Sequence
atgc intronic sequence ATGC exonic sequencegtaagcagagctatttactctgttctcttctctgtacttaatgtgaaagctgattatgcttttggatgatataatactacacagATTGGGTGGATTTATGGCTCGGTCACTGAGGATATCTTAACGGGTTTCAAGATGCATTGCCATGGATGGAGATCTGTATATTGTATGCCAAAGCGAGCGG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G21770.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G21770.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM5G840940_T01 (Zea mays), 3'ss of exon 3
------------------------------------------------gtaagcagagctattta--ctctgttctcttctctgtacttaatgtgaaagctg--------------attatgcttttggatgat---ataatactacacagATTGGGTGGATTTATGGCTCGGTCACTGAGGATATCTTAACGGGTTTCAAGATGCATTGCCATGGATGGAGATCTGTATATTGTATGCCAAAGCGAGCGG
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gtaactttggcccatcatgtctttgtttttccttctcccatgtagtttccagatcaggctcttcaaactgtgtttgtgcccttgaaataaattgaaaaactgcaacctagcatccaagaatacttttagctaactcgatgaaaatatctagGTTGGTTGGATTTATGGATCTGTCACTGAGGATATCCTCACGGGCTTCAAGATGCACTGCCATGGTTGGCGATCTGTGTACTGCATGCCCAAGAGACCAG
upper sequence: AT2G21770.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA08G15380.1 (Glycine max), 3'ss of exon 12
---------gta-agcagagctatttactctgttctcttctc--------tgtacttaatgtgaaagctgatta--tgcttttggat-gatataatactacacagATTGGGTGGATTTATGGCTCGGTCACTGAGGATATCTTAACGGGTTTCAAGATGCATTGCCATGGATGGAGATCTGTATATTGTATGCCAAAGCGAGCGG
|| | | | | ||| | |||| || | | || | | | | | | | |||| | | | | | ||| ||| |||||||||| ||||| || || || ||||||||||| || || || || |||||||||||||| ||| | ||||| ||||| || || ||||| | |
gtaagtatcatagaaaaaaattgttttgttaattctttttgaaaaattagtcttctcattcttatatttattctcttgctcataaaccgttggcgttttac-cagGTTGGGTGGATATATGGTTCTGTGACAGAGGATATCTTGACTGGATTTAAAATGCATTGCCATGGTTGGCGGTCTGTGTATTGCATTCCTAAGCGGCCTG
upper sequence: AT2G21770.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA05G32100.1 (Glycine max), 3'ss of exon 12
-----------gtaagcagagctatttactctgttctcttctc--------tgtacttaatgtgaaa--gctgattatgcttttggatgatataatactacacagATTGGGTGGATTTATGGCTCGGTCACTGAGGATATCTTAACGGGTTTCAAGATGCATTGCCATGGATGGAGATCTGTATATTGTATGCCAAAGCGAGCGG
|| | | | ||| | |||| || | | || | | | | | || | |||| | | | | |||| ||| |||||||||| ||||| || || || ||||||||||| || || || || |||||||||||||| ||| | ||||| ||||| || || ||||| | |
gtaagtatcatagaaagaaatttgttttgtaaattctttttgaaaaattagtcttctcattcttatatttcttctcttgctcataatcgttggcttgctac-cagGTTGGGTGGATATATGGTTCTGTGACAGAGGATATCTTGACTGGATTTAAAATGCATTGCCATGGTTGGCGGTCTGTGTATTGCATTCCTAAGCGGCCTG
upper sequence: AT2G21770.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv07s0031g02060.t01 (Vitis vinifera), 3'ss of exon 12
------------gtaagcagagctatttactctgttctcttctctgtacttaatgtgaaagctgattatgcttttggatgatataatactacac-agATTGGGTGGATTTATGGCTCGGTCACTGAGGATATCTTAACGGGTTTCAAGATGCATTGCCATGGATGGAGATCTGTATATTGTATGCCAAAGCGAGCGG
| || || | | | | ||| || | || | | || | || | || | || ||| || || |||| ||||| |||||||| || || |||||||| |||| || ||||||||||| |||||||||||| | ||||| || || || || ||||| | |
gtaaggagaaaaaaattcaaagttctgaaaacc-ttccattagcaagttctaccattatcacttcattcctttctaaattttcaaacactgaaccagGTTGGCTGGATATATGGCTCTGTGACAGAGGATATACTAACAGGGTTCAAGATGCACTGCCATGGATGGCGGTCTGTTTACTGCATACCCAAGCGGCCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctctgtacttaatgtgaaagctgattatgcttttggatgatataatactacacagATTGGGTGGATTTATGGCTCGGTCACTGAGGATATCTTAACGGGTTTCAAGATGCATTGCCATGGATGGAGATCTGTATATTGTATGCCAAAGCGAGCGG
agctgat putative branch site (score: 4)
atgatataatacta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcagagctatttactctgttctcttctctgtacttaatgtgaaagctgattatgcttttggatgatataatactacacagATTGGGTGGATTTATGGCTCGGTCACTGAGGATATCTTAACGGGTTTCAAGATGCATTGCCATGGATGGAGATCTGTATATTGTATGCCAAAGCGAGCGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC