Sequence
atgc intronic sequence ATGC exonic sequence...aaatttctaatctttgttgtgttggccagtgatactgtacagtaaaagaaaggagaaatttctgtgattgctgatgttttgtttgtgtttttccattcagCGTCGCAATCTGTGAAGAAGATTATTGAAATTAATCCTTATATGCTTGGTACAATGGCTGGTGGTGCTGCTGATTGTCAATTCTGGCACAGAAATCTGGG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G26340.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G26340.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os06g06030.1 (Oryza sativa), 3'ss of exon 2
aaatttctaatctttgttgtgttggccagtgatactgtacagtaaaagaaaggagaaatttct--gtgattgctgatgttttgtttgtgtttttccattcagCGTCGCAATCTGTGAAGAAGATTATTGAAATTAATCCTTATATGCTTGGTACAATGGCTGGTGGTGCTGCTGATTGTCAATTCTGGCACAGAAATCTGGG
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aaaatgcttgttgctgtttcagaagaccttgctttattgcaaggatggtcacttaatcttacttattgggtcttaatatcacatttct--tcttacctgcagCTTCGCAAACTGTGAGGAAAATTATTGAAATAAATCCGTACATGCTTGGAACAATGGCAGGAGGTGCTGCTGATTGTCAATTTTGGCATAGGAACTTGGG
upper sequence: AT3G26340.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G102596_T02 (Zea mays), 3'ss of exon 2
aaatttctaatctttgttgtgttggccagtgatactgtacagtaaaagaaaggagaaatttctgtgattgctgatgttttgtttgtgtttttccatt---cagCGTCGCAATCTGTGAAGAAGATTATTGAAATTAATCCTTATATGCTTGGTACAATGGCTGGTGGTGCTGCTGATTGTCAATTCTGGCACAGAAATCTGGG
| | |||| ||| | | | | ||| || | || | |||| | || || | | | | | ||||| ||| |||| || ||| | |||| ||| ||||||||||| |||||||| ||||| || ||||||||||| |||||||||||||| ||||| ||||| || || || ||
--ctgggttctcttagttaagaaaatcgggactgatgttcatttgt-gacatgagattgtatactgtttcatatgatctcactgttctttttatatttcgcagCCTCACAAACCGTGAGGAAAATTATTGAAATAAATCCTTACATGCTGGGGACAATGGCTGGAGGTGCTGCTGATTGCCAATTTTGGCATAGGAACCTAGG
upper sequence: AT3G26340.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA06G17960.1 (Glycine max), 3'ss of exon 3
------------------------aaattt--ctaatctttgttgtgttggccagtgata---ctgtacagtaaaagaaaggagaaatt-tctgtgattgctgatgtttt----gtttgtgtttt---tccattcagCGTCGCAATCTGTGAAGAAGATTATTGAAATTAATCCTTATATGCTTGGTACAATGGCTGGTGGTGCTGCTGATTGTCAATTCTGGCACAGAAATCTGGG
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gtgagtgtttgttaattttaactttaatttcactattctttgttcctttggtgaatgctgagtttttatgttacttgttacttttatctatttgtggttgtctttgttcttgaattttgagtgttggctgtctccagCATCGCAGTCTGTGAAGAAGATTATTGAAATTAATCCGTATATGCTTGGGACAATGGCTGGAGGTGCTGCTGATTGTCAGTTTTGGCACAGGAATCTTGG
upper sequence: AT3G26340.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA04G37030.3 (Glycine max), 3'ss of exon 3
-------------------------------------------------------------aaatttctaatctttgttgtgttggccagtgatactgtacagtaaaagaaaggagaaattt---ctgtgattgctgatgttttgtttgtgttt-ttccattcagCGTCGCAATCTGTGAAGAAGATTATTGAAATTAATCCTTATATGCTTGGTACAATGGCTGGTGGTGCTGCTGATTGTCAATTCTGGCACAGAAATCTGGG
| ||| | | ||||| | | || || || | | | | | |||| |||| ||| | || || | |||| | | |||||||||| ||||||||||| ||||| ||||| ||||| ||||||||||| |||||||||||||||||||||||||| || || |||||||| ||||| ||
gtgagtatttgttagattttaatttcatttttcactgttctttgttcctttggctgaggcagagttttttgtttttgtgctaattgctgcaaat----taaaatgatgggttttatctatttgcattgtgtttgatcttgaattctgactgttggctgtctccagCGTCGCAGTCTGTGAAGAAAATTATCGAAATCAATCCGTATATGCTTGGGACAATGGCTGGTGGTGCTGCTGATTGCCAGTTTTGGCACAGGAATCTCGG
upper sequence: AT3G26340.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv01s0010g02900.t01 (Vitis vinifera), 3'ss of exon 3
--aaatt--tctaatctttgttgtgttggccagtgatactgtacagtaaaagaaaggagaaatttctgtgattgctgatgttttgtttgtgtttttccatt-cagCGTCGCAATCTGTGAAGAAGATTATTGAAATTAATCCTTATATGCTTGGTACAATGGCTGGTGGTGCTGCTGATTGTCAATTCTGGCACAGAAATCTGGG
| | || || ||||| | || || | | | | ||| ||| | | ||| | || | || | || || |||| || |||||||||||||| ||||||||||||||||| || |||||||| ||||||||||| || ||||||||||| || || |||||||||||| ||||
ctcatctgatcaaaactttgaaccatgaaatagggagatctt----ttggactttggatgcattgcc-tatttgttttcattgtcttccttccttatttttgcagCATCACAATCTGTGAAGAAAATTATTGAAATTAATCCCTACATGCTTGGCACAATGGCTGGAGGAGCTGCTGATTGCCAGTTTTGGCACAGAAATTTGGG
upper sequence: AT3G26340.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S2_300V6.1 (Physcomitrella patens), 3'ss of exon 2
----aaatttctaatctttgttgtgttggccagtgatactgtacagtaaaagaaaggagaaatttctgtga-ttgctgatgttttgtttgtgtttttccatt-cagCGTCGCAATCTGTGAAGAAGATTATTGAAATTAATCCTTATATGCTTGGTACAATGGCTGGTGGTGCTGCTGATTGTCAATTCTGGCACAGAAATCTGGG
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agtgaggtttcccaag---gttgcactatttaaatgtatggagca-tgaagaaagggtttagttggtacatcttgctgacaagtgcattg--tttttccatcacagCCTCGCAATCGGTGAAGAAAATTTTGGAAATCAACCCTTACTTGTTGGGCACAATGGCTGGAGGTGCTGCAGATTGTCAGTTTTGGCAACGAAATCTAGGMapped 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|124806235|gb|EH893180.1|EH893180EST: AGGTGTTATGGTAGCTGCTGATTCTCGAGCTAGCATGGGAGGATATATCT CGTCGCAATCTGTGAAGAAGATT
genomic: AGGTGTTATGGTAGCTGCTGATTCTCGAGCTAGCATGGGAGGATATATCTgtatgtttct ... ttccattcagCGTCGCAATCTGTGAAGAAGATT
EST:
gi|124992948|gb|EL065217.1|EL065217EST: AGGTGTTATGGTAGCTGCTGATTCTCGAGCTAGCATGGTAGGATATATCT CGTCGCAATCTGTGAAG
genomic: AGGTGTTATGGTAGCTGCTGATTCTCGAGCTAGCATGGGAGGATATATCTgtatgtttct ... ttccattcagCGTCGCAATCTGTGAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagaaaggagaaatttctgtgattgctgatgttttgtttgtgtttttccattcagCGTCGCAATCTGTGAAGAAGATTATTGAAATTAATCCTTATATGCTTGGTACAATGGCTGGTGGTGCTGCTGATTGTCAATTCTGGCACAGAAATCTGGG
tgctgat putative branch site (score: 3)
tttttccattc putative PPT
agaaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaatttctaatctttgttgtgttggccagtgatactgtacagtaaaagaaaggagaaatttctgtgattgctgatgttttgtttgtgtttttccattcagCGTCGCAATCTGTGAAGAAGATTATTGAAATTAATCCTTATATGCTTGGTACAATGGCTGGTGGTGCTGCTGATTGTCAATTCTGGCACAGAAATCTGGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - -aaaagaa
- - - - - - - - - - - - - - - - - - - - - - - - - -ggagaaa