Sequence
atgc intronic sequence ATGC exonic sequencegttagtgatacctcttctttttgagtttttactaggacaaattttgatgttgttagcatttctttgtatacttagaagctattcttatgtacgtgcagAGGTACGCGGATTAAGACCCGCAAACGGAATATTGCTGCTCCTCTGGACCCTGCAGCCTTTTCTGATGCAGTGGTCCAGATTTACCATGATAATGCTGGT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G36230.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G36230.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os11g21990.1 (Oryza sativa), 3'ss of exon 2
--------gttagtgatacctcttct--ttttgagtttttactaggacaaattttgatgttgttagcatttctttgtatacttagaagctattcttatgtacgtgcagAGGTACGCGGATTAAGACCCGCAAACGGAATATTGCTGCTCCTCTGGACCCTGCAGCCTTTTCTGATGCAGTGGTCCAGATTTACCATGATAATGCTGGT
|| | || | |||| || ||| | || | | || | || || | |||| | || | ||| || ||| |||||||| ||||||||||||||||||||||||||||||||||||| ||||||||||| | || ||||||||| | ||||||||||| | |||||||||||
ttgtgtcaattcatagtattgtgtgaagttttcagctttctttgcaacta----tcatatagtaaggctatcttaatgattttttttgttatgct---atac-tgcagAGGCCAGCGGATTAAGACCCGCAAACGGAATATTGCTGCTCCTTTGGACCCTGCATCATTCTCTGATGCAATTGTCCAGATTTATCTGGATAATGCTGGA
upper sequence: AT5G36230.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM5G877316_T03 (Zea mays), 3'ss of exon 2
-------------gttagtgatacctcttctttttgagtttttactaggacaaattttgatgttgttagcatttctttgtatacttagaagctattcttatgtacgtgcagAGGTACGCGGATTAAGACCCGCAAACGGAATATTGCTGCTCCTCTGGACCCTGCAGCCTTTTCTGATGCAGTGGTCCAGATTTACCATGATAATGCTGGT
|| || || ||| ||| ||| | | || || ||||| | | ||| | | | | | |||| || ||||||| |||||||||||||||||||| ||||| ||||| |||||| ||||||||||| | || ||||||||| | ||||||||||| | ||||||| |||
catgtttatactatataatggtaaaacttatttgcagagtttg--catggcagtattgcatgtt-caggtaattcaccttgttttctgcaattattatt--------gcagAGGCACGCGGATTAAGACCCGCAAGCGGAACATTGCAGCTCCTTTGGACCCTGCATCATTCTCTGATGCAATTGTCCAGATTTATCTGGATAATGGTGGA
upper sequence: AT5G36230.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G012416_T04 (Zea mays), 3'ss of exon 2
gttagtgatacctcttctttttgagtttttactaggacaaattttgatgttgt-tagcatttctttgtatacttagaagctattcttatgtacg--tgcagAGGTACGCGGATTAAGACCCGCAAACGGAATATTGCTGCTCCTCTGGACCCTGCAGCCTTTTCTGATGCAGTGGTCCAGATTTACCATGATAATGCTGGT
|| || | || || || ||| | ||| | || | || | |||| | |||| | | | || | || |||||||| |||||||||||||||||||| ||||||||||| |||||| ||||||||||| | || ||||||||| | || ||||| || ||||||| |||
-tttatgtttatactgtattggtagaacttatttggagagtttgcatggcagtattgcatgttcatgtaatccactttattttcctcaattattattgcagAGGCACGCGGATTAAGACCCGCAAGCGGAATATTGCAGCTCCTTTGGACCCTGCATCATTCTCTGATGCAATTGTTCAGATCTATTTGGATAATGGTGGA
upper sequence: AT5G36230.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA09G38530.1 (Glycine max), 3'ss of exon 2
gttagtgatacctcttctttttgagtttttactaggacaaattttgatgttgttagcatttctttgtatacttagaagctattcttatgt--acgtgcagAGGTACGCGGATTAAGACCCGCAAACGGAATATTGCTGCTCCTCTGGACCCTGCAGCCTTTTCTGATGCAGTGGTCCAGATTTACCATGATAATGCTGGT
|| | | | | | | | | | | | | | || | |||| || |||| | | | || | | |||| | | ||| || ||||||||||||||||||||||||||||||||||| || |||||||||||||| || || |||||||||||||||||||| ||||||||||||
attttgtaggctattgcatgtagcttctattattgtgttatttatcatgtatgtataatttatgttgaggctcttttcttttgtttatctcaatccccagTGGCACGCGGATTAAGACCCGCAAACGGAATATTGCTGCGCCGCTGGACCCTGCAGCATTCTCGGATGCAGTGGTCCAGATTTATTTGGATAATGCTGGT
upper sequence: AT5G36230.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA18G47780.1 (Glycine max), 3'ss of exon 2
gttagtgatacctcttctttttgagtttttacta--ggacaaattttgatgt-tgttagcatttctttgta--tacttagaagctattcttatgtacgtgcagAGGTACGCGGATTAAGACCCGCAAACGGAATATTGCTGCTCCTCTGGACCCTGCAGCCTTTTCTGATGCAGTGGTCCAGATTTACCATGATAATGCTGGT
| || || || | |||| || || || | | || | |||| |||| || |||| ||||| | || | | | ||| || ||||||||||||||||||||||| ||||||||||| || |||||||||||||| || || |||||||||||||||||||| |||||||||||
--ttttgtaggctattgcatgtgagcttatattattgtgttatttatcatgtatgtttaatttatgttgtgggcacttatcttttgtttatctccatccccaGTGGCACGCGGATTAAGACCCGCAAACGAAATATTGCTGCGCCGCTGGACCCTGCAGCATTCTCGGATGCAGTGGTCCAGATTTATTTGGATAATGCTGG-
upper sequence: AT5G36230.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv04s0023g00670.t01 (Vitis vinifera), 3'ss of exon 3
--gttagtgatacctcttctttttgagtttttactaggacaaattttgatgttgttagcatttctttgtatac-----ttagaagctattcttatgtacgtgcagAGGTACGCGGATTAAGACCCGCAAACGGAATATTGCTGCTCCTCTGGACCCTGCAGCCTTTTCTGATGCAGTGGTCCAGATTTACCATGATAATGCTGGT
|| || || | | || | ||| | || |||| | | |||| || ||| || | | || ||| | | ||| || |||||||||||||||||||||||||||||||| || || |||||||||||| | ||| | |||||||||||||||||||| | ||||||||||||
tggtggaaagtaactacagtagcgaacattctt----gacgtgtgtttttgttatcaa-atttgttgacataagcctgttgtcatttgtttctatttttttccagTGGCACGCGGATTAAGACCCGCAAACGGAATATTGCAGCGCCGCTGGACCCTGCAACATTTGCAGATGCAGTGGTCCAGATTTATCTGGATAATGCTGGT
upper sequence: AT5G36230.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ06557 (Selaginella moellendorffii), 3'ss of exon 2
gttagtgatacctcttctttttgagtttttactaggacaaattttgatgttgttagcatttctttgtatacttagaagctattcttatgtacgtgcagAGGTACGCGGATTAAGACCCGCAAACGGAATATTGCTGCTCCTCTGGACCCTGCAGCCTTTTCTGATGCAGTGGTCCAGATTTACCATGATAATGCTGGT
| || || | || || || | || | | || || | | | | || | || || || |||||||||||||||||||||||||||||||| ||| ||||||| | | || | ||||| | |||||||| ||| ||| ||||||||
--------------------gtaagggctt--tgagattc-ttgcattggttttggtttggtttggtttgttcatga------tttgggcgtgtatagTGGCACGCGGATTAAGACCCGCAAACGGAATATTGCAATTCCGTTGGACCCATCTTCTTTCGCGGATGCTATAGTCCAGATCTACTTGGATCATGCTGGTMapped 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|125224240|gb|EL238325.1|EL238325EST: GCTCGAAGGAGAAACCCACTCTCGG AGGTACGCGGTATTAAGACCCGCAAACGGAATATTGCTGCTCCTCTGGACC
genomic: GCTCGAAGGAGAAACCCACTCTCGGgttagtgata ... gtacgtgcagAGGTACGCGG-ATTAAGACCCGCAAACGGAATATTGCTGCTCCTCTGGACC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgatgttgttagcatttctttgtatacttagaagctattcttatgtacgtgcagAGGTACGCGGATTAAGACCCGCAAACGGAATATTGCTGCTCCTCTGGACCCTGCAGCCTTTTCTGATGCAGTGGTCCAGATTTACCATGATAATGCTGGT
ttttgat putative branch site (score: 4)
tattcttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtgatacctcttctttttgagtttttactaggacaaattttgatgttgttagcatttctttgtatacttagaagctattcttatgtacgtgcagAGGTACGCGGATTAAGACCCGCAAACGGAATATTGCTGCTCCTCTGGACCCTGCAGCCTTTTCTGATGCAGTGGTCCAGATTTACCATGATAATGCTGGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG