Sequence
atgc intronic sequence ATGC exonic sequencegtcttattctcttattcttttctcatacagcgtttgctattgaacagtatttcctaatttgtactctcttgtagcaatgctgagcagtggacatgtttattggcttacctgtttctttcagCTAAGCAATCCTTGGGAAATAGTCAGAAATGATGTCTCATATCCTATTAAGTTCTATGGGAAAGTGGTTTTTGGATCAGATGGTAAGAAACGGTGGATTG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G29320.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G29320.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os03g55090.1 (Oryza sativa), 3'ss of exon 4
gtcttattctcttattcttttctcatacagcgtttgctattgaacagtatttcctaatttgtactctcttgtagcaatgctgagcagtggacatgtttattggcttacctgtttctttcagCTAAGCAATCCTTGGGAAATAGTCAGAAATGATGTCTCATATCCTATTAAGTTCTATGGGAAAGTGGTTTTTGGATCAGATGGTAAGAAACGGTGGATTG
|| | | |||| | | | ||| || ||| |||| | ||| | | | || || | ||||| || ||||| | | | |||| ||| | | ||||||||||| || || |||| |||||||| |||||| | ||||||||||| ||||||||| || | ||||| | || | |||||||
---gtactgatatgccctttcattttttgctgcttgaaatc---cagaattt--tgatt---atgttgatatactgattat-agcagctaac-catttatgacttcatacttatcttccagATGGGAAATCCTTGGGAGATTGTAAGAACCGATGTCTCCTATCCTGTGAAGTTCTATGGTAAAGTGGTTGAAGGCACTGATGGGAGGATGCACTGGATTG
upper sequence: AT3G29320.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G074158_T01 (Zea mays), 3'ss of exon 4
gtcttattctcttattcttttctcatacagcgtttgctattgaacagtatttcctaatttgtactctcttgtagcaatgctgagcagtggacatgtttattggcttacctgtttctttcagCTAAGCAATCCTTGGGAAATAGTCAGAAATGATGTCTCATATCCTATTAAGTTCTATGGGAAAGTGGTTTTTGGATCAGATGGTAAGAAACGGTGGATTG
| | | |||| || ||||||| | | | || || || || | | | |||| | || || | ||||| | || ||| | | |||||||||| | || |||||||||||||| |||||| | || |||||||| |||||||| || | ||||||| ||| | |||||||
------gtaccaagatgccttcttat------tttgctactaggaaattattaaagatctgc-ctattatcttcttatgccaatca-tgcccgcatttatg------------ttttccagATGGGATATCCTTGGGAGGTTGTAAGAAATGATGTCTCTTATCCTGTGAAATTCTATGGTAAAGTGGTGGAAGGCACTGATGGTAGGAAGCACTGGATTG
upper sequence: AT3G29320.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA13G06040.1 (Glycine max), 3'ss of exon 4
gtcttattctcttattcttttctcatac-agcgtttgctattgaacagtatttcctaatttgtactctcttgtagcaatgc---tgagcagtggacatgtttattggcttacctgt------ttctttcagCTAAGCAATCCTTGGGAAATAGTCAGAAATGATGTCTCATATCCTATTAAGTTCTATGGGAAAGTGGTTTTTGGATCAGATGGTAAGAAACGGTGGATTG
|| | ||| | || || | | | || | || | || | | || ||| | | | ||| | | || || || ||| || || | ||| ||| ||| | ||||||| ||||| || | ||||||||||| ||||||||| | ||||||||||| || || |||| || ||||||||||| |||| |||||||
gtatgtttcattatttgttggcaagtgctagtggcatgtacttaaaaattaaaattataatgtttgcaccaacaccaaagtctttcagttctgttaatatttctttctttgcttgtgatctcgtctaacagATGGGCAATCCCTGGGAGATTATTAGAAATGATGTTTCATATCCTGTAAAGTTCTATGGCAAGGTTGTTTCAGGGTCAGATGGTAAAAAACATTGGATTG
upper sequence: AT3G29320.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA19G03490.1 (Glycine max), 3'ss of exon 4
----gtcttattctcttattcttttctcatac-agcgtttgctattgaac-agtatttcctaatttgtactctcttgtagcaatgctgagcagtggacatgtttattggcttacctgtttcttt------cagCTAAGCAATCCTTGGGAAATAGTCAGAAATGATGTCTCATATCCTATTAAGTTCTATGGGAAAGTGGTTTTTGGATCAGATGGTAAGAAACGGTGGATTG
|| | ||| | ||||| | || || | | || || | ||| |||| | | | | | || || || ||| || || | ||| | | ||| | ||||||| ||||| || | ||||||||||| ||||||||| | ||||||||||| || || |||| || ||||||||||| |||| |||||||
gtatgtttaattat-ttattgacaagtgctattggcatgtacttaaaaattaaaattataatgtttgcatcaacac-caaaatctttcagttctgttaatatttctttctttgcttgtgacctcgtcaaacagATGGGCAATCCCTGGGAGATTATTAGAAATGATGTTTCATATCCTGTAAAGTTCTATGGCAAGGTTGTTTCAGGGTCAGATGGTAAAAAACATTGGATTG
upper sequence: AT3G29320.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv14s0108g01560.t01 (Vitis vinifera), 3'ss of exon 4
---------------------------------------------------------------------gtcttattctcttattcttttctcataca-gcgtttgctattgaacagtatttcctaatttgtactctcttgtagcaatgctgagcagtggacatgtttattggcttac--ctgtttcttt---cagCTAAGCAATCCTTGGGAAATAGTCAGAAATGATGTCTCATATCCTATTAAGTTCTATGGGAAAGTGGTTTTTGGATCAGATGGTAAGAAACGGTGGATTG
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gtattcttgctttttgttcatttattttcattttaagtacttccttgtgtatgtgtttaaaaataaatggtcct-ttcagttattaaatttccagaaacataattagtgttc--tgttggtagcgaaattat-ttctttaagtttcataatggaaagcctcattatctgttggttaagtacagtttctctttgcagATGGGCAATCCCTGGGAAATTGTGAGAAATGATGTCTCATATCCTGTGAAATTTTATGGAAAGGTTATTGAAGGATCAGATGGAAAAAGACACTGGATTGMapped 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|125016697|gb|EL088966.1|EL088966EST: AGAGAATTACAAAAGATGGACAGGAGGAAGCTGCAGAAGATTGGCTTGAG CTAAGCAATCCTTGGGAAATAGTCAGAAATGATGTCTCATA
genomic: AGAGAATTACAAAAGATGGACAGGAGGAAGCTGCAGAAGATTGGCTTGAGgtcttattct ... tttctttcagCTAAGCAATCCTTGGGAAATAGTCAGAAATGATGTCTCATA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttgtagcaatgctgagcagtggacatgtttattggcttacctgtttctttcagCTAAGCAATCCTTGGGAAATAGTCAGAAATGATGTCTCATATCCTATTAAGTTCTATGGGAAAGTGGTTTTTGGATCAGATGGTAAGAAACGGTGGATTG
ggcttac putative branch site (score: 3)
cttacctgtttctttc CT-rich tract
atgtttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcttattctcttattcttttctcatacagcgtttgctattgaacagtatttcctaatttgtactctcttgtagcaatgctgagcagtggacatgtttattggcttacctgtttctttcagCTAAGCAATCCTTGGGAAATAGTCAGAAATGATGTCTCATATCCTATTAAGTTCTATGGGAAAGTGGTTTTTGGATCAGATGGTAAGAAACGGTGGATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA