Sequence
atgc intronic sequence ATGC exonic sequence...tgagataatatagtcacccagtatctttctcgctgatagcagcacagttgtggtggtacatgttggtttcattgttttctgaccaacaaatttgtttcagGGTCGTAGTAACCCTCAGCGATTTTTTCCACCAAAACCCGATGATGTTGCAACCATATGCTATACAAGCGGAACAACTGGGACACCCAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G05970.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G05970.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA20G28200.1 (Glycine max), 3'ss of exon 9
--tgagataatatagtcacccagtatctt-tctcgctg-atagcagcacagttgtggtggtacatgttggtttcattgttttctgaccaacaaatttgtttcagGGTCGTAGTAACCCTCAGCGATTTTTTCCACCAAAACCCGATGATGTTGCAACCATATGCTATACAAGCGGAACAACTGGGACACCCAAG
| || | || ||| ||| | ||| ||| | | | | || | ||||| || | | || | || |||| | |||| ||||| |||| ||||| |||| |||||||||||| ||||| |||||||||| ||||| ||||| || |||||||| || || ||
tatcagttt-taagttcattttgtaaatggtcttgctatggatttgatctgctgctatttattatgtttattacctcattgtttgtgtggt---tttgacttagGGACGTAGCAACCTTCAGCCCTTTTGTCCACCAAAACCTGATGACATTGCAACCATTTGCTACACAAGTGGTACAACTGGAACCCCAAAA
upper sequence: AT3G05970.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA10G39540.1 (Glycine max), 3'ss of exon 9
--tgagataatatagtcacccagtatctttctcgctgatagcagcacagttgtggtggtacatgttggtttcattgttttctgaccaaca-aatttgtttcagGGTCGTAGTAACCCTCAGCGATTTTTTCCACCAAAACCCGATGATGTTGCAACCATATGCTATACAAGCGGAACAACTGGGACACCCAAG
| | || ||| ||| | | || || | || || || | || || || | | || | ||| | |||| || || |||| ||||| || | |||||||||||| ||||| |||||||||| ||||||||||| || |||||||| || || ||
gtataagttttaagttcattttgtaaatggt--gttgctattgatttgatc-tgctgctatttcttatgtttgttagctcattacttgcgtggttttgattagGGACGCAGCAACCTTCAGCTCTTCTGTCCACCAAAACCTGATGACATTGCAACCATTTGCTATACAAGTGGTACAACTGGAACCCCAAAA
upper sequence: AT3G05970.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv05s0020g03080.t01 (Vitis vinifera), 3'ss of exon 9
tgagataatatagtcacccagtatctttctcgctgatagcagcacagttgtggtggtacatgttggtttcattgttttctgacca-acaa--atttgtttcagGGTCGTAGTAACCCTCAGCGATTTTTTCCACCAAAACCCGATGATGTTGCAACCATATGCTATACAAGCGGAACAACTGGGACACCCAAG
|| | | | | | ||| | | | | | | || | | | || |||| || | |||| || ||| ||||||| ||| || || | |||| || ||||| || ||||||||||||||||| ||||||||||| || |||||||||||||| |||
---tattgcaaatcctttttttttttttttaattataaattaaattaaattattttctcacagtaatctaatggtttccttattttacaatggttccttttagGGTCGCAGTCGTCCCCAACCTTTTTGCCCCCCAAAGCCTGATGATGTTGCAACCATTTGCTATACAAGTGGTACAACTGGGACACCTAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agttgtggtggtacatgttggtttcattgttttctgaccaacaaatttgtttcagGGTCGTAGTAACCCTCAGCGATTTTTTCCACCAAAACCCGATGATGTTGCAACCATATGCTATACAAGCGGAACAACTGGGACACCCAAG
ttctgac putative branch site (score: 2)
tttgtttc putative PPT
aaatttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgagataatatagtcacccagtatctttctcgctgatagcagcacagttgtggtggtacatgttggtttcattgttttctgaccaacaaatttgtttcagGGTCGTAGTAACCCTCAGCGATTTTTTCCACCAAAACCCGATGATGTTGCAACCATATGCTATACAAGCGGAACAACTGGGACACCCAAG
- - - - - - - cacccag
- - - - - - - - - - - - - - - - - - - -cagcaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccaacaa