Sequence
atgc intronic sequence ATGC exonic sequenceAACCATTGAGCATCTGTTACCAATTTTTCTTTCCCTTTTGAAAGATGAATTTCCTGATGTGCGCCTTAACATCATAAGCAAGTTAGATCAAGTCAACCAGgtttgttgcatctctcttgtgtgctttagatactacttttattgcttccttatttagttggtgactgaattatcttttacggcag
Basic information
species | Arabidopsis thaliana |
transcript | AT1G25490.1 |
intron # | 8 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G25490.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GRMZM2G164352_T04 (Zea mays), 5'ss of exon 8
AACCATTGAGCATCTGTTACCAATTTTTCTTTCCCTTTTGAAAGATGAATTTCCTGATGTGCGCCTTAACATCATAAGCAAGTTAGATCAAGTCAACCAGgtttgttgcatctctcttgtgtgctttagatactacttttattgcttccttatttagttggtgactgaattatcttttacggcag--------------------------------------------------------------------------------------------------------
|||||||| || || | |||||||| || || | |||||||| |||||||||||||| || |||||||| || ||||| | |||||||| || ||||| || ||| | | |||| | | | || | || || ||| || ||||| | | | || | | | || || | ||
TACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGACGAATTTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAGgtcagtaccattttttttgt-tattagatttatttgcctt-ttcctttctgttttagatttttaatgtaatcttttataagctagctagccattagtatgctagatttttttaagttgatgtccttgaaagccttgcctttctcttcaaaattatctgatgattgctgatttttgttttgatctttcag
upper sequence: AT1G25490.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA02G10790.2 (Glycine max), 5'ss of exon 8
AACCATTGAGCATCTGTTACCAATTTTTCTTTCCCTTTTGAAAGATGAATTTCCTGATGTGCGCCTTAACATCATAAGCAAGTTAGATCAAGTCAACCAGgtttgttgcatctctcttgtgtgctttagatactactt---ttattgcttccttatttagttggtgactgaattatcttttacggcag-------------
||| |||||||| || | || |||||||| ||||||||||| ||||||||||||||||| ||||| || |||||||||||| | |||||||| || ||||||||| | | || | ||| | || | | | || |||| | | ||| | || | | || | || |
AACAATTGAGCAGCTTCTTCCTATTTTTCTCTCCCTTTTGAAGGATGAATTTCCTGATGTACGCCTAAATATCATAAGCAAGCTTGATCAAGTGAATCAGgtttgtag-agcttttgagtggtttctatttgcaaattgctttataaactttcgacaaccttgtttcctttttgtttttctctggtaatgctgttaattct
upper sequence: AT1G25490.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA10G42250.1 (Glycine max), 5'ss of exon 8
AACCATTGAGCATCTGTTACCAATTTTTCTTTCCCTTTTGAAAGATGAATTTCCTGATGTGCGCCTTAACATCATAAGCAAGTTAGATCAAGTCAACCAGgtttgttgcatctctcttgtgtgctttagatactacttttattgcttccttatttagttggtgactgaattatctttta-cggcag-------------------
||| |||||||| || | || ||||| |||||||||||||| ||||||||||| || |||||||| ||||| || |||||| | |||||||| || |||||| ||| | | ||| || | || | | | ||||| || |||| || | |||| | || |
AACAATTGAGCAGCTTCTTCCTATTTTCCTTTCCCTTTTGAAGGATGAATTTCCCGACGTGCGCCTAAACATTATCAGCAAGCTTGATCAAGTGAATCAGgtt-gttatagtttc----tgtagttaatttaattttcagaatgctttagatttcttttggcaaccttttctcctttcctctgctgatataattaattcgagcat
upper sequence: AT1G25490.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA20G24790.1 (Glycine max), 5'ss of exon 8
AACCATTGAGCATCTGTTACCAATTTTTCTTTCCCTTTTGAAAGATGAATTTCCTGATGTGCGCCTTAACATCATAAGCAAGTTAGATCAAGTCAACCAGgtttgttgcatctctcttgtgtgctttagatactacttttattgcttccttatttagttggtgac-tgaattatcttttacggcag-------------------
||| |||||||| || | || ||||| |||||||||||||| |||||||||||||| || ||||| ||||| || |||||| | |||||||| || |||||| ||| || | ||| || | || | | | | ||||| || |||| || | || ||| | || |
AACAATTGAGCAGCTTCTTCCTATTTTCCTTTCCCTTTTGAAGGATGAATTTCCTGACGTACGCCTAAACATTATCAGCAAGCTTGATCAAGTGAATCAGgtt-gttatattttc----tgtaattaatttaattttctgaatgctttagatttcttttggcaacctttgttccttttctctgctgatataattaattctagcat
upper sequence: AT1G25490.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: Vv01s0011g03280.t01 (Vitis vinifera), 5'ss of exon 7
AACCATTGAGCATCTGTTACCAATTTTTCTTTCCCTTTTGAAAGATGAATTTCCTGATGTGCGCCTTAACATCATAAGCAAGTTAGATCAAGTCAACCAGgtttgttgca------------tctctcttgtgtgctttagatactacttttattgcttccttatttagttggtgactgaattatcttttacggcag---
||| ||||| || || | |||||||||||||| |||||||| ||||| ||||||||||| || || || ||||| |||||| | |||||| | || ||||||||| | || | | | ||| || || | ||| | ||| | ||| | | | | | | ||| | |||
AACAATTGATCAACTTCTTCCAATTTTTCTTTCTCTTTTGAAGGATGACTTTCCTGATGTACGACTAAATATCATTAGCAAGCTTGATCAAATAAATCAGgtttgtcataatttaaggagtttcacatcagcctttttttaattttatgtgctctgcctacttgtctagccagctattctactttttttaaatgcaattt
upper sequence: AT1G25490.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: PP1S197_114V6.1 (Physcomitrella patens), 5'ss of exon 7
AACCATTGAGCATCTGTTACCAATTTTTCTTTCCCTTTTGAAAGATGAATTTCCTGATGTGCGCCTTAACATCATAAGCAAGTTAGATCAAGTCAACCAGgtt-tgttgcatctctcttgtgtgc----tttagatac---tacttttattgcttccttatttagttggtgactgaattatcttttacggcag------------------------------------------------------------------------------------------------------
|| |||||||| || ||||| || || || || || ||||| ||||||||||| || ||||| || || ||||| |||||| |||||||||||||||| || || | || | ||| ||| ||| | | | | ||| | | | | | | ||| | | |||| | || |||
TACTATTGAGCAACTTTTACCCATATTCCTATCACTGTTGAAGGATGAATTTCCAGACGTGCGGCTAAATATCATCAGCAAGCTAGATCAAGTCAACCAAgtaatgatcaattctattagtgaaggacatttcattacatgtccctatcttgttgctctgataaatctttgatttagttatgtattgtggcctttctttaatggacatgacattagttgggttcacatcaagacactggatgtgttccacaaagaaaagaaccaatggatctgaatttggactttttgatcacag
upper sequence: AT1G25490.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: EFJ35758 (Selaginella moellendorffii), 5'ss of exon 7
AACCATTGAGCATCTGTTACCAATTTTTCTTTCCCTTTTGAAAGATGAATTTCCTGATGTGCGCCTTAACATCATAAGCAAGTTAGATCAAGTCAACCAGgtttgttgcatctctcttgtgtgctttagatactacttttattgcttccttatttagttggtgactgaattatcttttacggcag
|| || || || || |||||||| ||| | |||||||||| |||||||| ||||| || | || ||||||||||||||| | |||||||||||| ||| ||| | | | | | || | | || || ||| |||
GACAATCGAACAGCTTTTACCAATATTTTTGGCCCTTTTGAAGGATGAATTCCCTGACGTTAGGCTCAACATCATAAGCAAGCTGGATCAAGTCAACAAGgcaagtt-cgcccaacgaagattcatt--gttttgaattgatcttttcgttacag------------------------------
upper sequence: AT1G25490.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: EFJ10709 (Selaginella moellendorffii), 5'ss of exon 7
-----AACCATTGAGCATCTGTTACCAATTTTTCTTTCCCTTTTGAAAGATGAATTTCCTGATGTGCGCCTTAACATCATAAGCAAGTTAGATCAAGTCAACCAGgtttgttgcatctctcttgtgtgctttagatactacttttattgcttccttatttagttggtgactgaattatcttttacggcag
|| || || || || |||||||| ||| | |||||||||| |||||||| ||||| || | || ||||||||||||||| | |||||||||||| ||| ||| | | | | | || | | || || ||| |||
GACGCGACAATCGAACAACTTTTACCAATATTTTTGGCCCTTTTGAAGGATGAATTCCCTGACGTTAGGCTCAACATCATAAGCAAGCTGGATCAAgtcaacaaggcaagtt-cgcccaacgaagattcatt--gttttgagttgatcttttcgttacag------------------------------Mapped 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|47830292|gb|CK119976.1|CK119976EST: TTCCTGATGTGCGCCTTAACATCATAAGCAAGTTAGATCAAGTCAACCAG GTTATTGGAATTGATCTACTATCTCAATCCTTGTTACCGGCCATTGTAGAA
genomic: TTCCTGATGTGCGCCTTAACATCATAAGCAAGTTAGATCAAGTCAACCAGgtttgttgca ... tttacggcagGTTATTGGAATTGATCTACTATCTCAATCCTTGTTACCGGCCATTGTAGAA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AACCATTGAGCATCTGTTACCAATTTTTCTTTCCCTTTTGAAAGATGAATTTCCTGATGTGCGCCTTAACATCATAAGCAAGTTAGATCAAGTCAACCAGgtttgttgcatctctcttgtgtgctttagatactacttttattgcttccttatttagttggtgactgaattatcttttacggcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA