Sequence
atgc intronic sequence ATGC exonic sequenceTGCTGTAGCAATGGTGTATTTTGTTCAAGGTGTTTTAGGACTCGCTAGGCTCGCTGTTAGTTTCTATTTAAAAGATGACTTGCATCTTGATCCTGCTGAGgtatgctttttgtagttccttgttggactttcatgggaatatctctttataggctgacaaatatatacctcttgactag
Basic information
species | Arabidopsis thaliana |
transcript | AT2G32040.1 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G32040.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: LOC_Os07g07654.1 (Oryza sativa), 5'ss of exon 2
TGCTGTAGCAATGGTGTATTTTGTTCAAGGTGTTTTAGGACTCGCTAGGCTCGCTGTTAGTTTCTATTTAAAAGATGACTTGCATCTTGATCCTGCTGAGgt----------------atgct---ttttgtagttccttgttggactttcatgggaatatctcttt-----------ataggctgacaaatatatacctcttgactag--------------------------
|| || |||| ||||||||||| ||||| |||||||| || ||| | || ||||| ||||| || ||||||||||| | |||||||||||||| ||||| ||||| |||| | || | |||| ||| | ||||| || || | ||| |||||| |||||| ||
GGCAGTTGCAACTGTGTATTTTGTGCAAGGGGTTTTAGGCCTTGCTCGACTTGCTGTGAGTTTTTACTTAAAAGATGATCTTCATCTTGATCCTGCAGAGgtctgtgttcccctctaaatgctatcttttttgttttggtattggtatttatttatgtaatctcattccacccatacagtaagttgattcctatataggtcttgataagtgatcaatatgttttctcccatgtag
upper sequence: AT2G32040.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA10G39220.1 (Glycine max), 5'ss of exon 2
TGCTGTAGCAATGGTGTATTTTGTTCAAGGTGTTTTAGGACTCGCTAGGCTCGCTGTTAGTTTCTATTTAAAAGATGACTTGCATCTTGATCCTGCTGAGgtatgctttttgtagttccttgttggactttcatgggaatatctctttataggctgac----aaatatatacctcttgactag------------------
|||||| || ||||||||||||||||||||||||||||| || || || || ||||| | || || ||||||||||| |||||| | || ||||||||||| || | || || | | | | | | |||| || || | | || | |||| || | |
TGCTGTTGCGATGGTGTATTTTGTTCAAGGTGTTTTAGGGCTTGCAAGACTGGCTGTGAACTTTTACTTAAAAGATGATTTGCATTTGGACCCTGCTGAGgtgtgtcatcatggtttaattaatatgcagtta-atgtacatcttttgattgatttcatttgaattttatagctacagctcaattacctaatccaaggtgt
upper sequence: AT2G32040.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA20G28510.1 (Glycine max), 5'ss of exon 3
TGCTGTAGCAATGGTGTATTTTGTTCAAGGTGTTTTAGGACTCGCTAGGCTCGCTGTTAGTTTCTATTTAAAAGATGACTTGCATCTTGATCCTGCTGAGgtatgctttt----tgtagttcct-------tgttggactttcatgggaatatctctttataggctgacaaatatatacctcttgactag----------
|||||| || ||||| ||||||||||||||||||||||| || || || || ||||| | || || ||||||||||| |||||| | || ||||||||||| || || | || || | | || || | | | || || || | || | || || | | || | |
TGCTGTTGCGATGGTTTATTTTGTTCAAGGTGTTTTAGGGCTTGCAAGACTGGCTGTGAACTTTTACTTAAAAGATGATTTGCATTTAGACCCTGCTGAGgtgtgtccttatggtttaattaatatgcagttaatgcacatcttttgattaatttcatttgaatcttataactacagctcaattacccaatccaaggtgt
upper sequence: AT2G32040.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv05s0020g03660.t01 (Vitis vinifera), 5'ss of exon 2
TGCTGTAGCAATGGTGTATTTTGTTCAAGGTGTTTTAGGACTCGCTAGGCTCGCTGTTAGTTTCTATTTAAAAGATGACTTGCATCTTGATCCTGCTGAGgtatgctttttgtagttccttgttggactt---tcatgggaatatctctttataggctgacaa---atatatacctcttgactag---------------
||| || || ||||| |||||||| |||||||||||||| || ||||||| ||||| ||||| |||||||||||||| ||||||| |||||||| ||||| || | | | || | | || | |||| | | |||| || | || ||| |||| | |
TGCCGTTGCCATGGTATATTTTGTCCAAGGTGTTTTAGGCCTTTCTAGGCTTGCTGTCAGTTTTTATTTAAAAGATGATCTGCATCTAGATCCTGCAGAGgtgtgtgatcttaactttcataaattttttaggttatggtagaactcatttagtcgcatataatccatactattttctttctttgctttaactttttaggMapped 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|116448948|gb|EG491540.1|EG491540EST: TCGCTGTTAGTTTCTATTTAAAAGATGACTTGCATCTTGATCCTGCTGAG ACAGCTGTGATAACGGGTCTTTCTTCATTGCCGTGGCTTGTTAAGCCTCTC
genomic: TCGCTGTTAGTTTCTATTTAAAAGATGACTTGCATCTTGATCCTGCTGAGgtatgctttt ... tcttgactagACAGCTGTGATAACGGGTCTTTCTTCATTGCCGTGGCTTGTTAAGCCTCTC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TGCTGTAGCAATGGTGTATTTTGTTCAAGGTGTTTTAGGACTCGCTAGGCTCGCTGTTAGTTTCTATTTAAAAGATGACTTGCATCTTGATCCTGCTGAGgtatgctttttgtagttccttgttggactttcatgggaatatctctttataggctgacaaatatatacctcttgactag
- - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG