Sequence
atgc intronic sequence ATGC exonic sequencegttagccctctgagctatcgattcgtcatttcttcttttatcattctgctttgtagcaacttttctaagcgaatgctctgcttttgtagGAAAATAGTTTTGGCTACAAACATTGCCGAGAGTAGTATTACAATTGATGATGTTGTATATGTTGTGGATTGTGGTAAAGCAAAGGAAACTAGCTATGAT
Basic information
species | Arabidopsis thaliana |
transcript | AT2G35920.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G35920.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os10g33275.2 (Oryza sativa), 3'ss of exon 10
gttagccctctgagctatcgattcgtcatttcttcttttatcattctgctttgt---agcaacttttctaagcgaatgct-ctgc-------ttttgtagGAAAATAGTTTTGGCTACAAACATTGCCGAGAGTAGTATTACAATTGATGATGTTGTATATGTTGTGGATTGTGGTAAAGCAAAGGAAACTAGCTATGAT
| | | | | | | | | | |||| | | || || ||| | | |||| | | | | |||| ||| |||| |||||||| |||||||| ||||| ||||| || || ||||||||||| ||||||||||| ||||| | |||||||| |||||||||||||| || ||||||
gctttttatgttacatttgagctagctgtgtcttaatggctaatcctattttatttgaacaacctgtattgcttattgctgttgcatatgtatttttcagGAAAATTGTTTTGGCAACAAATATTGCAGAAAGCAGTATTACAATAGATGATGTTGTCTATGTAATTGATTGTGGCAAAGCAAAGGAAACAAGTTATGAT
upper sequence: AT2G35920.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G399212_T01 (Zea mays), 3'ss of exon 12
-------------gttagccctctgagctatcgattcgtcatttcttcttttatcattctgctttgtagcaacttttctaagcgaatgctctgcttttgtagGAAAATAGTTTTGGCTACAAACATTGCCGAGAGTAGTATTACAATTGATGATGTTGTATATGTTGTGGATTGTGGTAAAGCAAAGGAAACTAGCTATGAT
|||| | | | | || | || ||| || | |||| | | | | | | || | | || || || ||||| |||||||| || |||||||| ||||||||||| || || ||||||||||| ||||| | ||||||||||| || ||||| || |||||||||
ctctttataaatggttaacaattcctttcag-atcttatcgagaaattttagatccttttacttt-tcttattgtctattaacggtttgtttgtaatttcagAAAAATTGTTTTGGCAACCAACATTGCGGAGAGTAGTATCACTATAGATGATGTTGTCTATGTGATTGATTGTGGTAAGGCCAAGGAGACAAGCTATGAT
upper sequence: AT2G35920.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G119671_T01 (Zea mays), 3'ss of exon 3
-------------gttagccctctgagctatcgattcgtcatttcttcttttatcattctgctttgtagcaacttttctaagcgaatgctctgcttttgtagGAAAATAGTTTTGGCTACAAACATTGCCGAGAGTAGTATTACAATTGATGATGTTGTATATGTTGTGGATTGTGGTAAAGCAAAGGAAACTAGCTATGAT
|||| | | | | || | | || ||| || | |||| | | | | | | || | | || || || ||||| |||||||| || |||||||| ||||||||||| || || ||||||||||| ||||| | |||||||
ctctttataaatggttaacaattcctttcag-atcttatcgagtaattttagatccttttacttt-tcttattgtctattaacggtttgtttgtaatttcagAAAAATTGTTTTGGCAACCAACATTGCGGAGAGTAGTATCACTATAGATGATGTTGTCTATGTGATTGATTGTG--------------------------
upper sequence: AT2G35920.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G052798_T01 (Zea mays), 3'ss of exon 4
------------gttagccctct--gagctatcgattcgtcatttcttcttttatcattctgctttgtagc----aacttttctaagcg------aatgctctgctt-----ttgtagGAAAATAGTTTTGGCTACAAACATTGCCGAGAGTAGTATTACAATTGATGATGTTGTATATGTTGTGGATTGTGGTAAAGCAAAGGAAACTAGCTATGAT
|||| || | | | | || |||| | |||||| ||| | | |||||||| | | || | || || || ||||| |||||||| || |||||| | ||||||||||| || || ||||||||||| ||||| | ||||||||||| ||
gtttgaactaattgtagctctttataaatggttaacaattcctttcagatcttatcaagtaattttagatccttttacttttcttattgtctattaacagTTTGTTTGTAATTTCAGAAAAAATTGTTTTGGCAACCAACATTACGGAGAGTAGTATCACTATAGATGATGTTGTCTATGTGATTGATTGTGGTAAGGCC------------------
upper sequence: AT2G35920.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv08s0032g01230.t01 (Vitis vinifera), 3'ss of exon 10
gttagc-cctctgagctatcgattcgtcatttcttcttttatcattctgctttgtagcaacttt----tctaagcgaatgctctgcttttgtagGAAAATAGTTTTGGCTACAAACATTGCCGAGAGTAGTATTACAATTGATGATGTTGTATATGTTGTGGATTGTGGTAAAGCAAAGGAAACTAGCTATGAT
| ||| | | | ||| | | || | | | || |||| | | ||| ||||| | | || |||||||||||| || | || ||||||||||| ||||||||||| || || |||||||||||||| || | || ||||| || ||||||||||| || || |||
gcaagcatccttcatctactaagccttctatctattagtgatgcatctgaaacagattatttttcaattctaaattgctttgcatctattgtagGAAAATTGTGCTAGCCACAAACATTGCAGAGAGTAGTATCACCATAGATGATGTTGTATACGTCATAGACTGTGGAAAGGCAAAGGAAACAAGTTACGAT
upper sequence: AT2G35920.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: PP1S36_206V6.1 (Physcomitrella patens), 3'ss of exon 11
gttagccctctgagct---atcgattcgtcatttcttcttttatcattctgctttgt-agcaactttt----ctaa-gcgaatgctctgctt--ttgtagGAAAATAGTTTTGGCTACAAACATTGCCGAGAGTAGTATTACAATTGATGATGTTGTATATGTTGTGGATTGTGGTAAAGCAAAGGAAACTAGCTATGAT
|| | ||| | || | | || || | | || || | | | | |||| | | ||| || || || | | |||||||||||| || |||| || ||||| ||||||| ||||||||| || |||||||| || || || | |||||||| || |||||||| || ||||||||
tttctctagttgaacactaataaaacggacagtttctatgctagtatacagggatatcagcagagtctaatgctagtgctgttgaccttcctggttgtagGAAAATTGTGCTGGCCACCAACATAGCCGAGACTAGTATTACGATCGATGATGTAGTCTACGTGATTGATTGTGGGAAGGCAAAGGAGACAAGCTATGAC
upper sequence: AT2G35920.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: EFJ25900 (Selaginella moellendorffii), 3'ss of exon 7
gttagccctctgagctatcgattcgtcatttcttcttttatcattctgctttgtagcaacttttctaag--cgaatgctctgcttt---tgtagGAAAATAGTTTTGGCTACAAACATTGCCGAGAGTAGTATTACAATTGATGATGTTGTATATGTTGTGGATTGTGGTAAAGCAAAGGAAACTAGCTATGAT
| ||||| | || | | | || |||||||| || || ||||| || || || || || ||||| || | ||| || || |||||||| ||||| |||||| | || ||||| ||||| ||||||||||||||||||
------------------------------------------gtaatgcttccggctgatcgttttgatttctaactttctgctttcaatgcagAAAAATTGTCTTAGCGACGAATATTGCAGAAACTAGCATAACTATTGATGACGTTGTGTATGTTATCGACTGTGGGAAAGCTAAGGAAACTAGCTATGAT
upper sequence: AT2G35920.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: EFJ10915 (Selaginella moellendorffii), 3'ss of exon 10
gttagccctctgagctatcgattcgtcatttcttcttttatcattctgctttgtagcaacttttctaagcgaatgctctgcttttgtagGAAAATAGTTTTGGCTACAAACATTGCCGAGAGTAGTATTACAATTGATGATGTTGTATATGTTGTGGATTGTGGTAAAGCAAAGGAAACTAGCTATGAT
| || ||| | | | ||||||| |||| | || || ||||| || || || || || ||||| || | ||| || || |||||||| ||||| |||||| | || ||||| ||||| ||||||||||||||||||
------------------------------------gtaatgcttccggccgatcgtttgatttctaactttctgcttt--caatgcagAAAAATTGTCTTAGCGACGAATATTGCAGAAACTAGCATAACTATTGATGACGTTGTGTATGTTATCGACTGTGGGAAAGCTAAGGAAACTAGCTATGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttttatcattctgctttgtagcaacttttctaagcgaatgctctgcttttgtagGAAAATAGTTTTGGCTACAAACATTGCCGAGAGTAGTATTACAATTGATGATGTTGTATATGTTGTGGATTGTGGTAAAGCAAAGGAAACTAGCTATGAT
ctctgctttt CT-rich tract
ttttctaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagccctctgagctatcgattcgtcatttcttcttttatcattctgctttgtagcaacttttctaagcgaatgctctgcttttgtagGAAAATAGTTTTGGCTACAAACATTGCCGAGAGTAGTATTACAATTGATGATGTTGTATATGTTGTGGATTGTGGTAAAGCAAAGGAAACTAGCTATGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA