Sequence
atgc intronic sequence ATGC exonic sequencegtatgtatcaaaatctccctccttacgatcatgatttggctggatatctgattatgaactatgttgcagAATCTAGAAATCAAGAAGATCAATGAGGAGAAGAAGGCTTCCATGGCTGCTCAGTTTGCTGCTGAAGCTACCTTAAGAAGGGTCCATGCTGCTCAAAAGG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G68060.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G68060.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os06g14080.1 (Oryza sativa), 3'ss of exon 3
gtatgtatc--aaaatct----ccctccttac-----gatcatgatttggctggatatctgattatgaactatg-------ttgcagAATCTAGAAATCAAGAAGATCAATGAGGAGAAGAAGGCTTCCATGGCTGCTCAGTTTGCTGCTGAAGCTACCTTAAGAAGGGTCCATGCTGCTCAAAAGG
||||||||| | ||| | || || | || ||| |||| | | ||| || || |||||||||||||| |||||||||| ||||| ||||| |||||| | ||||||||||||||||| || ||||| || || | || || ||||| || |||||||
gtatgtatcttataatttgtgtttatctgtatccgttgtctctgttttagctgatcttttctttaacaatgataaaaacaaatgcagAATCTAGAAGTCAAGAAGATTAATGATGAGAAAAAGGCTGCAATGGCTGCTCAGTTTGCAGCAGAAGCGACTTTGCGGAGAGTACATGCAGCCCAAAAGG
upper sequence: AT1G68060.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os02g50320.2 (Oryza sativa), 3'ss of exon 3
------------gtatgtatcaaaatctccctccttacgatcatgatttggctggatatctgattatgaactatgttgcagAATCTAGAAATCAAGAAGATCAATGAGGAGAAGAAGGCTTCCATGGCTGCTCAGTTTGCTGCTGAAGCTACCTTAAGAAGGGTCCATGCTGCTCAAAAGG
|| | | ||| | | | | | | ||| | | | | ||||| |||| || ||||||||||||||| ||||||| | ||||| ||||| ||||| | ||||||||||||||||| || ||||| || | |||| || ||||| || ||||| |
gtatctatctttatactttttaaagttg---tttctgcccccctctttttgattgctccctgatggagaac-attttgcagAATCTAGAACTCAAGAAAACAAATGATGAGAAAAAGGCGGCTATGGCTGCTCAGTTTGCAGCAGAAGCAACTCTGCGAAGAGTGCATGCAGCCCAAAAAG
upper sequence: AT1G68060.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM5G832989_T01 (Zea mays), 3'ss of exon 3
----gtatgtatcaaa-atctccctccttacgatcatg---atttggctggata---tctgattatgaactatgttgcagAATCTAGAAATCAAGAAGATCAATGAGGAGAAGAAGGCTTCCATGGCTGCTCAGTTTGCTGCTGAAGCTACCTTAAGAAGGGTCCATGCTGCTCAAAAGG
||| |||| | |||||| | | || | ||| | | |||| | | | |||||||| |||||| | ||||| | ||||| ||||| |||||| | ||||||||||||||||| || ||||| || || |||| || |||| ||||| || |
gtatgtacatatcctatgactcccttttgttgtctctgccccctcaattggttgctctttgatcactaga-gttttgcagAACCTAGAACTGAAGAAAACAAATGATGAGAAAAAGGCTGCTATGGCTGCTCAGTTTGCGGCGGAAGCAACACTACGAAGAGTACATGGAGCTCAGAAAG
upper sequence: AT1G68060.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G05100.1 (Glycine max), 3'ss of exon 3
---------------------gtatgtatcaaaatctccctccttacgatcatgatttggctggatatctgattatgaactatgttgcagAATCTAGAAATCAAGAAGATCAATGAGGAGAAGAAGGCTTCCATGGCTGCTCAGTTTGCTGCTGAAGCTACCTTAAGAAGGGTCCATGCTGCTCAAAAGG
|| | | | | | | | | | || | || | | | | | ||||||||||| ||||| ||||| || ||||| || ||||| || || ||||| ||||||||||| |||||||| || | ||||||||||||||||||| ||||
gtaatgcttgaagcctctatcaagcttagcgaggagtaaatttctgaggttacgtggtgtgtttttactaaactggatatt-tcttgcagAATCTTGAAATAAAGAAAATTAATGATGAAAAGAAAGCATCGATGGCAGCTCAGTTTGCAGCTGAAGCCACTCTTCGAAGGGTCCATGCTGCTCAGAAGG
upper sequence: AT1G68060.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA05G34560.1 (Glycine max), 3'ss of exon 3
gtatgtatcaaaatctccctc---cttac---gatcatgatttggctggatatctga------ttatgaactatg------ttgcagAATCTAGAAATCAAGAAGATCAATGAGGAGAAGAAGGCTTCCATGGCTGCTCAGTTTGCTGCTGAAGCTACCTTAAGAAGGGTCCATGCTGCTCAAAAGG
||| | || ||| || |||| || |||| || || || | || |||| | ||||||||||| ||||| ||||| |||||||| || || || || || ||||| ||||||||||| |||||||| || | ||||||||||||||||||| ||||
gtaatgcttgaagcctctatcaagcttagtgagaggtaaattttttaggttacgtggtgtgtttaataaactgggtatttcttgcagAATCTTGAAATAAAGAAAATCAATGATGAAAAAAAAGCATCGATGGCAGCTCAGTTTGCAGCTGAAGCCACTCTTCGAAGGGTCCATGCTGCTCAGAAGG
upper sequence: AT1G68060.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA07G26540.1 (Glycine max), 3'ss of exon 3
------------------gtatgtatcaaaatctccctccttacgatcatgatttggctggatatctgattatgaactatgttgcagAATCTAGAAATCAAGAAGATCAATGAGGAGAAGAAGGCTTCCATGGCTGCTCAGTTTGCTGCTGAAGCTACCTTAAGAAGGGTCCATGCTGCTCAAAAGG
| | | | | || | | | ||| | | ||||| | | | | | ||||||||| ||||| || || ||||| || || ||||| || || ||||| ||||||||||| |||||||| || | ||||||||||||||||| || || |
gtattgcatgaagcctctatcaactttaggaaatagtcattttcccaggttaggtggtatgttttctgaatcgaatatttctggcagAATCTTGAAATTAAAAAAATCAACGATGAAAAGAAAGCATCAATGGCAGCTCAGTTTGCAGCTGAAGCCACTCTTAGAAGGGTCCATGCTGCCCAGAAAG
upper sequence: AT1G68060.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA02G09390.1 (Glycine max), 3'ss of exon 3
gtatgtatcaaaatctccctc--ctt------acgatcat-------gatttggctggata---tctgattatgaactatgttgcagAATCTAGAAATCAAGAAGATCAATGAGGAGAAGAAGGCTTCCATGGCTGCTCAGTTTGCTGCTGAAGCTACCTTAAGAAGGGTCCATGCTGCTCAAAAGG
|||| | | || |||| || ||| | |||| | || || | || ||||| | | | | | ||||||||| ||||| || || ||||| || || |||||||| || ||||| ||||||||||| |||||||| || | |||||||||| ||||| || || |
gtatttcttgaagcctccatcaactttagtaaatagtcattttcccaggttaggtggtatgttttctgaattaaatatttctggcagAATCTTGAAATAAAAAAAATCAACGATGAAAAGAAGGCATCAATGGCAGCTCAGTTTGCAGCTGAAGCCACTCTTCGAAGGGTCCACGCTGCCCAGAAAG
upper sequence: AT1G68060.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv01s0011g05790.t01 (Vitis vinifera), 3'ss of exon 3
gtat-gtatcaaaatctccc-----tccttacgatcatgatttggctggatatc-tgattatgaacta---------tgttgcagAATCTAGAAATCAAGAAGATCAATGAGGAGAAGAAGGCTTCCATGGCTGCTCAGTTTGCTGCTGAAGCTACCTTAAGAAGGGTCCATGCTGCTCAAAAGG
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gtattgcatgaaacccttccatttttctttataagttttgtgtgtgtgtgttttgcagttttgtcctaacaattgttttttgcagAATCTCGAGATCAAGAAAATCAATGATGAAAAGAAGGCCTCCATGGCTGCTCAATTTGCAGCAGAAGCCACTCTTAGAAGGGTTCATGCTGCGCAGAAGGMapped 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|163981443|gb|ES117585.1|ES117585EST: TAAGTTGGATGGGAAGCTCAAGTTAACTGAATCGCTTCTACCAAAGCAAA AATCTAGAAATCAAGAAGAT
genomic: TAAGTTGGATGGGAAGCTCAAGTTAACTGAATCGCTTCT-CCAAAGCAAAgtatgtatca ... tatgttgcagAATCTAGAAATCAAGAAGAT
EST:
gi|125014213|gb|EL086482.1|EL086482EST: CTAAGTTGGATGGGAAGCTCAAGTTAACTGAATCGCTTCTCCAAAGCAAA AATCTAGAAATCAAGAAGATCAATGAGGAGAAGAAGGCTTCCA
genomic: CTAAGTTGGATGGGAAGCTCAAGTTAACTGAATCGCTTCTCCAAAGCAAAgtatgtatca ... tatgttgcagAATCTAGAAATCAAGAAGATCAATGAGGAGAAGAAGGCTTCCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctccctccttacgatcatgatttggctggatatctgattatgaactatgttgcagAATCTAGAAATCAAGAAGATCAATGAGGAGAAGAAGGCTTCCATGGCTGCTCAGTTTGCTGCTGAAGCTACCTTAAGAAGGGTCCATGCTGCTCAAAAGG
attatgaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtatcaaaatctccctccttacgatcatgatttggctggatatctgattatgaactatgttgcagAATCTAGAAATCAAGAAGATCAATGAGGAGAAGAAGGCTTCCATGGCTGCTCAGTTTGCTGCTGAAGCTACCTTAAGAAGGGTCCATGCTGCTCAAAAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT