Sequence
atgc intronic sequence ATGC exonic sequence...ttagtttcttgttgatgtttttgatatctaccaatctcttttcaatttatgtctatatgttgctaaatatcttgttcaatgactgatttcttaaactcagGGTGGAAATTCTGCCATGGCGGAGCATTTGGCTTCAATCTTTGGTACTGAGAAAGACAGAGTGAATTGCCCTTTCTACTTCAAGATTGGCGCTTGCCGTC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G27650.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G27650.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os05g48960.1 (Oryza sativa), 3'ss of exon 2
-----ttagtttcttgttgatgtttttgatatctaccaatctcttttcaatttatgtctatatgttgctaaatatcttgttcaatgact--gatttcttaaactcagG-----GTGGAAATTCT------GCCATGGCGGAGCATTTGGCTTCAATCTTTGGTACTGAGAAAGACAGAGTGAATTGCCCTTTCTACTTCAAGATTGGCGCTTGCCGTC
| || || | | |||| || | | || | || | | ||| || || | || || || ||| | | | | | | |||| | || ||| | | | |||||||||||||||||||||||| ||||| |||||||| || || || || ||||| || |||||||||
gttaccagataagccattcatatacat-atatatagaagcacttcttgagatttggacaataaatt-ctgacaattttttttaatctttttgttatgtacagCTCAAGTGTCAGTTGAAGTGTTTTGAAAGTCATGGCGGAGCATTTGGCTTCAATATTTGGGACTGAGAAGGATAGGGTTAACTGCCCCTTTTACTTCAAG----------------
upper sequence: AT1G27650.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os01g47750.1 (Oryza sativa), 3'ss of exon 3
-ttagtttcttgttgatgtttttgatatctaccaatctc--ttttcaatttatgtctatatgttgctaaat----atcttgttcaatgactga--tttcttaaactcagGGTGGAAATTCT----GCCATGGC-GGAGCATTTGGCTTCAATCTTTGGTACTGAGAAAGACAG---AGTGAATTGCCCTTTCTAC-TTCAAGATTGGCGCTTGCCGTC-----------------
|| ||| || |||| | | | | | || | || | | | || | || | || || | | || || || | || | | ||| ||| | || || | | || | || | || | || | || | || | | ||| ||| | |
gttcgttgatt-ttgaatcatggcagagcacttagcttcaatatttggtacagagaaagataaggtcaactgcccattttacttcaagattggggcttgccgtcatggggatcggtgctcttgtcttcataacagGCCCACCATATCACCAACTGTTGTGTTTGCGAACATGTATCAGCGCCCTGATATGATCACGCCCGGGGTTGATGCTCAAGGCCAGCCGATAGATCCCCGC
upper sequence: AT1G27650.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os05g48960.2 (Oryza sativa), 3'ss of exon 3
----------------ttagtttcttgttgatgtttttg-------atatctaccaatctcttttcaatttatgtctatatgttgctaaatatcttgttcaatgac--tgatttcttaaactcagG-----GTGGAAATTCT------GCCATGGCGGAGCATTTGGCTTCAATCTTTGGTACTGAGAAAGACAGAGTGAATTGCCCTTTCTACTTCAAGATTGGCGCTTGCCGTC
||||| | | | | || |||| || | | || | || | | ||| || || | || || || ||| || | | | | |||| | || ||| | | | |||||||||||||||||||||||| ||||| |||||||| || || || || ||||| || |||||||||
gtatttctttctccctgtagttaccagataagccattcatatacatatatatagaagcacttcttgagatttggacaataaatt-ctgacaattttttttaatctttttgttatgtacagCTCAAGTGTCAGTTGAAGTGTTTTGAAAGTCATGGCGGAGCATTTGGCTTCAATATTTGGGACTGAGAAGGATAGGGTTAACTGCCCCTTTTACTTCAAG----------------
upper sequence: AT1G27650.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G031827_T02 (Zea mays), 3'ss of exon 1
-----ttagtttcttgttgat--gtttttgatatctaccaatctcttttcaatttatgtctat-atgttgctaaatatcttgttcaatgactgatttcttaaactcagGGTGGAAATTCTGCCATGGCGGAGCATTTGGCTTCAATCTTTGGTACTGAGAAAGACAGAGTGAATTGCCCTTTCTACTTCAAGATTGGCGCTTGCCGTC
| |||||| | | | | | | |||| | ||||| |||| | | ||| | ||| ||||| | | || ||| | |||| || || || |||||||||||| |||||||| ||||||||||| ||||| ||||| || || |||||||| |||||||||||||| ||||| ||||
atccccatggttcttgataacaggccatgagtttataccccctccatttcaccttatattgaagatgatactat---tcttgctta-tgcttgaaggttg----tcagTCTGCAAGTTGAATCATGGCGGAGCACTTGGCTTCGATCTTTGGTACCGAGAAGGACAGGGTCAACTGCCCTTTTTACTTCAAGATTGGGGCTTGTCGTC
upper sequence: AT1G27650.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G031827_T06 (Zea mays), 3'ss of exon 1
------ttagtttcttgttgatgtttttgatat-ctaccaatctcttttcaatttatgtc--tatatgttgctaaatatcttgttcaatgactgatttcttaaact---cagGGTGGAAATTCTGCCATGGCGGAGCATTTGGCTTCAATCTTTGGTACTGAGAAAGACAGAGTGAATTGCCCTTTCTACTTCAAGATTGGCGCTTGCCGTC
| | | | | | | || | | | | | | | | | | | || || ||| ||| | || | ||| | || || | || | ||| || || || |||||||||||| |||||||| ||||||||||| ||||| ||||| || || |||||||| |||||||||||||| ||
gtattccttgatccccatggttcttgataacaggccatgagtttataccccctccatttcaccttatattgaagatgatactattc--ttgcttatgcttgaagGTTGTCAGTCTGCAAGTTGAATCATGGCGGAGCACTTGGCTTCGATCTTTGGTACCGAGAAGGACAGGGTCAACTGCCCTTTTTACTTCAAGATTGGGGC--------
upper sequence: AT1G27650.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G031827_T05 (Zea mays), 3'ss of exon 1
----ttagtttcttgttgatgtttttgatat-ctaccaatctcttttcaatttatgt--ctatatgttgctaaatatcttgttcaatgactgatttcttaaa---ctcagGGTGGAAATTCTGCCATGGCGGAGCATTTGGCTTCAATCTTTGGTACTGAGAAAGACAGAGTGAATTGCCCTTTCTACTTCAAGATTGGCGCTTGCCGTC
| | | | | | | || | | | | | | | | | | | || | | ||| ||| | || | ||| | || || | || |||| || || || |||||||||||| |||||||| ||||||||||| ||||| ||||| || || |||||||| |||||||||||||| ||
attccttgatccccatggttcttgataacaggccatgagtttataccccctccatttcaccttatattgaagatgatactattc--ttgcttatgcttgaagGTTGTCAGTCTGCAAGTTGAATCATGGCGGAGCACTTGGCTTCGATCTTTGGTACCGAGAAGGACAGGGTCAACTGCCCTTTTTACTTCAAGATTGGGGC--------
upper sequence: AT1G27650.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G020928_T03 (Zea mays), 3'ss of exon 2
ttagtttcttgttgat--gtttttgatatctaccaatctcttttcaatttatgtctatatgttgctaaatatcttgttcaatgactgattt--cttaaac----tcagGGTGGAAATTCTGCCATGGCGGAGCATTTGGCTTCAATCTTTGGTACTGAGAAAGACAGAGTGAATTGCCCTTTCTACTTCAAGATTGGCGCTTGCCGTC
| |||| | | | | | | || || | || || || | | ||| | | | | | | || | || ||| || | | || || |||||||||||| |||||||| ||||| || |||||||| ||||| || || |||||||| |||||||||||||| ||
catggttctagataacaaaccatgagtttatatcattatcccctctatctcaccttgtattgaacatggtttttgatactattcttctttgtgcttgaagGTTGCCGGTCTGCGGGTTGAATCATGGCGGAGCACTTGGCTTCGATCTTCGGCACTGAGAAGGACAGGGTCAACTGCCCTTTTTACTTCAAGATTGGGGC--------
upper sequence: AT1G27650.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G020928_T02 (Zea mays), 3'ss of exon 3
---------------ttagtttcttgttgatg--tttttgatatctaccaatctcttttcaatttatgtctatatgttgctaaatatcttgttcaatgactgatt--tcttaaac----tcagGGTGGAAATTCTGCCATGGCGGAGCATTTGGCTTCAATCTTTGGTACTGAGAAAGACAGAGTGAATTGCCCTTTCTACTTCAAGATTGGCGCTTGCCGTC
| |||| | | | | | | || || | || || || | | ||| | | | | | | || | || ||| || | | || || |||||||||||| |||||||| ||||| || |||||||| ||||| || || |||||||| |||||||||||||| ||
gtattccttgatccccatggttctagataacaaaccatgagtttatatcattatcccctctatctcaccttgtattgaacatggtttttgatactattcttctttgtgcttgaagGTTGCCGGTCTGCGGGTTGAATCATGGCGGAGCACTTGGCTTCGATCTTCGGCACTGAGAAGGACAGGGTCAACTGCCCTTTTTACTTCAAGATTGGGGC--------
upper sequence: AT1G27650.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G025014_T01 (Zea mays), 3'ss of exon 2
ttagtttcttgttgat--gtttttgatatctaccaatctcttttcaatttatgtctatatgttgctaaatatcttgttcaatgactgattt--cttaaac----tcagGGTGGAAATTCTGCCATGGCGGAGCATTTGGCTTCAATCTTTGGTACTGAGAAAGACAGAGTGAATTGCCCTTTCTACTTCAAGATTGGCGCTTGCCGTC
| |||| | | | | | | | || | || || || | ||||| | | | | | | || | || ||| || | | || | || |||||||||||| |||||||| ||||| || |||||||| ||||| || || |||||||| |||||||||||||| ||
catggttctagataacaaaccatgagtttacatcattatcccctctatctcaccttatattgaacatggtttttgatactattcttctttgtgcttgaagGTTGCCGGTCTGCGAGTTGAATCATGGCGGAGCACTTGGCTTCGATCTTCGGCACTGAGAAGGACAGGGTCAACTGCCCTTTTTACTTCAAGATTGGGGC-------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttatgtctatatgttgctaaatatcttgttcaatgactgatttcttaaactcagGGTGGAAATTCTGCCATGGCGGAGCATTTGGCTTCAATCTTTGGTACTGAGAAAGACAGAGTGAATTGCCCTTTCTACTTCAAGATTGGCGCTTGCCGTC
tttctt CT-rich tract
taaatatctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttagtttcttgttgatgtttttgatatctaccaatctcttttcaatttatgtctatatgttgctaaatatcttgttcaatgactgatttcttaaactcagGGTGGAAATTCTGCCATGGCGGAGCATTTGGCTTCAATCTTTGGTACTGAGAAAGACAGAGTGAATTGCCCTTTCTACTTCAAGATTGGCGCTTGCCGTC
- - - - - - - - gtttttg
- - - - - - - - - - - - - -ctaccaa