Sequence
atgc intronic sequence ATGC exonic sequencegtaacggtgttatctcttgttgtgtctaatgtgtaatcaggtgtgaaatcgatttgtagattttgaaaagcttttgctgtttgtttagGTTGAGCTTGAGGATCCAGTTGAGAACATTGGTGCTAAGCTAGTGAGACAAGCTGCTTCCAAGACTAATGACTTAGCTGGTGATGGAACAACGACTTCTG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G56500.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G56500.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os02g01280.1 (Oryza sativa), 3'ss of exon 3
-------------------------------------------------------------------------------------gtaac-ggtgttatctcttgttgtgtctaatgtgtaatcaggt-gtgaaatcgatttgtagattt-tgaaaagcttttgc-tgtttgtt------tagGTTGAGCTTGAGGATCCAGTTGAGAACATTGGTGCTAAGCTAGTGAGACAAGCTGCTTCCAAGACTAATGACTTAGCTGGTGATGGAACAACGACTTCTG
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gtatgccacgtatagtaaactgttcgtgttcttatgatgcaatcctatcattgcttaaattcagagttttctgaaaaatgactgaacatttggcataaactgtttgttttcttatgatgcaatcctatcatagcttaaattcagagttttctgaaaaatgagtgaacatttggcatgcaccagGTTGAGCTGGAGGACCCTGTTGAAAATATTGGAGCCAAATTAGTCCGGCAAGCTGCAGCCAAGACAAATGATTTGGCTGGTGATGGGACAACGACTTCTG
upper sequence: AT5G56500.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G015989_T01 (Zea mays), 3'ss of exon 3
---------------------------------------gtaacggtgttatctcttgttgtgtctaatgtgtaatcaggtgtgaaatcgatttgtagattttgaaaagcttttgctgtttgtttagGTTGAGCTTGAGGATCCAGTTGAGAACATTGGTGCTAAGCTAGTGAGACAAGCTGCTTCCAAGACTAATGACTTAGCTGGTGATGGAACAACGACTTCTG
| || | | || ||||| | | | | || | | | || || || ||| | || | ||||||| |||||||| || ||||| || ||||||||||| | || | ||||||||| | || || |||||||| ||||||||||| ||||| ||||| |
gtgcacatctgactacaaacttaccatcgtttgttcttgctcgtactgcaaccataccctgc-tctaacttcttgt-ggctgccgagtttcctcatatgttctgg---gctgtggccatgcacc-agGTTGAACTTGAGGACCCTGTTGAAAATATTGGTGCTAAATTGGTCCGCCAAGCTGCTGCTAAAACAAATGACTTGGCTGGTGATGGGACAACCACTTCGG
upper sequence: AT5G56500.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G18760.2 (Glycine max), 3'ss of exon 2
----------gtaacggtgttatctcttgttgtgtctaatgtgtaatcaggt-gtgaaatcg-atttgta--gattttgaaaagcttttgctgtttgtttagGTTGAGCTTGAGGATCCAGTTGAGAACATTGGTGCTAAGCTAGTGAGACAAGCTGCTTCCAAGACTAATGACTTAGCTGGTGATGGAACAACGACTTCTG
| ||| | || || | || | ||| ||| | | || | | |||||| ||| || | |||| ||||| | |||||||| | |||||||| |||||||| |||||||| ||| | ||||||||||| ||| ||||||| || ||||| |||||||||||||| ||||| || |
tttgaatttgtttacgtggataggatttcatttgaattgtgtttaagtggattgtttgtttgtgtttgtattgatgttttgttgaatttg--gtttggtaagGTTGAGTTGGAGGATCCCGTTGAGAATATTGGTGCCAAGTTGGTGAGACAAGCGGCTGCCAAGACAAACGACTTGGCTGGTGATGGAACCACGACCTCGG
upper sequence: AT5G56500.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA15G40110.1 (Glycine max), 3'ss of exon 2
-----gtaacggtgt---tatctcttgttgtgtctaatgtgtaatcaggtgtgaaatcgatttgtagattttgaaaagcttttgctgtttgttt----agGTTGAGCTTGAGGATCCAGTTGAGAACATTGGTGCTAAGCTAGTGAGACAAGCTGCTTCCAAGACTAATGACTTAGCTGGTGATGGAACAACGACTTCTG
| | || | | | || | | | | | | | ||| | | ||| |||||| | ||| || ||| |||||||| | |||||||| |||||||| ||||| || ||| | ||||||||||| ||| ||||||| || ||||| |||||||||||||| |||||||| |
tgtttgaatttgtttatgtggataggatttcatttgaattttgtttaagtgggttttttgggtgtttgttttgatgctttgttgaatttgatttgggaagGTTGAGTTGGAGGATCCGGTTGAGAATATTGGCGCCAAGTTGGTGAGACAAGCAGCTGCCAAGACAAACGACTTGGCTGGTGATGGAACCACGACTTCGG
upper sequence: AT5G56500.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 3
-------gtaacggtgttatctcttg---ttgtgtctaatgtgtaatcaggtgtgaaatcgatt-tgtagattttgaaaagcttttgctgtttgtt-tagGTTGAGCTTGAGGATCCAGTTGAGAACATTGGTGCTAAGCTAGTGAGACAAGCTGCTTCCAAGACTAATGACTTAGCTGGTGATGGAACAACGACTTCTG
| | || | ||| |||| || | | || || | | || | || | ||||| | | | ||||||||| | |||||||| |||||||| ||||||||||| ||||||||||||| ||| ||||||| || ||||| ||||| ||||| ||||| || ||||
atgcctaccatctgtccttgacgttgagattgtctccagtaaatatctcaacacaaatttgtccgtgaggcacttattgatgttttgttatcacctatagGTTGAGTTGGAGGATCCTGTTGAGAATATTGGTGCTAAATTAGTGAGACAAGCAGCTGCCAAGACCAACGACTTGGCTGGGGATGGGACAACAACATCTG
upper sequence: AT5G56500.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S14_298V6.1 (Physcomitrella patens), 3'ss of exon 2
-----------------------------------------------------------------------------------------------------gtaacggtgttatctcttgttgtgtctaatgtgtaatcaggtgtgaaatcga--tttgtagattttgaaaagcttttgctgtttgtttagGTTGAGCTTGAGGATCCAGTTGAGAACATTGGTGCTAAGCTAGTGAGACAAGCTGCTTCCAAGACTAATGACTTAGCTGGTGATGGAACAACGACTTCTG
| || | | | | ||| | ||| | || | ||| | || ||| | | | | | | | |||||||||||||||||||||| |||||||| ||||| ||| | ||||| ||||| || ||||||| |||||||| |||||||| || || || || ||||
gttagggcttgcatcctctctatgagcccggatttattatgttgtttacttggtttttttggataagcgcgattttttttttgaggggggcggggtgtagaatcttgggataaggtttcgttctttcttgaat-tagatgcgcatgagtttgagcttttcaattaacgcgctgaatctcggaactcaacagGTTGAGCTTGAGGATCCAGTCGAGAACATCGGTGCCAAGTTGGTGAGGCAAGCGGCAGCCAAGACGAATGACTTGGCTGGTGACGGTACCACCACCTCTG
upper sequence: AT5G56500.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ33580 (Selaginella moellendorffii), 3'ss of exon 2
gtaacggtgttatctcttgttgtgtctaatgtgtaatcaggtgtgaaatcg-atttgtagattttgaaaagcttttgctgtttgttt--agGTTGAGCTTGAGGATCCAGTTGAGAACATTGGTGCTAAGCTAGTGAGACAAGCTGCTTCCAAGACTAATGACTTAGCTGGTGATGGAACAACGACTTCTG
|| | | || ||| | | | | | | ||||||||| ||||||| |||| ||||| || ||| |||| |||||||||||||| ||| || ||||||||||| || || || |||||||| |||||||||||||| || || || |
------------------------------gtagagggaaaagttaaaatgcggctacaaagtcttttgtgcttttgctctttgtttgcagGTGGAGCTGGAAGATGCAGTCGAGAACATTGGTGCGCGGCTTGTAAGACAAGCTGCGTCGAAAACAAATGACTTGGCTGGTGATGGAACCACCACGTCCG
upper sequence: AT5G56500.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ32217 (Selaginella moellendorffii), 3'ss of exon 2
gtaacggtgttatctcttgttgtgtctaatgtgtaatcaggtgtgaaatcgatttgtagattttgaaaagcttttgctgtttgtttagGTTGAGCTTGAGGATCCAGTTGAGAACATTGGTGCTAAGCTAGTGAGACAAGCTGCTTCCAAGACTAATGACTTAGCTGGTGATGGAACAACGACTTCTG
| ||| ||| | | || | |||| || || ||| ||| | ||||| |||| | || || || |||||||||||||||| || || ||||| ||||||||||| || || || || || ||||| |||||||| ||||||||
-------------------gtatgtgccttgtctttcttgttgatgctgtggtttgctga---tggaaa--------tgtat-tttagATTGAATTGGAAGACCCGGTTGAGAACATTGGTGTGAAACTCGTGAGGCAAGCTGCTTCTAAAACCAACGATTTGGCTGGGGATGGAACGACGACTTCCT
upper sequence: AT5G56500.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ36935 (Selaginella moellendorffii), 3'ss of exon 2
gtaacggtgttatctcttgttgtgtctaatgtgtaatcaggtgtgaaatcgatttgtagattttgaaaagcttttgctgtttgttt--agGTTGAGCTTGAGGATCCAGTTGAGAACATTGGTGCTAAGCTAGTGAGACAAGCTGCTTCCAAGACTAATGACTTAGCTGGTGATGGAACAACGACTTCTG
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----------------------------gtaggaaggaaaagataaaatgcggctacaaagtcttttgtgtttttgctctttgtttgcagGTGGAGCTGGAAGATGCAGTCGAGAACATTGGTGCGCGGCTTGTAAGACAAGCTGCGTCAAAAACAAATGACTTGGCTGGTGATGGAACCACCACGTCCGMapped 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|19875387|gb|AU236218.1|AU236218EST: AATACGGTTCCCCTAGAATCGTTAATGATGGTGTTACGGTCGCTAGAGAG GTTGAGCTTGAGGATCCAGTTGAGAACATTGGTGCTAAGCTAGTGAGACAA
genomic: AATACGGTTCCCCTAGAATCGTTAATGATGGTGTTACGGTCGCTAGAGAGgtaacggtgt ... gtttgtttagGTTGAGCTTGAGGATCCAGTTGAGAACATTGGTGCTAAGCTAGTGAGACAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taatcaggtgtgaaatcgatttgtagattttgaaaagcttttgctgtttgtttagGTTGAGCTTGAGGATCCAGTTGAGAACATTGGTGCTAAGCTAGTGAGACAAGCTGCTTCCAAGACTAATGACTTAGCTGGTGATGGAACAACGACTTCTG
tttgttt CT-rich tract
attttgaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaacggtgttatctcttgttgtgtctaatgtgtaatcaggtgtgaaatcgatttgtagattttgaaaagcttttgctgtttgtttagGTTGAGCTTGAGGATCCAGTTGAGAACATTGGTGCTAAGCTAGTGAGACAAGCTGCTTCCAAGACTAATGACTTAGCTGGTGATGGAACAACGACTTCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA