Sequence
atgc intronic sequence ATGC exonic sequencegtataaacttatgtttcagataatttctgtgtaagagacttgtattgtaagtgaatctagttaaaaatagataacgtgacgacctattgacaagtatcaacaatcgtctgttttgttaccctcacactctctgatactacatgtctaaaaccatttttgaagGGTCGTAATGTCATCATCGAACAAAGCTGGGGTGCACCAAAGGTGACAAAGGATGGTGTGACTGTTGCCAAGAGCATTGAGTTCAAGGATAGAATTAAGA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G33210.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os10g32550.1 (Oryza sativa), 3'ss of exon 3
gtataaacttatgtttcagataatttctgtgtaagagacttgtattgtaagtgaatctagttaaaaatagataacgtgacgacctattgacaagtatcaacaatcgtctgttttgttaccctcacactctctgatactacatgtctaaaaccatttttgaagGGTCGTAATGTCATCATCGAACAAAGCTGGGGTGCACCAAAGGTGACAAAGGATGGTGTGACTGTTGCCAAGAGCATTGAGTTCAAGGATAGAATTAAGA
|| | | | ||| | | || | ||| | | | |||| ||||| || | | || || |||||| || || |||| || ||||| | || || || |||| ||| |||| || || |||||||| ||||||||||||||||||||||||||||||||||||||| | ||||
-------------------------------------------------agcacagtgtttgttgggcctacaactttttatgtttttattt--tgtcag-agtgctgtgttgtgttatttgcagattg---gacttaacgtgtcta-------ttatgcagGGACGCAATGTGGTTATTGAGCAGAGCTATGGTTCACCGAAAGTCACAAAGGACGGTGTGACTGTTGCCAAGAGCATTGAGTTCAAGGATAGAGTCAAGA
upper sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os03g04970.1 (Oryza sativa), 3'ss of exon 3
gtataaacttatgtttcagataatttctgtgtaagagacttgtattgtaagtgaatctagttaaaaatagataacgtgacgacctattgacaagtatcaaca-atcgtctgttttgttaccctcacactctctgatactacatgtctaaaaccatttttgaagGGTCGTAATGTCATCATCGAACAAAGCTGGGGTGCACCAAAGGTGACAAAGGATGGTGTGACTGTTGCCAAGAGCATTGAGTTCAAGGATAGAATTAAGA
| | | || | | | ||| || || || | || | | || | | | ||| | | | | || ||| | ||| |||| || | ||| | || || ||||||| ||||| || || || ||||||||||| || |||||||||||||||||||| |||| | || ||||||
--------------------------------------------------------gttatgtgagattgcttttttagttttttatggatctttaacagtacattttgggagttatcatgcaaacaatgttgagctcaatataacta-------tgttgcagGGACGCACTGTTGTTATTGAGCAAAGCTTTGGTGCTCCTAAAGTTACAAAGGATGGAGTTACTGTTGCCAAGAGCATTGAATTCAGTAACAGGGTTAAGA
upper sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G416120_T01 (Zea mays), 3'ss of exon 2
gtataaacttatgtttcagataatttctgtgtaagagacttgtattgtaagtgaatctagttaaaaatagataacgtgacgacctattgacaa-gtatcaacaatcgtctgttttgttaccctcacactctctgatactacatgtctaaaaccatttttgaagGGTCGTAATGTCATCATCGAACAAAGCTGGGGTGCACCAAAGGTGACAAAGGATGGTGTGACTGTTGCCAAGAGCATTGAGTTCAAGGATAGAATTAAGA
| | ||| || | | | | | | || | | | | || | | | || |||||||| || ||| || | || || | || |||| || ||||| | || || ||||||| |||||||| || || ||||||||||||||||||||||| ||||||||||| || ||||||||| | ||||
---------------------------------------------actcactgattccaatactgtttggtttgttttactttgttgtaatactgttgccttagttgtttgttttgta---cttgaact------tatcgcctgcct---------tctgtagGGGCGCAATGTGGTTATTGAGCAAAGCTTCGGTGCACCGAAAGTCACAAAGGATGGTGTGACTGTTGCGAAGAGCATTGAATTTAAGGATAGAGTAAAGA
upper sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G458208_T01 (Zea mays), 3'ss of exon 2
gtataaacttatgtttcagataatttctgtgtaagagacttgtattgtaagtgaatctagttaaaaatagataacgtgacgacctattgacaagtatcaacaatcgtctgttttgttaccctcacactctctgatactacatgtctaaaaccatttttgaagGGTCGTAATGTCATCATCGAACAAAGCTGGGGTGCACCAAAGGTGACAAAGGATGGTGTGACTGTTGCCAAGAGCATTGAGTTCAAGGATAGAATTAAGA
| | | | | | | || | ||| | || || || | | | | ||| ||| | ||| || | | || ||| || |||| || ||||| | || || ||||||| |||||||| || || |||||||||||||||||||| || ||||||||||| || ||||||||| | ||||
----------------------------------------------------gcactcactgattataatattgcttgatgtgct-ttactctgttgtagtactgttgcatttagtttgttttgtacttgaatttattgcctgc---------tttctgcagGGGCGCAATGTGGTTATTGAGCAAAGCTTTGGTGCACCGAAAGTCACAAAGGATGGTGTGACTGTAGCAAAGAGCATTGAATTTAAGGATAGAGTAAAGA
upper sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G33680.1 (Glycine max), 3'ss of exon 3
gtataaacttatgtttcagataatttctgtgtaagagacttgtattgtaagtgaatctagttaaaaatagataacgtgacgaccta---ttgacaagtatcaacaatcgtctgttttgttaccctcacactctctgatactacatgtctaaaacc---atttttgaagGGTCGTAATGTCATCATCGAACAAAGCTGGGGTGCACCAAAGGTGACAAAGGATGGTGTGACTGTTGCCAAGAGCATTGAGTTCAAGGATAGAATTAAGA
|| | | || | | |||| | |||||| | | ||| || || | | | | | | ||| ||||| |||| |||||||| | || || ||||| | || ||||| || |||||||| ||||| || || ||||| ||||||||||| |||||||||| | | ||||
--------------------------------------------------------------------gaatgtcttttggatccaggcttgaaacatatcaatagtagtcccttcattttgattggtgttgatcacgattgttattgttaaattggtgtttttatagGGGCGTAATGTGGTTATTGAGCAAAGTTTTGGAGCACCCAAAGTGACAAAAGATGGAGTAACCGTTGCTAAGAGCATTGAATTCAAGGATAAAGTCAAGA
upper sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv05s0051g00340.t01 (Vitis vinifera), 3'ss of exon 3
gtataaacttatgtttcagataatttctgtgtaagagacttgtattgtaagtgaatctagttaaaaatagataacgtgacgacctattgacaagtatcaacaatcgtctgttttgttaccctcacactctctgatactacatgtctaaaaccatttttgaagGGTCGTAATGTCATCATCGAACAAAGCTGGGGTGCACCAAAGGTGACAAAGGATGGTGTGACTGTTGCCAAGAGCATTGAGTTCAAGGATAGAATTAAGA
| || | || | | | | || | | || | || | | | ||| | | || | ||| |||| ||||| || | | || ||||| | ||||| ||||| |||||||| |||||||| |||||||| || |||||||||||||||||| |||| ||||
--------------------------------------------------------ttgattcttggtgcatcttatttcaattctctattgagggttgg--gttaattgatgtggt----ttatacttaaaaaaggttaatcagcgttttgttgtttccagGGGCGTAACGTGGTACTAGAGCAAAGTTTTGGTGCCCCAAAAGTGACAAAAGATGGTGTAACTGTTGCAAAAAGCATTGAGTTCAAGGATCGAATCAAGA
upper sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S52_245V6.1 (Physcomitrella patens), 3'ss of exon 3
------------gtataaacttatgtttcagataatttctgtgtaagagacttgtattgtaagtgaatctagttaaaaat---agataacgtgacgacctattgaca-agtatcaacaatcgtctgttttgttaccctcacact--ctctgatactac-atgtctaaaaccatttttga-agGGTCGTAATGTCATCATCGAACAAAGCTGGGGTGCACCAAAGGTGACAAAGGATGGTGTGACTGTTGCCAAGAGCATTGAGTTCAAGGATAGAATTAAGA
| | || |||||| || | | | ||| | || | ||||| | | || |||| ||| || | | ||| | | | | | | | | || | || | || | ||| | |||| || | ||| |||||||| ||| | || | || || ||||| ||||||||||| |||||||| || |||||||| |||||||| || ||||||
gtaacctgctgcctgctattttgcttttcagtagggatcaatcccgaactgtctaattcttggt-attctagctttagatccgagattttactttgacttagagtcgtagttttagggggatttgataacatagtttacgaattaactgtaatgtcgtgacgttgtgctctctttccaacagGGCCGGACTGTTATCATCGAGCAATCTTTTGGATCTCCTAAAGTGACCAAGGATGGTGTTACTGTTGCGAAAAGCATTGAATTCAAGGACAGGCTTAAGA
upper sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ32351 (Selaginella moellendorffii), 3'ss of exon 1
gtataaacttatgtttcagataatttctgtgtaagagacttgtattgtaagtgaatctagttaaaaatagataacgtgacgacctattgacaagtatcaacaatcgtctgttttgttaccctcacactctctgat-actacatgtctaaaaccatttttgaagGGTCGTAATGTCATCATCGAACAAAGCTGGGGTGCACCAAAGGTGACAAAGGATGGTGTGACTGTTGCCAAGAGCATTGAGTTCAAGGATAGAATTAAGA
| | | |||| || ||| ||| || ||| || | ||| || |||| |||| || || || | ||||| ||| ||| ||| | || ||||| || ||||||||||||||||||||||||||||| || |||||||| | | ||||
-------------------------------------------------------------------------------------------gtattctatccatcgcctttttccaatgaacaacaaactaagatcgctctttttctttttcc--ctttgcagGGGCGAAACGTTGTGATCGATCAAGGCTTTGGTTCTCCCAAGGTTACCAAGGATGGTGTGACTGTTGCCAAGAGCATCGACTTCAAGGACAAGCTGAAGA
upper sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ20894 (Selaginella moellendorffii), 3'ss of exon 1
gtataaacttatgtttcagataatttctgtgtaagagacttgtattgtaagtgaatctagttaaaaatagataacgtgacgacctattgacaagtatcaacaatcgtctgttttgttaccctcacactctctgatactacatgtctaaaaccatttttgaagGGTCGTAATGTCATCATCGAACAAAGCTGGGGTGCACCAAAGGTGACAAAGGATGGTGTGACTGTTGCCAAGAGCATTGAGTTCAAGGATAGAATTAAGA
| ||| | | || | | | || | | | ||||| |||| || || || | ||||| ||| ||| ||| | || ||||| || ||||||||||||||||||||||||||||| || |||||||| | | ||||
------------------------------------------------------------------------------------------------------gtattctatcc-atcgcctttttccaatgaacaacaaacttcttttttttccttttgtagGGGCGAAACGTTGTGATCGATCAAGGCTTTGGTTCTCCCAAGGTTACCAAGGATGGTGTGACTGTTGCCAAGAGCATCGACTTCAAGGACAAGCTGAAGAMapped 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|116483326|gb|EG525918.1|EG525918EST: GGGGTGTTGAGGATCTTGCTGATGCAGTTAAAGTCACTATGGGACCCAAG GGTCGTAATGTCATCATCGAACAAAGCTGGGGTGCACCAAAGGTGACAAAG
genomic: GGGGTGTTGAGGATCTTGCTGATGCAGTTAAAGTCACTATGGGACCCAAGgtataaactt ... atttttgaagGGTCGTAATGTCATCATCGAACAAAGCTGGGGTGCACCAAAGGTGACAAAG
EST:
gi|47829841|gb|CK119525.1|CK119525EST: GGGGTGTTGAGGATCTTGCTGATGCAGTTAAAGTCACTATGGGACCCAAG GGTCGTAATGTCATCATCGAACAAAGCTGGGGTGCACCAAAGGTGACAAAG
genomic: GGGGTGTTGAGGATCTTGCTGATGCAGTTAAAGTCACTATGGGACCCAAGgtataaactt ... atttttgaagGGTCGTAATGTCATCATCGAACAAAGCTGGGGTGCACCAAAGGTGACAAAG
EST:
gi|116483327|gb|EG525919.1|EG525919EST: GGGGTGTTGAGGATCTTGCTGATGCAGTTAAAGTCACTATGGGACCCAAG GGTCGTAATGTCATCATCGAACAAAGCTGGGGTGCACCAAAGGTGACAAAG
genomic: GGGGTGTTGAGGATCTTGCTGATGCAGTTAAAGTCACTATGGGACCCAAGgtataaactt ... atttttgaagGGTCGTAATGTCATCATCGAACAAAGCTGGGGTGCACCAAAGGTGACAAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgttttgttaccctcacactctctgatactacatgtctaaaaccatttttgaagGGTCGTAATGTCATCATCGAACAAAGCTGGGGTGCACCAAAGGTGACAAAGGATGGTGTGACTGTTGCCAAGAGCATTGAGTTCAAGGATAGAATTAAGA
gtctaaa putative branch site (score: 3)
ccattttt CT-rich tract
atttttgaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtataaacttatgtttcagataatttctgtgtaagagacttgtattgtaagtgaatctagttaaaaatagataacgtgacgacctattgacaagtatcaacaatcgtctgttttgttaccctcacactctctgatactacatgtctaaaaccatttttgaagGGTCGTAATGTCATCATCGAACAAAGCTGGGGTGCACCAAAGGTGACAAAGGATGGTGTGACTGTTGCCAAGAGCATTGAGTTCAAGGATAGAATTAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA