Sequence
atgc intronic sequence ATGC exonic sequencegtttgttcctatctcgttttcctcaagtggacaatgaaagattacagcttaaaatttattctgttccccaagtgaaaaagggttccttagcaatcttctttgctggcagATACGAGATATTTCAGCTTATGGTGAACCTGTATACCGAGAGATTCATACAAATGCTCAGATTGCTCAGTGACAGAGCAAACGATCTGACAAATATAGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G71820.2 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G71820.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GRMZM2G070045_T01 (Zea mays), 3'ss of exon 7
gtttgttcctatctcgttttcctca--agtggacaatgaaagattacagcttaaaatttattctgttccc-caagtgaaaaagggttccttagcaatcttctttgctggcagATACGAGATATTTCAGCTTATGGTGAACCTGTATACCGAGAGATTCATACAAATGCTCAGATTGCTCAGTGACAGAGCAAACGATCTGACAAATATAGAG
| | |||| | | | | | | ||| || | | | || | | || | || | | | | | | | | | ||| ||| || || || || ||||| ||||| ||||||||||| ||||||||||| || ||||| || | |||||||| |||||||||||| | ||||||| |
----------gcagggctatccttagaactagtgatttgcagaatatttcctgatggttttcttatttttgccagcgtattaaattgtcacattccttgtttctgc--acagGTATGAAATTTTCCAGCTCATGGTAAACCTGTATACTGAGAGATTCATTCAGATGCTTCGACTTCTCAGTGATAGAGCAAACGATATTCAAAATATAAAT
upper sequence: AT1G71820.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GRMZM2G579509_T01 (Zea mays), 3'ss of exon 2
gtttgttcctatctcgttt-tcctcaagtggacaatgaaagattacagcttaaaatttattctgttccccaagtgaaaaagggttccttagcaatcttctttgctg-gcagATACGAGATATTTCAGCTTATGGTGAACCTGTATACCGAGAGATTCATACAAATGCTCAGATTGCTCAGTGACAGAGCAAACGATCTGACAAATATAGAG
|||| | | |||| | || | || ||| || || ||| | | | || || || | || ||| ||||||| || || || ||||| ||||| ||||| || || ||||||||||| || ||||| || | |||||||| |||||||||||| | ||||||| |
----------atctgggctatcctagaactagtgatttac-ataacattttctgatggtttccttatctttgccaacgtgttaaatattcacattccttatttctgcgcagATATGAAATTTTCCAGCTCATGGTAAACCTATACACTGAGAGATTCATTCAGATGCTTCGACTTCTCAGTGATAGAGCAAACGATATTCAAAATATAAAC
upper sequence: AT1G71820.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA03G03120.1 (Glycine max), 3'ss of exon 13
------------------------------------------------------------------gtttgttcctatctcgttttcctcaagtggacaatgaaagattacagctta--aaatttattctgttccccaagtgaaaaagggttcctta-gca---atcttctttg--------ctggcagATACGAGATATTTCAGCTTATGGTGAACCTGTATACCGAGAGATTCATACAAATGCTCAGATTGCTCAGTGACAGAGCAAACGATCTGACAAATATAGAG
| | | | | | | | | ||| ||| | | ||| || | | | | | | || ||| ||| | | | || |||| ||||||||||||||||||| ||||| ||||| || ||||| || ||||| || || || ||||| |||||||| || ||||| || || || | ||||| || |||
gttttctctatattgaatatactacctttttaatcttcacagcttttggactggcttctctatgaaacacatcctaaacccatgcttgagcctatccgagtcaaactacacatttcacttaatctaaacaagtgtttattggtagagggcttctttatgtacatgttttatttgttctaattctggcagATACGAGATATTCCAGCTAATGGTAAATCTGTACACTGAGAGGTTTATTCAGATGCTAAGATTGCTTAGCGACAGGGCGAATGAATTAACAAACATTGAG
upper sequence: AT1G71820.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv12s0034g02360.t01 (Vitis vinifera), 3'ss of exon 12
-----gtttgttcc-tatctcgttttcctcaagtggacaatgaaagattacagcttaaaatttattctgttccccaagtgaaaaagggttccttagcaatcttctttgctggcagATACGAGATATTTCAGCTTATGGTGAACCTGTATACCGAGAGATTCATACAAATGCTCAGATTGCTCAGTGACAGAGCAAACGATCTGACAAATATAGAG
|||||| || | | | | ||| |||| || || | || | || |||| |||| ||||||| ||| | ||||||| || ||||| || || ||||| || || ||||| ||||| ||||| || ||||| || ||||||||||| ||||||| | |||||||||||||||
tgctcatttgttttgtacatttgtgtgcatctgtgtgttgtgaagactttcatccgtgaaaatgttttgttt---------------gttctaattcaatctttcttgattgcagATATGAAATATTCCAACTCATGGTAAATCTTTATACTGAGAGGTTCATTCAGATGCTTAGGCTGCTCAGTGACCGAGCAAATCAACTGACAAATATAGAG
upper sequence: AT1G71820.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv03s0097g00670.t01 (Vitis vinifera), 3'ss of exon 12
-----gtttgttcc-tatctcgttttcctcaagtggacaatgaaagattacagcttaaaatttattctgttccccaagtgaaaaagggttccttagcaatcttctttgctggcagATACGAGATATTTCAGCTTATGGTGAACCTGTATACCGAGAGATTCATACAAATGCTCAGATTGCTCAGTGACAGAGCAAACGATCTGACAAATATAGAG
|||||| | | | | | | ||| |||| || || | || | || |||| |||| ||||||| ||| | ||||||| || ||||| || || ||||| || || ||||| ||||| ||||| || |||||||| ||||||||||| ||||||| | |||||||||||||||
tgctcatttgtttcatgcatttgtgtgcatctgtgtgttgtgaagattttcatccacgaaaatgttttgttt---------------gttcaaattcaatctttcttgtttgcagATATGAAATATTCCAACTGATGGTAAATCTTTATACTGAGAGGTTCATTCAGATGCTCAGGCTGCTCAGTGACCGAGCAAATCAACTGACAAATATAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttattctgttccccaagtgaaaaagggttccttagcaatcttctttgctggcagATACGAGATATTTCAGCTTATGGTGAACCTGTATACCGAGAGATTCATACAAATGCTCAGATTGCTCAGTGACAGAGCAAACGATCTGACAAATATAGAG
tcttctttgct CT-rich tract
tgaaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgttcctatctcgttttcctcaagtggacaatgaaagattacagcttaaaatttattctgttccccaagtgaaaaagggttccttagcaatcttctttgctggcagATACGAGATATTTCAGCTTATGGTGAACCTGTATACCGAGAGATTCATACAAATGCTCAGATTGCTCAGTGACAGAGCAAACGATCTGACAAATATAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA