Sequence
atgc intronic sequence ATGC exonic sequencegtatggatgcacccattccttgcattgagtttattctgttctgtgtgagtcgtaggttaattgctttcatgtatctttttagGTTCTTCGACCATTTCTTCTTCGAAGACTAAAGTCAGATGTTGAGAAAGGTTTGCCACCGAAGAAGGAGACCATACTTAAAGTTGGTATGTCTCAGATGC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G06400.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 8
gta-tggat---gcacccattccttgcattgagtttattctgttctgtgtgagtcgtaggttaattgctttcatgt-atctttttagGTTCTTCGACCATTTCTTCTTCGAAGACTAAAGTCAGATGTTGAGAAAGGTTTGCCACCGAAGAAGGAGACCATACTTAAAGTTGGTATGTCTCAGATGC
||| ||| | |||| | ||||| | || |||| || | | ||| | | || | ||||| | || |||||||||| |||||||| ||||| || || || || ||||||||||||||||| ||||| || ||||| || |||||||||||||| |||||| ||||||
gtaacagatttgatatccatattctcaattga-tagatcatgttg-gttttccttgtatgatttgtg-taacatgttacacttgaagGTTCTTCGTCCATTTCTGCTTCGGAGGCTTAAATCTGATGTTGAGAAAGGTTTACCACCAAAAAAGGAAACTATACTTAAAGTTGGAATGTCTGAGATGC
upper sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os01g27040.1 (Oryza sativa), 3'ss of exon 8
----gtatggatgcacccattcct-----tgcattgagtttattctgttctgtgtgagtcgtaggttaattgctttcatgtatctttttagGTTCTTCGACCATTTCTTCTTCGAAGACTAAAGTCAGATGTTGAGAAAGGTTTGCCACCGAAGAAGGAGACCATACTTAAAGTTGGTATGTCTCAGATGC
||| | ||||| | |||| | | || | | | ||| | | | | || ||| | |||||||||| ||||||||||||||||| || || || |||||||| || || || || || || ||||| || || ||||| ||||| |||||||||||||
gtgagtaatataactcccatgctcaatggctcattatgctaataatttgggacaacctgcatagttcattcatgtaaattcttctatgaagGTTCTTCGCCCATTTCTTCTTCGAAGGCTTAAATCTGATGTTGAAAAGGGATTACCCCCCAAAAAGGAAACTATCCTTAAGGTTGGAATGTCTCAGATGC
upper sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 8
gtatggatgcacccattccttgcattgagtttattctgttctgtgtgagtcgtaggttaattgctttcatgtatctttt---tagGTTCTTCGACCATTTCTTCTTCGAAGACTAAAGTCAGATGTTGAGAAAGGTTTGCCACCGAAGAAGGAGACCATACTTAAAGTTGGTATGTCTCAGATGC
|| |||| | || | | | | || | || | || || |||||| |||| || | ||||| |||||||||| |||||||||||| | || || ||||| ||||| || || ||| | || ||||||||||| ||||||||||||||||| |||||||||||||
gttgggatataattatcatgataactaattatagtactttaaaatgaactcttaa--taattg-tttcttgcaacttttgcaaagGTTCTTCGCCCATTTCTTCTTAGGAGGCTCAAGTCTGATGTAGAAAAGGGTCTACCTCCGAAGAAGGAAACCATACTTAAAGTTGGAATGTCTCAGATGC
upper sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 8
gtatggatgca--cccattccttgcattgagtttattctgttctg-tgt-gagtcgtaggttaattgctttcatgtatctt-tttagGTTCTTCGACCATTTCTTCTTCGAAGACTAAAGTCAGATGTTGAGAAAGGTTTGCCACCGAAGAAGGAGACCATACTTAAAGTTGGTATGTCTCAGATGC
||| | | | | ||| ||| | || |||| || | ||| | | || | | |||| ||| | | || |||| || || ||||| || |||||||| | |||||||||||||||||||||||||||||||| ||||| ||||| || ||||| || ||||| || ||||
gtaagccttgaagcttcttcattgttaagggtctattgtgataaaatgttgtataataatgttttcattttc-tgtgtgtaattaagGTCCTCCGTCCATTCCTCCTTCGAAGGTTGAAGTCAGATGTTGAGAAAGGTTTGCCACCGAAAAAGGAAACCATTCTCAAAGTAGGCATGTCGCAAATGC
upper sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 8
----gtatggatgcacccattccttgcattgagtttattctgttctg-tgtga-gtcgtag-gttaattgctttcatgtatctttttagGTTCTTCGACCATTTCTTCTTCGAAGACTAAAGTCAGATGTTGAGAAAGGTTTGCCACCGAAGAAGGAGACCATACTTAAAGTTGGTATGTCTCAGATGC
| | || || | || ||| | | || || | || | ||| | | || ||| || || || || |||| || || ||||| || |||||||| | |||||||||||||||||||||||||||||||| ||||| ||||| || ||||| || ||||| || ||||
gtaagccttgaagcttct-ttgattgtttagggtctactgtgataaaatgttatataataatgttttcaatttctgtgcatgatta-agGTCCTCCGTCCATTCCTCCTTCGAAGGTTGAAGTCAGATGTTGAGAAAGGTTTGCCACCGAAAAAGGAAACCATTCTCAAAGTAGGCATGTCGCAAATGC
upper sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 8
-----gtatggatgcacccattccttgcattgagtttattctgttctgtgtgagtcgtag--gttaattgc-tttcatgtatctttttagGTTCTTCGACCATTTCTTCTTCGAAGACTAAAGTCAGATGTTGAGAAAGGTTTGCCACCGAAGAAGGAGACCATACTTAAAGTTGGTATGTCTCAGATGC
|| || | | || ||| ||| | |||| | || | || || | || | ||| | | | | | |||| || ||||||||||| |||||||| | |||||||||||||||||||| |||||||| || ||||| || || |||||||| || ||||| || ||||
gtaaattacagaaccttcttttgattgttggaagtccttgatgtta-atctggcacataattgtcattttcattttctatgtatatcaagGTCCTCCGACCATTTCTCCTTCGAAGGTTGAAGTCAGATGTTGAGAAAGGATTGCCACCAAAAAAGGAAACTATTCTTAAAGTAGGCATGTCCCAAATGC
upper sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 8
-----gtatggatgcacccattccttgcattgagtttattctgttctgtgtgagtcgtag--gttaattgc-tttcatgtatctttttagGTTCTTCGACCATTTCTTCTTCGAAGACTAAAGTCAGATGTTGAGAAAGGTTTGCCACCGAAGAAGGAGACCATACTTAAAGTTGGTATGTCTCAGATGC
|| || | | || ||| ||| | |||| | || | || || | || | ||| | | | | | |||| || || |||||||| |||||||| | |||||||||||||||||||| ||||||||||| ||||| || || ||||| || || ||||| || ||||
gtaaattacagaaccttcttttgattgttggaagtccttaatgtta-atctggcacataattgtcattttcattttctatgtatatcaagGTCCTCCGCCCATTTCTCCTTCGAAGGTTGAAGTCAGATGTTGAGAAAGGGTTGCCACCGAAAAAGGAAACTATTCTTAAGGTAGGCATGTCCCAAATGC
upper sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 8
gtatggatgcacccattccttgcattgagtttattctgttctgtgtgagtcgtaggttaattgctttcatgtatct---ttttagGTTCTTCGACCATTTCTTCTTCGAAGACTAAAGTCAGATGTTGAGAAAGGTTTGCCACCGAAGAAGGAGACCATACTTAAAGTTGGTATGTCTCAGATGC
||| || | || | || | || | | | | | ||| | || | | ||| |||||||| || || || || || ||||| ||||| |||||||||||||||||||| ||||| || || ||||| || ||||||||||| || |||||||| |||
gtaaacccaagacctcctaattttttagctctaccttatttcatctcatttactga--aatggtttctgtatttctgttttttagGTCCTCCGGCCTTTCCTCCTTCGGAGACTGAAGTCAGATGTTGAGAAAGGCTTGCCTCCAAAAAAGGAAACAATACTTAAAGTAGGCATGTCTCAATTGC
upper sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: EFJ06565 (Selaginella moellendorffii), 3'ss of exon 8
gtatggatgcacccattccttgcattgagtttattctgttctgtgtgagtcgtaggttaattgctttcatgtatctttttagGTTCTTCGACCATTTCTTCTTCGAAGACTAAAGTCAGATGTTGAGAAAGGTTTGCCACCGAAGAAGGAGACCATACTTAAAGTTGGTATGTCTCAGATGC
| |||| | | | | | | || | | | | | | || | |||| | || |||||||| | || | || ||||| |||||||| | ||| || || || ||||||||||| || || |||||||| |||||||||||||
--------------------------gtacttatccagcatt-tataaatcaaccatgagtaacact------ttttctcagGTCTTACGCCCATTTCTCTTAAGACGTCTCAAGTCGGATGTTGAAAGAGGATTACCCCCAAAGAAGGAGACAATCCTCAAAGTTGGGATGTCTCAGATGC
upper sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: EFJ31365 (Selaginella moellendorffii), 3'ss of exon 8
gtatggatgcacccattccttgcattgagtttattctgttctgtgtgagtcgtaggttaattgctttcatgtatctttttagGTTCTTCGACCATTTCTTCTTCGAAGACTAAAGTCAGATGTTGAGAAAGGTTTGCCACCGAAGAAGGAGACCATACTTAAAGTTGGTATGTCTCAGATGC
| |||| | | | | | | || | | | | | | || | |||| | || |||||||| | || | || ||||| |||||||| | ||| ||||| || ||||||||||| || || |||||||| |||||||||||||
--------------------------gtacttatccagcatt-tataaatcaaccatgagtaacact------ttttctcagGTCTTACGCCCATTTCTCTTAAGACGTCTCAAGTCGGATGTTGAAAGAGGATTGCCCCCAAAGAAGGAGACAATCCTCAAAGTTGGGATGTCTCAGATGCMapped 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|124885786|gb|EH964688.1|EH964688EST: AAATTTCTGGTGAGAATGACCAGCAAGAAGTTGTGCAACAACTGCACAAG GTTCTTCGACCATTTCTTCTTCGAAGACTAAAGTCAG
genomic: AAATTTCTGGTGAGAATGACCAGCAAGAAGTTGTGCAACAACTGCACAAGgtatggatgc ... atctttttagGTTCTTCGACCATTTCTTCTTCGAAGACTAAAGTCAG
EST:
gi|116481378|gb|EG523970.1|EG523970EST: AAATTTCTGGTGAGAATGACCAGCAAGAAGTTGTGCAACAACTGCACAAG GTTCTTCGACCATTTCTTCTTCGAAGACTAAAGTCAGATGTTGAGAAAGGT
genomic: AAATTTCTGGTGAGAATGACCAGCAAGAAGTTGTGCAACAACTGCACAAGgtatggatgc ... atctttttagGTTCTTCGACCATTTCTTCTTCGAAGACTAAAGTCAGATGTTGAGAAAGGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtttattctgttctgtgtgagtcgtaggttaattgctttcatgtatctttttagGTTCTTCGACCATTTCTTCTTCGAAGACTAAAGTCAGATGTTGAGAAAGGTTTGCCACCGAAGAAGGAGACCATACTTAAAGTTGGTATGTCTCAGATGC
ggttaat putative branch site (score: 4)
tatcttttt putative PPT
tatcttttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatggatgcacccattccttgcattgagtttattctgttctgtgtgagtcgtaggttaattgctttcatgtatctttttagGTTCTTCGACCATTTCTTCTTCGAAGACTAAAGTCAGATGTTGAGAAAGGTTTGCCACCGAAGAAGGAGACCATACTTAAAGTTGGTATGTCTCAGATGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG