| || | | | | | | | | | | || | ||| | ||| || | | | ||||| | || |||||||| ||||| |||||||||||||||||||| || || || || |||||||||||||| || || | || |||||||| |||||||||| |||||||
tagatttgtaagttggcaccaaattaactggatttttgttc-agttaggctataggttattgaagtgccatttttttcattttttttcttgtaaattgcagGTGATAGCAGCAACTAACCGTGCAGATATTCTTGATCCTGCCCTGATGCGTTCTGGTCGTTTGGATCGTAAAATTGAGTTTCCACACCCAAGTGAAGAAG
upper sequence: AT3G05530.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 7
---gtgagtgtctttatccattctaaggactaatcatactggtcttaaaaatcgtt---ctcaaagaaacagtaacaaccatacctttctattttttcagGTGATTGCAGCTACTAACCGTGCAGATATTCTGGACCCAGCACTCATGCGTTCTGGTCGATTAGACAGAAAGATTGAGTTCCCACACCCAACCGAAGAAG
| || | ||| |||| || || | || | ||| || | | | | || | | | ||||||| ||||| || ||||| || |||||||||||||| ||||| ||||| ||||||||||| || | || |||||||| ||||| || || |||||||
gcagctagaatgcctatgtattcagttacaatattttattcccttttaggatcaagaaattctcctatctaatgtttattctatttatggtaacatgtagGTGATAGCAGCAACAAACCGAGCTGATATTCTGGACCCTGCACTTATGCGATCTGGTCGATTGGATCGTAAAATTGAGTTTCCACATCCCACTGAAGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttaaaaatcgttctcaaagaaacagtaacaaccatacctttctattttttcagGTGATTGCAGCTACTAACCGTGCAGATATTCTGGACCCAGCACTCATGCGTTCTGGTCGATTAGACAGAAAGATTGAGTTCCCACACCCAACCGAAGAAG
cagtaac putative branch site (score: 2)
tacctttctatttttt putative PPT
tttctattttttca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtgtctttatccattctaaggactaatcatactggtcttaaaaatcgttctcaaagaaacagtaacaaccatacctttctattttttcagGTGATTGCAGCTACTAACCGTGCAGATATTCTGGACCCAGCACTCATGCGTTCTGGTCGATTAGACAGAAAGATTGAGTTCCCACACCCAACCGAAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG