Sequence
atgc intronic sequence ATGC exonic sequence...ctgaagttaagcagaattacggttgtctacatctcagcttcagtgtctttttatattataatattacagattttaagtatcttattgacattgatatcagATCAAGATTCGGTTAGATTATTGGCTGTTGAGGGTTGTGCTGCTCTTGGGAAATTGTTGGAGCCCCAGGACTGTGTTGCACACATTCTTCCTGTGATTGT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G13320.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G13320.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 3
--ctgaagttaagcagaattacggttgtctacatctcagcttcagtgtctttttatattataatattacagattttaagtatcttattgacatt--gatatcagATCAAGATTCGGTTAGATTATTGGCTGTTGAGGGTTGTGCTGCTCTTGGGAAATTGTTGGAGCCCCAGGACTGTGTTGCACACATTCTTCCTGTGATTGT
|| | ||| ||| | || | | || | | | | || |||| | || | ||| || || || | || || ||||||||||||| || | || ||||| ||||| || |||||||||||||||||||||||||| || || || ||||| ||||| || ||||| || |||||
ggagcaaatagtgcatgattgagccagttgggacatttactatacatgttctgcagccta-aataatgca---tctaacaatattgctggccttttattaccagATCAAGATTCCGTACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGAAATTGTTGGAACCACAAGATTGTGTAGCACATATCCTTCCAGTTATTGT
upper sequence: AT1G13320.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G122135_T04 (Zea mays), 3'ss of exon 3
ctgaagttaagcagaattacggttgtctacatctcagcttcagtgtctttttatattataatattacag--attttaagtatcttattgacattgatatcagATCAAGATTCGGTTAGATTATTGGCTGTTGAGGGTTGTGCTGCTCTTGGGAAATTGTTGGAGCCCCAGGACTGTGTTGCACACATTCTTCCTGTGATTGT
|| | | | |||| | | || | | | | || | | | |||| | || | | | | | | | || | |||||||||||||| || | || ||||||||||| ||||||||||||||||| |||||||||||||| || || ||||| || ||||||||||| || |||||
ctaatcattatt-gaatcattga-gttagtgtttgcatatagtcatacacttttgggacatcattagggctatgtctaaaacgtcgtggtctttattttcagATCAAGATTCAGTGCGTTTGTTGGCTGTTGAAGGTTGTGCTGCTCTTGGTAAATTGTTGGAGCCACAAGATTGTGTAGCTCACATTCTTCCAGTCATTGT
upper sequence: AT1G13320.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G102858_T01 (Zea mays), 3'ss of exon 3
---ctgaagttaagcagaattacggttgtctacatctcagcttcagtgtctttttatattataatattacagattttaagtatcttattgaca-ttgatatcagATCAAGATTCGGTTAGATTATTGGCTGTTGAGGGTTGTGCTGCTCTTGGGAAATTGTTGGAGCCCCAGGACTGTGTTGCACACATTCTTCCTGTGATTGT
| | | || | ||| | | | | |||| | || |||| | | ||| | | | ||||| || | ||||| |||||||| || || ||||||| |||||||||||||||||||||||||| |||||||||||||| || |||| ||||| ||||| || || |||||
ttgtttgaatgttacaaggcatcagttatttgaaattagttcacagtcaaatcatacattacatcagctaaga----agaaactgttttgactctttaactcagACCAAGATTCAGTGCGACTATTGGCAGTTGAGGGTTGTGCTGCTCTTGGGAAGTTGTTGGAGCCCCAAGATTGTGCAGCACATATTCTCCCAGTTATTGT
upper sequence: AT1G13320.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 3
-----ctgaagttaagcagaattacggttgtctacatctcagcttcagtgtctttttatattataatattacagattttaagtatcttattgacattgatatcagATCAAGATTCGGTTAGATTATTGGCTGTTGAGGGTTGTGCTGCTCTTGGGAAATTGTTGGAGCCCCAGGACTGTGTTGCACACATTCTTCCTGTGATTGT
|||| || | ||| | ||| | | | | | || | || || || || | ||| | || | | | || | |||||||||||||| || | | ||||||||||| || |||||||| ||||| ||||||||||| || || || || || |||||||||||||| || |||||
catgattgaatttgaatcattgggttagtgtttgcatatagtcatacgcat-ttgggacatcat--taggactatgtctaa--acctgctggtctttattttcagATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTAAATTGTTGGAACCACAAGATTGCGTAGCACACATTCTTCCAGTCATTGT
upper sequence: AT1G13320.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA02G10790.1 (Glycine max), 3'ss of exon 3
------------------ctgaagttaagcagaattacggttgtctacatctcagcttcagtgtc----tttttatattataatattacagattttaagtatcttattgacattgatatcagATCAAGATTCGGTTAGATTATTGGCTGTTGAGGGTTGTGCTGCTCTTGGGAAATTGTTGGAGCCCCAGGACTGTGTTGCACACATTCTTCCTGTGATTGT
|| | | || | | | | ||| | |||| | ||| || || ||| | | | | | | || | ||||||||||| || |||||||| |||||||| |||||||||||||||||||||||| || ||||||| || || || | |||| || || || || |||||
gtaattgaatacatatttctcattctttcttgatgtcttggcctgtcaatcataaattcaataataaattttccttaatacaattggcctagtatgcaatttaactttttaacctggctcagATCAAGACTCTGTTAGATTGTTGGCTGTGGAGGGTTGTGCTGCTCTTGGGAAACTGCTGGAGCCACAAGATTGCATCACACATATACTACCGGTTATTGT
upper sequence: AT1G13320.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA02G10790.2 (Glycine max), 3'ss of exon 3
------------------ctgaagttaagcagaattacggttgtctacatctcagcttcagt----gtctttttatattataatattacagattttaagtatcttattgacattgatatcagATCAAGATTCGGTTAGATTATTGGCTGTTGAGGGTTGTGCTGCTCTTGGGAAATTGTTGGAGCCCCAGGACTGTGTTGCACACATTCTTCCTGTGATTGT
|| | | || | | | | ||| | |||| | ||| || || ||| | | | | | | || | ||||||||||| || |||||||| |||||||| |||||||||||||||||||||||| || ||||||| || || || | |||| || || ||
gtaattgaatacatatttctcattctttcttgatgtcttggcctgtcaatcataaattcaataataaattttccttaatacaattggcctagtatgcaatttaactttttaacctggctcagATCAAGACTCTGTTAGATTGTTGGCTGTGGAGGGTTGTGCTGCTCTTGGGAAACTGCTGGAGCCACAAGATTGCATCACACATATACTACCG--------
upper sequence: AT1G13320.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 3
---------------------------------ctgaagttaagcagaattacggttgtctacatctcagcttcagt-gtctttttatattataatat-tacagattttaagtatct-tattgacat------tgatat-----cagATCAAGATTCGGTTAGATTATTGGCTGTTGAGGGTTGTGCTGCTCTTGGGAAATTGTTGGAGCCCCAGGACTGTGTTGCACACATTCTTCCTGTGATTGT
||| | ||| || | ||| | | | || || | || | || || || | | || | || | || | || | || | || | ||||||||||||| || ||||| |||||||| ||||| |||||||||||||| || |||||||||| || || ||||||||||| || || || || |||||
gtaattgaatacatatttcttgttctttgtagatggaaagtgtctgtcatttttgtctattgcatatttacattggttgtgtgattgtgttgtagaatctcctgaatgtactttcctcttttaatatgtgttgtaatcttggaacagATCAAGATTCTGTCAGATTGTTGGCTGTGGAGGGCTGTGCTGCTCTTGGCAAGCTGTTGGAGCCACAAGATTGTGTTGCACATATACTCCCGGTTATTGT
upper sequence: AT1G13320.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 3
--------------------------ctgaagttaagcagaatta--cggttgtctacatctcagcttca-gtgtctttttatattataatattacagat-----------tttaagtatcttattgacat-tgatatcagATCAAGATTCGGTTAGATTATTGGCTGTTGAGGGTTGTGCTGCTCTTGGGAAATTGTTGGAGCCCCAGGACTGTGTTGCACACATTCTTCCTGTGATTGT
|| || | || | | |||||| | | | || |||| || | | || | | | || || | ||| |||| || | | ||||||||||||| || ||||| |||||||| ||||| |||||||||||||| || |||||||||| || || ||||||||||| || || || || |||||
gtaattgaatacatatttcttgttctttgtagatggaaagtgtctgtcatttgtctgttacatatttacatgtgtgattgtgttgtagagtctcctgaatgtactttactcctttaatatgcaattgtaatcttggaacagATCAAGATTCTGTCAGATTGTTGGCTGTGGAGGGCTGTGCTGCTCTTGGCAAGCTGTTGGAGCCACAAGATTGTGTTGCACATATACTCCCGGTTATTGT
upper sequence: AT1G13320.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 2
---ctgaagttaagcagaattacggttgt-ctacatc-tcagcttcagtgtct-ttttatattataatattacagattttaagtatcttattgacattgatatcagATCAAGATTCGGTTAGATTATTGGCTGTTGAGGGTTGTGCTGCTCTTGGGAAATTGTTGGAGCCCCAGGACTGTGTTGCACACATTCTTCCTGTGATTGT
|| ||| | ||| | | || || ||| |||||| | | | || | | | | | ||||||| ||| |||| || | |||||||||||||| || || ||||||| ||||||||||||||| | || || || || || ||||||||||| || |||||| ||||| ||||| ||| |
atttctgttttttgcatatctaccatcatgttatataatcaagttcagtatttgtcttctcatctgcttctgaagatttt--gtaatttatc----ttcacctcagATCAAGATTCAGTCAGGTTATTGGTTGTTGAGGGTTGTGCCACACTGGGCAAGTTATTAGAGCCCCAGGAATGCATTGCACGTATTCTCCCTGTTATTATMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|116468454|gb|EG511046.1|EG511046EST: TCATTTGAAGACAGACATTATGTCCATGTTTGAGGATCTTACGCAAGATG ATCAAGATTCGGTTAGATTATTGGCTGTTGAGGGTTGTGCTGCTCTTGGGA
genomic: TCATTTGAAGACAGACATTATGTCCATGTTTGAGGATCTTACGCAAGATGgtatgctctc ... ttgatatcagATCAAGATTCGGTTAGATTATTGGCTGTTGAGGGTTGTGCTGCTCTTGGGA
EST:
gi|116468455|gb|EG511047.1|EG511047EST: TCATTTGAAGACAGACATTATGTCCATGTTTGAGGATCTTACGCAAGATG ATCAAGATTCGGTTAGATTATTGGCTGTTGAGGGTTGTGCTGCTCTTGGGA
genomic: TCATTTGAAGACAGACATTATGTCCATGTTTGAGGATCTTACGCAAGATGgtatgctctc ... ttgatatcagATCAAGATTCGGTTAGATTATTGGCTGTTGAGGGTTGTGCTGCTCTTGGGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctttttatattataatattacagattttaagtatcttattgacattgatatcagATCAAGATTCGGTTAGATTATTGGCTGTTGAGGGTTGTGCTGCTCTTGGGAAATTGTTGGAGCCCCAGGACTGTGTTGCACACATTCTTCCTGTGATTGT
ttatattataatatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctgaagttaagcagaattacggttgtctacatctcagcttcagtgtctttttatattataatattacagattttaagtatcttattgacattgatatcagATCAAGATTCGGTTAGATTATTGGCTGTTGAGGGTTGTGCTGCTCTTGGGAAATTGTTGGAGCCCCAGGACTGTGTTGCACACATTCTTCCTGTGATTGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - aagcaga
- - - - - - - - - - - - - ctacatc